{"id":473,"date":"2016-08-19T15:59:24","date_gmt":"2016-08-19T15:59:24","guid":{"rendered":"https:\/\/courses.lumenlearning.com\/umd-publichealthbio\/?post_type=chapter&#038;p=473"},"modified":"2016-08-19T15:59:25","modified_gmt":"2016-08-19T15:59:25","slug":"chapter-14-dna-structure-and-function","status":"publish","type":"chapter","link":"https:\/\/courses.lumenlearning.com\/umd-publichealthbio\/chapter\/chapter-14-dna-structure-and-function\/","title":{"raw":"Chapter\u00a014.\u00a0DNA Structure and Function","rendered":"Chapter\u00a014.\u00a0DNA Structure and Function"},"content":{"raw":"<div class=\"chapter\" title=\"Chapter&#xA0;14.&#xA0;DNA Structure and Function\" id=\"id501987\"><div class=\"titlepage\"><div><div><h1 class=\"title\"><span class=\"cnx-gentext-chapter cnx-gentext-autogenerated\">Chapter\u00a0<\/span><span class=\"cnx-gentext-chapter cnx-gentext-n\">14<\/span><span class=\"cnx-gentext-chapter cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-chapter cnx-gentext-t\">DNA Structure and Function<\/span><\/h1><\/div><\/div><\/div><div class=\"introduction\" id=\"m44484\"><div id=\"m44484-fig-ch14_00_01\" class=\"figure splash\" title=\"Figure&#xA0;14.1.&#xA0;\"><div class=\"body\"><div class=\"mediaobject\"><span id=\"m44484-fs-id1597120\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155639\/Figure_14_00_01.jpg\" width=\"600\" alt=\"Photo shows Dolly the sheep, which has been stuffed and placed in a glass case.\"\/><\/div><\/div><div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.1<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"\/><\/div><div class=\"caption\">Dolly the sheep was the first large mammal to be cloned.<\/div><\/div><h3 class=\"title\"><span>Introduction<sup><a href=\"co03.html#book-attribution-m44484\">*<\/a><\/sup><\/span><\/h3><p><span id=\"m44484-fs-id3011658\"> <\/span>The three letters \u201cDNA\u201d have now become synonymous with crime solving, paternity testing, human identification, and genetic testing. DNA can be retrieved from hair, blood, or saliva. Each person\u2019s DNA is unique, and it is possible to detect differences between individuals within a species on the basis of these unique features.<\/p><p><span id=\"m44484-fs-id1480610\"> <\/span>DNA analysis has many practical applications beyond forensics. In humans, DNA testing is applied to numerous uses: determining paternity, tracing genealogy, identifying pathogens, archeological research, tracing disease outbreaks, and studying human migration patterns. In the medical field, DNA is used in diagnostics, new vaccine development, and cancer therapy. It is now possible to determine predisposition to diseases by looking at genes.<\/p><p><span id=\"m44484-fs-id1396004\"> <\/span>Each human cell has 23 pairs of chromosomes: one set of chromosomes is inherited from the mother and the other set is inherited from the father. There is also a mitochondrial genome, inherited exclusively from the mother, which can be involved in inherited genetic disorders. On each chromosome, there are thousands of genes that are responsible for determining the genotype and phenotype of the individual. A gene is defined as a sequence of DNA that codes for a functional product. The human haploid genome contains 3 billion base pairs and has between 20,000 and 25,000 functional genes.<\/p><\/div><div xml:lang=\"en\" class=\"section module\" title=\"14.1.&#xA0;Historical Basis of Modern Understanding\"><div class=\"titlepage\"><div><div><h2 id=\"m44485\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.1<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Historical Basis of Modern Understanding<sup><a href=\"co03.html#book-attribution-m44485\">*<\/a><\/sup><\/span><\/span><\/h2><\/div><div class=\"abstract\"><div class=\"title\"><span><span class=\"cnx-gentext-abstract cnx-gentext-autogenerated\"><span class=\"cnx-gentext-abstract cnx-gentext-t\"\/><\/span><\/span><\/div><p>By the end of this section, you will be able to:\n<\/p><div class=\"itemizedlist\"><ul class=\"itemizedlist\"><li class=\"listitem\"><p>Explain transformation of DNA<\/p><\/li><li class=\"listitem\"><p>Describe the key experiments that helped identify that DNA is the genetic material<\/p><\/li><li class=\"listitem\"><p>State and explain Chargaff\u2019s rules<\/p><\/li><\/ul><\/div><\/div><\/div><\/div><div class=\"toc\"><ul\/><\/div><p><span id=\"m44485-fs-id1511467\"> <\/span>Modern understandings of DNA have evolved from the discovery of nucleic acid to the development of the double-helix model. In the 1860s, Friedrich Miescher (<a class=\"xref target-figure\" href=\"ch14.html#m44485-fig-ch14_01_01\" title=\"Figure&#xA0;14.2.&#xA0;\">Figure\u00a014.2<\/a>), a physician by profession, was the first person to isolate phosphate-rich chemicals from white blood cells or leukocytes. He named these chemicals (which would eventually be known as RNA and DNA) nuclein because they were isolated from the nuclei of the cells.<\/p><div id=\"m44485-fig-ch14_01_01\" class=\"figure\" title=\"Figure&#xA0;14.2.&#xA0;\"><div class=\"body\"><div class=\"mediaobject\"><span id=\"m44485-fs-id2081310\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155642\/Figure_14_01_01.jpg\" width=\"150\" alt=\"Photo of Friedrich Miescher.\"\/><\/div><\/div><div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.2<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"\/><\/div><div class=\"caption\">Friedrich Miescher (1844\u20131895) discovered nucleic acids.<\/div><\/div><div id=\"m44485-fs-id1964835\" class=\"note interactive\"><div class=\"title\"><span class=\"cnx-gentext-tip-t\">Link to Learning<\/span><\/div><div class=\"body\"><div class=\"mediaobject\"><span id=\"m44485-fs-id1482325\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155645\/miescher_levene.png\" width=\"120\" alt=\"QR Code representing a URL\"\/><\/div><p><span id=\"m44485-fs-id2009505\"> <\/span>To see Miescher conduct an experiment step-by-step, click through <a class=\"link\" href=\"http:\/\/openstaxcollege.org\/l\/miescher_levene\" target=\"\">this review<\/a> of how he discovered the key role of DNA and proteins in the nucleus.<\/p><\/div><\/div><p><span id=\"m44485-fs-id1430986\"> <\/span>A half century later, British bacteriologist Frederick Griffith was perhaps the first person to show that hereditary information could be transferred from one cell to another \u201chorizontally,\u201d rather than by descent. In 1928, he reported the first demonstration of bacterial <em class=\"glossterm\"><span id=\"m44485-autoid-cnx2dbk-id1280706\"> <\/span>transformation<\/em><a id=\"id502585\" class=\"indexterm\">, a process in which external DNA is taken up by a cell, thereby changing morphology and physiology. He was working with <span class=\"emphasis\"><em>Streptococcus pneumoniae,<\/em><\/span> the bacterium that causes pneumonia. Griffith worked with two strains, rough (R) and smooth (S). The R strain is non-pathogenic (does not cause disease) and is called rough because its outer surface is a cell wall and lacks a capsule; as a result, the cell surface appears uneven under the microscope. The S strain is pathogenic (disease-causing) and has a capsule outside its cell wall. As a result, it has a smooth appearance under the microscope. Griffith injected the live R strain into mice and they survived. In another experiment, when he injected mice with the heat-killed S strain, they also survived. In a third set of experiments, a mixture of live R strain and heat-killed S strain were injected into mice, and\u2014to his surprise\u2014the mice died. Upon isolating the live bacteria from the dead mouse, only the S strain of bacteria was recovered. When this isolated S strain was injected into fresh mice, the mice died. Griffith concluded that something had passed from the heat-killed S strain into the live R strain and transformed it into the pathogenic S strain, and he called this the transforming principle (<\/a><a class=\"xref target-figure\" href=\"ch14.html#m44485-fig-ch14_01_02\" title=\"Figure&#xA0;14.3.&#xA0;\">Figure\u00a014.3<\/a>). These experiments are now famously known as Griffith's transformation experiments.<\/p><div id=\"m44485-fig-ch14_01_02\" class=\"figure\" title=\"Figure&#xA0;14.3.&#xA0;\"><div class=\"body\"><div class=\"mediaobject\"><span id=\"m44485-fs-id1631652\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155647\/Figure_14_01_02.jpg\" width=\"525\" alt=\"On the left is a photo of a live mouse, representing a mouse injected with heat-killed, virulent S strain. On the right is a photo of a dead mouse, representing a mouse injected with heat-killed, virulent S strain and live, non-virulent R strain.\"\/><\/div><\/div><div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.3<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"\/><\/div><div class=\"caption\">Two strains of <span class=\"emphasis\"><em>S. pneumoniae<\/em><\/span> were used in Griffith\u2019s transformation experiments. The R strain is non-pathogenic. The S strain is pathogenic and causes death. When Griffith injected a mouse with the heat-killed S strain and a live R strain, the mouse died. The S strain was recovered from the dead mouse. Thus, Griffith concluded that something had passed from the heat-killed S strain to the R strain, transforming the R strain into S strain in the process. (credit \"living mouse\": modification of work by NIH; credit \"dead mouse\": modification of work by Sarah Marriage)<\/div><\/div><p><span id=\"m44485-fs-id2890946\"> <\/span>Scientists Oswald Avery, Colin MacLeod, and Maclyn McCarty (1944) were interested in exploring this transforming principle further. They isolated the S strain from the dead mice and isolated the proteins and nucleic acids, namely RNA and DNA, as these were possible candidates for the molecule of heredity. They conducted a systematic elimination study. They used enzymes that specifically degraded each component and then used each mixture separately to transform the R strain. They found that when DNA was degraded, the resulting mixture was no longer able to transform the bacteria, whereas all of the other combinations were able to transform the bacteria. This led them to conclude that DNA was the transforming principle.<\/p><div id=\"m44485-fs-id1772414\" class=\"note career\"><div class=\"title\"><span class=\"cnx-gentext-tip-t\">Career Connection<\/span><\/div><div class=\"body\"><p title=\"Forensic Scientists and DNA Analysis\"><span id=\"m44485-fs-id2115765\"> <\/span><\/p><div class=\"title\"><b>Forensic Scientists and DNA Analysis<\/b><\/div><p title=\"Forensic Scientists and DNA Analysis\">DNA evidence was used for the first time to solve an immigration case. The story started with a teenage boy returning to London from Ghana to be with his mother. Immigration authorities at the airport were suspicious of him, thinking that he was traveling on a forged passport. After much persuasion, he was allowed to go live with his mother, but the immigration authorities did not drop the case against him. All types of evidence, including photographs, were provided to the authorities, but deportation proceedings were started nevertheless. Around the same time, Dr. Alec Jeffreys of Leicester University in the United Kingdom had invented a technique known as DNA fingerprinting. The immigration authorities approached Dr. Jeffreys for help. He took DNA samples from the mother and three of her children, plus an unrelated mother, and compared the samples with the boy\u2019s DNA. Because the biological father was not in the picture, DNA from the three children was compared with the boy\u2019s DNA. He found a match in the boy\u2019s DNA for both the mother and his three siblings. He concluded that the boy was indeed the mother\u2019s son.<\/p><p><span id=\"m44485-fs-id1227579\"> <\/span>Forensic scientists analyze many items, including documents, handwriting, firearms, and biological samples. They analyze the DNA content of hair, semen, saliva, and blood, and compare it with a database of DNA profiles of known criminals. Analysis includes DNA isolation, sequencing, and sequence analysis; most forensic DNA analysis involves polymerase chain reaction (PCR) amplification of short tandem repeat (STR) loci and electrophoresis to determine the length of the PCR-amplified fragment. Only mitochondrial DNA is sequenced for forensics. Forensic scientists are expected to appear at court hearings to present their findings. They are usually employed in crime labs of city and state government agencies. Geneticists experimenting with DNA techniques also work for scientific and research organizations, pharmaceutical industries, and college and university labs. Students wishing to pursue a career as a forensic scientist should have at least a bachelor's degree in chemistry, biology, or physics, and preferably some experience working in a laboratory.<\/p><\/div><\/div><p><span id=\"m44485-fs-id2025461\"> <\/span>Experiments conducted by Martha Chase and Alfred Hershey in 1952 provided confirmatory evidence that DNA was the genetic material and not proteins. Chase and Hershey were studying a bacteriophage, which is a virus that infects bacteria. Viruses typically have a simple structure: a protein coat, called the capsid, and a nucleic acid core that contains the genetic material, either DNA or RNA. The bacteriophage infects the host bacterial cell by attaching to its surface, and then it injects its nucleic acids inside the cell. The phage DNA makes multiple copies of itself using the host machinery, and eventually the host cell bursts, releasing a large number of bacteriophages. Hershey and Chase labeled one batch of phage with radioactive sulfur, <sup>35<\/sup>S, to label the protein coat. Another batch of phage were labeled with radioactive phosphorus, <sup>32<\/sup>P. Because phosphorous is found in DNA, but not protein, the DNA and not the protein would be tagged with radioactive phosphorus.<\/p><p><span id=\"m44485-fs-id1352111\"> <\/span>Each batch of phage was allowed to infect the cells separately. After infection, the phage bacterial suspension was put in a blender, which caused the phage coat to be detached from the host cell. The phage and bacterial suspension was spun down in a centrifuge. The heavier bacterial cells settled down and formed a pellet, whereas the lighter phage particles stayed in the supernatant. In the tube that contained phage labeled with<sup> 35<\/sup>S, the supernatant contained the radioactively labeled phage, whereas no radioactivity was detected in the pellet. In the tube that contained the phage labeled with <sup>32<\/sup>P, the radioactivity was detected in the pellet that contained the heavier bacterial cells, and no radioactivity was detected in the supernatant.  Hershey and Chase concluded that it was the phage DNA that was injected\ninto the cell and carried information to produce more phage particles, thus providing evidence that DNA was the genetic material and not proteins (<a class=\"xref target-figure\" href=\"ch14.html#m44485-fig-ch14_01_03\" title=\"Figure&#xA0;14.4.&#xA0;\">Figure\u00a014.4<\/a>).<\/p><div id=\"m44485-fig-ch14_01_03\" class=\"figure\" title=\"Figure&#xA0;14.4.&#xA0;\"><div class=\"body\"><div class=\"mediaobject\"><span id=\"m44485-fs-id1879663\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155649\/Figure_14_01_03.jpg\" width=\"400\" alt=\"Illustration shows bacteria being infected by phage labeled with ^{35}S, which is incorporated into the protein coat, or ^{32}P, which is incorporated into the DNA. Infected bacteria were separated from phage by centrifugation and cultured. The bacteria that had been infected with phage containing ^{32}P-labeled DNA made radioactive phage. The bacteria that had been infected with ^{35}S-labeled phage produced unlabeled phage. The results support the hypothesis that DNA, and not protein, is the genetic material.\"\/><\/div><\/div><div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.4<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"\/><\/div><div class=\"caption\">In Hershey and Chase's experiments, bacteria were infected with phage radiolabeled with either <sup>35<\/sup>S, which labels protein, or <sup>32<\/sup>P, which labels DNA. Only <sup>32<\/sup>P entered the bacterial cells, indicating that DNA is the genetic material.<\/div><\/div><p><span id=\"m44485-fs-id1430603\"> <\/span>Around this same time, Austrian biochemist Erwin Chargaff examined the content of DNA in different species and found that the amounts of adenine, thymine, guanine, and cytosine were not found in equal quantities, and that it varied from species to species, but not between individuals of the same species. He found that the amount of adenine equals the amount of thymine, and the amount of cytosine equals the amount of guanine, or A = T and G = C. This is also known as Chargaff\u2019s rules. This finding proved immensely useful when Watson and Crick were getting ready to propose their DNA double helix model.<\/p><\/div><div xml:lang=\"en\" class=\"section module\" title=\"14.2.&#xA0;DNA Structure and Sequencing\"><div class=\"titlepage\"><div><div><h2 id=\"m44486\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.2<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Structure and Sequencing<sup><a href=\"co03.html#book-attribution-m44486\">*<\/a><\/sup><\/span><\/span><\/h2><\/div><div class=\"abstract\"><div class=\"title\"><span><span class=\"cnx-gentext-abstract cnx-gentext-autogenerated\"><span class=\"cnx-gentext-abstract cnx-gentext-t\"\/><\/span><\/span><\/div><p>By the end of this section, you will be able to:\n<\/p><div class=\"itemizedlist\"><ul class=\"itemizedlist\"><li class=\"listitem\"><p>Describe the structure of DNA<\/p><\/li><li class=\"listitem\"><p>Explain the Sanger method of DNA sequencing<\/p><\/li><li class=\"listitem\"><p>Discuss the similarities and differences between eukaryotic and prokaryotic DNA<\/p><\/li><\/ul><\/div><\/div><\/div><\/div><div class=\"toc\"><ul><li class=\"toc-section\"><a href=\"#m44486-fs-id1671532\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Sequencing Techniques<\/span><\/a><ul><li class=\"toc-section\"><a href=\"#m44486-fs-id3294130\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Packaging in Cells<\/span><\/a><\/li><\/ul><\/li><\/ul><\/div><p><span id=\"m44486-fs-id2164409\"> <\/span>The building blocks of DNA are nucleotides. The important components of the nucleotide are a nitrogenous base, deoxyribose (5-carbon sugar), and a phosphate group (<a class=\"xref target-figure\" href=\"ch14.html#m44486-fig-ch14_02_01\" title=\"Figure&#xA0;14.5.&#xA0;\">Figure\u00a014.5<\/a>). The nucleotide is named depending on the nitrogenous base. The nitrogenous base can be a purine such as adenine (A) and guanine (G), or a pyrimidine such as cytosine (C) and thymine (T).<\/p><div id=\"m44486-fig-ch14_02_01\" class=\"figure\" title=\"Figure&#xA0;14.5.&#xA0;\"><div class=\"body\"><div class=\"mediaobject\"><span id=\"m44486-fs-id1760452\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155652\/Figure_14_02_01.jpg\" width=\"500\" alt=\"Illustration depicts the structure of a nucleoside, which is made up of a pentose with a nitrogenous base attached at the 1' position. There are two kinds of nitrogenous bases: pyrimidines, which have one six-membered ring, and purines, which have a six-membered ring fused to a five-membered ring. Cytosine, thymine, and uracil are pyrimidines, and adenine and guanine are purines. A nucleoside with a phosphate attached at the 5' position is called a mononucleotide. A nucleoside with two or three phosphates attached is called a nucleotide diphosphate or nucleotide triphosphate, respectively.\"\/><\/div><\/div><div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.5<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"\/><\/div><div class=\"caption\">Each nucleotide is made up of a sugar, a phosphate group, and a nitrogenous base. The sugar is deoxyribose in DNA and ribose in RNA.<\/div><\/div><p><span id=\"m44486-fs-id1912233\"> <\/span>The nucleotides combine with each other by covalent bonds known as phosphodiester bonds or linkages. The purines have a double ring structure with a six-membered ring fused to a five-membered ring. Pyrimidines are smaller in size; they have a single six-membered ring structure. The carbon atoms of the five-carbon sugar are numbered 1', 2', 3', 4', and 5' (1' is read as \u201cone prime\u201d). The phosphate residue is attached to the hydroxyl group of the 5' carbon of one sugar of one nucleotide and the hydroxyl group of the 3' carbon of the sugar of the next nucleotide, thereby forming a 5'-3' phosphodiester bond.<\/p><p><span id=\"m44486-fs-id2019239\"> <\/span>In the 1950s, Francis Crick and James Watson worked together to determine the structure of DNA at the University of Cambridge, England. Other scientists like Linus Pauling and Maurice Wilkins were also actively exploring this field. Pauling had discovered the secondary structure of proteins using X-ray crystallography. In Wilkins\u2019 lab, researcher Rosalind Franklin was using X-ray diffraction methods to understand the structure of DNA. Watson and Crick were able to piece together the puzzle of the DNA molecule on the basis of Franklin's data because Crick had also studied X-ray diffraction (<a class=\"xref target-figure\" href=\"ch14.html#m44486-fig-ch14_02_02\" title=\"Figure&#xA0;14.6.&#xA0;\">Figure\u00a014.6<\/a>). In 1962, James Watson, Francis Crick, and Maurice Wilkins were awarded the Nobel Prize in Medicine. Unfortunately, by then Franklin had died, and Nobel prizes are not awarded posthumously.<\/p><div id=\"m44486-fig-ch14_02_02\" class=\"figure\" title=\"Figure&#xA0;14.6.&#xA0;\"><div class=\"body\"><div class=\"mediaobject\"><span id=\"m44486-fs-id2075482\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155654\/Figure_14_02_02ab_new.jpg\" width=\"500\" alt=\"The photo in part A shows James Watson, Francis Crick, and Maclyn McCarty. The x-ray diffraction pattern in part b is symmetrical, with dots in an x-shape\"\/><\/div><\/div><div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.6<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"\/><\/div><div class=\"caption\">The work of pioneering scientists (a) James Watson, Francis Crick, and Maclyn McCarty led to our present day understanding of DNA. Scientist Rosalind Franklin discovered (b) the X-ray diffraction pattern of DNA, which helped to elucidate its double helix structure. (credit a: modification of work by Marjorie McCarty, Public Library of Science)<\/div><\/div><p><span id=\"m44486-fs-id2317138\"> <\/span>Watson and Crick proposed that DNA is made up of two strands that are twisted around each other to form a right-handed helix. Base pairing takes place between a purine and pyrimidine; namely, A pairs with T and G pairs with C. Adenine and thymine are complementary base pairs, and cytosine and guanine are also complementary base pairs. The base pairs are stabilized by hydrogen bonds; adenine and thymine form two hydrogen bonds and cytosine and guanine form three hydrogen bonds. The two strands are anti-parallel in nature; that is, the 3' end of one strand faces the 5' end of the other strand. The sugar and phosphate of the nucleotides form the backbone of the structure, whereas the nitrogenous bases are stacked inside. Each base pair is separated from the other base pair by a distance of 0.34 nm, and each turn of the helix measures 3.4 nm. Therefore, ten base pairs are present per turn of the helix. The diameter of the DNA double helix is 2 nm, and it is uniform throughout. Only the pairing between a purine and pyrimidine can explain the uniform diameter. The twisting of the two strands around each other results in the formation of uniformly spaced major and minor grooves (<a class=\"xref target-figure\" href=\"ch14.html#m44486-fig-ch14_02_03\" title=\"Figure&#xA0;14.7.&#xA0;\">Figure\u00a014.7<\/a>).<\/p><div id=\"m44486-fig-ch14_02_03\" class=\"figure\" title=\"Figure&#xA0;14.7.&#xA0;\"><div class=\"body\"><div class=\"mediaobject\"><span id=\"m44486-fs-id2144919\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155657\/Figure_14_02_03abc.jpg\" width=\"450\" alt=\"Part A shows an illustration of a DNA double helix, which has a sugar-phosphate backbone on the outside and nitrogenous base pairs on the inside. Part B shows base pairing between thymine and adenine, which form two hydrogen bonds, and between guanine and cytosine, which form three hydrogen bonds. Part C shows a molecular model of the DNA double helix. The outside of the helix alternates between wide gaps, called major grooves, and narrow gaps, called minor grooves.\"\/><\/div><\/div><div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.7<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"\/><\/div><div class=\"caption\">DNA has (a) a double helix structure and (b) phosphodiester bonds. The (c) major and minor grooves are binding sites for DNA binding proteins during processes such as transcription (the copying of RNA from DNA) and replication.<\/div><\/div><div class=\"section\" title=\"DNA Sequencing Techniques\"><div class=\"titlepage\"><div><div><h3 id=\"m44486-fs-id1671532\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Sequencing Techniques<\/span><\/span><\/h3><\/div><\/div><\/div><p><span id=\"m44486-fs-id2060998\"> <\/span>Until the 1990s, the sequencing of DNA (reading the sequence of DNA) was a relatively expensive and long process. Using radiolabeled nucleotides also compounded the problem through safety concerns. With currently available technology and automated machines, the process is cheap, safer, and can be completed in a matter of hours. Fred Sanger developed the sequencing method used for the human genome sequencing project, which is widely used today (<a class=\"xref target-figure\" href=\"ch14.html#m44486-fig-ch14_02_04\" title=\"Figure&#xA0;14.8.&#xA0;\">Figure\u00a014.8<\/a>).<\/p><div id=\"m44486-fs-id2117592\" class=\"note interactive\"><div class=\"title\"><span class=\"cnx-gentext-tip-t\">Link to Learning<\/span><\/div><div class=\"body\"><div class=\"mediaobject\"><span id=\"m44486-fs-id1958775\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155659\/DNA_sequencing.png\" width=\"120\" alt=\"QR Code representing a URL\"\/><\/div><p><span id=\"m44486-fs-id2897121\"> <\/span>Visit <a class=\"link\" href=\"http:\/\/openstaxcollege.org\/l\/DNA_sequencing\" target=\"\">this site<\/a> to watch a video explaining the DNA sequence reading technique that resulted from Sanger\u2019s work.<\/p><\/div><\/div><p><span id=\"m44486-fs-id1695688\"> <\/span>The method is known as the dideoxy chain termination method. The sequencing method is based on the use of chain terminators, the dideoxynucleotides (ddNTPs). The dideoxynucleotides, or ddNTPSs, differ from the deoxynucleotides by the lack of a free 3' OH group on the five-carbon sugar. If a ddNTP is added to a growing a DNA strand, the chain is not extended any further because the free 3' OH group needed to add another nucleotide is not available. By using a predetermined ratio of deoxyribonucleotides to dideoxynucleotides, it is possible to generate DNA fragments of different sizes.<\/p><div id=\"m44486-fig-ch14_02_04\" class=\"figure\" title=\"Figure&#xA0;14.8.&#xA0;\"><div class=\"body\"><div class=\"mediaobject\"><span id=\"m44486-fs-id1822083\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155702\/Figure_14_02_04ab.jpg\" width=\"400\" alt=\"Part A shows a template DNA strand and newly synthesized strands that were generated in the presence of dideoxynucleotides that terminate the chain at different points to generate fragments of different sizes. Each dideoxynucleotide is labeled a different color. Part B shows a sequence readout that was generated after the DNA fragments were separated on the basis of size. The color of the fragment indicates the identity of the nucleotide at the end of a given fragment. By reading the colors in order, the DNA sequence can be determined.\"\/><\/div><\/div><div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.8<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"\/><\/div><div class=\"caption\">In Frederick Sanger's dideoxy chain termination method, dye-labeled dideoxynucleotides are used to generate DNA fragments that terminate at different points. The DNA is separated by capillary electrophoresis on the basis of size, and from the order of fragments formed, the DNA sequence can be read. The DNA sequence readout is shown on an electropherogram that is generated by a laser scanner.<\/div><\/div><p><span id=\"m44486-fs-id1797232\"> <\/span>The DNA sample to be sequenced is denatured or separated into two strands by heating it to high temperatures. The DNA is divided into four tubes in which a primer, DNA polymerase, and all four nucleotides (A, T, G, and C) are added. In addition to each of the four tubes, limited quantities of one of the four dideoxynucleotides are added to each tube respectively. The tubes are labeled as A, T, G, and C according to the ddNTP added. For detection purposes, each of the four dideoxynucleotides carries a different fluorescent label. Chain elongation continues until a fluorescent dideoxy nucleotide is incorporated, after which no further elongation takes place. After the reaction is over, electrophoresis is performed. Even a difference in length of a single base can be detected. The sequence is read from a laser scanner. For his work on DNA sequencing, Sanger received a Nobel Prize in chemistry in 1980.<\/p><div id=\"m44486-fs-id1352111\" class=\"note interactive\"><div class=\"title\"><span class=\"cnx-gentext-tip-t\">Link to Learning<\/span><\/div><div class=\"body\"><div class=\"mediaobject\"><span id=\"m44486-fs-id1483229\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155704\/DNA_and_genomes.png\" width=\"120\" alt=\"QR Code representing a URL\"\/><\/div><p><span id=\"m44486-fs-id1968434\"> <\/span>Sanger\u2019s genome sequencing has led to a race to sequence human genomes at a rapid speed and low cost, often referred to as the $1000 in one day sequence. Learn more by selecting the Sequencing at Speed animation <a class=\"link\" href=\"http:\/\/openstaxcollege.org\/l\/DNA_and_genomes\" target=\"\">here<\/a>.<\/p><\/div><\/div><p><span id=\"m44486-fs-id2573656\"> <\/span>Gel <em class=\"glossterm\"><span id=\"m44486-autoid-cnx2dbk-id1615069\"> <\/span>electrophoresis<\/em><a id=\"id503706\" class=\"indexterm\"> is a technique used to separate DNA fragments of different sizes. Usually the gel is made of a chemical called agarose. Agarose powder is added to a buffer and heated. After cooling, the gel solution is poured into a casting tray. Once the gel has solidified, the DNA is loaded on the gel and electric current is applied. The DNA has a net negative charge and moves from the negative electrode toward the positive electrode. The electric current is applied for sufficient time to let the DNA separate according to size; the smallest fragments will be farthest from the well (where the DNA was loaded), and the heavier molecular weight fragments will be closest to the well. Once the DNA is separated, the gel is stained with a DNA-specific dye for viewing it (<\/a><a class=\"xref target-figure\" href=\"ch14.html#m44486-fig-ch14_02_05\" title=\"Figure&#xA0;14.9.&#xA0;\">Figure\u00a014.9<\/a>).<\/p><div id=\"m44486-fig-ch14_02_05\" class=\"figure\" title=\"Figure&#xA0;14.9.&#xA0;\"><div class=\"body\"><div class=\"mediaobject\"><span id=\"m44486-fs-id2022421\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155706\/Figure_14_02_05.jpg\" width=\"320\" alt=\"Photo shows an agarose gel illuminated under UV light. The gel is nine lanes across. Each lane was loaded with a sample containing DNA fragments of differing size that have separated as they travel through the gel, from top to bottom. The DNA appears as thin, white bands on a black background. Lanes one and nine contain many bands from a DNA standard. These bands are closely spaced toward the top, and spaced farther apart further down the gel. Lanes two through eight contain one or two bands each. Some of these bands are identical in size and run the same distance into the gel. Others run a slightly different distance, indicating a small difference in size.\"\/><\/div><\/div><div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.9<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"\/><\/div><div class=\"caption\">DNA can be separated on the basis of size using gel electrophoresis. (credit: James Jacob, Tompkins Cortland Community College)<\/div><\/div><div id=\"m44486-fs-id1288287\" class=\"note evolution\"><div class=\"title\"><span class=\"cnx-gentext-tip-t\">Evolution Connection<\/span><\/div><div class=\"body\"><p title=\"Neanderthal Genome: How Are We Related?\"><span id=\"m44486-fs-id2013345\"> <\/span><\/p><div class=\"title\"><b>Neanderthal Genome: How Are We Related?<\/b><\/div><p title=\"Neanderthal Genome: How Are We Related?\">The first draft sequence of the Neanderthal genome was recently published by Richard E. Green et al. in 2010.<sup><sup>[<a id=\"m44486-fs-id1277293\" href=\"#ftn.m44486-fs-id1277293\" class=\"footnote\">11<\/a>]<\/sup><\/sup> Neanderthals are the closest ancestors of present-day humans. They were known to have lived in Europe and Western Asia before they disappeared from fossil records approximately 30,000 years ago. Green\u2019s team studied almost 40,000-year-old fossil remains that were selected from sites across the world. Extremely sophisticated means of sample preparation and DNA sequencing were employed because of the fragile nature of the bones and heavy microbial contamination. In their study, the scientists were able to sequence some four billion base pairs. The Neanderthal sequence was compared with that of present-day humans from across the world. After comparing the sequences, the researchers found that the Neanderthal genome had 2 to 3 percent greater similarity to people living outside Africa than to people in Africa. While current theories have suggested that all present-day humans can be traced to a small ancestral population in Africa, the data from the Neanderthal genome may contradict this view. Green and his colleagues also discovered DNA segments among people in Europe and Asia that are more similar to Neanderthal sequences than to other contemporary human sequences. Another interesting observation was that Neanderthals are as closely related to people from Papua New Guinea as to those from China or France. This is surprising because Neanderthal fossil remains have been located only in Europe and West Asia. Most likely, genetic exchange took place between Neanderthals and modern humans as modern humans emerged out of Africa, before the divergence of Europeans, East Asians, and Papua New Guineans.<\/p><p><span id=\"m44486-fs-id1471220\"> <\/span>Several genes seem to have undergone changes from Neanderthals during the evolution of present-day humans. These genes are involved in cranial structure, metabolism, skin morphology, and cognitive development. One of the genes that is of particular interest is <span class=\"emphasis\"><em>RUNX2<\/em><\/span>, which is different in modern day humans and Neanderthals. This gene is responsible for the prominent frontal bone, bell-shaped rib cage, and dental differences seen in Neanderthals. It is speculated that an evolutionary change in <span class=\"emphasis\"><em>RUNX2<\/em><\/span> was important in the origin of modern-day humans, and this affected the cranium and the upper body.<\/p><\/div><\/div><div id=\"m44486-fs-id1770393\" class=\"note interactive\"><div class=\"title\"><span class=\"cnx-gentext-tip-t\">Link to Learning<\/span><\/div><div class=\"body\"><div class=\"mediaobject\"><span id=\"m44486-fs-id2308662\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155708\/neanderthal.png\" width=\"120\" alt=\"QR Code representing a URL\"\/><\/div><p><span id=\"m44486-fs-id2026323\"> <\/span>Watch <a class=\"link\" href=\"http:\/\/openstaxcollege.org\/l\/neanderthal\" target=\"\">Svante P\u00e4\u00e4bo\u2019s talk<\/a> explaining the Neanderthal genome research at the 2011 annual TED (Technology, Entertainment, Design) conference.<\/p><\/div><\/div><div class=\"section\" title=\"DNA Packaging in Cells\"><div class=\"titlepage\"><div><div><h4 id=\"m44486-fs-id3294130\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Packaging in Cells<\/span><\/span><\/h4><\/div><\/div><\/div><p><span id=\"m44486-fs-id2215894\"> <\/span>When comparing prokaryotic cells to eukaryotic cells, prokaryotes are much simpler than eukaryotes in many of their features (<a class=\"xref target-figure\" href=\"ch14.html#m44486-fig-ch14_02_06\" title=\"Figure&#xA0;14.10.&#xA0;\">Figure\u00a014.10<\/a>). Most prokaryotes contain a single, circular chromosome that is found in an area of the cytoplasm called the nucleoid.<\/p><div id=\"m44486-fs-id1973249\" class=\"note art-connection\"><div class=\"title\"><span class=\"cnx-gentext-tip-t\">Art Connection<\/span><\/div><div class=\"body\"><p><span id=\"m44486-fs-id2589720\"> <\/span><\/p><div id=\"m44486-fig-ch14_02_06\" class=\"figure\" title=\"Figure&#xA0;14.10.&#xA0;\"><div class=\"body\"><span class=\"inlinemediaobject\"><span id=\"m44486-fs-id1970814\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155711\/Figure_14_02_06_new.png\" width=\"450\" alt=\"Illustration shows a eukaryotic cell, which has a membrane-bound nucleus containing chromatin and a nucleolus, and a prokaryotic cell, which has DNA contained in an area of the cytoplasm called the nucleoid. The prokaryotic cell is much smaller than the eukaryotic cell.\"\/><\/span><\/div><div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.10<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"\/><\/div><div class=\"caption\">A eukaryote contains a well-defined nucleus, whereas in prokaryotes, the chromosome lies in the cytoplasm in an area called the nucleoid.<\/div><\/div><p><span id=\"m44486-fs-id1512144\"> <\/span>In eukaryotic cells, DNA and RNA synthesis occur in a separate compartment from protein synthesis. In prokaryotic cells, both processes occur together. What advantages might there be to separating the processes? What advantages might there be to having them occur together?<\/p><\/div><\/div><p><span id=\"m44486-fs-id2962722\"> <\/span>The size of the genome in one of the most well-studied prokaryotes, <span class=\"emphasis\"><em>E.coli,<\/em><\/span> is 4.6 million base pairs (approximately 1.1 mm, if cut and stretched out). So how does this fit inside a small bacterial cell? The DNA is twisted by what is known as supercoiling. Supercoiling means that DNA is either under-wound (less than one turn of the helix per 10 base pairs) or over-wound (more than 1 turn per 10 base pairs) from its normal relaxed state. Some proteins are known to be involved in the supercoiling; other proteins and enzymes such as DNA gyrase help in maintaining the supercoiled structure.<\/p><p><span id=\"m44486-fs-id2235232\"> <\/span>Eukaryotes, whose chromosomes each consist of a linear DNA molecule, employ a different type of packing strategy to fit their DNA inside the nucleus (<a class=\"xref target-figure\" href=\"ch14.html#m44486-fig-ch14_02_07\" title=\"Figure&#xA0;14.11.&#xA0;\">Figure\u00a014.11<\/a>). At the most basic level, DNA is wrapped around proteins known as histones to form structures called nucleosomes. The histones are evolutionarily conserved proteins that are rich in basic amino acids and form an octamer. The DNA (which is negatively charged because of the phosphate groups) is wrapped tightly around the histone core. This nucleosome is linked to the next one with the help of a linker DNA. This is also known as the \u201cbeads on a string\u201d structure. This is further compacted into a 30 nm fiber, which is the diameter of the structure. At the metaphase stage, the chromosomes are at their most compact, are approximately 700 nm in width, and are found in association with scaffold proteins.<\/p><p><span id=\"m44486-fs-id2685429\"> <\/span>In interphase, eukaryotic chromosomes have two distinct regions that can be distinguished by staining. The tightly packaged region is known as heterochromatin, and the less dense region is known as euchromatin. Heterochromatin usually contains genes that are not expressed, and is found in the regions of the centromere and telomeres. The euchromatin usually contains genes that are transcribed, with DNA packaged around nucleosomes but not further compacted.<\/p><div id=\"m44486-fig-ch14_02_07\" class=\"figure\" title=\"Figure&#xA0;14.11.&#xA0;\"><div class=\"body\"><div class=\"mediaobject\"><span id=\"m44486-fs-id1987230\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155713\/Figure_14_02_07.jpg\" width=\"275\" alt=\"Illustration shows the levels of organization of eukaryotic chromosomes, starting with the DNA double helix, which wraps around histone proteins. The entire DNA molecule wraps around many clusters of histone proteins, forming a structure that looks like beads on a string. The chromatin is further condensed by wrapping around a protein core. The result is a compact chromosome, shown in duplicated form.\"\/><\/div><\/div><div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.11<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"\/><\/div><div class=\"caption\">These figures illustrate the compaction of the eukaryotic chromosome.<\/div><\/div><\/div><\/div><\/div><div xml:lang=\"en\" class=\"section module\" title=\"14.3.&#xA0;Basics of DNA Replication\"><div class=\"titlepage\"><div><div><h2 id=\"m44487\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.3<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Basics of DNA Replication<sup><a href=\"co03.html#book-attribution-m44487\">*<\/a><\/sup><\/span><\/span><\/h2><\/div><div class=\"abstract\"><div class=\"title\"><span><span class=\"cnx-gentext-abstract cnx-gentext-autogenerated\"><span class=\"cnx-gentext-abstract cnx-gentext-t\"\/><\/span><\/span><\/div><p>By the end of this section, you will be able to:\n<\/p><div class=\"itemizedlist\"><ul class=\"itemizedlist\"><li class=\"listitem\"><p>Explain how the structure of DNA reveals the replication process<\/p><\/li><li class=\"listitem\"><p>Describe the Meselson and Stahl experiments<\/p><\/li><\/ul><\/div><\/div><\/div><\/div><div class=\"toc\"><ul\/><\/div><p><span id=\"m44487-fs-id2265995\"> <\/span>The elucidation of the structure of the double helix provided a hint as to how DNA divides and makes copies of itself. This model suggests that the two strands of the double helix separate during replication, and each strand serves as a template from which the new complementary strand is copied. What was not clear was how the replication took place. There were three models suggested (<a class=\"xref target-figure\" href=\"ch14.html#m44487-fig-ch14_03_01\" title=\"Figure&#xA0;14.12.&#xA0;\">Figure\u00a014.12<\/a>): conservative, semi-conservative, and dispersive.<\/p><div id=\"m44487-fig-ch14_03_01\" class=\"figure\" title=\"Figure&#xA0;14.12.&#xA0;\"><div class=\"body\"><div class=\"mediaobject\"><span id=\"m44487-fs-id2051052\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155715\/Figure_14_03_01.jpg\" width=\"275\" alt=\"Illustration shows the conservative, semi-conservative, and dispersive models of DNA synthesis. In the conservative model, when DNA is replicated and both newly synthesized strands are paired together. In the semi-conservative model, each newly synthesized strand pairs with a parent strand. In the dispersive model, newly synthesized DNA is interspersed with parent DNA within both DNA strands.\"\/><\/div><\/div><div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.12<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"\/><\/div><div class=\"caption\">The three suggested models of DNA replication. Grey indicates the original DNA strands, and blue indicates newly synthesized DNA.<\/div><\/div><p><span id=\"m44487-fs-id1685167\"> <\/span>In conservative replication, the parental DNA remains together, and the newly formed daughter strands are together. The semi-conservative method suggests that each of the two parental DNA strands act as a template for new DNA to be synthesized; after replication, each double-stranded DNA includes one parental or \u201cold\u201d strand and one \u201cnew\u201d strand. In the dispersive model, both copies of DNA have double-stranded segments of parental DNA and newly synthesized DNA interspersed.<\/p><p><span id=\"m44487-fs-id2216817\"> <\/span>Meselson and Stahl were interested in understanding how DNA replicates. They grew <span class=\"emphasis\"><em>E. coli<\/em><\/span> for several generations in a medium containing a \u201cheavy\u201d isotope of nitrogen (<sup>15<\/sup>N) that gets incorporated into nitrogenous bases, and eventually into the DNA (<a class=\"xref target-figure\" href=\"ch14.html#m44487-fig-ch14_03_02\" title=\"Figure&#xA0;14.13.&#xA0;\">Figure\u00a014.13<\/a>).<\/p><div id=\"m44487-fig-ch14_03_02\" class=\"figure\" title=\"Figure&#xA0;14.13.&#xA0;\"><div class=\"body\"><div class=\"mediaobject\"><span id=\"m44487-fs-id1640010\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155717\/Figure_14_03_02.jpg\" width=\"350\" alt=\"Illustration shows an experiment in which E. coli was grown initially in media containing ^{15}N nucleotides. When the DNA was extracted and run in an ultracentrifuge, a band of DNA appeared low in the tube. The culture was next placed in ^{14}N medium. After one generation, all of the DNA appeared in the middle of the tube, indicating that the DNA was a mixture of half ^{14}N and half ^{15}N DNA. After two generations, half of the DNA appeared in the middle of the tube, and half appeared higher up, indicating that half the DNA contained 50% ^{15}N, and half contained ^{14}N only. In subsequent generations, more and more of the DNA appeared in the upper, ^{14}N band.\"\/><\/div><\/div><div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.13<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"\/><\/div><div class=\"caption\">Meselson and Stahl experimented with <span class=\"emphasis\"><em>E. coli<\/em><\/span> grown first in heavy nitrogen (<sup>15<\/sup>N) then in <sup>14<\/sup>N. DNA grown in <sup>15<\/sup>N (red band) is heavier than DNA grown in <sup>14<\/sup>N (orange band), and sediments to a lower level in cesium chloride solution in an ultracentrifuge. When DNA grown in <sup>15<\/sup>N is switched to media containing <sup>14<\/sup>N, after one round of cell division the DNA sediments halfway between the <sup>15<\/sup>N and <sup>14<\/sup>N levels, indicating that it now contains fifty percent <sup>14<\/sup>N. In subsequent cell divisions, an increasing amount of DNA contains <sup>14<\/sup>N only. This data supports the semi-conservative replication model. (credit: modification of work by Mariana Ruiz Villareal)<\/div><\/div><p><span id=\"m44487-fs-id2589720\"> <\/span>The <span class=\"emphasis\"><em>E. coli<\/em><\/span> culture was then shifted into medium containing <sup>14<\/sup>N and allowed to grow for one generation. The cells were harvested and the DNA was isolated. The DNA was centrifuged at high speeds in an ultracentrifuge. Some cells were allowed to grow for one more life cycle in <sup>14<\/sup>N and spun again. During the density gradient centrifugation, the DNA is loaded into a gradient (typically a salt such as cesium chloride or sucrose) and spun at high speeds of 50,000 to 60,000 rpm. Under these circumstances, the DNA will form a band according to its density in the gradient. DNA grown in <sup>15<\/sup>N will band at a higher density position than that grown in <sup>14<\/sup>N. Meselson and Stahl noted that after one generation of growth in <sup>14<\/sup>N after they had been shifted from <sup>15<\/sup>N, the single band observed was intermediate in position in between DNA of cells grown exclusively in<sup> 15<\/sup>N and <sup>14<\/sup>N. This suggested either a semi-conservative or dispersive mode of replication. The DNA harvested from cells grown for two generations in <sup>14<\/sup>N formed two bands: one DNA band was at the intermediate position between <sup>15<\/sup>N and <sup>14<\/sup>N, and the other corresponded to the band of <sup>14<\/sup>N DNA. These results could only be explained if DNA replicates in a semi-conservative manner. Therefore, the other two modes were ruled out.<\/p><p><span id=\"m44487-fs-id2854117\"> <\/span>During DNA replication, each of the two strands that make up the double helix serves as a template from which new strands are copied. The new strand will be complementary to the parental or \u201cold\u201d strand. When two daughter DNA copies are formed, they have the same sequence and are divided equally into the two daughter cells.<\/p><div id=\"m44487-fs-id1366889\" class=\"note interactive\"><div class=\"title\"><span class=\"cnx-gentext-tip-t\">Link to Learning<\/span><\/div><div class=\"body\"><div class=\"mediaobject\"><span id=\"m44487-fs-id1676042\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155720\/DNA_replication.png\" width=\"120\" alt=\"QR Code representing a URL\"\/><\/div><p><span id=\"m44487-fs-id2171177\"> <\/span>Click through <a class=\"link\" href=\"http:\/\/openstaxcollege.org\/l\/DNA_replicatio2\" target=\"\">this tutorial<\/a> on DNA replication.<\/p><\/div><\/div><\/div><div xml:lang=\"en\" class=\"section module\" title=\"14.4.&#xA0;DNA Replication in Prokaryotes\"><div class=\"titlepage\"><div><div><h2 id=\"m44488\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.4<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Replication in Prokaryotes<sup><a href=\"co03.html#book-attribution-m44488\">*<\/a><\/sup><\/span><\/span><\/h2><\/div><div class=\"abstract\"><div class=\"title\"><span><span class=\"cnx-gentext-abstract cnx-gentext-autogenerated\"><span class=\"cnx-gentext-abstract cnx-gentext-t\"\/><\/span><\/span><\/div><p>By the end of this section, you will be able to:\n<\/p><div class=\"itemizedlist\"><ul class=\"itemizedlist\"><li class=\"listitem\"><p>Explain the process of DNA replication in prokaryotes<\/p><\/li><li class=\"listitem\"><p>Discuss the role of different enzymes and proteins in supporting this process<\/p><\/li><\/ul><\/div><\/div><\/div><\/div><div class=\"toc\"><ul\/><\/div><p><span id=\"m44488-fs-id2571092\"> <\/span>DNA replication has been extremely well studied in prokaryotes primarily because of the small size of the genome and the mutants that are available. <span class=\"emphasis\"><em>E. coli <\/em><\/span>has 4.6 million base pairs in a single circular chromosome and all of it gets replicated in approximately 42 minutes, starting from a single origin of replication and proceeding around the circle in both directions. This means that approximately 1000 nucleotides are added per second. The process is quite rapid and occurs without many mistakes.<\/p><p><span id=\"m44488-fs-id1806393\"> <\/span>DNA replication employs a large number of proteins and enzymes, each of which plays a critical role during the process. One of the key players is the enzyme DNA polymerase, also known as DNA pol, which adds nucleotides one by one to the growing DNA chain that are complementary to the template strand. The addition of nucleotides requires energy; this energy is obtained from the nucleotides that have three phosphates attached to them, similar to ATP which has three phosphate groups attached. When the bond between the phosphates is broken, the energy released is used to form the phosphodiester bond between the incoming nucleotide and the growing chain. In prokaryotes, three main types of polymerases are known: DNA pol I, DNA pol II, and DNA pol III. It is now known that DNA pol III is the enzyme required for DNA synthesis; DNA pol I and DNA pol II are primarily required for repair.<\/p><p><span id=\"m44488-fs-id1676042\"> <\/span>How does the replication machinery know where to begin? It turns out that there are specific nucleotide sequences called origins of replication where replication begins. In <span class=\"emphasis\"><em>E. coli, <\/em><\/span>which has a single origin of replication on its one chromosome (as do most prokaryotes), it is approximately 245 base pairs long and is rich in AT sequences. The origin of replication is recognized by certain proteins that bind to this site. An enzyme called <em class=\"glossterm\"><span id=\"m44488-autoid-cnx2dbk-id1589581\"> <\/span>helicase<\/em><a id=\"id505329\" class=\"indexterm\"> unwinds the DNA by breaking the hydrogen bonds between the nitrogenous base pairs. ATP hydrolysis is required for this process. As the DNA opens up, Y-shaped structures called <em class=\"glossterm\"><span id=\"m44488-autoid-cnx2dbk-id1589586\"> <\/span>replication forks<\/em><\/a><a id=\"id505344\" class=\"indexterm\"> are formed. Two replication forks are formed at the origin of replication and these get extended bi- directionally as replication proceeds. <em class=\"glossterm\"><span id=\"m44488-autoid-cnx2dbk-id1589591\"> <\/span>Single-strand binding proteins<\/em><\/a><a id=\"id505359\" class=\"indexterm\"> coat the single strands of DNA near the replication fork to prevent the single-stranded DNA from winding back into a double helix. DNA polymerase is able to add nucleotides only in the 5' to 3' direction (a new DNA strand can be only extended in this direction). It also requires a free 3'-OH group to which it can add nucleotides by forming a phosphodiester bond between the 3'-OH end and the 5' phosphate of the next nucleotide. This essentially means that it cannot add nucleotides if a free 3'-OH group is not available. Then how does it add the first nucleotide? The problem is solved with the help of a primer that provides the free 3'-OH end. Another enzyme, RNA <em class=\"glossterm\"><span id=\"m44488-autoid-cnx2dbk-id1589600\"> <\/span>primase<\/em><\/a><a id=\"id505378\" class=\"indexterm\">, synthesizes an RNA primer that is about five to ten nucleotides long and complementary to the DNA. Because this sequence primes the DNA synthesis, it is appropriately called the <em class=\"glossterm\"><span id=\"m44488-autoid-cnx2dbk-id1589605\"> <\/span>primer<\/em><\/a><a id=\"id505394\" class=\"indexterm\">. DNA polymerase can now extend this RNA primer, adding nucleotides one by one that are complementary to the template strand (<\/a><a class=\"xref target-figure\" href=\"ch14.html#m44488-fig-ch14_04_01\" title=\"Figure&#xA0;14.14.&#xA0;\">Figure\u00a014.14<\/a>).<\/p><div id=\"m44488-fs-id1305287\" class=\"note art-connection\"><div class=\"title\"><span class=\"cnx-gentext-tip-t\">Art Connection<\/span><\/div><div class=\"body\"><p><span id=\"m44488-fs-id2979157\"> <\/span>\n<\/p><div id=\"m44488-fig-ch14_04_01\" class=\"figure\" title=\"Figure&#xA0;14.14.&#xA0;\"><div class=\"body\"><span class=\"inlinemediaobject\"><span id=\"m44488-fs-id2897265\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155722\/Figure_14_04_01.png\" width=\"400\" alt=\"Illustration shows the replication fork. Helicase unwinds the helix, and single-strand binding proteins prevent the helix from re-forming. Topoisomerase prevents the DNA from getting too tightly coiled ahead of the replication fork. DNA primase forms an RNA primer, and DNA polymerase extends the DNA strand from the RNA primer. DNA synthesis occurs only in the 5' to 3' direction. On the leading strand, DNA synthesis occurs continuously. On the lagging strand, DNA synthesis restarts many times as the helix unwinds, resulting in many short fragments called &#x201C;Okazaki fragments.&#x201D; DNA ligase joins the Okazaki fragments together into a single DNA molecule.\"\/><\/span><\/div><div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.14<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"\/><\/div><div class=\"caption\">A replication fork is formed when helicase separates the DNA strands at the origin of replication. The DNA tends to become more highly coiled ahead of the replication fork. Topoisomerase breaks and reforms DNA\u2019s phosphate backbone ahead of the replication fork, thereby relieving the pressure that results from this supercoiling. Single-strand binding proteins bind to the single-stranded DNA to prevent the helix from re-forming. Primase synthesizes an RNA primer. DNA polymerase III uses this primer to synthesize the daughter DNA strand. On the leading strand, DNA is synthesized continuously, whereas on the lagging strand, DNA is synthesized in short stretches called Okazaki fragments. DNA polymerase I replaces the RNA primer with DNA. DNA ligase seals the gaps between the Okazaki fragments, joining the fragments into a single DNA molecule. (credit: modification of work by Mariana Ruiz Villareal)<\/div><\/div><p><span id=\"m44488-fs-id1368727\"> <\/span>You isolate a cell strain in which the joining together of Okazaki fragments is impaired and suspect that a mutation has occurred in an enzyme found at the replication fork. Which enzyme is most likely to be mutated?<\/p><\/div><\/div><p><span id=\"m44488-fs-id1385221\"> <\/span>The replication fork moves at the rate of 1000 nucleotides per second. DNA polymerase can only extend in the 5' to 3' direction, which poses a slight problem at the replication fork. As we know, the DNA double helix is anti-parallel; that is, one strand is in the 5' to 3' direction and the other is oriented in the 3' to 5' direction. One strand, which is complementary to the 3' to 5' parental DNA strand, is synthesized continuously towards the replication fork because the polymerase can add nucleotides in this direction. This continuously synthesized strand is known as the <em class=\"glossterm\"><span id=\"m44488-autoid-cnx2dbk-id1237696\"> <\/span>leading strand<\/em><a id=\"id505512\" class=\"indexterm\">. The other strand, complementary to the 5' to 3' parental DNA, is extended away from the replication fork, in small fragments known as <em class=\"glossterm\"><span id=\"m44488-autoid-cnx2dbk-id1237700\"> <\/span>Okazaki fragments<\/em><\/a><a id=\"id505527\" class=\"indexterm\">, each requiring a primer to start the synthesis. Okazaki fragments are named after the Japanese scientist who first discovered them. The strand with the Okazaki fragments is known as the <em class=\"glossterm\"><span id=\"m44488-autoid-cnx2dbk-id1237706\"> <\/span>lagging strand<\/em><\/a><a id=\"id505542\" class=\"indexterm\">.<\/a><\/p><p><span id=\"m44488-fs-id2962574\"> <\/span>The leading strand can be extended by one primer alone, whereas the lagging strand needs a new primer for each of the short Okazaki fragments. The overall direction of the lagging strand will be 3' to 5', and that of the leading strand 5' to 3'. A protein called the <em class=\"glossterm\"><span id=\"m44488-autoid-cnx2dbk-id1237718\"> <\/span>sliding clamp<\/em><a id=\"id505565\" class=\"indexterm\"> holds the DNA polymerase in place as it continues to add nucleotides. The sliding clamp is a ring-shaped protein that binds to the DNA and holds the polymerase in place. <em class=\"glossterm\"><span id=\"m44488-autoid-cnx2dbk-id1237723\"> <\/span>Topoisomerase<\/em><\/a><a id=\"id505580\" class=\"indexterm\"> prevents the over-winding of the DNA double helix ahead of the replication fork as the DNA is opening up; it does so by causing temporary nicks in the DNA helix and then resealing it. As synthesis proceeds, the RNA primers are replaced by DNA. The primers are removed by the exonuclease activity of DNA pol I, and the gaps are filled in by deoxyribonucleotides. The nicks that remain between the newly synthesized DNA (that replaced the RNA primer) and the previously synthesized DNA are sealed by the enzyme DNA <em class=\"glossterm\"><span id=\"m44488-autoid-cnx2dbk-id1237730\"> <\/span>ligase<\/em><\/a><a id=\"id505598\" class=\"indexterm\"> that catalyzes the formation of phosphodiester linkage between the 3'-OH end of one nucleotide and the 5' phosphate end of the other fragment.<\/a><\/p><p><span id=\"m44488-fs-id1752302\"> <\/span>Once the chromosome has been completely replicated, the two DNA copies move into two different cells during cell division. The process of DNA replication can be summarized as follows:<\/p><div class=\"orderedlist\"><span id=\"m44488-fs-id2017788\"> <\/span><ol class=\"orderedlist\" type=\"1\"><li class=\"listitem\"><p>DNA unwinds at the origin of replication.<\/p><\/li><li class=\"listitem\"><p>Helicase opens up the DNA-forming replication forks; these are extended bidirectionally.<\/p><\/li><li class=\"listitem\"><p>Single-strand binding proteins coat the DNA around the replication fork to prevent rewinding of the DNA.<\/p><\/li><li class=\"listitem\"><p>Topoisomerase binds at the region ahead of the replication fork to prevent supercoiling.<\/p><\/li><li class=\"listitem\"><p>Primase synthesizes RNA primers complementary to the DNA strand.<\/p><\/li><li class=\"listitem\"><p>DNA polymerase starts adding nucleotides to the 3'-OH end of the primer.<\/p><\/li><li class=\"listitem\"><p>Elongation of both the lagging and the leading strand continues.<\/p><\/li><li class=\"listitem\"><p>RNA primers are removed by exonuclease activity.<\/p><\/li><li class=\"listitem\"><p>Gaps are filled by DNA pol by adding dNTPs.<\/p><\/li><li class=\"listitem\"><p>The gap between the two DNA fragments is sealed by DNA ligase, which helps in the formation of phosphodiester bonds.<\/p><\/li><\/ol><\/div><p><span id=\"m44488-fs-id2235232\"> <\/span>&lt;!--cnx.newline--&gt;<br\/><a class=\"xref target-table\" href=\"ch14.html#m44488-tab-ch14_04_01\" title=\"Table&#xA0;14.1.&#xA0;\">Table\u00a014.1<\/a> summarizes the enzymes involved in prokaryotic DNA replication and the functions of each.<\/p><div class=\"table\" id=\"m44488-tab-ch14_04_01\"><table cellpadding=\"0\" style=\"border: 1px solid; border-spacing: 0px;\"><caption><span class=\"cnx-gentext-caption cnx-gentext-t\">Table <\/span><span class=\"cnx-gentext-caption cnx-gentext-n\">14.1. <\/span><\/caption><thead valign=\"bottom\"><tr><th colspan=\"2\" style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">Prokaryotic DNA Replication: Enzymes and Their Function<\/th><\/tr><tr><th style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">Enzyme\/protein<\/th><th style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">Specific Function<\/th><\/tr><\/thead><tbody valign=\"top\"><tr><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">DNA pol I<\/td><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">Exonuclease activity removes RNA primer and replaces with newly synthesized DNA<\/td><\/tr><tr><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">DNA pol II<\/td><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">Repair function<\/td><\/tr><tr><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">DNA pol III<\/td><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">Main enzyme that adds nucleotides in the 5'-3' direction<\/td><\/tr><tr><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">Helicase<\/td><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">Opens the DNA helix by breaking hydrogen bonds between the nitrogenous bases<\/td><\/tr><tr><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">Ligase<\/td><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">Seals the gaps between the Okazaki fragments to create one continuous DNA strand<\/td><\/tr><tr><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">Primase<\/td><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">Synthesizes RNA primers needed to start replication<\/td><\/tr><tr><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">Sliding Clamp<\/td><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">Helps to hold the DNA polymerase in place when nucleotides are being added<\/td><\/tr><tr><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">Topoisomerase<\/td><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">Helps relieve the stress on DNA when unwinding by causing breaks and then resealing the DNA<\/td><\/tr><tr><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 0 !important; text-align: left !important;\">Single-strand binding proteins (SSB)<\/td><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 0 !important; text-align: left !important;\">Binds to single-stranded DNA to avoid DNA rewinding back.<\/td><\/tr><\/tbody><\/table><\/div><div id=\"m44488-fs-id1672176\" class=\"note interactive\"><div class=\"title\"><span class=\"cnx-gentext-tip-t\">Link to Learning<\/span><\/div><div class=\"body\"><div class=\"mediaobject\"><span id=\"m44488-fs-id2914259\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155724\/replication_DNA.png\" width=\"120\" alt=\"QR Code representing a URL\"\/><\/div><p><span id=\"m44488-fs-id2010960\"> <\/span>Review the full process of DNA replication <a class=\"link\" href=\"http:\/\/openstaxcollege.org\/l\/replication_DNA\" target=\"\">here<\/a>.<\/p><\/div><\/div><\/div><div xml:lang=\"en\" class=\"section module\" title=\"14.5.&#xA0;DNA Replication in Eukaryotes\"><div class=\"titlepage\"><div><div><h2 id=\"m44517\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.5<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Replication in Eukaryotes<sup><a href=\"co03.html#book-attribution-m44517\">*<\/a><\/sup><\/span><\/span><\/h2><\/div><div class=\"abstract\"><div class=\"title\"><span><span class=\"cnx-gentext-abstract cnx-gentext-autogenerated\"><span class=\"cnx-gentext-abstract cnx-gentext-t\"\/><\/span><\/span><\/div><p>By the end of this section, you will be able to:\n<\/p><div class=\"itemizedlist\"><ul class=\"itemizedlist\"><li class=\"listitem\"><p>Discuss the similarities and differences between DNA replication in eukaryotes and prokaryotes<\/p><\/li><li class=\"listitem\"><p>State the role of telomerase in DNA replication<\/p><\/li><\/ul><\/div><\/div><\/div><\/div><div class=\"toc\"><ul><li class=\"toc-section\"><a href=\"#m44517-fs-id1272063\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">Telomere replication<\/span><\/a><ul><li class=\"toc-section\"><a href=\"#m44517-fs-id2150202\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">Telomerase and Aging<\/span><\/a><\/li><\/ul><\/li><\/ul><\/div><p><span id=\"m44517-fs-id1975225\"> <\/span>Eukaryotic genomes are much more complex and larger in size than prokaryotic genomes. The human genome has three billion base pairs per haploid set of chromosomes, and 6 billion base pairs are replicated during the S phase of the cell cycle. There are multiple origins of replication on the eukaryotic chromosome; humans can have up to 100,000 origins of replication. The rate of replication is approximately 100 nucleotides per second, much slower than prokaryotic replication. In yeast, which is a eukaryote, special sequences known as Autonomously Replicating Sequences (ARS) are found on the chromosomes. These are equivalent to the origin of replication in <span class=\"emphasis\"><em>E. coli<\/em><\/span>.<\/p><p><span id=\"m44517-fs-id1482304\"> <\/span>The number of DNA polymerases in eukaryotes is much more than prokaryotes: 14 are known, of which five are known to have major roles during replication and have been well studied. They are known as pol <span class=\"emphasis\"><em>\u03b1<\/em><\/span>, pol <span class=\"emphasis\"><em>\u03b2<\/em><\/span>, pol <span class=\"emphasis\"><em>\u03b3<\/em><\/span>, pol <span class=\"emphasis\"><em>\u03b4<\/em><\/span>, and pol <span class=\"emphasis\"><em>\u03b5<\/em><\/span>.<\/p><p><span id=\"m44517-fs-id2904988\"> <\/span>The essential steps of replication are the same as in prokaryotes. Before replication can start, the DNA has to be made available as template. Eukaryotic DNA is bound to basic proteins known as histones to form structures called nucleosomes. The chromatin (the complex between DNA and proteins) may undergo some chemical modifications, so that the DNA may be able to slide off the proteins or be accessible to the enzymes of the DNA replication machinery. At the origin of replication, a pre-replication complex is made with other initiator proteins. Other proteins are then recruited to start the replication process (<a class=\"xref target-table\" href=\"ch14.html#m44517-tab-ch14_05_01\" title=\"Table&#xA0;14.2.&#xA0;\">Table\u00a014.2<\/a>).<\/p><p><span id=\"m44517-fs-id2018337\"> <\/span> A helicase using the energy from ATP hydrolysis opens up the DNA helix. Replication forks are formed at each replication origin as the DNA unwinds. The opening of the double helix causes over-winding, or supercoiling, in the DNA ahead of the replication fork. These are resolved with the action of topoisomerases. Primers are formed by the enzyme primase, and using the primer, DNA pol can start synthesis. While the leading strand is continuously synthesized by the enzyme pol <span class=\"emphasis\"><em>\u03b4<\/em><\/span>, the lagging strand is synthesized by pol <span class=\"emphasis\"><em>\u03b5<\/em><\/span>. A sliding clamp protein known as PCNA (Proliferating Cell Nuclear Antigen) holds the DNA pol in place so that it does not slide off the DNA. RNase H removes the RNA primer, which is then replaced with DNA nucleotides. The Okazaki fragments in the lagging strand are joined together after the replacement of the RNA primers with DNA. The gaps that remain are sealed by DNA ligase, which forms the phosphodiester bond.<\/p><div class=\"section\" title=\"Telomere replication\"><div class=\"titlepage\"><div><div><h3 id=\"m44517-fs-id1272063\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">Telomere replication<\/span><\/span><\/h3><\/div><\/div><\/div><p><span id=\"m44517-fs-id2030086\"> <\/span>Unlike prokaryotic chromosomes, eukaryotic chromosomes are linear. As you\u2019ve learned, the enzyme DNA pol can add nucleotides only in the 5' to 3' direction. In the leading strand, synthesis continues until the end of the chromosome is reached. On the lagging strand, DNA is synthesized in short stretches, each of which is initiated by a separate primer. When the replication fork reaches the end of the linear chromosome, there is no place for a primer to be made for the DNA fragment to be copied at the end of the chromosome. These ends thus remain unpaired, and over time these ends may get progressively shorter as cells continue to divide.<\/p><p><span id=\"m44517-fs-id1318769\"> <\/span>The ends of the linear chromosomes are known as <em class=\"glossterm\"><span id=\"m44517-autoid-cnx2dbk-id1756920\"> <\/span>telomeres<\/em><a id=\"id506690\" class=\"indexterm\">, which have repetitive sequences that code for no particular gene. In a way, these telomeres protect the genes from getting deleted as cells continue to divide. In humans, a six base pair sequence, TTAGGG, is repeated 100 to 1000 times. The discovery of the enzyme telomerase (<\/a><a class=\"xref target-figure\" href=\"ch14.html#m44517-fig-ch14_05_02\" title=\"Figure&#xA0;14.16.&#xA0;\">Figure\u00a014.16<\/a>) helped in the understanding of how chromosome ends are maintained. The <em class=\"glossterm\"><span id=\"m44517-autoid-cnx2dbk-id1766081\"> <\/span>telomerase<\/em><a id=\"id506715\" class=\"indexterm\"> enzyme contains a catalytic part and a built-in RNA template. It attaches to the end of the chromosome, and complementary bases to the RNA template are added on the 3' end of the DNA strand. Once the 3' end of the lagging strand template is sufficiently elongated, DNA polymerase can add the nucleotides complementary to the ends of the chromosomes. Thus, the ends of the chromosomes are replicated.<\/a><\/p><div id=\"m44517-fig-ch14_05_01\" class=\"figure\" title=\"Figure&#xA0;14.15.&#xA0;\"><div class=\"body\"><div class=\"mediaobject\"><span id=\"m44517-fs-id1986139\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155727\/Figure_14_05_01.jpg\" width=\"300\" alt=\"Telomerase has an associated RNA that complements the 5' overhang at the end of the chromosome. The RNA template is used to synthesize the complementary strand. Telomerase then shifts, and the process is repeated. Next, primase and DNA polymerase synthesize the rest of the complementary strand.\"\/><\/div><\/div><div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.15<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"\/><\/div><div class=\"caption\">The ends of linear chromosomes are maintained by the action of the telomerase enzyme.<\/div><\/div><p><span id=\"m44517-fs-id1721035\"> <\/span>Telomerase is typically active in germ cells and adult stem cells. It is not active in adult somatic cells. For her discovery of telomerase and its action, Elizabeth Blackburn (<a class=\"xref target-figure\" href=\"ch14.html#m44517-fig-ch14_05_02\" title=\"Figure&#xA0;14.16.&#xA0;\">Figure\u00a014.16<\/a>) received the Nobel Prize for Medicine and Physiology in 2009.<\/p><div id=\"m44517-fig-ch14_05_02\" class=\"figure\" title=\"Figure&#xA0;14.16.&#xA0;\"><div class=\"body\"><div class=\"mediaobject\"><span id=\"m44517-fs-id2318509\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155728\/Figure_14_05_02.jpg\" width=\"320\" alt=\"Photo of Elizabeth Blackburn.\"\/><\/div><\/div><div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.16<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"\/><\/div><div class=\"caption\">Elizabeth Blackburn, 2009 Nobel Laureate, is the scientist who discovered how telomerase works. (credit: US Embassy Sweden)<\/div><\/div><div class=\"section\" title=\"Telomerase and Aging\"><div class=\"titlepage\"><div><div><h4 id=\"m44517-fs-id2150202\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">Telomerase and Aging<\/span><\/span><\/h4><\/div><\/div><\/div><p><span id=\"m44517-fs-id2199338\"> <\/span>Cells that undergo cell division continue to have their telomeres shortened because most somatic cells do not make telomerase. This essentially means that telomere shortening is associated with aging. With the advent of modern medicine, preventative health care, and healthier lifestyles, the human life span has increased, and there is an increasing demand for people to look younger and have a better quality of life as they grow older.<\/p><p><span id=\"m44517-fs-id2196973\"> <\/span>In 2010, scientists found that telomerase can reverse some age-related conditions in mice. This may have potential in regenerative medicine.<sup><sup>[<a id=\"m44517-fs-id1477114\" href=\"#ftn.m44517-fs-id1477114\" class=\"footnote\">12<\/a>]<\/sup><\/sup> Telomerase-deficient mice were used in these studies; these mice have tissue atrophy, stem cell depletion, organ system failure, and impaired tissue injury responses. Telomerase reactivation in these mice caused extension of telomeres, reduced DNA damage, reversed neurodegeneration, and improved the function of the testes, spleen, and intestines. Thus, telomere reactivation may have potential for treating age-related diseases in humans.<\/p><p><span id=\"m44517-fs-id2370326\"> <\/span>Cancer is characterized by uncontrolled cell division of abnormal cells. The cells accumulate mutations, proliferate uncontrollably, and can migrate to different parts of the body through a process called metastasis. Scientists have observed that cancerous cells have considerably shortened telomeres and that telomerase is active in these cells. Interestingly, only after the telomeres were shortened in the cancer cells did the telomerase become active. If the action of telomerase in these cells can be inhibited by drugs during cancer therapy, then the cancerous cells could potentially be stopped from further division.<\/p><div class=\"table\" id=\"m44517-tab-ch14_05_01\"><table cellpadding=\"0\" style=\"border: 1px solid; border-spacing: 0px;\"><caption><span class=\"cnx-gentext-caption cnx-gentext-t\">Table <\/span><span class=\"cnx-gentext-caption cnx-gentext-n\">14.2. <\/span><\/caption><thead valign=\"bottom\"><tr><th colspan=\"3\" style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">Difference between Prokaryotic and Eukaryotic Replication<\/th><\/tr><tr><th style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">Property<\/th><th style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">Prokaryotes<\/th><th style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">Eukaryotes<\/th><\/tr><\/thead><tbody valign=\"top\"><tr><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">Origin of replication<\/td><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">Single<\/td><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">Multiple<\/td><\/tr><tr><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">Rate of replication<\/td><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">1000 nucleotides\/s<\/td><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">50 to 100 nucleotides\/s<\/td><\/tr><tr><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">DNA polymerase types<\/td><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">5<\/td><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">14<\/td><\/tr><tr><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">Telomerase<\/td><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">Not present<\/td><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">Present<\/td><\/tr><tr><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">RNA primer removal<\/td><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">DNA pol I<\/td><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">RNase H<\/td><\/tr><tr><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">Strand elongation<\/td><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">DNA pol III<\/td><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">Pol \u03b4, pol \u03b5<\/td><\/tr><tr><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 0 !important; text-align: left !important;\">Sliding clamp<\/td><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 0 !important; text-align: left !important;\">Sliding clamp<\/td><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 0 !important; text-align: left !important;\">PCNA<\/td><\/tr><\/tbody><\/table><\/div><\/div><\/div><\/div><div xml:lang=\"en\" class=\"section module\" title=\"14.6.&#xA0;DNA Repair\"><div class=\"titlepage\"><div><div><h2 id=\"m44513\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.6<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Repair<sup><a href=\"co03.html#book-attribution-m44513\">*<\/a><\/sup><\/span><\/span><\/h2><\/div><div class=\"abstract\"><div class=\"title\"><span><span class=\"cnx-gentext-abstract cnx-gentext-autogenerated\"><span class=\"cnx-gentext-abstract cnx-gentext-t\"\/><\/span><\/span><\/div><p>By the end of this section, you will be able to:\n<\/p><div class=\"itemizedlist\"><ul class=\"itemizedlist\"><li class=\"listitem\"><p>Discuss the different types of mutations in DNA<\/p><\/li><li class=\"listitem\"><p>Explain DNA repair mechanisms<\/p><\/li><\/ul><\/div><\/div><\/div><\/div><div class=\"toc\"><ul\/><\/div><p><span id=\"m44513-fs-id1976493\"> <\/span>DNA replication is a highly accurate process, but mistakes can occasionally occur, such as a DNA polymerase inserting a wrong base. Uncorrected mistakes may sometimes lead to serious consequences, such as cancer. Repair mechanisms correct the mistakes. In rare cases, mistakes are not corrected, leading to mutations; in other cases, repair enzymes are themselves mutated or defective.<\/p><p><span id=\"m44513-fs-id2348700\"> <\/span>Most of the mistakes during DNA replication are promptly corrected by DNA polymerase by proofreading the base that has been just added (<a class=\"xref target-figure\" href=\"ch14.html#m44513-fig-ch14_06_01\" title=\"Figure&#xA0;14.17.&#xA0;\">Figure\u00a014.17<\/a>). In <em class=\"glossterm\"><span id=\"m44513-autoid-cnx2dbk-id1749376\"> <\/span>proofreading<\/em><a id=\"id507339\" class=\"indexterm\">, the DNA pol reads the newly added base before adding the next one, so a correction can be made. The polymerase checks whether the newly added base has paired correctly with the base in the template strand. If it is the right base, the next nucleotide is added. If an incorrect base has been added, the enzyme makes a cut at the phosphodiester bond and releases the wrong nucleotide. This is performed by the exonuclease action of DNA pol III. Once the incorrect nucleotide has been removed, a new one will be added again.<\/a><\/p><div id=\"m44513-fig-ch14_06_01\" class=\"figure\" title=\"Figure&#xA0;14.17.&#xA0;\"><div class=\"body\"><div class=\"mediaobject\"><span id=\"m44513-fs-id2321057\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155730\/Figure_14_06_01.jpg\" width=\"320\" alt=\"Illustration shows DNA polymerase replicating a strand of DNA. The enzyme has accidentally inserted G opposite A, resulting in a bulge. The enzyme backs up to fix the error.\"\/><\/div><\/div><div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.17<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"\/><\/div><div class=\"caption\">Proofreading by DNA polymerase corrects errors during replication.<\/div><\/div><p><span id=\"m44513-fs-id2186525\"> <\/span>Some errors are not corrected during replication, but are instead corrected after replication is completed; this type of repair is known as <em class=\"glossterm\"><span id=\"m44513-autoid-cnx2dbk-id1749419\"> <\/span>mismatch repair<\/em><a id=\"id507399\" class=\"indexterm\"> (<\/a><a class=\"xref target-figure\" href=\"ch14.html#m44513-fig-ch14_06_02\" title=\"Figure&#xA0;14.18.&#xA0;\">Figure\u00a014.18<\/a>). The enzymes recognize the incorrectly added nucleotide and excise it; this is then replaced by the correct base. If this remains uncorrected, it may lead to more permanent damage. How do mismatch repair enzymes recognize which of the two bases is the incorrect one? In <span class=\"emphasis\"><em>E. coli<\/em><\/span>, after replication, the nitrogenous base adenine acquires a methyl group; the parental DNA strand will have methyl groups, whereas the newly synthesized strand lacks them. Thus, DNA polymerase is able to remove the wrongly incorporated bases from the newly synthesized, non-methylated strand. In eukaryotes, the mechanism is not very well understood, but it is believed to involve recognition of unsealed nicks in the new strand, as well as a short-term continuing association of some of the replication proteins with the new daughter strand after replication has completed.<\/p><div id=\"m44513-fig-ch14_06_02\" class=\"figure\" title=\"Figure&#xA0;14.18.&#xA0;\"><div class=\"body\"><div class=\"mediaobject\"><span id=\"m44513-fs-id2025027\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155732\/Figure_14_06_02.jpg\" width=\"250\" alt=\"The top illustration shows a replicated DNA strand with G-T base mismatch. The bottom illustration shows the repaired DNA, which has the correct G-C base pairing.\"\/><\/div><\/div><div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.18<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"\/><\/div><div class=\"caption\">In mismatch repair, the incorrectly added base is detected after replication. The mismatch repair proteins detect this base and remove it from the newly synthesized strand by nuclease action. The gap is now filled with the correctly paired base.<\/div><\/div><p><span id=\"m44513-fs-id3000290\"> <\/span>In another type of repair mechanism, <em class=\"glossterm\"><span id=\"m44513-autoid-cnx2dbk-id1761231\"> <\/span>nucleotide excision repair<\/em><a id=\"id507474\" class=\"indexterm\">, enzymes replace incorrect bases by making a cut on both the 3' and 5' ends of the incorrect base (<\/a><a class=\"xref target-figure\" href=\"ch14.html#m44513-fig-ch14_06_03\" title=\"Figure&#xA0;14.19.&#xA0;\">Figure\u00a014.19<\/a>). The segment of DNA is removed and replaced with the correctly paired nucleotides by the action of DNA pol. Once the bases are filled in, the remaining gap is sealed with a phosphodiester linkage catalyzed by DNA ligase. This repair mechanism is often employed when UV exposure causes the formation of pyrimidine dimers.<\/p><div id=\"m44513-fig-ch14_06_03\" class=\"figure\" title=\"Figure&#xA0;14.19.&#xA0;\"><div class=\"body\"><div class=\"mediaobject\"><span id=\"m44513-fs-id1695253\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155733\/Figure_14_06_03.jpg\" width=\"200\" alt=\"Illustration shows a DNA strand in which a thymine dimer has formed. Excision repair enzyme cut out the section of DNA that contains the dimer so it can be replaced with normal base pairs.\"\/><\/div><\/div><div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.19<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"\/><\/div><div class=\"caption\">Nucleotide excision repairs thymine dimers. When exposed to UV, thymines lying adjacent to each other can form thymine dimers. In normal cells, they are excised and replaced.<\/div><\/div><p><span id=\"m44513-fs-id2078153\"> <\/span>A well-studied example of mistakes not being corrected is seen in people suffering from xeroderma pigmentosa (<a class=\"xref target-figure\" href=\"ch14.html#m44513-fig-ch14_06_04\" title=\"Figure&#xA0;14.20.&#xA0;\">Figure\u00a014.20<\/a>). Affected individuals have skin that is highly sensitive to UV rays from the sun. When individuals are exposed to UV, pyrimidine dimersespecially those of thymineare formed; people with xeroderma pigmentosa are not able to repair the damage. These are not repaired because of a defect in the nucleotide excision repair enzymes, whereas in normal individuals, the thymine dimers are excised and the defect is corrected. The thymine dimers distort the structure of the DNA double helix, and this may cause problems during DNA replication. People with xeroderma pigmentosa may have a higher risk of contracting skin cancer than those who dont have the condition.<\/p><div id=\"m44513-fig-ch14_06_04\" class=\"figure\" title=\"Figure&#xA0;14.20.&#xA0;\"><div class=\"body\"><div class=\"mediaobject\"><span id=\"m44513-fs-id2583496\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155735\/Figure_14_06_04.jpg\" width=\"320\" alt=\"Photo shows a person with mottled skin lesions that result from xermoderma pigmentosa.\"\/><\/div><\/div><div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.20<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"\/><\/div><div class=\"caption\">Xeroderma pigmentosa is a condition in which thymine dimerization from exposure to UV is not repaired.  Exposure to sunlight results in skin lesions. (credit: James Halpern et al.)<\/div><\/div><p><span id=\"m44513-fs-id1310247\"> <\/span>Errors during DNA replication are not the only reason why mutations arise in DNA. <em class=\"glossterm\"><span id=\"m44513-autoid-cnx2dbk-id1768504\"> <\/span>Mutations<\/em><a id=\"id507596\" class=\"indexterm\">, variations in the nucleotide sequence of a genome, can also occur because of damage to DNA. Such mutations may be of two types: induced or spontaneous. <em class=\"glossterm\"><span id=\"m44513-autoid-cnx2dbk-id1768509\"> <\/span>Induced mutations<\/em><\/a><a id=\"id507611\" class=\"indexterm\"> are those that result from an exposure to chemicals, UV rays, x-rays, or some other environmental agent. <em class=\"glossterm\"><span id=\"m44513-autoid-cnx2dbk-id1768514\"> <\/span>Spontaneous mutations<\/em><\/a><a id=\"id507626\" class=\"indexterm\"> occur without any exposure to any environmental agent; they are a result of natural reactions taking place within the body.<\/a><\/p><p><span id=\"m44513-fs-id1368727\"> <\/span>Mutations may have a wide range of effects. Some mutations are not expressed; these are known as <em class=\"glossterm\"><span id=\"m44513-autoid-cnx2dbk-id1768527\"> <\/span>silent mutations<\/em><a id=\"id507648\" class=\"indexterm\">. <em class=\"glossterm\"><span id=\"m44513-autoid-cnx2dbk-id1768531\"> <\/span>Point mutations<\/em><\/a><a id=\"id507662\" class=\"indexterm\"> are those mutations that affect a single base pair. The most common nucleotide mutations are substitutions, in which one base is replaced by another. These can be of two types, either transitions or transversions. <em class=\"glossterm\"><span id=\"m44513-autoid-cnx2dbk-id1768803\"> <\/span>Transition substitution<\/em><\/a><a id=\"id507677\" class=\"indexterm\"> refers to a purine or pyrimidine being replaced by a base of the same kind; for example, a purine such as adenine may be replaced by the purine guanine. <em class=\"glossterm\"><span id=\"m44513-autoid-cnx2dbk-id1768808\"> <\/span>Transversion substitution<\/em><\/a><a id=\"id507692\" class=\"indexterm\"> refers to a purine being replaced by a pyrimidine, or vice versa; for example, cytosine, a pyrimidine, is replaced by adenine, a purine. Mutations can also be the result of the addition of a base, known as an insertion, or the removal of a base, also known as deletion. Sometimes a piece of DNA from one chromosome may get translocated to another chromosome or to another region of the same chromosome; this is also known as translocation. These mutation types are shown in <\/a><a class=\"xref target-figure\" href=\"ch14.html#m44513-fig-ch14_06_05\" title=\"Figure&#xA0;14.21.&#xA0;\">Figure\u00a014.21<\/a>.<\/p><div id=\"m44513-fs-id2046784\" class=\"note art-connection\"><div class=\"title\"><span class=\"cnx-gentext-tip-t\">Art Connection<\/span><\/div><div class=\"body\"><p><span id=\"m44513-fs-id2216817\"> <\/span><\/p><div id=\"m44513-fig-ch14_06_05\" class=\"figure\" title=\"Figure&#xA0;14.21.&#xA0;\"><div class=\"body\"><span class=\"inlinemediaobject\"><span id=\"m44513-fs-id2221137\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155739\/Figure_14_06_05.png\" width=\"325\" alt=\"Illustration shows different types of point mutations that result from a single amino acid substitution. In a silent mutation, no change in the amino acid sequence occurs. In a missense mutation, one amino acid is substituted for another. In a nonsense mutation, a stop codon is substituted for an amino acid. In a frameshift mutation, one or more bases is added or deleted, resulting in a change in the reading frame.\"\/><\/span><\/div><div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.21<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"\/><\/div><div class=\"caption\">Mutations can lead to changes in the protein sequence encoded by the DNA.<\/div><\/div><p><span id=\"m44513-fs-id1813148\"> <\/span>A frameshift mutation that results in the insertion of three nucleotides is often less deleterious than a mutation that results in the insertion of one nucleotide. Why?<\/p><\/div><\/div><p><span id=\"m44513-fs-id2936137\"> <\/span>Mutations in repair genes have been known to cause cancer. Many mutated repair genes have been implicated in certain forms of pancreatic cancer, colon cancer, and colorectal cancer. Mutations can affect either somatic cells or germ cells. If many mutations accumulate in a somatic cell, they may lead to problems such as the uncontrolled cell division observed in cancer. If a mutation takes place in germ cells, the mutation will be passed on to the next generation, as in the case of hemophilia and xeroderma pigmentosa.<\/p><\/div><div class=\"glossary\" title=\"Glossary\" id=\"id508089\"><div class=\"titlepage\"><div><div><h2 class=\"title\"><span class=\"cnx-gentext-glossary cnx-gentext-autogenerated\"><span class=\"cnx-gentext-glossary cnx-gentext-t\">Glossary<\/span><\/span><\/h2><\/div><\/div><\/div><dl><dt>electrophoresis<\/dt><dd><p>technique used to separate DNA fragments according to size<\/p><\/dd><dt>helicase<\/dt><dd><p>during replication, this enzyme helps to open up the DNA helix by breaking the hydrogen bonds<\/p><\/dd><dt>induced mutation<\/dt><dd><p>mutation that results from exposure to chemicals or environmental agents<\/p><\/dd><dt>lagging strand<\/dt><dd><p>during replication, the strand that is replicated in short fragments and away from the replication fork<\/p><\/dd><dt>leading strand<\/dt><dd><p>strand that is synthesized continuously in the 5'-3' direction which is synthesized in the direction of the replication fork<\/p><\/dd><dt>ligase<\/dt><dd><p>enzyme that catalyzes the formation of a phosphodiester linkage between the 3' OH and 5' phosphate ends of the DNA<\/p><\/dd><dt>mismatch repair<\/dt><dd><p>type of repair mechanism in which mismatched bases are removed after replication<\/p><\/dd><dt>mutation<\/dt><dd><p>variation in the nucleotide sequence of a genome<\/p><\/dd><dt>nucleotide excision repair<\/dt><dd><p>type of DNA repair mechanism in which the wrong base, along with a few nucleotides upstream or downstream, are removed<\/p><\/dd><dt>Okazaki fragment<\/dt><dd><p>DNA fragment that is synthesized in short stretches on the lagging strand<\/p><\/dd><dt>point mutation<\/dt><dd><p>mutation that affects a single base<\/p><\/dd><dt>primase<\/dt><dd><p>enzyme that synthesizes the RNA primer; the primer is needed for DNA pol to start synthesis of a new DNA strand<\/p><\/dd><dt>primer<\/dt><dd><p>short stretch of nucleotides that is required to initiate replication; in the case of replication, the primer has RNA nucleotides<\/p><\/dd><dt>proofreading<\/dt><dd><p>function of DNA pol in which it reads the newly added base before adding the next one<\/p><\/dd><dt>replication fork<\/dt><dd><p>Y-shaped structure formed during initiation of replication<\/p><\/dd><dt>silent mutation<\/dt><dd><p>mutation that is not expressed<\/p><\/dd><dt>single-strand binding protein<\/dt><dd><p>during replication, protein that binds to the single-stranded DNA; this helps in keeping the two strands of DNA apart so that they may serve as templates<\/p><\/dd><dt>sliding clamp<\/dt><dd><p>ring-shaped protein that holds the DNA pol on the DNA strand<\/p><\/dd><dt>spontaneous mutation<\/dt><dd><p>mutation that takes place in the cells as a result of chemical reactions taking place naturally without exposure to any external agent<\/p><\/dd><dt>telomerase<\/dt><dd><p>enzyme that contains a catalytic part and an inbuilt RNA template; it functions to maintain telomeres at chromosome ends<\/p><\/dd><dt>telomere<\/dt><dd><p>DNA at the end of linear chromosomes<\/p><\/dd><dt>topoisomerase<\/dt><dd><p>enzyme that causes underwinding or overwinding of DNA when DNA replication is taking place<\/p><\/dd><dt>transformation<\/dt><dd><p>process in which external DNA is taken up by a cell<\/p><\/dd><dt>transition substitution<\/dt><dd><p>when a purine is replaced with a purine or a pyrimidine is replaced with another pyrimidine<\/p><\/dd><dt>transversion substitution<\/dt><dd><p>when a purine is replaced by a pyrimidine or a pyrimidine is replaced by a purine<\/p><\/dd><\/dl><\/div>&lt;!--CNX: Start Area: \"Sections Summary\"--&gt;<div class=\"cnx-eoc summary\"><div class=\"title\"><span>Sections Summary<\/span><\/div><div class=\"section empty\"><div class=\"title\"><a href=\"#m44484\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Introduction<\/span><\/span><\/a><\/div><div class=\"body\"><div class=\"section\"><div class=\"title\"><a href=\"#m44485\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.1<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Historical Basis of Modern Understanding<\/span><\/span><\/a><\/div><div class=\"body\"><p><span id=\"m44485-fs-id2984818\"> <\/span>DNA was first isolated from white blood cells by Friedrich Miescher, who called it nuclein because it was isolated from nuclei. Frederick Griffith's experiments with strains of <span class=\"emphasis\"><em>Streptococcus pneumoniae<\/em><\/span> provided the first hint that DNA may be the transforming principle. Avery, MacLeod, and McCarty proved that DNA is required for the transformation of bacteria. Later experiments by Hershey and Chase using bacteriophage T2 proved that DNA is the genetic material. Chargaff found that the ratio of A = T and C = G, and that the percentage content of A, T, G, and C is different for different species.<\/p><\/div><\/div><div class=\"section\"><div class=\"title\"><a href=\"#m44486\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.2<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Structure and Sequencing<\/span><\/span><\/a><\/div><div class=\"body\"><p><span id=\"m44486-fs-id1342929\"> <\/span>The currently accepted model of the double-helix structure of DNA was proposed by Watson and Crick. Some of the salient features are that the two strands that make up the double helix are complementary and anti-parallel in nature. Deoxyribose sugars and phosphates form the backbone of the structure, and the nitrogenous bases are stacked inside. The diameter of the double helix, 2 nm, is uniform throughout. A purine always pairs with a pyrimidine; A pairs with T, and G pairs with C. One turn of the helix has ten base pairs. During cell division, each daughter cell receives a copy of the DNA by a process known as DNA replication. Prokaryotes are much simpler than eukaryotes in many of their features. Most prokaryotes contain a single, circular chromosome. In general, eukaryotic chromosomes contain a linear DNA molecule packaged into nucleosomes, and have two distinct regions that can be distinguished by staining, reflecting different states of packaging and compaction.<\/p><\/div><\/div><div class=\"section\"><div class=\"title\"><a href=\"#m44487\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.3<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Basics of DNA Replication<\/span><\/span><\/a><\/div><div class=\"body\"><p><span id=\"m44487-fs-id2682756\"> <\/span>The model for DNA replication suggests that the two strands of the double helix separate during replication, and each strand serves as a template from which the new complementary strand is copied. In conservative replication, the parental DNA is conserved, and the daughter DNA is newly synthesized. The semi-conservative method suggests that each of the two parental DNA strands acts as template for new DNA to be synthesized; after replication, each double-stranded DNA includes one parental or \u201cold\u201d strand and one \u201cnew\u201d strand. The dispersive mode suggested that the two copies of the DNA would have segments of parental DNA and newly synthesized DNA.<\/p><\/div><\/div><div class=\"section\"><div class=\"title\"><a href=\"#m44488\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.4<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Replication in Prokaryotes<\/span><\/span><\/a><\/div><div class=\"body\"><p><span id=\"m44488-fs-id1437221\"> <\/span>Replication in prokaryotes starts from a sequence found on the chromosome called the origin of replication\u2014the point at which the DNA opens up. Helicase opens up the DNA double helix, resulting in the formation of the replication fork. Single-strand binding proteins bind to the single-stranded DNA near the replication fork to keep the fork open. Primase synthesizes an RNA primer to initiate synthesis by DNA polymerase, which can add nucleotides only in the 5' to 3' direction. One strand is synthesized continuously in the direction of the replication fork; this is called the leading strand. The other strand is synthesized in a direction away from the replication fork, in short stretches of DNA known as Okazaki fragments. This strand is known as the lagging strand. Once replication is completed, the RNA primers are replaced by DNA nucleotides and the DNA is sealed with DNA ligase, which creates phosphodiester bonds between the 3'-OH of one end and the 5' phosphate of the other strand.<\/p><\/div><\/div><div class=\"section\"><div class=\"title\"><a href=\"#m44517\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.5<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Replication in Eukaryotes<\/span><\/span><\/a><\/div><div class=\"body\"><p><span id=\"m44517-fs-id2694542\"> <\/span>Replication in eukaryotes starts at multiple origins of replication. The mechanism is quite similar to prokaryotes. A primer is required to initiate synthesis, which is then extended by DNA polymerase as it adds nucleotides one by one to the growing chain. The leading strand is synthesized continuously, whereas the lagging strand is synthesized in short stretches called Okazaki fragments. The RNA primers are replaced with DNA nucleotides; the DNA remains one continuous strand by linking the DNA fragments with DNA ligase. The ends of the chromosomes pose a problem as polymerase is unable to extend them without a primer. Telomerase, an enzyme with an inbuilt RNA template, extends the ends by copying the RNA template and extending one end of the chromosome. DNA polymerase can then extend the DNA using the primer. In this way, the ends of the chromosomes are protected.<\/p><\/div><\/div><div class=\"section\"><div class=\"title\"><a href=\"#m44513\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.6<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Repair<\/span><\/span><\/a><\/div><div class=\"body\"><p><span id=\"m44513-fs-id1242469\"> <\/span>DNA polymerase can make mistakes while adding nucleotides. It edits the DNA by proofreading every newly added base. Incorrect bases are removed and replaced by the correct base, and then a new base is added. Most mistakes are corrected during replication, although when this does not happen, the mismatch repair mechanism is employed. Mismatch repair enzymes recognize the wrongly incorporated base and excise it from the DNA, replacing it with the correct base. In yet another type of repair, nucleotide excision repair, the incorrect base is removed along with a few bases on the 5' and 3' end, and these are replaced by copying the template with the help of DNA polymerase. The ends of the newly synthesized fragment are attached to the rest of the DNA using DNA ligase, which creates a phosphodiester bond.<\/p><p><span id=\"m44513-fs-id2595588\"> <\/span>Most mistakes are corrected, and if they are not, they may result in a mutation defined as a permanent change in the DNA sequence. Mutations can be of many types, such as substitution, deletion, insertion, and translocation. Mutations in repair genes may lead to serious consequences such as cancer. Mutations can be induced or may occur spontaneously.<\/p><\/div><\/div><\/div>&lt;!--CNX: Start Area: \"Art Connections\"--&gt;<div class=\"cnx-eoc art-exercise\"><div class=\"title\"><span>Art Connections<\/span><\/div><div class=\"section empty\"><div class=\"title\"><a href=\"#m44484\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Introduction<\/span><\/span><\/a><\/div><div class=\"body\"><div class=\"section empty\"><div class=\"title\"><a href=\"#m44485\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.1<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Historical Basis of Modern Understanding<\/span><\/span><\/a><\/div><div class=\"body\"><div class=\"section\"><div class=\"title\"><a href=\"#m44486\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.2<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Structure and Sequencing<\/span><\/span><\/a><\/div><div class=\"body\"><div id=\"m44486-fs-idp2462496\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44486-fs-idm104265760\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">5.<\/span><\/a><\/span><\/div><div class=\"body\">&lt;!--calling informal.object--&gt;<div class=\"problem\"><span id=\"m44486-fs-idm14998192\"> <\/span>\n<p><span id=\"m44486-fs-idp65790208\"> <\/span><a class=\"xref target-figure\" href=\"ch14.html#m44486-fig-ch14_02_06\" title=\"Figure&#xA0;14.10.&#xA0;\">Figure\u00a014.10<\/a> In eukaryotic cells, DNA and RNA synthesis occur in a separate compartment from protein synthesis. In prokaryotic cells, both processes occur together. What advantages might there be to separating the processes? What advantages might there be to having them occur together?<\/p>\n<\/div><div id=\"m44486-fs-idm104265760\" class=\"solution\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44486-fs-idp2462496\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><a class=\"xref target-figure\" href=\"ch14.html#m44486-fig-ch14_02_06\" title=\"Figure&#xA0;14.10.&#xA0;\">Figure\u00a014.10<\/a> Compartmentalization enables a eukaryotic cell to divide processes into discrete steps so it can build more complex protein and RNA products. But there is an advantage to having a single compartment as well: RNA and protein synthesis occurs much more quickly in a prokaryotic cell.<\/div><\/div><\/div><\/div><\/div><\/div><div class=\"section empty\"><div class=\"title\"><a href=\"#m44487\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.3<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Basics of DNA Replication<\/span><\/span><\/a><\/div><div class=\"body\"><div class=\"section\"><div class=\"title\"><a href=\"#m44488\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.4<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Replication in Prokaryotes<\/span><\/span><\/a><\/div><div class=\"body\"><div id=\"m44488-fs-idm104376352\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44488-fs-idp76857456\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">13.<\/span><\/a><\/span><\/div><div class=\"body\">&lt;!--calling informal.object--&gt;<div class=\"problem\"><span id=\"m44488-fs-idm62690592\"> <\/span>\n<p><span id=\"m44488-fs-idp29378960\"> <\/span><a class=\"xref target-figure\" href=\"ch14.html#m44488-fig-ch14_04_01\" title=\"Figure&#xA0;14.14.&#xA0;\">Figure\u00a014.14<\/a> You isolate a cell strain in which the joining together of Okazaki fragments is impaired and suspect that a mutation has occurred in an enzyme found at the replication fork. Which enzyme is most likely to be mutated?<\/p>\n<\/div><div id=\"m44488-fs-idp76857456\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44488-fs-idm104376352\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44488-fs-idp125877360\"> <\/span><a class=\"xref target-figure\" href=\"ch14.html#m44488-fig-ch14_04_01\" title=\"Figure&#xA0;14.14.&#xA0;\">Figure\u00a014.14<\/a> DNA ligase, as this enzyme joins together Okazaki fragments.<\/p><\/div><\/div><\/div><\/div><\/div><\/div><div class=\"section empty\"><div class=\"title\"><a href=\"#m44517\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.5<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Replication in Eukaryotes<\/span><\/span><\/a><\/div><div class=\"body\"><div class=\"section\"><div class=\"title\"><a href=\"#m44513\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.6<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Repair<\/span><\/span><\/a><\/div><div class=\"body\"><div id=\"m44513-fs-idp163052304\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44513-fs-idp122564624\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">24.<\/span><\/a><\/span><\/div><div class=\"body\">&lt;!--calling informal.object--&gt;<div class=\"problem\"><span id=\"m44513-fs-idp152472016\"> <\/span>\n            <p><span id=\"m44513-fs-idp131842896\"> <\/span><a class=\"xref target-figure\" href=\"ch14.html#m44513-fig-ch14_06_05\" title=\"Figure&#xA0;14.21.&#xA0;\">Figure\u00a014.21<\/a> A frameshift mutation that results in the insertion of three nucleotides is often less deleterious than a mutation that results in the insertion of one nucleotide. Why?<\/p>\n            <\/div><div id=\"m44513-fs-idp122564624\" class=\"solution\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44513-fs-idp163052304\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><a class=\"xref target-figure\" href=\"ch14.html#m44513-fig-ch14_06_05\" title=\"Figure&#xA0;14.21.&#xA0;\">Figure\u00a014.21<\/a> If three nucleotides are added, one additional amino acid will be incorporated into the protein chain, but the reading frame wont shift.<\/div><\/div><\/div><\/div><\/div><\/div><\/div>&lt;!--CNX: Start Area: \"Multiple Choice\"--&gt;<div class=\"cnx-eoc multiple-choice\"><div class=\"title\"><span>Multiple Choice<\/span><\/div><div class=\"section empty\"><div class=\"title\"><a href=\"#m44484\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Introduction<\/span><\/span><\/a><\/div><div class=\"body\"><div class=\"section\"><div class=\"title\"><a href=\"#m44485\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.1<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Historical Basis of Modern Understanding<\/span><\/span><\/a><\/div><div class=\"body\"><div id=\"m44485-fs-id2897046\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44485-fs-id1425482\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">1.<\/span><\/a><\/span><\/div><div class=\"body\">&lt;!--calling informal.object--&gt;<div class=\"problem\"><span id=\"m44485-fs-id2072379\"> <\/span><p><span id=\"m44485-fs-id1341900\"> <\/span>If DNA of a particular species was analyzed and it was found that it contains 27 percent A, what would be the percentage of C?<\/p>\n<div class=\"orderedlist\"><span id=\"m44485-fs-id1602896\"> <\/span><ol class=\"orderedlist\" type=\"a\"><li class=\"listitem\"><p>27 percent<\/p><\/li><li class=\"listitem\"><p>30 percent<\/p><\/li><li class=\"listitem\"><p>23 percent<\/p><\/li><li class=\"listitem\"><p>54 percent<\/p><\/li><\/ol><\/div>\n<\/div><div id=\"m44485-fs-id1425482\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44485-fs-id2897046\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44485-fs-id1450506\"> <\/span>C<\/p><\/div><\/div><\/div><\/div><div id=\"m44485-fs-id1435268\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44485-fs-id1439092\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">2.<\/span><\/a><\/span><\/div><div class=\"body\">&lt;!--calling informal.object--&gt;<div class=\"problem\"><span id=\"m44485-fs-id1393700\"> <\/span><p><span id=\"m44485-fs-id2638298\"> <\/span>The experiments by Hershey and Chase helped confirm that DNA was the hereditary material on the basis of the finding that:<\/p>\n<div class=\"orderedlist\"><span id=\"m44485-fs-id1694835\"> <\/span><ol class=\"orderedlist\" type=\"a\"><li class=\"listitem\"><p>radioactive phage were found in the pellet<\/p><\/li><li class=\"listitem\"><p>radioactive cells were found in the supernatant<\/p><\/li><li class=\"listitem\"><p>radioactive sulfur was found inside the cell<\/p><\/li><li class=\"listitem\"><p>radioactive phosphorus was found in the cell<\/p><\/li><\/ol><\/div>\n<\/div><div id=\"m44485-fs-id1439092\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44485-fs-id1435268\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44485-fs-id1685167\"> <\/span>D<\/p><\/div><\/div><\/div><\/div><\/div><\/div><div class=\"section\"><div class=\"title\"><a href=\"#m44486\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.2<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Structure and Sequencing<\/span><\/span><\/a><\/div><div class=\"body\"><div id=\"m44486-fs-id2709296\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44486-fs-id1728094\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">6.<\/span><\/a><\/span><\/div><div class=\"body\">&lt;!--calling informal.object--&gt;<div class=\"problem\"><span id=\"m44486-fs-id1640010\"> <\/span><p><span id=\"m44486-fs-id2984818\"> <\/span>DNA double helix does not have which of the following?<\/p>\n<div class=\"orderedlist\"><span id=\"m44486-fs-id2701000\"> <\/span><ol class=\"orderedlist\" type=\"a\"><li class=\"listitem\"><p>antiparallel configuration<\/p><\/li><li class=\"listitem\"><p>complementary base pairing<\/p><\/li><li class=\"listitem\"><p>major and minor grooves<\/p><\/li><li class=\"listitem\"><p>uracil<\/p><\/li><\/ol><\/div>\n<\/div><div id=\"m44486-fs-id1728094\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44486-fs-id2709296\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44486-fs-id1466731\"> <\/span>D<\/p><\/div><\/div><\/div><\/div><div id=\"m44486-fs-id2688539\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44486-fs-id2904571\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">7.<\/span><\/a><\/span><\/div><div class=\"body\">&lt;!--calling informal.object--&gt;<div class=\"problem\"><span id=\"m44486-fs-id662862\"> <\/span><p><span id=\"m44486-fs-id2681297\"> <\/span>In eukaryotes, what is the DNA wrapped around?<\/p>\n<div class=\"orderedlist\"><span id=\"m44486-fs-id3070802\"> <\/span><ol class=\"orderedlist\" type=\"a\"><li class=\"listitem\"><p>single-stranded binding proteins<\/p><\/li><li class=\"listitem\"><p>sliding clamp<\/p><\/li><li class=\"listitem\"><p>polymerase<\/p><\/li><li class=\"listitem\"><p>histones<\/p><\/li><\/ol><\/div>\n<\/div><div id=\"m44486-fs-id2904571\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44486-fs-id2688539\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44486-fs-id2569081\"> <\/span>D<\/p><\/div><\/div><\/div><\/div><\/div><\/div><div class=\"section\"><div class=\"title\"><a href=\"#m44487\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.3<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Basics of DNA Replication<\/span><\/span><\/a><\/div><div class=\"body\"><div id=\"m44487-fs-id2956539\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44487-fs-id1396004\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">10.<\/span><\/a><\/span><\/div><div class=\"body\">&lt;!--calling informal.object--&gt;<div class=\"problem\"><span id=\"m44487-fs-id1439092\"> <\/span><p><span id=\"m44487-fs-id1561237\"> <\/span>Meselson and Stahl's experiments proved that DNA replicates by which mode?<\/p>\n<div class=\"orderedlist\"><span id=\"m44487-fs-id2199309\"> <\/span><ol class=\"orderedlist\" type=\"a\"><li class=\"listitem\"><p>conservative<\/p><\/li><li class=\"listitem\"><p>semi-conservative<\/p><\/li><li class=\"listitem\"><p>dispersive<\/p><\/li><li class=\"listitem\"><p>none of the above<\/p><\/li><\/ol><\/div>\n<\/div><div id=\"m44487-fs-id1396004\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44487-fs-id2956539\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44487-fs-id1262008\"> <\/span>B<\/p><\/div><\/div><\/div><\/div><div id=\"m44487-fs-id2300016\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44487-fs-id2581969\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">11.<\/span><\/a><\/span><\/div><div class=\"body\">&lt;!--calling informal.object--&gt;<div class=\"problem\"><span id=\"m44487-fs-id1812902\"> <\/span><p><span id=\"m44487-fs-id2089930\"> <\/span>If the sequence of the 5'-3' strand is AATGCTAC, then the complementary sequence has the following sequence:<\/p>\n<div class=\"orderedlist\"><span id=\"m44487-fs-id2334300\"> <\/span><ol class=\"orderedlist\" type=\"a\"><li class=\"listitem\"><p>3'-AATGCTAC-5'<\/p><\/li><li class=\"listitem\"><p>3'-CATCGTAA-5'<\/p><\/li><li class=\"listitem\"><p>3'-TTACGATG-5'<\/p><\/li><li class=\"listitem\"><p>3'-GTAGCATT-5'<\/p><\/li><\/ol><\/div>\n<\/div><div id=\"m44487-fs-id2581969\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44487-fs-id2300016\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44487-fs-id2022386\"> <\/span>C<\/p><\/div><\/div><\/div><\/div><\/div><\/div><div class=\"section\"><div class=\"title\"><a href=\"#m44488\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.4<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Replication in Prokaryotes<\/span><\/span><\/a><\/div><div class=\"body\"><div id=\"m44488-fs-id1341900\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44488-fs-id2345394\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">14.<\/span><\/a><\/span><\/div><div class=\"body\">&lt;!--calling informal.object--&gt;<div class=\"problem\"><span id=\"m44488-fs-id1519179\"> <\/span><p><span id=\"m44488-fs-id2329090\"> <\/span>Which of the following components is not involved during the formation of the replication fork?<\/p>\n<div class=\"orderedlist\"><span id=\"m44488-fs-id1602896\"> <\/span><ol class=\"orderedlist\" type=\"a\"><li class=\"listitem\"><p>single-strand binding proteins<\/p><\/li><li class=\"listitem\"><p>helicase<\/p><\/li><li class=\"listitem\"><p>origin of replication<\/p><\/li><li class=\"listitem\"><p>ligase<\/p><\/li><\/ol><\/div>\n<\/div><div id=\"m44488-fs-id2345394\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44488-fs-id1341900\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44488-fs-id2643307\"> <\/span>D<\/p><\/div><\/div><\/div><\/div><div id=\"m44488-fs-id2075108\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44488-fs-id1910465\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">15.<\/span><\/a><\/span><\/div><div class=\"body\">&lt;!--calling informal.object--&gt;<div class=\"problem\"><span id=\"m44488-fs-id1396394\"> <\/span><p><span id=\"m44488-fs-id2138308\"> <\/span>Which of the following does the enzyme primase synthesize?<\/p>\n<div class=\"orderedlist\"><span id=\"m44488-fs-id2228365\"> <\/span><ol class=\"orderedlist\" type=\"a\"><li class=\"listitem\"><p>DNA primer<\/p><\/li><li class=\"listitem\"><p>RNA primer<\/p><\/li><li class=\"listitem\"><p>Okazaki fragments<\/p><\/li><li class=\"listitem\"><p>phosphodiester linkage<\/p><\/li><\/ol><\/div>\n<\/div><div id=\"m44488-fs-id1910465\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44488-fs-id2075108\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44488-fs-id2010183\"> <\/span>B<\/p><\/div><\/div><\/div><\/div><div id=\"m44488-fs-id1406784\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44488-fs-id1512007\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">16.<\/span><\/a><\/span><\/div><div class=\"body\">&lt;!--calling informal.object--&gt;<div class=\"problem\"><span id=\"m44488-fs-id2019618\"> <\/span><p><span id=\"m44488-fs-id1798381\"> <\/span>In which direction does DNA replication take place?<\/p>\n<div class=\"orderedlist\"><span id=\"m44488-fs-id3241387\"> <\/span><ol class=\"orderedlist\" type=\"a\"><li class=\"listitem\"><p>5'-3'<\/p><\/li><li class=\"listitem\"><p>3'-5'<\/p><\/li><li class=\"listitem\"><p>5'<\/p><\/li><li class=\"listitem\"><p>3'<\/p><\/li><\/ol><\/div>\n<\/div><div id=\"m44488-fs-id1512007\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44488-fs-id1406784\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44488-fs-id2979133\"> <\/span>A<\/p><\/div><\/div><\/div><\/div><\/div><\/div><div class=\"section\"><div class=\"title\"><a href=\"#m44517\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.5<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Replication in Eukaryotes<\/span><\/span><\/a><\/div><div class=\"body\"><div id=\"m44517-fs-id2739491\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44517-fs-id2075482\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">22.<\/span><\/a><\/span><\/div><div class=\"body\">&lt;!--calling informal.object--&gt;<div class=\"problem\"><span id=\"m44517-fs-id1631701\"> <\/span><p><span id=\"m44517-fs-id2024527\"> <\/span>The ends of the linear chromosomes are maintained by<\/p>\n<div class=\"orderedlist\"><span id=\"m44517-fs-id3000420\"> <\/span><ol class=\"orderedlist\" type=\"a\"><li class=\"listitem\"><p>helicase<\/p><\/li><li class=\"listitem\"><p>primase<\/p><\/li><li class=\"listitem\"><p>DNA pol<\/p><\/li><li class=\"listitem\"><p>telomerase<\/p><\/li><\/ol><\/div>\n<\/div><div id=\"m44517-fs-id2075482\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44517-fs-id2739491\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44517-fs-id2314747\"> <\/span>D<\/p><\/div><\/div><\/div><\/div><\/div><\/div><div class=\"section\"><div class=\"title\"><a href=\"#m44513\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.6<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Repair<\/span><\/span><\/a><\/div><div class=\"body\"><div id=\"m44513-fs-id1951731\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44513-fs-id2750351\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">25.<\/span><\/a><\/span><\/div><div class=\"body\">&lt;!--calling informal.object--&gt;<div class=\"problem\"><span id=\"m44513-fs-id1477381\"> <\/span><p><span id=\"m44513-fs-id1685167\"> <\/span>During proofreading, which of the following enzymes reads the DNA?<\/p>\n<div class=\"orderedlist\"><span id=\"m44513-fs-id2781180\"> <\/span><ol class=\"orderedlist\" type=\"a\"><li class=\"listitem\"><p>primase<\/p><\/li><li class=\"listitem\"><p>topoisomerase<\/p><\/li><li class=\"listitem\"><p>DNA pol<\/p><\/li><li class=\"listitem\"><p>helicase<\/p><\/li><\/ol><\/div>\n<\/div><div id=\"m44513-fs-id2750351\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44513-fs-id1951731\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44513-fs-id1477929\"> <\/span>C<\/p><\/div><\/div><\/div><\/div><div id=\"m44513-fs-id1414909\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44513-fs-id1837280\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">26.<\/span><\/a><\/span><\/div><div class=\"body\">&lt;!--calling informal.object--&gt;<div class=\"problem\"><span id=\"m44513-fs-id2415145\"> <\/span><p><span id=\"m44513-fs-id2073382\"> <\/span>The initial mechanism for repairing nucleotide errors in DNA is ________.<\/p>\n<div class=\"orderedlist\"><span id=\"m44513-fs-id1794075\"> <\/span><ol class=\"orderedlist\" type=\"a\"><li class=\"listitem\"><p>mismatch repair<\/p><\/li><li class=\"listitem\"><p>DNA polymerase proofreading<\/p><\/li><li class=\"listitem\"><p>nucleotide excision repair<\/p><\/li><li class=\"listitem\"><p>thymine dimers<\/p><\/li><\/ol><\/div>\n<\/div><div id=\"m44513-fs-id1837280\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44513-fs-id1414909\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44513-fs-id2051151\"> <\/span>B<\/p><\/div><\/div><\/div><\/div><\/div><\/div><\/div>&lt;!--CNX: Start Area: \"Free Response\"--&gt;<div class=\"cnx-eoc free-response\"><div class=\"title\"><span>Free Response<\/span><\/div><div class=\"section empty\"><div class=\"title\"><a href=\"#m44484\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Introduction<\/span><\/span><\/a><\/div><div class=\"body\"><div class=\"section\"><div class=\"title\"><a href=\"#m44485\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.1<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Historical Basis of Modern Understanding<\/span><\/span><\/a><\/div><div class=\"body\"><div id=\"m44485-fs-id1426300\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44485-fs-id2100648\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">3.<\/span><\/a><\/span><\/div><div class=\"body\">&lt;!--calling informal.object--&gt;<div class=\"problem\"><span id=\"m44485-fs-id2334828\"> <\/span><p><span id=\"m44485-fs-id2739498\"> <\/span>Explain Griffith's transformation experiments. What did he conclude from them?<\/p><\/div><div id=\"m44485-fs-id2100648\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44485-fs-id1426300\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44485-fs-id2168285\"> <\/span>Live R cells acquired genetic information from the heat-killed S cells that \u201ctransformed\u201d the R cells into S cells.<\/p><\/div><\/div><\/div><\/div><div id=\"m44485-fs-id2763427\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44485-fs-id2137450\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">4.<\/span><\/a><\/span><\/div><div class=\"body\">&lt;!--calling informal.object--&gt;<div class=\"problem\"><span id=\"m44485-fs-id1760961\"> <\/span><p><span id=\"m44485-fs-id2926691\"> <\/span>Why were radioactive sulfur and phosphorous used to label bacteriophage in Hershey and Chase's experiments?<\/p><\/div><div id=\"m44485-fs-id2137450\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44485-fs-id2763427\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44485-fs-id2571119\"> <\/span>Sulfur is an element found in proteins and phosphorus is a component of nucleic acids.<\/p><\/div><\/div><\/div><\/div><\/div><\/div><div class=\"section\"><div class=\"title\"><a href=\"#m44486\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.2<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Structure and Sequencing<\/span><\/span><\/a><\/div><div class=\"body\"><div id=\"m44486-fs-id1286460\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44486-fs-id2274570\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">8.<\/span><\/a><\/span><\/div><div class=\"body\">&lt;!--calling informal.object--&gt;<div class=\"problem\"><span id=\"m44486-fs-id1986198\"> <\/span><p><span id=\"m44486-fs-id1704961\"> <\/span>Provide a brief summary of the Sanger sequencing method.<\/p><\/div><div id=\"m44486-fs-id2274570\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44486-fs-id1286460\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44486-fs-id2196933\"> <\/span>The template DNA strand is mixed with a DNA polymerase, a primer, the 4 deoxynucleotides, and a limiting concentration of 4 dideoxynucleotides. DNA polymerase synthesizes a strand complementary to the template. Incorporation of ddNTPs at different locations results in DNA fragments that have terminated at every possible base in the template. These fragments are separated by gel electrophoresis and visualized by a laser detector to determine the sequence of bases.<\/p><\/div><\/div><\/div><\/div><div id=\"m44486-fs-id2926746\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44486-fs-id1569099\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">9.<\/span><\/a><\/span><\/div><div class=\"body\">&lt;!--calling informal.object--&gt;<div class=\"problem\"><span id=\"m44486-fs-id1479286\"> <\/span><p><span id=\"m44486-fs-id2914790\"> <\/span>Describe the structure and complementary base pairing of DNA.<\/p><\/div><div id=\"m44486-fs-id1569099\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44486-fs-id2926746\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44486-fs-id2150246\"> <\/span>DNA has two strands in anti-parallel orientation. The sugar-phosphate linkages form a backbone on the outside, and the bases are paired on the inside: A with T, and G with C, like rungs on a spiral ladder.<\/p><\/div><\/div><\/div><\/div><\/div><\/div><div class=\"section\"><div class=\"title\"><a href=\"#m44487\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.3<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Basics of DNA Replication<\/span><\/span><\/a><\/div><div class=\"body\"><div id=\"m44487-fs-id1958775\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44487-fs-id1384287\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">12.<\/span><\/a><\/span><\/div><div class=\"body\">&lt;!--calling informal.object--&gt;<div class=\"problem\"><span id=\"m44487-fs-id2025461\"> <\/span><p><span id=\"m44487-fs-id2072379\"> <\/span>How did the scientific community learn that DNA replication takes place in a semi-conservative fashion?<\/p><\/div><div id=\"m44487-fs-id1384287\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44487-fs-id1958775\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44487-fs-id1478330\"> <\/span>Meselson\u2019s experiments with <span class=\"emphasis\"><em>E. coli <\/em><\/span>grown in <sup>15<\/sup>N deduced this finding.<\/p><\/div><\/div><\/div><\/div><\/div><\/div><div class=\"section\"><div class=\"title\"><a href=\"#m44488\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.4<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Replication in Prokaryotes<\/span><\/span><\/a><\/div><div class=\"body\"><div id=\"m44488-fs-id1286460\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44488-fs-id2936597\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">17.<\/span><\/a><\/span><\/div><div class=\"body\">&lt;!--calling informal.object--&gt;<div class=\"problem\"><span id=\"m44488-fs-id1441996\"> <\/span><p><span id=\"m44488-fs-id2198448\"> <\/span>DNA replication is bidirectional and discontinuous; explain your understanding of those concepts.<\/p><\/div><div id=\"m44488-fs-id2936597\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44488-fs-id1286460\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44488-fs-id1268735\"> <\/span>At an origin of replication, two replication forks are formed that are extended in two directions. On the lagging strand, Okazaki fragments are formed in a discontinuous manner.<\/p><\/div><\/div><\/div><\/div><div id=\"m44488-fs-id1805432\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44488-fs-id2114708\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">18.<\/span><\/a><\/span><\/div><div class=\"body\">&lt;!--calling informal.object--&gt;<div class=\"problem\"><span id=\"m44488-fs-id1569099\"> <\/span><p><span id=\"m44488-fs-id2257887\"> <\/span>What are Okazaki fragments and how they are formed?<\/p><\/div><div id=\"m44488-fs-id2114708\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44488-fs-id1805432\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44488-fs-id2336863\"> <\/span>Short DNA fragments are formed on the lagging strand synthesized in a direction away from the replication fork. These are synthesized by DNA pol.<\/p><\/div><\/div><\/div><\/div><div id=\"m44488-fs-id1720501\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44488-fs-id3165297\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">19.<\/span><\/a><\/span><\/div><div class=\"body\">&lt;!--calling informal.object--&gt;<div class=\"problem\"><span id=\"m44488-fs-id2228028\"> <\/span><p><span id=\"m44488-fs-id1778374\"> <\/span>If the rate of replication in a particular prokaryote is 900 nucleotides per second, how long would it take 1.2 million base pair genomes to make two copies?<\/p><\/div><div id=\"m44488-fs-id3165297\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44488-fs-id1720501\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44488-fs-id2279649\"> <\/span>1333 seconds or 22.2 minutes.<\/p><\/div><\/div><\/div><\/div><div id=\"m44488-fs-id2126300\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44488-fs-id1286063\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">20.<\/span><\/a><\/span><\/div><div class=\"body\">&lt;!--calling informal.object--&gt;<div class=\"problem\"><span id=\"m44488-fs-id671101\"> <\/span><p><span id=\"m44488-fs-id1986681\"> <\/span>Explain the events taking place at the replication fork. If the gene for helicase is mutated, what part of replication will be affected?<\/p><\/div><div id=\"m44488-fs-id1286063\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44488-fs-id2126300\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44488-fs-id1436147\"> <\/span>At the replication fork, the events taking place are helicase action, binding of single-strand binding proteins, primer synthesis, and synthesis of new strands. If there is a mutated helicase gene, the replication fork will not be extended.<\/p><\/div><\/div><\/div><\/div><div id=\"m44488-fs-id1403064\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44488-fs-id1986827\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">21.<\/span><\/a><\/span><\/div><div class=\"body\">&lt;!--calling informal.object--&gt;<div class=\"problem\"><span id=\"m44488-fs-id2115858\"> <\/span><p><span id=\"m44488-fs-id1387702\"> <\/span>What is the role of a primer in DNA replication? What would happen if you forgot to add a primer in a tube containing the reaction mix for a DNA sequencing reaction?<\/p><\/div><div id=\"m44488-fs-id1986827\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44488-fs-id1403064\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44488-fs-id2385726\"> <\/span>Primer provides a 3'-OH group for DNA pol to start adding nucleotides. There would be no reaction in the tube without a primer, and no bands would be visible on the electrophoresis.<\/p><\/div><\/div><\/div><\/div><\/div><\/div><div class=\"section\"><div class=\"title\"><a href=\"#m44517\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.5<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Replication in Eukaryotes<\/span><\/span><\/a><\/div><div class=\"body\"><div id=\"m44517-fs-id2896348\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44517-fs-id2746188\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">23.<\/span><\/a><\/span><\/div><div class=\"body\">&lt;!--calling informal.object--&gt;<div class=\"problem\"><span id=\"m44517-fs-id2167973\"> <\/span><p><span id=\"m44517-fs-id2694648\"> <\/span>How do the linear chromosomes in eukaryotes ensure that its ends are replicated completely?<\/p><\/div><div id=\"m44517-fs-id2746188\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44517-fs-id2896348\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44517-fs-id2190591\"> <\/span>Telomerase has an inbuilt RNA template that extends the 3' end, so primer is synthesized and extended. Thus, the ends are protected.<\/p><\/div><\/div><\/div><\/div><\/div><\/div><div class=\"section\"><div class=\"title\"><a href=\"#m44513\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.6<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Repair<\/span><\/span><\/a><\/div><div class=\"body\"><div id=\"m44513-fs-id2008893\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44513-fs-id1385923\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">27.<\/span><\/a><\/span><\/div><div class=\"body\">&lt;!--calling informal.object--&gt;<div class=\"problem\"><span id=\"m44513-fs-id2763212\"> <\/span><p><span id=\"m44513-fs-id3044550\"> <\/span>What is the consequence of mutation of a mismatch repair enzyme? How will this affect the function of a gene?<\/p><\/div><div id=\"m44513-fs-id1385923\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44513-fs-id2008893\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44513-fs-id1712102\"> <\/span>Mutations are not repaired, as in the case of xeroderma pigmentosa. Gene function may be affected or it may not be expressed.<\/p><\/div><\/div><\/div><\/div><\/div><\/div><\/div><div class=\"cnx-eoc cnx-solutions\"><div class=\"title\">Solutions<\/div>&lt;!--CNX: Start Area: \"Art Connections\"--&gt;<div class=\"solution\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44486-fs-idp2462496\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><a class=\"xref target-figure\" href=\"ch14.html#m44486-fig-ch14_02_06\" title=\"Figure&#xA0;14.10.&#xA0;\">Figure\u00a014.10<\/a> Compartmentalization enables a eukaryotic cell to divide processes into discrete steps so it can build more complex protein and RNA products. But there is an advantage to having a single compartment as well: RNA and protein synthesis occurs much more quickly in a prokaryotic cell.<\/div><\/div><div class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44488-fs-idm104376352\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span> <\/span><a class=\"xref target-figure\" href=\"ch14.html#m44488-fig-ch14_04_01\" title=\"Figure&#xA0;14.14.&#xA0;\">Figure\u00a014.14<\/a> DNA ligase, as this enzyme joins together Okazaki fragments.<\/p><\/div><\/div><div class=\"solution\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44513-fs-idp163052304\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><a class=\"xref target-figure\" href=\"ch14.html#m44513-fig-ch14_06_05\" title=\"Figure&#xA0;14.21.&#xA0;\">Figure\u00a014.21<\/a> If three nucleotides are added, one additional amino acid will be incorporated into the protein chain, but the reading frame wont shift.<\/div><\/div>&lt;!--CNX: Start Area: \"Multiple Choice\"--&gt;<div class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44485-fs-id2897046\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span> <\/span>C<\/p><\/div><\/div><div class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44485-fs-id1435268\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span> <\/span>D<\/p><\/div><\/div><div class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44486-fs-id2709296\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span> <\/span>D<\/p><\/div><\/div><div class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44486-fs-id2688539\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span> <\/span>D<\/p><\/div><\/div><div class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44487-fs-id2956539\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span> <\/span>B<\/p><\/div><\/div><div class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44487-fs-id2300016\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span> <\/span>C<\/p><\/div><\/div><div class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44488-fs-id1341900\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span> <\/span>D<\/p><\/div><\/div><div class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44488-fs-id2075108\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span> <\/span>B<\/p><\/div><\/div><div class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44488-fs-id1406784\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span> <\/span>A<\/p><\/div><\/div><div class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44517-fs-id2739491\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span> <\/span>D<\/p><\/div><\/div><div class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44513-fs-id1951731\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span> <\/span>C<\/p><\/div><\/div><div class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44513-fs-id1414909\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span> <\/span>B<\/p><\/div><\/div>&lt;!--CNX: Start Area: \"Free Response\"--&gt;<div class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44485-fs-id1426300\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span> <\/span>Live R cells acquired genetic information from the heat-killed S cells that \u201ctransformed\u201d the R cells into S cells.<\/p><\/div><\/div><div class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44485-fs-id2763427\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span> <\/span>Sulfur is an element found in proteins and phosphorus is a component of nucleic acids.<\/p><\/div><\/div><div class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44486-fs-id1286460\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span> <\/span>The template DNA strand is mixed with a DNA polymerase, a primer, the 4 deoxynucleotides, and a limiting concentration of 4 dideoxynucleotides. DNA polymerase synthesizes a strand complementary to the template. Incorporation of ddNTPs at different locations results in DNA fragments that have terminated at every possible base in the template. These fragments are separated by gel electrophoresis and visualized by a laser detector to determine the sequence of bases.<\/p><\/div><\/div><div class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44486-fs-id2926746\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span> <\/span>DNA has two strands in anti-parallel orientation. The sugar-phosphate linkages form a backbone on the outside, and the bases are paired on the inside: A with T, and G with C, like rungs on a spiral ladder.<\/p><\/div><\/div><div class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44487-fs-id1958775\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span> <\/span>Meselson\u2019s experiments with <span class=\"emphasis\"><em>E. coli <\/em><\/span>grown in <sup>15<\/sup>N deduced this finding.<\/p><\/div><\/div><div class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44488-fs-id1286460\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span> <\/span>At an origin of replication, two replication forks are formed that are extended in two directions. On the lagging strand, Okazaki fragments are formed in a discontinuous manner.<\/p><\/div><\/div><div class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44488-fs-id1805432\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span> <\/span>Short DNA fragments are formed on the lagging strand synthesized in a direction away from the replication fork. These are synthesized by DNA pol.<\/p><\/div><\/div><div class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44488-fs-id1720501\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span> <\/span>1333 seconds or 22.2 minutes.<\/p><\/div><\/div><div class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44488-fs-id2126300\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span> <\/span>At the replication fork, the events taking place are helicase action, binding of single-strand binding proteins, primer synthesis, and synthesis of new strands. If there is a mutated helicase gene, the replication fork will not be extended.<\/p><\/div><\/div><div class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44488-fs-id1403064\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span> <\/span>Primer provides a 3'-OH group for DNA pol to start adding nucleotides. There would be no reaction in the tube without a primer, and no bands would be visible on the electrophoresis.<\/p><\/div><\/div><div class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44517-fs-id2896348\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span> <\/span>Telomerase has an inbuilt RNA template that extends the 3' end, so primer is synthesized and extended. Thus, the ends are protected.<\/p><\/div><\/div><div class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44513-fs-id2008893\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span> <\/span>Mutations are not repaired, as in the case of xeroderma pigmentosa. Gene function may be affected or it may not be expressed.<\/p><\/div><\/div><\/div><\/div><\/div><\/div><\/div><\/div><\/div><\/div><\/div><\/div><\/div><\/div><\/div><\/div><\/div><\/div>","rendered":"<div class=\"chapter\" title=\"Chapter&#xa0;14.&#xa0;DNA Structure and Function\" id=\"id501987\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h1 class=\"title\"><span class=\"cnx-gentext-chapter cnx-gentext-autogenerated\">Chapter\u00a0<\/span><span class=\"cnx-gentext-chapter cnx-gentext-n\">14<\/span><span class=\"cnx-gentext-chapter cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-chapter cnx-gentext-t\">DNA Structure and Function<\/span><\/h1>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"introduction\" id=\"m44484\">\n<div id=\"m44484-fig-ch14_00_01\" class=\"figure splash\" title=\"Figure&#xa0;14.1.&#xa0;\">\n<div class=\"body\">\n<div class=\"mediaobject\"><span id=\"m44484-fs-id1597120\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155639\/Figure_14_00_01.jpg\" width=\"600\" alt=\"Photo shows Dolly the sheep, which has been stuffed and placed in a glass case.\" \/><\/div>\n<\/div>\n<div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.1<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"><\/span><\/div>\n<div class=\"caption\">Dolly the sheep was the first large mammal to be cloned.<\/div>\n<\/div>\n<h3 class=\"title\"><span>Introduction<sup><a href=\"co03.html#book-attribution-m44484\">*<\/a><\/sup><\/span><\/h3>\n<p><span id=\"m44484-fs-id3011658\"> <\/span>The three letters \u201cDNA\u201d have now become synonymous with crime solving, paternity testing, human identification, and genetic testing. DNA can be retrieved from hair, blood, or saliva. Each person\u2019s DNA is unique, and it is possible to detect differences between individuals within a species on the basis of these unique features.<\/p>\n<p><span id=\"m44484-fs-id1480610\"> <\/span>DNA analysis has many practical applications beyond forensics. In humans, DNA testing is applied to numerous uses: determining paternity, tracing genealogy, identifying pathogens, archeological research, tracing disease outbreaks, and studying human migration patterns. In the medical field, DNA is used in diagnostics, new vaccine development, and cancer therapy. It is now possible to determine predisposition to diseases by looking at genes.<\/p>\n<p><span id=\"m44484-fs-id1396004\"> <\/span>Each human cell has 23 pairs of chromosomes: one set of chromosomes is inherited from the mother and the other set is inherited from the father. There is also a mitochondrial genome, inherited exclusively from the mother, which can be involved in inherited genetic disorders. On each chromosome, there are thousands of genes that are responsible for determining the genotype and phenotype of the individual. A gene is defined as a sequence of DNA that codes for a functional product. The human haploid genome contains 3 billion base pairs and has between 20,000 and 25,000 functional genes.<\/p>\n<\/div>\n<div xml:lang=\"en\" class=\"section module\" title=\"14.1.&#xa0;Historical Basis of Modern Understanding\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h2 id=\"m44485\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.1<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Historical Basis of Modern Understanding<sup><a href=\"co03.html#book-attribution-m44485\">*<\/a><\/sup><\/span><\/span><\/h2>\n<\/div>\n<div class=\"abstract\">\n<div class=\"title\"><span><span class=\"cnx-gentext-abstract cnx-gentext-autogenerated\"><span class=\"cnx-gentext-abstract cnx-gentext-t\"><\/span><\/span><\/span><\/div>\n<p>By the end of this section, you will be able to:\n<\/p>\n<div class=\"itemizedlist\">\n<ul class=\"itemizedlist\">\n<li class=\"listitem\">\n<p>Explain transformation of DNA<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>Describe the key experiments that helped identify that DNA is the genetic material<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>State and explain Chargaff\u2019s rules<\/p>\n<\/li>\n<\/ul>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"toc\">\n<ul><\/ul>\n<\/div>\n<p><span id=\"m44485-fs-id1511467\"> <\/span>Modern understandings of DNA have evolved from the discovery of nucleic acid to the development of the double-helix model. In the 1860s, Friedrich Miescher (<a class=\"xref target-figure\" href=\"ch14.html#m44485-fig-ch14_01_01\" title=\"Figure&#xa0;14.2.&#xa0;\">Figure\u00a014.2<\/a>), a physician by profession, was the first person to isolate phosphate-rich chemicals from white blood cells or leukocytes. He named these chemicals (which would eventually be known as RNA and DNA) nuclein because they were isolated from the nuclei of the cells.<\/p>\n<div id=\"m44485-fig-ch14_01_01\" class=\"figure\" title=\"Figure&#xa0;14.2.&#xa0;\">\n<div class=\"body\">\n<div class=\"mediaobject\"><span id=\"m44485-fs-id2081310\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155642\/Figure_14_01_01.jpg\" width=\"150\" alt=\"Photo of Friedrich Miescher.\" \/><\/div>\n<\/div>\n<div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.2<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"><\/span><\/div>\n<div class=\"caption\">Friedrich Miescher (1844\u20131895) discovered nucleic acids.<\/div>\n<\/div>\n<div id=\"m44485-fs-id1964835\" class=\"note interactive\">\n<div class=\"title\"><span class=\"cnx-gentext-tip-t\">Link to Learning<\/span><\/div>\n<div class=\"body\">\n<div class=\"mediaobject\"><span id=\"m44485-fs-id1482325\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155645\/miescher_levene.png\" width=\"120\" alt=\"QR Code representing a URL\" \/><\/div>\n<p><span id=\"m44485-fs-id2009505\"> <\/span>To see Miescher conduct an experiment step-by-step, click through <a class=\"link\" href=\"http:\/\/openstaxcollege.org\/l\/miescher_levene\" target=\"\">this review<\/a> of how he discovered the key role of DNA and proteins in the nucleus.<\/p>\n<\/div>\n<\/div>\n<p><span id=\"m44485-fs-id1430986\"> <\/span>A half century later, British bacteriologist Frederick Griffith was perhaps the first person to show that hereditary information could be transferred from one cell to another \u201chorizontally,\u201d rather than by descent. In 1928, he reported the first demonstration of bacterial <em class=\"glossterm\"><span id=\"m44485-autoid-cnx2dbk-id1280706\"> <\/span>transformation<\/em><a id=\"id502585\" class=\"indexterm\">, a process in which external DNA is taken up by a cell, thereby changing morphology and physiology. He was working with <span class=\"emphasis\"><em>Streptococcus pneumoniae,<\/em><\/span> the bacterium that causes pneumonia. Griffith worked with two strains, rough (R) and smooth (S). The R strain is non-pathogenic (does not cause disease) and is called rough because its outer surface is a cell wall and lacks a capsule; as a result, the cell surface appears uneven under the microscope. The S strain is pathogenic (disease-causing) and has a capsule outside its cell wall. As a result, it has a smooth appearance under the microscope. Griffith injected the live R strain into mice and they survived. In another experiment, when he injected mice with the heat-killed S strain, they also survived. In a third set of experiments, a mixture of live R strain and heat-killed S strain were injected into mice, and\u2014to his surprise\u2014the mice died. Upon isolating the live bacteria from the dead mouse, only the S strain of bacteria was recovered. When this isolated S strain was injected into fresh mice, the mice died. Griffith concluded that something had passed from the heat-killed S strain into the live R strain and transformed it into the pathogenic S strain, and he called this the transforming principle (<\/a><a class=\"xref target-figure\" href=\"ch14.html#m44485-fig-ch14_01_02\" title=\"Figure&#xa0;14.3.&#xa0;\">Figure\u00a014.3<\/a>). These experiments are now famously known as Griffith&#8217;s transformation experiments.<\/p>\n<div id=\"m44485-fig-ch14_01_02\" class=\"figure\" title=\"Figure&#xa0;14.3.&#xa0;\">\n<div class=\"body\">\n<div class=\"mediaobject\"><span id=\"m44485-fs-id1631652\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155647\/Figure_14_01_02.jpg\" width=\"525\" alt=\"On the left is a photo of a live mouse, representing a mouse injected with heat-killed, virulent S strain. On the right is a photo of a dead mouse, representing a mouse injected with heat-killed, virulent S strain and live, non-virulent R strain.\" \/><\/div>\n<\/div>\n<div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.3<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"><\/span><\/div>\n<div class=\"caption\">Two strains of <span class=\"emphasis\"><em>S. pneumoniae<\/em><\/span> were used in Griffith\u2019s transformation experiments. The R strain is non-pathogenic. The S strain is pathogenic and causes death. When Griffith injected a mouse with the heat-killed S strain and a live R strain, the mouse died. The S strain was recovered from the dead mouse. Thus, Griffith concluded that something had passed from the heat-killed S strain to the R strain, transforming the R strain into S strain in the process. (credit &#8220;living mouse&#8221;: modification of work by NIH; credit &#8220;dead mouse&#8221;: modification of work by Sarah Marriage)<\/div>\n<\/div>\n<p><span id=\"m44485-fs-id2890946\"> <\/span>Scientists Oswald Avery, Colin MacLeod, and Maclyn McCarty (1944) were interested in exploring this transforming principle further. They isolated the S strain from the dead mice and isolated the proteins and nucleic acids, namely RNA and DNA, as these were possible candidates for the molecule of heredity. They conducted a systematic elimination study. They used enzymes that specifically degraded each component and then used each mixture separately to transform the R strain. They found that when DNA was degraded, the resulting mixture was no longer able to transform the bacteria, whereas all of the other combinations were able to transform the bacteria. This led them to conclude that DNA was the transforming principle.<\/p>\n<div id=\"m44485-fs-id1772414\" class=\"note career\">\n<div class=\"title\"><span class=\"cnx-gentext-tip-t\">Career Connection<\/span><\/div>\n<div class=\"body\">\n<p title=\"Forensic Scientists and DNA Analysis\"><span id=\"m44485-fs-id2115765\"> <\/span><\/p>\n<div class=\"title\"><b>Forensic Scientists and DNA Analysis<\/b><\/div>\n<p title=\"Forensic Scientists and DNA Analysis\">DNA evidence was used for the first time to solve an immigration case. The story started with a teenage boy returning to London from Ghana to be with his mother. Immigration authorities at the airport were suspicious of him, thinking that he was traveling on a forged passport. After much persuasion, he was allowed to go live with his mother, but the immigration authorities did not drop the case against him. All types of evidence, including photographs, were provided to the authorities, but deportation proceedings were started nevertheless. Around the same time, Dr. Alec Jeffreys of Leicester University in the United Kingdom had invented a technique known as DNA fingerprinting. The immigration authorities approached Dr. Jeffreys for help. He took DNA samples from the mother and three of her children, plus an unrelated mother, and compared the samples with the boy\u2019s DNA. Because the biological father was not in the picture, DNA from the three children was compared with the boy\u2019s DNA. He found a match in the boy\u2019s DNA for both the mother and his three siblings. He concluded that the boy was indeed the mother\u2019s son.<\/p>\n<p><span id=\"m44485-fs-id1227579\"> <\/span>Forensic scientists analyze many items, including documents, handwriting, firearms, and biological samples. They analyze the DNA content of hair, semen, saliva, and blood, and compare it with a database of DNA profiles of known criminals. Analysis includes DNA isolation, sequencing, and sequence analysis; most forensic DNA analysis involves polymerase chain reaction (PCR) amplification of short tandem repeat (STR) loci and electrophoresis to determine the length of the PCR-amplified fragment. Only mitochondrial DNA is sequenced for forensics. Forensic scientists are expected to appear at court hearings to present their findings. They are usually employed in crime labs of city and state government agencies. Geneticists experimenting with DNA techniques also work for scientific and research organizations, pharmaceutical industries, and college and university labs. Students wishing to pursue a career as a forensic scientist should have at least a bachelor&#8217;s degree in chemistry, biology, or physics, and preferably some experience working in a laboratory.<\/p>\n<\/div>\n<\/div>\n<p><span id=\"m44485-fs-id2025461\"> <\/span>Experiments conducted by Martha Chase and Alfred Hershey in 1952 provided confirmatory evidence that DNA was the genetic material and not proteins. Chase and Hershey were studying a bacteriophage, which is a virus that infects bacteria. Viruses typically have a simple structure: a protein coat, called the capsid, and a nucleic acid core that contains the genetic material, either DNA or RNA. The bacteriophage infects the host bacterial cell by attaching to its surface, and then it injects its nucleic acids inside the cell. The phage DNA makes multiple copies of itself using the host machinery, and eventually the host cell bursts, releasing a large number of bacteriophages. Hershey and Chase labeled one batch of phage with radioactive sulfur, <sup>35<\/sup>S, to label the protein coat. Another batch of phage were labeled with radioactive phosphorus, <sup>32<\/sup>P. Because phosphorous is found in DNA, but not protein, the DNA and not the protein would be tagged with radioactive phosphorus.<\/p>\n<p><span id=\"m44485-fs-id1352111\"> <\/span>Each batch of phage was allowed to infect the cells separately. After infection, the phage bacterial suspension was put in a blender, which caused the phage coat to be detached from the host cell. The phage and bacterial suspension was spun down in a centrifuge. The heavier bacterial cells settled down and formed a pellet, whereas the lighter phage particles stayed in the supernatant. In the tube that contained phage labeled with<sup> 35<\/sup>S, the supernatant contained the radioactively labeled phage, whereas no radioactivity was detected in the pellet. In the tube that contained the phage labeled with <sup>32<\/sup>P, the radioactivity was detected in the pellet that contained the heavier bacterial cells, and no radioactivity was detected in the supernatant.  Hershey and Chase concluded that it was the phage DNA that was injected<br \/>\ninto the cell and carried information to produce more phage particles, thus providing evidence that DNA was the genetic material and not proteins (<a class=\"xref target-figure\" href=\"ch14.html#m44485-fig-ch14_01_03\" title=\"Figure&#xa0;14.4.&#xa0;\">Figure\u00a014.4<\/a>).<\/p>\n<div id=\"m44485-fig-ch14_01_03\" class=\"figure\" title=\"Figure&#xa0;14.4.&#xa0;\">\n<div class=\"body\">\n<div class=\"mediaobject\"><span id=\"m44485-fs-id1879663\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155649\/Figure_14_01_03.jpg\" width=\"400\" alt=\"Illustration shows bacteria being infected by phage labeled with ^{35}S, which is incorporated into the protein coat, or ^{32}P, which is incorporated into the DNA. Infected bacteria were separated from phage by centrifugation and cultured. The bacteria that had been infected with phage containing ^{32}P-labeled DNA made radioactive phage. The bacteria that had been infected with ^{35}S-labeled phage produced unlabeled phage. The results support the hypothesis that DNA, and not protein, is the genetic material.\" \/><\/div>\n<\/div>\n<div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.4<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"><\/span><\/div>\n<div class=\"caption\">In Hershey and Chase&#8217;s experiments, bacteria were infected with phage radiolabeled with either <sup>35<\/sup>S, which labels protein, or <sup>32<\/sup>P, which labels DNA. Only <sup>32<\/sup>P entered the bacterial cells, indicating that DNA is the genetic material.<\/div>\n<\/div>\n<p><span id=\"m44485-fs-id1430603\"> <\/span>Around this same time, Austrian biochemist Erwin Chargaff examined the content of DNA in different species and found that the amounts of adenine, thymine, guanine, and cytosine were not found in equal quantities, and that it varied from species to species, but not between individuals of the same species. He found that the amount of adenine equals the amount of thymine, and the amount of cytosine equals the amount of guanine, or A = T and G = C. This is also known as Chargaff\u2019s rules. This finding proved immensely useful when Watson and Crick were getting ready to propose their DNA double helix model.<\/p>\n<\/div>\n<div xml:lang=\"en\" class=\"section module\" title=\"14.2.&#xa0;DNA Structure and Sequencing\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h2 id=\"m44486\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.2<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Structure and Sequencing<sup><a href=\"co03.html#book-attribution-m44486\">*<\/a><\/sup><\/span><\/span><\/h2>\n<\/div>\n<div class=\"abstract\">\n<div class=\"title\"><span><span class=\"cnx-gentext-abstract cnx-gentext-autogenerated\"><span class=\"cnx-gentext-abstract cnx-gentext-t\"><\/span><\/span><\/span><\/div>\n<p>By the end of this section, you will be able to:\n<\/p>\n<div class=\"itemizedlist\">\n<ul class=\"itemizedlist\">\n<li class=\"listitem\">\n<p>Describe the structure of DNA<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>Explain the Sanger method of DNA sequencing<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>Discuss the similarities and differences between eukaryotic and prokaryotic DNA<\/p>\n<\/li>\n<\/ul>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"toc\">\n<ul>\n<li class=\"toc-section\"><a href=\"#m44486-fs-id1671532\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Sequencing Techniques<\/span><\/a>\n<ul>\n<li class=\"toc-section\"><a href=\"#m44486-fs-id3294130\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Packaging in Cells<\/span><\/a><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/div>\n<p><span id=\"m44486-fs-id2164409\"> <\/span>The building blocks of DNA are nucleotides. The important components of the nucleotide are a nitrogenous base, deoxyribose (5-carbon sugar), and a phosphate group (<a class=\"xref target-figure\" href=\"ch14.html#m44486-fig-ch14_02_01\" title=\"Figure&#xa0;14.5.&#xa0;\">Figure\u00a014.5<\/a>). The nucleotide is named depending on the nitrogenous base. The nitrogenous base can be a purine such as adenine (A) and guanine (G), or a pyrimidine such as cytosine (C) and thymine (T).<\/p>\n<div id=\"m44486-fig-ch14_02_01\" class=\"figure\" title=\"Figure&#xa0;14.5.&#xa0;\">\n<div class=\"body\">\n<div class=\"mediaobject\"><span id=\"m44486-fs-id1760452\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155652\/Figure_14_02_01.jpg\" width=\"500\" alt=\"Illustration depicts the structure of a nucleoside, which is made up of a pentose with a nitrogenous base attached at the 1' position. There are two kinds of nitrogenous bases: pyrimidines, which have one six-membered ring, and purines, which have a six-membered ring fused to a five-membered ring. Cytosine, thymine, and uracil are pyrimidines, and adenine and guanine are purines. A nucleoside with a phosphate attached at the 5' position is called a mononucleotide. A nucleoside with two or three phosphates attached is called a nucleotide diphosphate or nucleotide triphosphate, respectively.\" \/><\/div>\n<\/div>\n<div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.5<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"><\/span><\/div>\n<div class=\"caption\">Each nucleotide is made up of a sugar, a phosphate group, and a nitrogenous base. The sugar is deoxyribose in DNA and ribose in RNA.<\/div>\n<\/div>\n<p><span id=\"m44486-fs-id1912233\"> <\/span>The nucleotides combine with each other by covalent bonds known as phosphodiester bonds or linkages. The purines have a double ring structure with a six-membered ring fused to a five-membered ring. Pyrimidines are smaller in size; they have a single six-membered ring structure. The carbon atoms of the five-carbon sugar are numbered 1&#8242;, 2&#8242;, 3&#8242;, 4&#8242;, and 5&#8242; (1&#8242; is read as \u201cone prime\u201d). The phosphate residue is attached to the hydroxyl group of the 5&#8242; carbon of one sugar of one nucleotide and the hydroxyl group of the 3&#8242; carbon of the sugar of the next nucleotide, thereby forming a 5&#8242;-3&#8242; phosphodiester bond.<\/p>\n<p><span id=\"m44486-fs-id2019239\"> <\/span>In the 1950s, Francis Crick and James Watson worked together to determine the structure of DNA at the University of Cambridge, England. Other scientists like Linus Pauling and Maurice Wilkins were also actively exploring this field. Pauling had discovered the secondary structure of proteins using X-ray crystallography. In Wilkins\u2019 lab, researcher Rosalind Franklin was using X-ray diffraction methods to understand the structure of DNA. Watson and Crick were able to piece together the puzzle of the DNA molecule on the basis of Franklin&#8217;s data because Crick had also studied X-ray diffraction (<a class=\"xref target-figure\" href=\"ch14.html#m44486-fig-ch14_02_02\" title=\"Figure&#xa0;14.6.&#xa0;\">Figure\u00a014.6<\/a>). In 1962, James Watson, Francis Crick, and Maurice Wilkins were awarded the Nobel Prize in Medicine. Unfortunately, by then Franklin had died, and Nobel prizes are not awarded posthumously.<\/p>\n<div id=\"m44486-fig-ch14_02_02\" class=\"figure\" title=\"Figure&#xa0;14.6.&#xa0;\">\n<div class=\"body\">\n<div class=\"mediaobject\"><span id=\"m44486-fs-id2075482\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155654\/Figure_14_02_02ab_new.jpg\" width=\"500\" alt=\"The photo in part A shows James Watson, Francis Crick, and Maclyn McCarty. The x-ray diffraction pattern in part b is symmetrical, with dots in an x-shape\" \/><\/div>\n<\/div>\n<div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.6<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"><\/span><\/div>\n<div class=\"caption\">The work of pioneering scientists (a) James Watson, Francis Crick, and Maclyn McCarty led to our present day understanding of DNA. Scientist Rosalind Franklin discovered (b) the X-ray diffraction pattern of DNA, which helped to elucidate its double helix structure. (credit a: modification of work by Marjorie McCarty, Public Library of Science)<\/div>\n<\/div>\n<p><span id=\"m44486-fs-id2317138\"> <\/span>Watson and Crick proposed that DNA is made up of two strands that are twisted around each other to form a right-handed helix. Base pairing takes place between a purine and pyrimidine; namely, A pairs with T and G pairs with C. Adenine and thymine are complementary base pairs, and cytosine and guanine are also complementary base pairs. The base pairs are stabilized by hydrogen bonds; adenine and thymine form two hydrogen bonds and cytosine and guanine form three hydrogen bonds. The two strands are anti-parallel in nature; that is, the 3&#8242; end of one strand faces the 5&#8242; end of the other strand. The sugar and phosphate of the nucleotides form the backbone of the structure, whereas the nitrogenous bases are stacked inside. Each base pair is separated from the other base pair by a distance of 0.34 nm, and each turn of the helix measures 3.4 nm. Therefore, ten base pairs are present per turn of the helix. The diameter of the DNA double helix is 2 nm, and it is uniform throughout. Only the pairing between a purine and pyrimidine can explain the uniform diameter. The twisting of the two strands around each other results in the formation of uniformly spaced major and minor grooves (<a class=\"xref target-figure\" href=\"ch14.html#m44486-fig-ch14_02_03\" title=\"Figure&#xa0;14.7.&#xa0;\">Figure\u00a014.7<\/a>).<\/p>\n<div id=\"m44486-fig-ch14_02_03\" class=\"figure\" title=\"Figure&#xa0;14.7.&#xa0;\">\n<div class=\"body\">\n<div class=\"mediaobject\"><span id=\"m44486-fs-id2144919\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155657\/Figure_14_02_03abc.jpg\" width=\"450\" alt=\"Part A shows an illustration of a DNA double helix, which has a sugar-phosphate backbone on the outside and nitrogenous base pairs on the inside. Part B shows base pairing between thymine and adenine, which form two hydrogen bonds, and between guanine and cytosine, which form three hydrogen bonds. Part C shows a molecular model of the DNA double helix. The outside of the helix alternates between wide gaps, called major grooves, and narrow gaps, called minor grooves.\" \/><\/div>\n<\/div>\n<div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.7<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"><\/span><\/div>\n<div class=\"caption\">DNA has (a) a double helix structure and (b) phosphodiester bonds. The (c) major and minor grooves are binding sites for DNA binding proteins during processes such as transcription (the copying of RNA from DNA) and replication.<\/div>\n<\/div>\n<div class=\"section\" title=\"DNA Sequencing Techniques\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h3 id=\"m44486-fs-id1671532\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Sequencing Techniques<\/span><\/span><\/h3>\n<\/div>\n<\/div>\n<\/div>\n<p><span id=\"m44486-fs-id2060998\"> <\/span>Until the 1990s, the sequencing of DNA (reading the sequence of DNA) was a relatively expensive and long process. Using radiolabeled nucleotides also compounded the problem through safety concerns. With currently available technology and automated machines, the process is cheap, safer, and can be completed in a matter of hours. Fred Sanger developed the sequencing method used for the human genome sequencing project, which is widely used today (<a class=\"xref target-figure\" href=\"ch14.html#m44486-fig-ch14_02_04\" title=\"Figure&#xa0;14.8.&#xa0;\">Figure\u00a014.8<\/a>).<\/p>\n<div id=\"m44486-fs-id2117592\" class=\"note interactive\">\n<div class=\"title\"><span class=\"cnx-gentext-tip-t\">Link to Learning<\/span><\/div>\n<div class=\"body\">\n<div class=\"mediaobject\"><span id=\"m44486-fs-id1958775\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155659\/DNA_sequencing.png\" width=\"120\" alt=\"QR Code representing a URL\" \/><\/div>\n<p><span id=\"m44486-fs-id2897121\"> <\/span>Visit <a class=\"link\" href=\"http:\/\/openstaxcollege.org\/l\/DNA_sequencing\" target=\"\">this site<\/a> to watch a video explaining the DNA sequence reading technique that resulted from Sanger\u2019s work.<\/p>\n<\/div>\n<\/div>\n<p><span id=\"m44486-fs-id1695688\"> <\/span>The method is known as the dideoxy chain termination method. The sequencing method is based on the use of chain terminators, the dideoxynucleotides (ddNTPs). The dideoxynucleotides, or ddNTPSs, differ from the deoxynucleotides by the lack of a free 3&#8242; OH group on the five-carbon sugar. If a ddNTP is added to a growing a DNA strand, the chain is not extended any further because the free 3&#8242; OH group needed to add another nucleotide is not available. By using a predetermined ratio of deoxyribonucleotides to dideoxynucleotides, it is possible to generate DNA fragments of different sizes.<\/p>\n<div id=\"m44486-fig-ch14_02_04\" class=\"figure\" title=\"Figure&#xa0;14.8.&#xa0;\">\n<div class=\"body\">\n<div class=\"mediaobject\"><span id=\"m44486-fs-id1822083\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155702\/Figure_14_02_04ab.jpg\" width=\"400\" alt=\"Part A shows a template DNA strand and newly synthesized strands that were generated in the presence of dideoxynucleotides that terminate the chain at different points to generate fragments of different sizes. Each dideoxynucleotide is labeled a different color. Part B shows a sequence readout that was generated after the DNA fragments were separated on the basis of size. The color of the fragment indicates the identity of the nucleotide at the end of a given fragment. By reading the colors in order, the DNA sequence can be determined.\" \/><\/div>\n<\/div>\n<div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.8<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"><\/span><\/div>\n<div class=\"caption\">In Frederick Sanger&#8217;s dideoxy chain termination method, dye-labeled dideoxynucleotides are used to generate DNA fragments that terminate at different points. The DNA is separated by capillary electrophoresis on the basis of size, and from the order of fragments formed, the DNA sequence can be read. The DNA sequence readout is shown on an electropherogram that is generated by a laser scanner.<\/div>\n<\/div>\n<p><span id=\"m44486-fs-id1797232\"> <\/span>The DNA sample to be sequenced is denatured or separated into two strands by heating it to high temperatures. The DNA is divided into four tubes in which a primer, DNA polymerase, and all four nucleotides (A, T, G, and C) are added. In addition to each of the four tubes, limited quantities of one of the four dideoxynucleotides are added to each tube respectively. The tubes are labeled as A, T, G, and C according to the ddNTP added. For detection purposes, each of the four dideoxynucleotides carries a different fluorescent label. Chain elongation continues until a fluorescent dideoxy nucleotide is incorporated, after which no further elongation takes place. After the reaction is over, electrophoresis is performed. Even a difference in length of a single base can be detected. The sequence is read from a laser scanner. For his work on DNA sequencing, Sanger received a Nobel Prize in chemistry in 1980.<\/p>\n<div id=\"m44486-fs-id1352111\" class=\"note interactive\">\n<div class=\"title\"><span class=\"cnx-gentext-tip-t\">Link to Learning<\/span><\/div>\n<div class=\"body\">\n<div class=\"mediaobject\"><span id=\"m44486-fs-id1483229\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155704\/DNA_and_genomes.png\" width=\"120\" alt=\"QR Code representing a URL\" \/><\/div>\n<p><span id=\"m44486-fs-id1968434\"> <\/span>Sanger\u2019s genome sequencing has led to a race to sequence human genomes at a rapid speed and low cost, often referred to as the $1000 in one day sequence. Learn more by selecting the Sequencing at Speed animation <a class=\"link\" href=\"http:\/\/openstaxcollege.org\/l\/DNA_and_genomes\" target=\"\">here<\/a>.<\/p>\n<\/div>\n<\/div>\n<p><span id=\"m44486-fs-id2573656\"> <\/span>Gel <em class=\"glossterm\"><span id=\"m44486-autoid-cnx2dbk-id1615069\"> <\/span>electrophoresis<\/em><a id=\"id503706\" class=\"indexterm\"> is a technique used to separate DNA fragments of different sizes. Usually the gel is made of a chemical called agarose. Agarose powder is added to a buffer and heated. After cooling, the gel solution is poured into a casting tray. Once the gel has solidified, the DNA is loaded on the gel and electric current is applied. The DNA has a net negative charge and moves from the negative electrode toward the positive electrode. The electric current is applied for sufficient time to let the DNA separate according to size; the smallest fragments will be farthest from the well (where the DNA was loaded), and the heavier molecular weight fragments will be closest to the well. Once the DNA is separated, the gel is stained with a DNA-specific dye for viewing it (<\/a><a class=\"xref target-figure\" href=\"ch14.html#m44486-fig-ch14_02_05\" title=\"Figure&#xa0;14.9.&#xa0;\">Figure\u00a014.9<\/a>).<\/p>\n<div id=\"m44486-fig-ch14_02_05\" class=\"figure\" title=\"Figure&#xa0;14.9.&#xa0;\">\n<div class=\"body\">\n<div class=\"mediaobject\"><span id=\"m44486-fs-id2022421\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155706\/Figure_14_02_05.jpg\" width=\"320\" alt=\"Photo shows an agarose gel illuminated under UV light. The gel is nine lanes across. Each lane was loaded with a sample containing DNA fragments of differing size that have separated as they travel through the gel, from top to bottom. The DNA appears as thin, white bands on a black background. Lanes one and nine contain many bands from a DNA standard. These bands are closely spaced toward the top, and spaced farther apart further down the gel. Lanes two through eight contain one or two bands each. Some of these bands are identical in size and run the same distance into the gel. Others run a slightly different distance, indicating a small difference in size.\" \/><\/div>\n<\/div>\n<div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.9<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"><\/span><\/div>\n<div class=\"caption\">DNA can be separated on the basis of size using gel electrophoresis. (credit: James Jacob, Tompkins Cortland Community College)<\/div>\n<\/div>\n<div id=\"m44486-fs-id1288287\" class=\"note evolution\">\n<div class=\"title\"><span class=\"cnx-gentext-tip-t\">Evolution Connection<\/span><\/div>\n<div class=\"body\">\n<p title=\"Neanderthal Genome: How Are We Related?\"><span id=\"m44486-fs-id2013345\"> <\/span><\/p>\n<div class=\"title\"><b>Neanderthal Genome: How Are We Related?<\/b><\/div>\n<p title=\"Neanderthal Genome: How Are We Related?\">The first draft sequence of the Neanderthal genome was recently published by Richard E. Green et al. in 2010.<sup><sup>[<a id=\"m44486-fs-id1277293\" href=\"#ftn.m44486-fs-id1277293\" class=\"footnote\">11<\/a>]<\/sup><\/sup> Neanderthals are the closest ancestors of present-day humans. They were known to have lived in Europe and Western Asia before they disappeared from fossil records approximately 30,000 years ago. Green\u2019s team studied almost 40,000-year-old fossil remains that were selected from sites across the world. Extremely sophisticated means of sample preparation and DNA sequencing were employed because of the fragile nature of the bones and heavy microbial contamination. In their study, the scientists were able to sequence some four billion base pairs. The Neanderthal sequence was compared with that of present-day humans from across the world. After comparing the sequences, the researchers found that the Neanderthal genome had 2 to 3 percent greater similarity to people living outside Africa than to people in Africa. While current theories have suggested that all present-day humans can be traced to a small ancestral population in Africa, the data from the Neanderthal genome may contradict this view. Green and his colleagues also discovered DNA segments among people in Europe and Asia that are more similar to Neanderthal sequences than to other contemporary human sequences. Another interesting observation was that Neanderthals are as closely related to people from Papua New Guinea as to those from China or France. This is surprising because Neanderthal fossil remains have been located only in Europe and West Asia. Most likely, genetic exchange took place between Neanderthals and modern humans as modern humans emerged out of Africa, before the divergence of Europeans, East Asians, and Papua New Guineans.<\/p>\n<p><span id=\"m44486-fs-id1471220\"> <\/span>Several genes seem to have undergone changes from Neanderthals during the evolution of present-day humans. These genes are involved in cranial structure, metabolism, skin morphology, and cognitive development. One of the genes that is of particular interest is <span class=\"emphasis\"><em>RUNX2<\/em><\/span>, which is different in modern day humans and Neanderthals. This gene is responsible for the prominent frontal bone, bell-shaped rib cage, and dental differences seen in Neanderthals. It is speculated that an evolutionary change in <span class=\"emphasis\"><em>RUNX2<\/em><\/span> was important in the origin of modern-day humans, and this affected the cranium and the upper body.<\/p>\n<\/div>\n<\/div>\n<div id=\"m44486-fs-id1770393\" class=\"note interactive\">\n<div class=\"title\"><span class=\"cnx-gentext-tip-t\">Link to Learning<\/span><\/div>\n<div class=\"body\">\n<div class=\"mediaobject\"><span id=\"m44486-fs-id2308662\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155708\/neanderthal.png\" width=\"120\" alt=\"QR Code representing a URL\" \/><\/div>\n<p><span id=\"m44486-fs-id2026323\"> <\/span>Watch <a class=\"link\" href=\"http:\/\/openstaxcollege.org\/l\/neanderthal\" target=\"\">Svante P\u00e4\u00e4bo\u2019s talk<\/a> explaining the Neanderthal genome research at the 2011 annual TED (Technology, Entertainment, Design) conference.<\/p>\n<\/div>\n<\/div>\n<div class=\"section\" title=\"DNA Packaging in Cells\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h4 id=\"m44486-fs-id3294130\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Packaging in Cells<\/span><\/span><\/h4>\n<\/div>\n<\/div>\n<\/div>\n<p><span id=\"m44486-fs-id2215894\"> <\/span>When comparing prokaryotic cells to eukaryotic cells, prokaryotes are much simpler than eukaryotes in many of their features (<a class=\"xref target-figure\" href=\"ch14.html#m44486-fig-ch14_02_06\" title=\"Figure&#xa0;14.10.&#xa0;\">Figure\u00a014.10<\/a>). Most prokaryotes contain a single, circular chromosome that is found in an area of the cytoplasm called the nucleoid.<\/p>\n<div id=\"m44486-fs-id1973249\" class=\"note art-connection\">\n<div class=\"title\"><span class=\"cnx-gentext-tip-t\">Art Connection<\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44486-fs-id2589720\"> <\/span><\/p>\n<div id=\"m44486-fig-ch14_02_06\" class=\"figure\" title=\"Figure&#xa0;14.10.&#xa0;\">\n<div class=\"body\"><span class=\"inlinemediaobject\"><span id=\"m44486-fs-id1970814\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155711\/Figure_14_02_06_new.png\" width=\"450\" alt=\"Illustration shows a eukaryotic cell, which has a membrane-bound nucleus containing chromatin and a nucleolus, and a prokaryotic cell, which has DNA contained in an area of the cytoplasm called the nucleoid. The prokaryotic cell is much smaller than the eukaryotic cell.\" \/><\/span><\/div>\n<div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.10<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"><\/span><\/div>\n<div class=\"caption\">A eukaryote contains a well-defined nucleus, whereas in prokaryotes, the chromosome lies in the cytoplasm in an area called the nucleoid.<\/div>\n<\/div>\n<p><span id=\"m44486-fs-id1512144\"> <\/span>In eukaryotic cells, DNA and RNA synthesis occur in a separate compartment from protein synthesis. In prokaryotic cells, both processes occur together. What advantages might there be to separating the processes? What advantages might there be to having them occur together?<\/p>\n<\/div>\n<\/div>\n<p><span id=\"m44486-fs-id2962722\"> <\/span>The size of the genome in one of the most well-studied prokaryotes, <span class=\"emphasis\"><em>E.coli,<\/em><\/span> is 4.6 million base pairs (approximately 1.1 mm, if cut and stretched out). So how does this fit inside a small bacterial cell? The DNA is twisted by what is known as supercoiling. Supercoiling means that DNA is either under-wound (less than one turn of the helix per 10 base pairs) or over-wound (more than 1 turn per 10 base pairs) from its normal relaxed state. Some proteins are known to be involved in the supercoiling; other proteins and enzymes such as DNA gyrase help in maintaining the supercoiled structure.<\/p>\n<p><span id=\"m44486-fs-id2235232\"> <\/span>Eukaryotes, whose chromosomes each consist of a linear DNA molecule, employ a different type of packing strategy to fit their DNA inside the nucleus (<a class=\"xref target-figure\" href=\"ch14.html#m44486-fig-ch14_02_07\" title=\"Figure&#xa0;14.11.&#xa0;\">Figure\u00a014.11<\/a>). At the most basic level, DNA is wrapped around proteins known as histones to form structures called nucleosomes. The histones are evolutionarily conserved proteins that are rich in basic amino acids and form an octamer. The DNA (which is negatively charged because of the phosphate groups) is wrapped tightly around the histone core. This nucleosome is linked to the next one with the help of a linker DNA. This is also known as the \u201cbeads on a string\u201d structure. This is further compacted into a 30 nm fiber, which is the diameter of the structure. At the metaphase stage, the chromosomes are at their most compact, are approximately 700 nm in width, and are found in association with scaffold proteins.<\/p>\n<p><span id=\"m44486-fs-id2685429\"> <\/span>In interphase, eukaryotic chromosomes have two distinct regions that can be distinguished by staining. The tightly packaged region is known as heterochromatin, and the less dense region is known as euchromatin. Heterochromatin usually contains genes that are not expressed, and is found in the regions of the centromere and telomeres. The euchromatin usually contains genes that are transcribed, with DNA packaged around nucleosomes but not further compacted.<\/p>\n<div id=\"m44486-fig-ch14_02_07\" class=\"figure\" title=\"Figure&#xa0;14.11.&#xa0;\">\n<div class=\"body\">\n<div class=\"mediaobject\"><span id=\"m44486-fs-id1987230\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155713\/Figure_14_02_07.jpg\" width=\"275\" alt=\"Illustration shows the levels of organization of eukaryotic chromosomes, starting with the DNA double helix, which wraps around histone proteins. The entire DNA molecule wraps around many clusters of histone proteins, forming a structure that looks like beads on a string. The chromatin is further condensed by wrapping around a protein core. The result is a compact chromosome, shown in duplicated form.\" \/><\/div>\n<\/div>\n<div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.11<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"><\/span><\/div>\n<div class=\"caption\">These figures illustrate the compaction of the eukaryotic chromosome.<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div xml:lang=\"en\" class=\"section module\" title=\"14.3.&#xa0;Basics of DNA Replication\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h2 id=\"m44487\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.3<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Basics of DNA Replication<sup><a href=\"co03.html#book-attribution-m44487\">*<\/a><\/sup><\/span><\/span><\/h2>\n<\/div>\n<div class=\"abstract\">\n<div class=\"title\"><span><span class=\"cnx-gentext-abstract cnx-gentext-autogenerated\"><span class=\"cnx-gentext-abstract cnx-gentext-t\"><\/span><\/span><\/span><\/div>\n<p>By the end of this section, you will be able to:\n<\/p>\n<div class=\"itemizedlist\">\n<ul class=\"itemizedlist\">\n<li class=\"listitem\">\n<p>Explain how the structure of DNA reveals the replication process<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>Describe the Meselson and Stahl experiments<\/p>\n<\/li>\n<\/ul>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"toc\">\n<ul><\/ul>\n<\/div>\n<p><span id=\"m44487-fs-id2265995\"> <\/span>The elucidation of the structure of the double helix provided a hint as to how DNA divides and makes copies of itself. This model suggests that the two strands of the double helix separate during replication, and each strand serves as a template from which the new complementary strand is copied. What was not clear was how the replication took place. There were three models suggested (<a class=\"xref target-figure\" href=\"ch14.html#m44487-fig-ch14_03_01\" title=\"Figure&#xa0;14.12.&#xa0;\">Figure\u00a014.12<\/a>): conservative, semi-conservative, and dispersive.<\/p>\n<div id=\"m44487-fig-ch14_03_01\" class=\"figure\" title=\"Figure&#xa0;14.12.&#xa0;\">\n<div class=\"body\">\n<div class=\"mediaobject\"><span id=\"m44487-fs-id2051052\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155715\/Figure_14_03_01.jpg\" width=\"275\" alt=\"Illustration shows the conservative, semi-conservative, and dispersive models of DNA synthesis. In the conservative model, when DNA is replicated and both newly synthesized strands are paired together. In the semi-conservative model, each newly synthesized strand pairs with a parent strand. In the dispersive model, newly synthesized DNA is interspersed with parent DNA within both DNA strands.\" \/><\/div>\n<\/div>\n<div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.12<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"><\/span><\/div>\n<div class=\"caption\">The three suggested models of DNA replication. Grey indicates the original DNA strands, and blue indicates newly synthesized DNA.<\/div>\n<\/div>\n<p><span id=\"m44487-fs-id1685167\"> <\/span>In conservative replication, the parental DNA remains together, and the newly formed daughter strands are together. The semi-conservative method suggests that each of the two parental DNA strands act as a template for new DNA to be synthesized; after replication, each double-stranded DNA includes one parental or \u201cold\u201d strand and one \u201cnew\u201d strand. In the dispersive model, both copies of DNA have double-stranded segments of parental DNA and newly synthesized DNA interspersed.<\/p>\n<p><span id=\"m44487-fs-id2216817\"> <\/span>Meselson and Stahl were interested in understanding how DNA replicates. They grew <span class=\"emphasis\"><em>E. coli<\/em><\/span> for several generations in a medium containing a \u201cheavy\u201d isotope of nitrogen (<sup>15<\/sup>N) that gets incorporated into nitrogenous bases, and eventually into the DNA (<a class=\"xref target-figure\" href=\"ch14.html#m44487-fig-ch14_03_02\" title=\"Figure&#xa0;14.13.&#xa0;\">Figure\u00a014.13<\/a>).<\/p>\n<div id=\"m44487-fig-ch14_03_02\" class=\"figure\" title=\"Figure&#xa0;14.13.&#xa0;\">\n<div class=\"body\">\n<div class=\"mediaobject\"><span id=\"m44487-fs-id1640010\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155717\/Figure_14_03_02.jpg\" width=\"350\" alt=\"Illustration shows an experiment in which E. coli was grown initially in media containing ^{15}N nucleotides. When the DNA was extracted and run in an ultracentrifuge, a band of DNA appeared low in the tube. The culture was next placed in ^{14}N medium. After one generation, all of the DNA appeared in the middle of the tube, indicating that the DNA was a mixture of half ^{14}N and half ^{15}N DNA. After two generations, half of the DNA appeared in the middle of the tube, and half appeared higher up, indicating that half the DNA contained 50% ^{15}N, and half contained ^{14}N only. In subsequent generations, more and more of the DNA appeared in the upper, ^{14}N band.\" \/><\/div>\n<\/div>\n<div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.13<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"><\/span><\/div>\n<div class=\"caption\">Meselson and Stahl experimented with <span class=\"emphasis\"><em>E. coli<\/em><\/span> grown first in heavy nitrogen (<sup>15<\/sup>N) then in <sup>14<\/sup>N. DNA grown in <sup>15<\/sup>N (red band) is heavier than DNA grown in <sup>14<\/sup>N (orange band), and sediments to a lower level in cesium chloride solution in an ultracentrifuge. When DNA grown in <sup>15<\/sup>N is switched to media containing <sup>14<\/sup>N, after one round of cell division the DNA sediments halfway between the <sup>15<\/sup>N and <sup>14<\/sup>N levels, indicating that it now contains fifty percent <sup>14<\/sup>N. In subsequent cell divisions, an increasing amount of DNA contains <sup>14<\/sup>N only. This data supports the semi-conservative replication model. (credit: modification of work by Mariana Ruiz Villareal)<\/div>\n<\/div>\n<p><span id=\"m44487-fs-id2589720\"> <\/span>The <span class=\"emphasis\"><em>E. coli<\/em><\/span> culture was then shifted into medium containing <sup>14<\/sup>N and allowed to grow for one generation. The cells were harvested and the DNA was isolated. The DNA was centrifuged at high speeds in an ultracentrifuge. Some cells were allowed to grow for one more life cycle in <sup>14<\/sup>N and spun again. During the density gradient centrifugation, the DNA is loaded into a gradient (typically a salt such as cesium chloride or sucrose) and spun at high speeds of 50,000 to 60,000 rpm. Under these circumstances, the DNA will form a band according to its density in the gradient. DNA grown in <sup>15<\/sup>N will band at a higher density position than that grown in <sup>14<\/sup>N. Meselson and Stahl noted that after one generation of growth in <sup>14<\/sup>N after they had been shifted from <sup>15<\/sup>N, the single band observed was intermediate in position in between DNA of cells grown exclusively in<sup> 15<\/sup>N and <sup>14<\/sup>N. This suggested either a semi-conservative or dispersive mode of replication. The DNA harvested from cells grown for two generations in <sup>14<\/sup>N formed two bands: one DNA band was at the intermediate position between <sup>15<\/sup>N and <sup>14<\/sup>N, and the other corresponded to the band of <sup>14<\/sup>N DNA. These results could only be explained if DNA replicates in a semi-conservative manner. Therefore, the other two modes were ruled out.<\/p>\n<p><span id=\"m44487-fs-id2854117\"> <\/span>During DNA replication, each of the two strands that make up the double helix serves as a template from which new strands are copied. The new strand will be complementary to the parental or \u201cold\u201d strand. When two daughter DNA copies are formed, they have the same sequence and are divided equally into the two daughter cells.<\/p>\n<div id=\"m44487-fs-id1366889\" class=\"note interactive\">\n<div class=\"title\"><span class=\"cnx-gentext-tip-t\">Link to Learning<\/span><\/div>\n<div class=\"body\">\n<div class=\"mediaobject\"><span id=\"m44487-fs-id1676042\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155720\/DNA_replication.png\" width=\"120\" alt=\"QR Code representing a URL\" \/><\/div>\n<p><span id=\"m44487-fs-id2171177\"> <\/span>Click through <a class=\"link\" href=\"http:\/\/openstaxcollege.org\/l\/DNA_replicatio2\" target=\"\">this tutorial<\/a> on DNA replication.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<div xml:lang=\"en\" class=\"section module\" title=\"14.4.&#xa0;DNA Replication in Prokaryotes\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h2 id=\"m44488\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.4<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Replication in Prokaryotes<sup><a href=\"co03.html#book-attribution-m44488\">*<\/a><\/sup><\/span><\/span><\/h2>\n<\/div>\n<div class=\"abstract\">\n<div class=\"title\"><span><span class=\"cnx-gentext-abstract cnx-gentext-autogenerated\"><span class=\"cnx-gentext-abstract cnx-gentext-t\"><\/span><\/span><\/span><\/div>\n<p>By the end of this section, you will be able to:\n<\/p>\n<div class=\"itemizedlist\">\n<ul class=\"itemizedlist\">\n<li class=\"listitem\">\n<p>Explain the process of DNA replication in prokaryotes<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>Discuss the role of different enzymes and proteins in supporting this process<\/p>\n<\/li>\n<\/ul>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"toc\">\n<ul><\/ul>\n<\/div>\n<p><span id=\"m44488-fs-id2571092\"> <\/span>DNA replication has been extremely well studied in prokaryotes primarily because of the small size of the genome and the mutants that are available. <span class=\"emphasis\"><em>E. coli <\/em><\/span>has 4.6 million base pairs in a single circular chromosome and all of it gets replicated in approximately 42 minutes, starting from a single origin of replication and proceeding around the circle in both directions. This means that approximately 1000 nucleotides are added per second. The process is quite rapid and occurs without many mistakes.<\/p>\n<p><span id=\"m44488-fs-id1806393\"> <\/span>DNA replication employs a large number of proteins and enzymes, each of which plays a critical role during the process. One of the key players is the enzyme DNA polymerase, also known as DNA pol, which adds nucleotides one by one to the growing DNA chain that are complementary to the template strand. The addition of nucleotides requires energy; this energy is obtained from the nucleotides that have three phosphates attached to them, similar to ATP which has three phosphate groups attached. When the bond between the phosphates is broken, the energy released is used to form the phosphodiester bond between the incoming nucleotide and the growing chain. In prokaryotes, three main types of polymerases are known: DNA pol I, DNA pol II, and DNA pol III. It is now known that DNA pol III is the enzyme required for DNA synthesis; DNA pol I and DNA pol II are primarily required for repair.<\/p>\n<p><span id=\"m44488-fs-id1676042\"> <\/span>How does the replication machinery know where to begin? It turns out that there are specific nucleotide sequences called origins of replication where replication begins. In <span class=\"emphasis\"><em>E. coli, <\/em><\/span>which has a single origin of replication on its one chromosome (as do most prokaryotes), it is approximately 245 base pairs long and is rich in AT sequences. The origin of replication is recognized by certain proteins that bind to this site. An enzyme called <em class=\"glossterm\"><span id=\"m44488-autoid-cnx2dbk-id1589581\"> <\/span>helicase<\/em><a id=\"id505329\" class=\"indexterm\"> unwinds the DNA by breaking the hydrogen bonds between the nitrogenous base pairs. ATP hydrolysis is required for this process. As the DNA opens up, Y-shaped structures called <em class=\"glossterm\"><span id=\"m44488-autoid-cnx2dbk-id1589586\"> <\/span>replication forks<\/em><\/a><a id=\"id505344\" class=\"indexterm\"> are formed. Two replication forks are formed at the origin of replication and these get extended bi- directionally as replication proceeds. <em class=\"glossterm\"><span id=\"m44488-autoid-cnx2dbk-id1589591\"> <\/span>Single-strand binding proteins<\/em><\/a><a id=\"id505359\" class=\"indexterm\"> coat the single strands of DNA near the replication fork to prevent the single-stranded DNA from winding back into a double helix. DNA polymerase is able to add nucleotides only in the 5&#8242; to 3&#8242; direction (a new DNA strand can be only extended in this direction). It also requires a free 3&#8242;-OH group to which it can add nucleotides by forming a phosphodiester bond between the 3&#8242;-OH end and the 5&#8242; phosphate of the next nucleotide. This essentially means that it cannot add nucleotides if a free 3&#8242;-OH group is not available. Then how does it add the first nucleotide? The problem is solved with the help of a primer that provides the free 3&#8242;-OH end. Another enzyme, RNA <em class=\"glossterm\"><span id=\"m44488-autoid-cnx2dbk-id1589600\"> <\/span>primase<\/em><\/a><a id=\"id505378\" class=\"indexterm\">, synthesizes an RNA primer that is about five to ten nucleotides long and complementary to the DNA. Because this sequence primes the DNA synthesis, it is appropriately called the <em class=\"glossterm\"><span id=\"m44488-autoid-cnx2dbk-id1589605\"> <\/span>primer<\/em><\/a><a id=\"id505394\" class=\"indexterm\">. DNA polymerase can now extend this RNA primer, adding nucleotides one by one that are complementary to the template strand (<\/a><a class=\"xref target-figure\" href=\"ch14.html#m44488-fig-ch14_04_01\" title=\"Figure&#xa0;14.14.&#xa0;\">Figure\u00a014.14<\/a>).<\/p>\n<div id=\"m44488-fs-id1305287\" class=\"note art-connection\">\n<div class=\"title\"><span class=\"cnx-gentext-tip-t\">Art Connection<\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44488-fs-id2979157\"> <\/span>\n<\/p>\n<div id=\"m44488-fig-ch14_04_01\" class=\"figure\" title=\"Figure&#xa0;14.14.&#xa0;\">\n<div class=\"body\"><span class=\"inlinemediaobject\"><span id=\"m44488-fs-id2897265\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155722\/Figure_14_04_01.png\" width=\"400\" alt=\"Illustration shows the replication fork. Helicase unwinds the helix, and single-strand binding proteins prevent the helix from re-forming. Topoisomerase prevents the DNA from getting too tightly coiled ahead of the replication fork. DNA primase forms an RNA primer, and DNA polymerase extends the DNA strand from the RNA primer. DNA synthesis occurs only in the 5' to 3' direction. On the leading strand, DNA synthesis occurs continuously. On the lagging strand, DNA synthesis restarts many times as the helix unwinds, resulting in many short fragments called &#x201c;Okazaki fragments.&#x201d; DNA ligase joins the Okazaki fragments together into a single DNA molecule.\" \/><\/span><\/div>\n<div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.14<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"><\/span><\/div>\n<div class=\"caption\">A replication fork is formed when helicase separates the DNA strands at the origin of replication. The DNA tends to become more highly coiled ahead of the replication fork. Topoisomerase breaks and reforms DNA\u2019s phosphate backbone ahead of the replication fork, thereby relieving the pressure that results from this supercoiling. Single-strand binding proteins bind to the single-stranded DNA to prevent the helix from re-forming. Primase synthesizes an RNA primer. DNA polymerase III uses this primer to synthesize the daughter DNA strand. On the leading strand, DNA is synthesized continuously, whereas on the lagging strand, DNA is synthesized in short stretches called Okazaki fragments. DNA polymerase I replaces the RNA primer with DNA. DNA ligase seals the gaps between the Okazaki fragments, joining the fragments into a single DNA molecule. (credit: modification of work by Mariana Ruiz Villareal)<\/div>\n<\/div>\n<p><span id=\"m44488-fs-id1368727\"> <\/span>You isolate a cell strain in which the joining together of Okazaki fragments is impaired and suspect that a mutation has occurred in an enzyme found at the replication fork. Which enzyme is most likely to be mutated?<\/p>\n<\/div>\n<\/div>\n<p><span id=\"m44488-fs-id1385221\"> <\/span>The replication fork moves at the rate of 1000 nucleotides per second. DNA polymerase can only extend in the 5&#8242; to 3&#8242; direction, which poses a slight problem at the replication fork. As we know, the DNA double helix is anti-parallel; that is, one strand is in the 5&#8242; to 3&#8242; direction and the other is oriented in the 3&#8242; to 5&#8242; direction. One strand, which is complementary to the 3&#8242; to 5&#8242; parental DNA strand, is synthesized continuously towards the replication fork because the polymerase can add nucleotides in this direction. This continuously synthesized strand is known as the <em class=\"glossterm\"><span id=\"m44488-autoid-cnx2dbk-id1237696\"> <\/span>leading strand<\/em><a id=\"id505512\" class=\"indexterm\">. The other strand, complementary to the 5&#8242; to 3&#8242; parental DNA, is extended away from the replication fork, in small fragments known as <em class=\"glossterm\"><span id=\"m44488-autoid-cnx2dbk-id1237700\"> <\/span>Okazaki fragments<\/em><\/a><a id=\"id505527\" class=\"indexterm\">, each requiring a primer to start the synthesis. Okazaki fragments are named after the Japanese scientist who first discovered them. The strand with the Okazaki fragments is known as the <em class=\"glossterm\"><span id=\"m44488-autoid-cnx2dbk-id1237706\"> <\/span>lagging strand<\/em><\/a><a id=\"id505542\" class=\"indexterm\">.<\/a><\/p>\n<p><span id=\"m44488-fs-id2962574\"> <\/span>The leading strand can be extended by one primer alone, whereas the lagging strand needs a new primer for each of the short Okazaki fragments. The overall direction of the lagging strand will be 3&#8242; to 5&#8242;, and that of the leading strand 5&#8242; to 3&#8242;. A protein called the <em class=\"glossterm\"><span id=\"m44488-autoid-cnx2dbk-id1237718\"> <\/span>sliding clamp<\/em><a id=\"id505565\" class=\"indexterm\"> holds the DNA polymerase in place as it continues to add nucleotides. The sliding clamp is a ring-shaped protein that binds to the DNA and holds the polymerase in place. <em class=\"glossterm\"><span id=\"m44488-autoid-cnx2dbk-id1237723\"> <\/span>Topoisomerase<\/em><\/a><a id=\"id505580\" class=\"indexterm\"> prevents the over-winding of the DNA double helix ahead of the replication fork as the DNA is opening up; it does so by causing temporary nicks in the DNA helix and then resealing it. As synthesis proceeds, the RNA primers are replaced by DNA. The primers are removed by the exonuclease activity of DNA pol I, and the gaps are filled in by deoxyribonucleotides. The nicks that remain between the newly synthesized DNA (that replaced the RNA primer) and the previously synthesized DNA are sealed by the enzyme DNA <em class=\"glossterm\"><span id=\"m44488-autoid-cnx2dbk-id1237730\"> <\/span>ligase<\/em><\/a><a id=\"id505598\" class=\"indexterm\"> that catalyzes the formation of phosphodiester linkage between the 3&#8242;-OH end of one nucleotide and the 5&#8242; phosphate end of the other fragment.<\/a><\/p>\n<p><span id=\"m44488-fs-id1752302\"> <\/span>Once the chromosome has been completely replicated, the two DNA copies move into two different cells during cell division. The process of DNA replication can be summarized as follows:<\/p>\n<div class=\"orderedlist\"><span id=\"m44488-fs-id2017788\"> <\/span><\/p>\n<ol class=\"orderedlist\" type=\"1\">\n<li class=\"listitem\">\n<p>DNA unwinds at the origin of replication.<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>Helicase opens up the DNA-forming replication forks; these are extended bidirectionally.<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>Single-strand binding proteins coat the DNA around the replication fork to prevent rewinding of the DNA.<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>Topoisomerase binds at the region ahead of the replication fork to prevent supercoiling.<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>Primase synthesizes RNA primers complementary to the DNA strand.<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>DNA polymerase starts adding nucleotides to the 3&#8242;-OH end of the primer.<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>Elongation of both the lagging and the leading strand continues.<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>RNA primers are removed by exonuclease activity.<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>Gaps are filled by DNA pol by adding dNTPs.<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>The gap between the two DNA fragments is sealed by DNA ligase, which helps in the formation of phosphodiester bonds.<\/p>\n<\/li>\n<\/ol>\n<\/div>\n<p><span id=\"m44488-fs-id2235232\"> <\/span>&lt;!&#8211;cnx.newline&#8211;&gt;<br \/><a class=\"xref target-table\" href=\"ch14.html#m44488-tab-ch14_04_01\" title=\"Table&#xa0;14.1.&#xa0;\">Table\u00a014.1<\/a> summarizes the enzymes involved in prokaryotic DNA replication and the functions of each.<\/p>\n<div class=\"table\" id=\"m44488-tab-ch14_04_01\">\n<table cellpadding=\"0\" style=\"border: 1px solid; border-spacing: 0px;\">\n<caption><span class=\"cnx-gentext-caption cnx-gentext-t\">Table <\/span><span class=\"cnx-gentext-caption cnx-gentext-n\">14.1. <\/span><\/caption>\n<thead valign=\"bottom\">\n<tr>\n<th colspan=\"2\" style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">Prokaryotic DNA Replication: Enzymes and Their Function<\/th>\n<\/tr>\n<tr>\n<th style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">Enzyme\/protein<\/th>\n<th style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">Specific Function<\/th>\n<\/tr>\n<\/thead>\n<tbody valign=\"top\">\n<tr>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">DNA pol I<\/td>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">Exonuclease activity removes RNA primer and replaces with newly synthesized DNA<\/td>\n<\/tr>\n<tr>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">DNA pol II<\/td>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">Repair function<\/td>\n<\/tr>\n<tr>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">DNA pol III<\/td>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">Main enzyme that adds nucleotides in the 5&#8242;-3&#8242; direction<\/td>\n<\/tr>\n<tr>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">Helicase<\/td>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">Opens the DNA helix by breaking hydrogen bonds between the nitrogenous bases<\/td>\n<\/tr>\n<tr>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">Ligase<\/td>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">Seals the gaps between the Okazaki fragments to create one continuous DNA strand<\/td>\n<\/tr>\n<tr>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">Primase<\/td>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">Synthesizes RNA primers needed to start replication<\/td>\n<\/tr>\n<tr>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">Sliding Clamp<\/td>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">Helps to hold the DNA polymerase in place when nucleotides are being added<\/td>\n<\/tr>\n<tr>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">Topoisomerase<\/td>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">Helps relieve the stress on DNA when unwinding by causing breaks and then resealing the DNA<\/td>\n<\/tr>\n<tr>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 0 !important; text-align: left !important;\">Single-strand binding proteins (SSB)<\/td>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 0 !important; text-align: left !important;\">Binds to single-stranded DNA to avoid DNA rewinding back.<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n<div id=\"m44488-fs-id1672176\" class=\"note interactive\">\n<div class=\"title\"><span class=\"cnx-gentext-tip-t\">Link to Learning<\/span><\/div>\n<div class=\"body\">\n<div class=\"mediaobject\"><span id=\"m44488-fs-id2914259\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155724\/replication_DNA.png\" width=\"120\" alt=\"QR Code representing a URL\" \/><\/div>\n<p><span id=\"m44488-fs-id2010960\"> <\/span>Review the full process of DNA replication <a class=\"link\" href=\"http:\/\/openstaxcollege.org\/l\/replication_DNA\" target=\"\">here<\/a>.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<div xml:lang=\"en\" class=\"section module\" title=\"14.5.&#xa0;DNA Replication in Eukaryotes\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h2 id=\"m44517\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.5<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Replication in Eukaryotes<sup><a href=\"co03.html#book-attribution-m44517\">*<\/a><\/sup><\/span><\/span><\/h2>\n<\/div>\n<div class=\"abstract\">\n<div class=\"title\"><span><span class=\"cnx-gentext-abstract cnx-gentext-autogenerated\"><span class=\"cnx-gentext-abstract cnx-gentext-t\"><\/span><\/span><\/span><\/div>\n<p>By the end of this section, you will be able to:\n<\/p>\n<div class=\"itemizedlist\">\n<ul class=\"itemizedlist\">\n<li class=\"listitem\">\n<p>Discuss the similarities and differences between DNA replication in eukaryotes and prokaryotes<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>State the role of telomerase in DNA replication<\/p>\n<\/li>\n<\/ul>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"toc\">\n<ul>\n<li class=\"toc-section\"><a href=\"#m44517-fs-id1272063\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">Telomere replication<\/span><\/a>\n<ul>\n<li class=\"toc-section\"><a href=\"#m44517-fs-id2150202\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">Telomerase and Aging<\/span><\/a><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/div>\n<p><span id=\"m44517-fs-id1975225\"> <\/span>Eukaryotic genomes are much more complex and larger in size than prokaryotic genomes. The human genome has three billion base pairs per haploid set of chromosomes, and 6 billion base pairs are replicated during the S phase of the cell cycle. There are multiple origins of replication on the eukaryotic chromosome; humans can have up to 100,000 origins of replication. The rate of replication is approximately 100 nucleotides per second, much slower than prokaryotic replication. In yeast, which is a eukaryote, special sequences known as Autonomously Replicating Sequences (ARS) are found on the chromosomes. These are equivalent to the origin of replication in <span class=\"emphasis\"><em>E. coli<\/em><\/span>.<\/p>\n<p><span id=\"m44517-fs-id1482304\"> <\/span>The number of DNA polymerases in eukaryotes is much more than prokaryotes: 14 are known, of which five are known to have major roles during replication and have been well studied. They are known as pol <span class=\"emphasis\"><em>\u03b1<\/em><\/span>, pol <span class=\"emphasis\"><em>\u03b2<\/em><\/span>, pol <span class=\"emphasis\"><em>\u03b3<\/em><\/span>, pol <span class=\"emphasis\"><em>\u03b4<\/em><\/span>, and pol <span class=\"emphasis\"><em>\u03b5<\/em><\/span>.<\/p>\n<p><span id=\"m44517-fs-id2904988\"> <\/span>The essential steps of replication are the same as in prokaryotes. Before replication can start, the DNA has to be made available as template. Eukaryotic DNA is bound to basic proteins known as histones to form structures called nucleosomes. The chromatin (the complex between DNA and proteins) may undergo some chemical modifications, so that the DNA may be able to slide off the proteins or be accessible to the enzymes of the DNA replication machinery. At the origin of replication, a pre-replication complex is made with other initiator proteins. Other proteins are then recruited to start the replication process (<a class=\"xref target-table\" href=\"ch14.html#m44517-tab-ch14_05_01\" title=\"Table&#xa0;14.2.&#xa0;\">Table\u00a014.2<\/a>).<\/p>\n<p><span id=\"m44517-fs-id2018337\"> <\/span> A helicase using the energy from ATP hydrolysis opens up the DNA helix. Replication forks are formed at each replication origin as the DNA unwinds. The opening of the double helix causes over-winding, or supercoiling, in the DNA ahead of the replication fork. These are resolved with the action of topoisomerases. Primers are formed by the enzyme primase, and using the primer, DNA pol can start synthesis. While the leading strand is continuously synthesized by the enzyme pol <span class=\"emphasis\"><em>\u03b4<\/em><\/span>, the lagging strand is synthesized by pol <span class=\"emphasis\"><em>\u03b5<\/em><\/span>. A sliding clamp protein known as PCNA (Proliferating Cell Nuclear Antigen) holds the DNA pol in place so that it does not slide off the DNA. RNase H removes the RNA primer, which is then replaced with DNA nucleotides. The Okazaki fragments in the lagging strand are joined together after the replacement of the RNA primers with DNA. The gaps that remain are sealed by DNA ligase, which forms the phosphodiester bond.<\/p>\n<div class=\"section\" title=\"Telomere replication\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h3 id=\"m44517-fs-id1272063\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">Telomere replication<\/span><\/span><\/h3>\n<\/div>\n<\/div>\n<\/div>\n<p><span id=\"m44517-fs-id2030086\"> <\/span>Unlike prokaryotic chromosomes, eukaryotic chromosomes are linear. As you\u2019ve learned, the enzyme DNA pol can add nucleotides only in the 5&#8242; to 3&#8242; direction. In the leading strand, synthesis continues until the end of the chromosome is reached. On the lagging strand, DNA is synthesized in short stretches, each of which is initiated by a separate primer. When the replication fork reaches the end of the linear chromosome, there is no place for a primer to be made for the DNA fragment to be copied at the end of the chromosome. These ends thus remain unpaired, and over time these ends may get progressively shorter as cells continue to divide.<\/p>\n<p><span id=\"m44517-fs-id1318769\"> <\/span>The ends of the linear chromosomes are known as <em class=\"glossterm\"><span id=\"m44517-autoid-cnx2dbk-id1756920\"> <\/span>telomeres<\/em><a id=\"id506690\" class=\"indexterm\">, which have repetitive sequences that code for no particular gene. In a way, these telomeres protect the genes from getting deleted as cells continue to divide. In humans, a six base pair sequence, TTAGGG, is repeated 100 to 1000 times. The discovery of the enzyme telomerase (<\/a><a class=\"xref target-figure\" href=\"ch14.html#m44517-fig-ch14_05_02\" title=\"Figure&#xa0;14.16.&#xa0;\">Figure\u00a014.16<\/a>) helped in the understanding of how chromosome ends are maintained. The <em class=\"glossterm\"><span id=\"m44517-autoid-cnx2dbk-id1766081\"> <\/span>telomerase<\/em><a id=\"id506715\" class=\"indexterm\"> enzyme contains a catalytic part and a built-in RNA template. It attaches to the end of the chromosome, and complementary bases to the RNA template are added on the 3&#8242; end of the DNA strand. Once the 3&#8242; end of the lagging strand template is sufficiently elongated, DNA polymerase can add the nucleotides complementary to the ends of the chromosomes. Thus, the ends of the chromosomes are replicated.<\/a><\/p>\n<div id=\"m44517-fig-ch14_05_01\" class=\"figure\" title=\"Figure&#xa0;14.15.&#xa0;\">\n<div class=\"body\">\n<div class=\"mediaobject\"><span id=\"m44517-fs-id1986139\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155727\/Figure_14_05_01.jpg\" width=\"300\" alt=\"Telomerase has an associated RNA that complements the 5' overhang at the end of the chromosome. The RNA template is used to synthesize the complementary strand. Telomerase then shifts, and the process is repeated. Next, primase and DNA polymerase synthesize the rest of the complementary strand.\" \/><\/div>\n<\/div>\n<div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.15<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"><\/span><\/div>\n<div class=\"caption\">The ends of linear chromosomes are maintained by the action of the telomerase enzyme.<\/div>\n<\/div>\n<p><span id=\"m44517-fs-id1721035\"> <\/span>Telomerase is typically active in germ cells and adult stem cells. It is not active in adult somatic cells. For her discovery of telomerase and its action, Elizabeth Blackburn (<a class=\"xref target-figure\" href=\"ch14.html#m44517-fig-ch14_05_02\" title=\"Figure&#xa0;14.16.&#xa0;\">Figure\u00a014.16<\/a>) received the Nobel Prize for Medicine and Physiology in 2009.<\/p>\n<div id=\"m44517-fig-ch14_05_02\" class=\"figure\" title=\"Figure&#xa0;14.16.&#xa0;\">\n<div class=\"body\">\n<div class=\"mediaobject\"><span id=\"m44517-fs-id2318509\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155728\/Figure_14_05_02.jpg\" width=\"320\" alt=\"Photo of Elizabeth Blackburn.\" \/><\/div>\n<\/div>\n<div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.16<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"><\/span><\/div>\n<div class=\"caption\">Elizabeth Blackburn, 2009 Nobel Laureate, is the scientist who discovered how telomerase works. (credit: US Embassy Sweden)<\/div>\n<\/div>\n<div class=\"section\" title=\"Telomerase and Aging\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h4 id=\"m44517-fs-id2150202\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">Telomerase and Aging<\/span><\/span><\/h4>\n<\/div>\n<\/div>\n<\/div>\n<p><span id=\"m44517-fs-id2199338\"> <\/span>Cells that undergo cell division continue to have their telomeres shortened because most somatic cells do not make telomerase. This essentially means that telomere shortening is associated with aging. With the advent of modern medicine, preventative health care, and healthier lifestyles, the human life span has increased, and there is an increasing demand for people to look younger and have a better quality of life as they grow older.<\/p>\n<p><span id=\"m44517-fs-id2196973\"> <\/span>In 2010, scientists found that telomerase can reverse some age-related conditions in mice. This may have potential in regenerative medicine.<sup><sup>[<a id=\"m44517-fs-id1477114\" href=\"#ftn.m44517-fs-id1477114\" class=\"footnote\">12<\/a>]<\/sup><\/sup> Telomerase-deficient mice were used in these studies; these mice have tissue atrophy, stem cell depletion, organ system failure, and impaired tissue injury responses. Telomerase reactivation in these mice caused extension of telomeres, reduced DNA damage, reversed neurodegeneration, and improved the function of the testes, spleen, and intestines. Thus, telomere reactivation may have potential for treating age-related diseases in humans.<\/p>\n<p><span id=\"m44517-fs-id2370326\"> <\/span>Cancer is characterized by uncontrolled cell division of abnormal cells. The cells accumulate mutations, proliferate uncontrollably, and can migrate to different parts of the body through a process called metastasis. Scientists have observed that cancerous cells have considerably shortened telomeres and that telomerase is active in these cells. Interestingly, only after the telomeres were shortened in the cancer cells did the telomerase become active. If the action of telomerase in these cells can be inhibited by drugs during cancer therapy, then the cancerous cells could potentially be stopped from further division.<\/p>\n<div class=\"table\" id=\"m44517-tab-ch14_05_01\">\n<table cellpadding=\"0\" style=\"border: 1px solid; border-spacing: 0px;\">\n<caption><span class=\"cnx-gentext-caption cnx-gentext-t\">Table <\/span><span class=\"cnx-gentext-caption cnx-gentext-n\">14.2. <\/span><\/caption>\n<thead valign=\"bottom\">\n<tr>\n<th colspan=\"3\" style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">Difference between Prokaryotic and Eukaryotic Replication<\/th>\n<\/tr>\n<tr>\n<th style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">Property<\/th>\n<th style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">Prokaryotes<\/th>\n<th style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">Eukaryotes<\/th>\n<\/tr>\n<\/thead>\n<tbody valign=\"top\">\n<tr>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">Origin of replication<\/td>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">Single<\/td>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">Multiple<\/td>\n<\/tr>\n<tr>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">Rate of replication<\/td>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">1000 nucleotides\/s<\/td>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">50 to 100 nucleotides\/s<\/td>\n<\/tr>\n<tr>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">DNA polymerase types<\/td>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">5<\/td>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">14<\/td>\n<\/tr>\n<tr>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">Telomerase<\/td>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">Not present<\/td>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">Present<\/td>\n<\/tr>\n<tr>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">RNA primer removal<\/td>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">DNA pol I<\/td>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">RNase H<\/td>\n<\/tr>\n<tr>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">Strand elongation<\/td>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">DNA pol III<\/td>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">Pol \u03b4, pol \u03b5<\/td>\n<\/tr>\n<tr>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 0 !important; text-align: left !important;\">Sliding clamp<\/td>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 0 !important; text-align: left !important;\">Sliding clamp<\/td>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 0 !important; text-align: left !important;\">PCNA<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div xml:lang=\"en\" class=\"section module\" title=\"14.6.&#xa0;DNA Repair\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h2 id=\"m44513\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.6<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Repair<sup><a href=\"co03.html#book-attribution-m44513\">*<\/a><\/sup><\/span><\/span><\/h2>\n<\/div>\n<div class=\"abstract\">\n<div class=\"title\"><span><span class=\"cnx-gentext-abstract cnx-gentext-autogenerated\"><span class=\"cnx-gentext-abstract cnx-gentext-t\"><\/span><\/span><\/span><\/div>\n<p>By the end of this section, you will be able to:\n<\/p>\n<div class=\"itemizedlist\">\n<ul class=\"itemizedlist\">\n<li class=\"listitem\">\n<p>Discuss the different types of mutations in DNA<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>Explain DNA repair mechanisms<\/p>\n<\/li>\n<\/ul>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"toc\">\n<ul><\/ul>\n<\/div>\n<p><span id=\"m44513-fs-id1976493\"> <\/span>DNA replication is a highly accurate process, but mistakes can occasionally occur, such as a DNA polymerase inserting a wrong base. Uncorrected mistakes may sometimes lead to serious consequences, such as cancer. Repair mechanisms correct the mistakes. In rare cases, mistakes are not corrected, leading to mutations; in other cases, repair enzymes are themselves mutated or defective.<\/p>\n<p><span id=\"m44513-fs-id2348700\"> <\/span>Most of the mistakes during DNA replication are promptly corrected by DNA polymerase by proofreading the base that has been just added (<a class=\"xref target-figure\" href=\"ch14.html#m44513-fig-ch14_06_01\" title=\"Figure&#xa0;14.17.&#xa0;\">Figure\u00a014.17<\/a>). In <em class=\"glossterm\"><span id=\"m44513-autoid-cnx2dbk-id1749376\"> <\/span>proofreading<\/em><a id=\"id507339\" class=\"indexterm\">, the DNA pol reads the newly added base before adding the next one, so a correction can be made. The polymerase checks whether the newly added base has paired correctly with the base in the template strand. If it is the right base, the next nucleotide is added. If an incorrect base has been added, the enzyme makes a cut at the phosphodiester bond and releases the wrong nucleotide. This is performed by the exonuclease action of DNA pol III. Once the incorrect nucleotide has been removed, a new one will be added again.<\/a><\/p>\n<div id=\"m44513-fig-ch14_06_01\" class=\"figure\" title=\"Figure&#xa0;14.17.&#xa0;\">\n<div class=\"body\">\n<div class=\"mediaobject\"><span id=\"m44513-fs-id2321057\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155730\/Figure_14_06_01.jpg\" width=\"320\" alt=\"Illustration shows DNA polymerase replicating a strand of DNA. The enzyme has accidentally inserted G opposite A, resulting in a bulge. The enzyme backs up to fix the error.\" \/><\/div>\n<\/div>\n<div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.17<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"><\/span><\/div>\n<div class=\"caption\">Proofreading by DNA polymerase corrects errors during replication.<\/div>\n<\/div>\n<p><span id=\"m44513-fs-id2186525\"> <\/span>Some errors are not corrected during replication, but are instead corrected after replication is completed; this type of repair is known as <em class=\"glossterm\"><span id=\"m44513-autoid-cnx2dbk-id1749419\"> <\/span>mismatch repair<\/em><a id=\"id507399\" class=\"indexterm\"> (<\/a><a class=\"xref target-figure\" href=\"ch14.html#m44513-fig-ch14_06_02\" title=\"Figure&#xa0;14.18.&#xa0;\">Figure\u00a014.18<\/a>). The enzymes recognize the incorrectly added nucleotide and excise it; this is then replaced by the correct base. If this remains uncorrected, it may lead to more permanent damage. How do mismatch repair enzymes recognize which of the two bases is the incorrect one? In <span class=\"emphasis\"><em>E. coli<\/em><\/span>, after replication, the nitrogenous base adenine acquires a methyl group; the parental DNA strand will have methyl groups, whereas the newly synthesized strand lacks them. Thus, DNA polymerase is able to remove the wrongly incorporated bases from the newly synthesized, non-methylated strand. In eukaryotes, the mechanism is not very well understood, but it is believed to involve recognition of unsealed nicks in the new strand, as well as a short-term continuing association of some of the replication proteins with the new daughter strand after replication has completed.<\/p>\n<div id=\"m44513-fig-ch14_06_02\" class=\"figure\" title=\"Figure&#xa0;14.18.&#xa0;\">\n<div class=\"body\">\n<div class=\"mediaobject\"><span id=\"m44513-fs-id2025027\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155732\/Figure_14_06_02.jpg\" width=\"250\" alt=\"The top illustration shows a replicated DNA strand with G-T base mismatch. The bottom illustration shows the repaired DNA, which has the correct G-C base pairing.\" \/><\/div>\n<\/div>\n<div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.18<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"><\/span><\/div>\n<div class=\"caption\">In mismatch repair, the incorrectly added base is detected after replication. The mismatch repair proteins detect this base and remove it from the newly synthesized strand by nuclease action. The gap is now filled with the correctly paired base.<\/div>\n<\/div>\n<p><span id=\"m44513-fs-id3000290\"> <\/span>In another type of repair mechanism, <em class=\"glossterm\"><span id=\"m44513-autoid-cnx2dbk-id1761231\"> <\/span>nucleotide excision repair<\/em><a id=\"id507474\" class=\"indexterm\">, enzymes replace incorrect bases by making a cut on both the 3&#8242; and 5&#8242; ends of the incorrect base (<\/a><a class=\"xref target-figure\" href=\"ch14.html#m44513-fig-ch14_06_03\" title=\"Figure&#xa0;14.19.&#xa0;\">Figure\u00a014.19<\/a>). The segment of DNA is removed and replaced with the correctly paired nucleotides by the action of DNA pol. Once the bases are filled in, the remaining gap is sealed with a phosphodiester linkage catalyzed by DNA ligase. This repair mechanism is often employed when UV exposure causes the formation of pyrimidine dimers.<\/p>\n<div id=\"m44513-fig-ch14_06_03\" class=\"figure\" title=\"Figure&#xa0;14.19.&#xa0;\">\n<div class=\"body\">\n<div class=\"mediaobject\"><span id=\"m44513-fs-id1695253\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155733\/Figure_14_06_03.jpg\" width=\"200\" alt=\"Illustration shows a DNA strand in which a thymine dimer has formed. Excision repair enzyme cut out the section of DNA that contains the dimer so it can be replaced with normal base pairs.\" \/><\/div>\n<\/div>\n<div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.19<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"><\/span><\/div>\n<div class=\"caption\">Nucleotide excision repairs thymine dimers. When exposed to UV, thymines lying adjacent to each other can form thymine dimers. In normal cells, they are excised and replaced.<\/div>\n<\/div>\n<p><span id=\"m44513-fs-id2078153\"> <\/span>A well-studied example of mistakes not being corrected is seen in people suffering from xeroderma pigmentosa (<a class=\"xref target-figure\" href=\"ch14.html#m44513-fig-ch14_06_04\" title=\"Figure&#xa0;14.20.&#xa0;\">Figure\u00a014.20<\/a>). Affected individuals have skin that is highly sensitive to UV rays from the sun. When individuals are exposed to UV, pyrimidine dimersespecially those of thymineare formed; people with xeroderma pigmentosa are not able to repair the damage. These are not repaired because of a defect in the nucleotide excision repair enzymes, whereas in normal individuals, the thymine dimers are excised and the defect is corrected. The thymine dimers distort the structure of the DNA double helix, and this may cause problems during DNA replication. People with xeroderma pigmentosa may have a higher risk of contracting skin cancer than those who dont have the condition.<\/p>\n<div id=\"m44513-fig-ch14_06_04\" class=\"figure\" title=\"Figure&#xa0;14.20.&#xa0;\">\n<div class=\"body\">\n<div class=\"mediaobject\"><span id=\"m44513-fs-id2583496\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155735\/Figure_14_06_04.jpg\" width=\"320\" alt=\"Photo shows a person with mottled skin lesions that result from xermoderma pigmentosa.\" \/><\/div>\n<\/div>\n<div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.20<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"><\/span><\/div>\n<div class=\"caption\">Xeroderma pigmentosa is a condition in which thymine dimerization from exposure to UV is not repaired.  Exposure to sunlight results in skin lesions. (credit: James Halpern et al.)<\/div>\n<\/div>\n<p><span id=\"m44513-fs-id1310247\"> <\/span>Errors during DNA replication are not the only reason why mutations arise in DNA. <em class=\"glossterm\"><span id=\"m44513-autoid-cnx2dbk-id1768504\"> <\/span>Mutations<\/em><a id=\"id507596\" class=\"indexterm\">, variations in the nucleotide sequence of a genome, can also occur because of damage to DNA. Such mutations may be of two types: induced or spontaneous. <em class=\"glossterm\"><span id=\"m44513-autoid-cnx2dbk-id1768509\"> <\/span>Induced mutations<\/em><\/a><a id=\"id507611\" class=\"indexterm\"> are those that result from an exposure to chemicals, UV rays, x-rays, or some other environmental agent. <em class=\"glossterm\"><span id=\"m44513-autoid-cnx2dbk-id1768514\"> <\/span>Spontaneous mutations<\/em><\/a><a id=\"id507626\" class=\"indexterm\"> occur without any exposure to any environmental agent; they are a result of natural reactions taking place within the body.<\/a><\/p>\n<p><span id=\"m44513-fs-id1368727\"> <\/span>Mutations may have a wide range of effects. Some mutations are not expressed; these are known as <em class=\"glossterm\"><span id=\"m44513-autoid-cnx2dbk-id1768527\"> <\/span>silent mutations<\/em><a id=\"id507648\" class=\"indexterm\">. <em class=\"glossterm\"><span id=\"m44513-autoid-cnx2dbk-id1768531\"> <\/span>Point mutations<\/em><\/a><a id=\"id507662\" class=\"indexterm\"> are those mutations that affect a single base pair. The most common nucleotide mutations are substitutions, in which one base is replaced by another. These can be of two types, either transitions or transversions. <em class=\"glossterm\"><span id=\"m44513-autoid-cnx2dbk-id1768803\"> <\/span>Transition substitution<\/em><\/a><a id=\"id507677\" class=\"indexterm\"> refers to a purine or pyrimidine being replaced by a base of the same kind; for example, a purine such as adenine may be replaced by the purine guanine. <em class=\"glossterm\"><span id=\"m44513-autoid-cnx2dbk-id1768808\"> <\/span>Transversion substitution<\/em><\/a><a id=\"id507692\" class=\"indexterm\"> refers to a purine being replaced by a pyrimidine, or vice versa; for example, cytosine, a pyrimidine, is replaced by adenine, a purine. Mutations can also be the result of the addition of a base, known as an insertion, or the removal of a base, also known as deletion. Sometimes a piece of DNA from one chromosome may get translocated to another chromosome or to another region of the same chromosome; this is also known as translocation. These mutation types are shown in <\/a><a class=\"xref target-figure\" href=\"ch14.html#m44513-fig-ch14_06_05\" title=\"Figure&#xa0;14.21.&#xa0;\">Figure\u00a014.21<\/a>.<\/p>\n<div id=\"m44513-fs-id2046784\" class=\"note art-connection\">\n<div class=\"title\"><span class=\"cnx-gentext-tip-t\">Art Connection<\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44513-fs-id2216817\"> <\/span><\/p>\n<div id=\"m44513-fig-ch14_06_05\" class=\"figure\" title=\"Figure&#xa0;14.21.&#xa0;\">\n<div class=\"body\"><span class=\"inlinemediaobject\"><span id=\"m44513-fs-id2221137\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155739\/Figure_14_06_05.png\" width=\"325\" alt=\"Illustration shows different types of point mutations that result from a single amino acid substitution. In a silent mutation, no change in the amino acid sequence occurs. In a missense mutation, one amino acid is substituted for another. In a nonsense mutation, a stop codon is substituted for an amino acid. In a frameshift mutation, one or more bases is added or deleted, resulting in a change in the reading frame.\" \/><\/span><\/div>\n<div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">14.21<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"><\/span><\/div>\n<div class=\"caption\">Mutations can lead to changes in the protein sequence encoded by the DNA.<\/div>\n<\/div>\n<p><span id=\"m44513-fs-id1813148\"> <\/span>A frameshift mutation that results in the insertion of three nucleotides is often less deleterious than a mutation that results in the insertion of one nucleotide. Why?<\/p>\n<\/div>\n<\/div>\n<p><span id=\"m44513-fs-id2936137\"> <\/span>Mutations in repair genes have been known to cause cancer. Many mutated repair genes have been implicated in certain forms of pancreatic cancer, colon cancer, and colorectal cancer. Mutations can affect either somatic cells or germ cells. If many mutations accumulate in a somatic cell, they may lead to problems such as the uncontrolled cell division observed in cancer. If a mutation takes place in germ cells, the mutation will be passed on to the next generation, as in the case of hemophilia and xeroderma pigmentosa.<\/p>\n<\/div>\n<div class=\"glossary\" title=\"Glossary\" id=\"id508089\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h2 class=\"title\"><span class=\"cnx-gentext-glossary cnx-gentext-autogenerated\"><span class=\"cnx-gentext-glossary cnx-gentext-t\">Glossary<\/span><\/span><\/h2>\n<\/div>\n<\/div>\n<\/div>\n<dl>\n<dt>electrophoresis<\/dt>\n<dd>\n<p>technique used to separate DNA fragments according to size<\/p>\n<\/dd>\n<dt>helicase<\/dt>\n<dd>\n<p>during replication, this enzyme helps to open up the DNA helix by breaking the hydrogen bonds<\/p>\n<\/dd>\n<dt>induced mutation<\/dt>\n<dd>\n<p>mutation that results from exposure to chemicals or environmental agents<\/p>\n<\/dd>\n<dt>lagging strand<\/dt>\n<dd>\n<p>during replication, the strand that is replicated in short fragments and away from the replication fork<\/p>\n<\/dd>\n<dt>leading strand<\/dt>\n<dd>\n<p>strand that is synthesized continuously in the 5&#8242;-3&#8242; direction which is synthesized in the direction of the replication fork<\/p>\n<\/dd>\n<dt>ligase<\/dt>\n<dd>\n<p>enzyme that catalyzes the formation of a phosphodiester linkage between the 3&#8242; OH and 5&#8242; phosphate ends of the DNA<\/p>\n<\/dd>\n<dt>mismatch repair<\/dt>\n<dd>\n<p>type of repair mechanism in which mismatched bases are removed after replication<\/p>\n<\/dd>\n<dt>mutation<\/dt>\n<dd>\n<p>variation in the nucleotide sequence of a genome<\/p>\n<\/dd>\n<dt>nucleotide excision repair<\/dt>\n<dd>\n<p>type of DNA repair mechanism in which the wrong base, along with a few nucleotides upstream or downstream, are removed<\/p>\n<\/dd>\n<dt>Okazaki fragment<\/dt>\n<dd>\n<p>DNA fragment that is synthesized in short stretches on the lagging strand<\/p>\n<\/dd>\n<dt>point mutation<\/dt>\n<dd>\n<p>mutation that affects a single base<\/p>\n<\/dd>\n<dt>primase<\/dt>\n<dd>\n<p>enzyme that synthesizes the RNA primer; the primer is needed for DNA pol to start synthesis of a new DNA strand<\/p>\n<\/dd>\n<dt>primer<\/dt>\n<dd>\n<p>short stretch of nucleotides that is required to initiate replication; in the case of replication, the primer has RNA nucleotides<\/p>\n<\/dd>\n<dt>proofreading<\/dt>\n<dd>\n<p>function of DNA pol in which it reads the newly added base before adding the next one<\/p>\n<\/dd>\n<dt>replication fork<\/dt>\n<dd>\n<p>Y-shaped structure formed during initiation of replication<\/p>\n<\/dd>\n<dt>silent mutation<\/dt>\n<dd>\n<p>mutation that is not expressed<\/p>\n<\/dd>\n<dt>single-strand binding protein<\/dt>\n<dd>\n<p>during replication, protein that binds to the single-stranded DNA; this helps in keeping the two strands of DNA apart so that they may serve as templates<\/p>\n<\/dd>\n<dt>sliding clamp<\/dt>\n<dd>\n<p>ring-shaped protein that holds the DNA pol on the DNA strand<\/p>\n<\/dd>\n<dt>spontaneous mutation<\/dt>\n<dd>\n<p>mutation that takes place in the cells as a result of chemical reactions taking place naturally without exposure to any external agent<\/p>\n<\/dd>\n<dt>telomerase<\/dt>\n<dd>\n<p>enzyme that contains a catalytic part and an inbuilt RNA template; it functions to maintain telomeres at chromosome ends<\/p>\n<\/dd>\n<dt>telomere<\/dt>\n<dd>\n<p>DNA at the end of linear chromosomes<\/p>\n<\/dd>\n<dt>topoisomerase<\/dt>\n<dd>\n<p>enzyme that causes underwinding or overwinding of DNA when DNA replication is taking place<\/p>\n<\/dd>\n<dt>transformation<\/dt>\n<dd>\n<p>process in which external DNA is taken up by a cell<\/p>\n<\/dd>\n<dt>transition substitution<\/dt>\n<dd>\n<p>when a purine is replaced with a purine or a pyrimidine is replaced with another pyrimidine<\/p>\n<\/dd>\n<dt>transversion substitution<\/dt>\n<dd>\n<p>when a purine is replaced by a pyrimidine or a pyrimidine is replaced by a purine<\/p>\n<\/dd>\n<\/dl>\n<\/div>\n<p>&lt;!&#8211;CNX: Start Area: &#8220;Sections Summary&#8221;&#8211;&gt;<\/p>\n<div class=\"cnx-eoc summary\">\n<div class=\"title\"><span>Sections Summary<\/span><\/div>\n<div class=\"section empty\">\n<div class=\"title\"><a href=\"#m44484\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Introduction<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<div class=\"section\">\n<div class=\"title\"><a href=\"#m44485\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.1<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Historical Basis of Modern Understanding<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<p><span id=\"m44485-fs-id2984818\"> <\/span>DNA was first isolated from white blood cells by Friedrich Miescher, who called it nuclein because it was isolated from nuclei. Frederick Griffith&#8217;s experiments with strains of <span class=\"emphasis\"><em>Streptococcus pneumoniae<\/em><\/span> provided the first hint that DNA may be the transforming principle. Avery, MacLeod, and McCarty proved that DNA is required for the transformation of bacteria. Later experiments by Hershey and Chase using bacteriophage T2 proved that DNA is the genetic material. Chargaff found that the ratio of A = T and C = G, and that the percentage content of A, T, G, and C is different for different species.<\/p>\n<\/div>\n<\/div>\n<div class=\"section\">\n<div class=\"title\"><a href=\"#m44486\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.2<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Structure and Sequencing<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<p><span id=\"m44486-fs-id1342929\"> <\/span>The currently accepted model of the double-helix structure of DNA was proposed by Watson and Crick. Some of the salient features are that the two strands that make up the double helix are complementary and anti-parallel in nature. Deoxyribose sugars and phosphates form the backbone of the structure, and the nitrogenous bases are stacked inside. The diameter of the double helix, 2 nm, is uniform throughout. A purine always pairs with a pyrimidine; A pairs with T, and G pairs with C. One turn of the helix has ten base pairs. During cell division, each daughter cell receives a copy of the DNA by a process known as DNA replication. Prokaryotes are much simpler than eukaryotes in many of their features. Most prokaryotes contain a single, circular chromosome. In general, eukaryotic chromosomes contain a linear DNA molecule packaged into nucleosomes, and have two distinct regions that can be distinguished by staining, reflecting different states of packaging and compaction.<\/p>\n<\/div>\n<\/div>\n<div class=\"section\">\n<div class=\"title\"><a href=\"#m44487\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.3<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Basics of DNA Replication<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<p><span id=\"m44487-fs-id2682756\"> <\/span>The model for DNA replication suggests that the two strands of the double helix separate during replication, and each strand serves as a template from which the new complementary strand is copied. In conservative replication, the parental DNA is conserved, and the daughter DNA is newly synthesized. The semi-conservative method suggests that each of the two parental DNA strands acts as template for new DNA to be synthesized; after replication, each double-stranded DNA includes one parental or \u201cold\u201d strand and one \u201cnew\u201d strand. The dispersive mode suggested that the two copies of the DNA would have segments of parental DNA and newly synthesized DNA.<\/p>\n<\/div>\n<\/div>\n<div class=\"section\">\n<div class=\"title\"><a href=\"#m44488\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.4<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Replication in Prokaryotes<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<p><span id=\"m44488-fs-id1437221\"> <\/span>Replication in prokaryotes starts from a sequence found on the chromosome called the origin of replication\u2014the point at which the DNA opens up. Helicase opens up the DNA double helix, resulting in the formation of the replication fork. Single-strand binding proteins bind to the single-stranded DNA near the replication fork to keep the fork open. Primase synthesizes an RNA primer to initiate synthesis by DNA polymerase, which can add nucleotides only in the 5&#8242; to 3&#8242; direction. One strand is synthesized continuously in the direction of the replication fork; this is called the leading strand. The other strand is synthesized in a direction away from the replication fork, in short stretches of DNA known as Okazaki fragments. This strand is known as the lagging strand. Once replication is completed, the RNA primers are replaced by DNA nucleotides and the DNA is sealed with DNA ligase, which creates phosphodiester bonds between the 3&#8242;-OH of one end and the 5&#8242; phosphate of the other strand.<\/p>\n<\/div>\n<\/div>\n<div class=\"section\">\n<div class=\"title\"><a href=\"#m44517\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.5<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Replication in Eukaryotes<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<p><span id=\"m44517-fs-id2694542\"> <\/span>Replication in eukaryotes starts at multiple origins of replication. The mechanism is quite similar to prokaryotes. A primer is required to initiate synthesis, which is then extended by DNA polymerase as it adds nucleotides one by one to the growing chain. The leading strand is synthesized continuously, whereas the lagging strand is synthesized in short stretches called Okazaki fragments. The RNA primers are replaced with DNA nucleotides; the DNA remains one continuous strand by linking the DNA fragments with DNA ligase. The ends of the chromosomes pose a problem as polymerase is unable to extend them without a primer. Telomerase, an enzyme with an inbuilt RNA template, extends the ends by copying the RNA template and extending one end of the chromosome. DNA polymerase can then extend the DNA using the primer. In this way, the ends of the chromosomes are protected.<\/p>\n<\/div>\n<\/div>\n<div class=\"section\">\n<div class=\"title\"><a href=\"#m44513\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.6<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Repair<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<p><span id=\"m44513-fs-id1242469\"> <\/span>DNA polymerase can make mistakes while adding nucleotides. It edits the DNA by proofreading every newly added base. Incorrect bases are removed and replaced by the correct base, and then a new base is added. Most mistakes are corrected during replication, although when this does not happen, the mismatch repair mechanism is employed. Mismatch repair enzymes recognize the wrongly incorporated base and excise it from the DNA, replacing it with the correct base. In yet another type of repair, nucleotide excision repair, the incorrect base is removed along with a few bases on the 5&#8242; and 3&#8242; end, and these are replaced by copying the template with the help of DNA polymerase. The ends of the newly synthesized fragment are attached to the rest of the DNA using DNA ligase, which creates a phosphodiester bond.<\/p>\n<p><span id=\"m44513-fs-id2595588\"> <\/span>Most mistakes are corrected, and if they are not, they may result in a mutation defined as a permanent change in the DNA sequence. Mutations can be of many types, such as substitution, deletion, insertion, and translocation. Mutations in repair genes may lead to serious consequences such as cancer. Mutations can be induced or may occur spontaneously.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<p>&lt;!&#8211;CNX: Start Area: &#8220;Art Connections&#8221;&#8211;&gt;<\/p>\n<div class=\"cnx-eoc art-exercise\">\n<div class=\"title\"><span>Art Connections<\/span><\/div>\n<div class=\"section empty\">\n<div class=\"title\"><a href=\"#m44484\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Introduction<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<div class=\"section empty\">\n<div class=\"title\"><a href=\"#m44485\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.1<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Historical Basis of Modern Understanding<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<div class=\"section\">\n<div class=\"title\"><a href=\"#m44486\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.2<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Structure and Sequencing<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<div id=\"m44486-fs-idp2462496\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44486-fs-idm104265760\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">5.<\/span><\/a><\/span><\/div>\n<div class=\"body\">&lt;!&#8211;calling informal.object&#8211;&gt;<\/p>\n<div class=\"problem\"><span id=\"m44486-fs-idm14998192\"> <\/span><\/p>\n<p><span id=\"m44486-fs-idp65790208\"> <\/span><a class=\"xref target-figure\" href=\"ch14.html#m44486-fig-ch14_02_06\" title=\"Figure&#xa0;14.10.&#xa0;\">Figure\u00a014.10<\/a> In eukaryotic cells, DNA and RNA synthesis occur in a separate compartment from protein synthesis. In prokaryotic cells, both processes occur together. What advantages might there be to separating the processes? What advantages might there be to having them occur together?<\/p>\n<\/div>\n<div id=\"m44486-fs-idm104265760\" class=\"solution\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44486-fs-idp2462496\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\"><a class=\"xref target-figure\" href=\"ch14.html#m44486-fig-ch14_02_06\" title=\"Figure&#xa0;14.10.&#xa0;\">Figure\u00a014.10<\/a> Compartmentalization enables a eukaryotic cell to divide processes into discrete steps so it can build more complex protein and RNA products. But there is an advantage to having a single compartment as well: RNA and protein synthesis occurs much more quickly in a prokaryotic cell.<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"section empty\">\n<div class=\"title\"><a href=\"#m44487\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.3<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Basics of DNA Replication<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<div class=\"section\">\n<div class=\"title\"><a href=\"#m44488\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.4<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Replication in Prokaryotes<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<div id=\"m44488-fs-idm104376352\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44488-fs-idp76857456\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">13.<\/span><\/a><\/span><\/div>\n<div class=\"body\">&lt;!&#8211;calling informal.object&#8211;&gt;<\/p>\n<div class=\"problem\"><span id=\"m44488-fs-idm62690592\"> <\/span><\/p>\n<p><span id=\"m44488-fs-idp29378960\"> <\/span><a class=\"xref target-figure\" href=\"ch14.html#m44488-fig-ch14_04_01\" title=\"Figure&#xa0;14.14.&#xa0;\">Figure\u00a014.14<\/a> You isolate a cell strain in which the joining together of Okazaki fragments is impaired and suspect that a mutation has occurred in an enzyme found at the replication fork. Which enzyme is most likely to be mutated?<\/p>\n<\/div>\n<div id=\"m44488-fs-idp76857456\" class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44488-fs-idm104376352\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44488-fs-idp125877360\"> <\/span><a class=\"xref target-figure\" href=\"ch14.html#m44488-fig-ch14_04_01\" title=\"Figure&#xa0;14.14.&#xa0;\">Figure\u00a014.14<\/a> DNA ligase, as this enzyme joins together Okazaki fragments.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"section empty\">\n<div class=\"title\"><a href=\"#m44517\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.5<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Replication in Eukaryotes<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<div class=\"section\">\n<div class=\"title\"><a href=\"#m44513\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.6<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Repair<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<div id=\"m44513-fs-idp163052304\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44513-fs-idp122564624\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">24.<\/span><\/a><\/span><\/div>\n<div class=\"body\">&lt;!&#8211;calling informal.object&#8211;&gt;<\/p>\n<div class=\"problem\"><span id=\"m44513-fs-idp152472016\"> <\/span><\/p>\n<p><span id=\"m44513-fs-idp131842896\"> <\/span><a class=\"xref target-figure\" href=\"ch14.html#m44513-fig-ch14_06_05\" title=\"Figure&#xa0;14.21.&#xa0;\">Figure\u00a014.21<\/a> A frameshift mutation that results in the insertion of three nucleotides is often less deleterious than a mutation that results in the insertion of one nucleotide. Why?<\/p>\n<\/p><\/div>\n<div id=\"m44513-fs-idp122564624\" class=\"solution\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44513-fs-idp163052304\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\"><a class=\"xref target-figure\" href=\"ch14.html#m44513-fig-ch14_06_05\" title=\"Figure&#xa0;14.21.&#xa0;\">Figure\u00a014.21<\/a> If three nucleotides are added, one additional amino acid will be incorporated into the protein chain, but the reading frame wont shift.<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<p>&lt;!&#8211;CNX: Start Area: &#8220;Multiple Choice&#8221;&#8211;&gt;<\/p>\n<div class=\"cnx-eoc multiple-choice\">\n<div class=\"title\"><span>Multiple Choice<\/span><\/div>\n<div class=\"section empty\">\n<div class=\"title\"><a href=\"#m44484\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Introduction<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<div class=\"section\">\n<div class=\"title\"><a href=\"#m44485\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.1<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Historical Basis of Modern Understanding<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<div id=\"m44485-fs-id2897046\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44485-fs-id1425482\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">1.<\/span><\/a><\/span><\/div>\n<div class=\"body\">&lt;!&#8211;calling informal.object&#8211;&gt;<\/p>\n<div class=\"problem\"><span id=\"m44485-fs-id2072379\"> <\/span><\/p>\n<p><span id=\"m44485-fs-id1341900\"> <\/span>If DNA of a particular species was analyzed and it was found that it contains 27 percent A, what would be the percentage of C?<\/p>\n<div class=\"orderedlist\"><span id=\"m44485-fs-id1602896\"> <\/span><\/p>\n<ol class=\"orderedlist\" type=\"a\">\n<li class=\"listitem\">\n<p>27 percent<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>30 percent<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>23 percent<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>54 percent<\/p>\n<\/li>\n<\/ol>\n<\/div>\n<\/div>\n<div id=\"m44485-fs-id1425482\" class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44485-fs-id2897046\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44485-fs-id1450506\"> <\/span>C<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div id=\"m44485-fs-id1435268\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44485-fs-id1439092\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">2.<\/span><\/a><\/span><\/div>\n<div class=\"body\">&lt;!&#8211;calling informal.object&#8211;&gt;<\/p>\n<div class=\"problem\"><span id=\"m44485-fs-id1393700\"> <\/span><\/p>\n<p><span id=\"m44485-fs-id2638298\"> <\/span>The experiments by Hershey and Chase helped confirm that DNA was the hereditary material on the basis of the finding that:<\/p>\n<div class=\"orderedlist\"><span id=\"m44485-fs-id1694835\"> <\/span><\/p>\n<ol class=\"orderedlist\" type=\"a\">\n<li class=\"listitem\">\n<p>radioactive phage were found in the pellet<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>radioactive cells were found in the supernatant<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>radioactive sulfur was found inside the cell<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>radioactive phosphorus was found in the cell<\/p>\n<\/li>\n<\/ol>\n<\/div>\n<\/div>\n<div id=\"m44485-fs-id1439092\" class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44485-fs-id1435268\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44485-fs-id1685167\"> <\/span>D<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"section\">\n<div class=\"title\"><a href=\"#m44486\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.2<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Structure and Sequencing<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<div id=\"m44486-fs-id2709296\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44486-fs-id1728094\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">6.<\/span><\/a><\/span><\/div>\n<div class=\"body\">&lt;!&#8211;calling informal.object&#8211;&gt;<\/p>\n<div class=\"problem\"><span id=\"m44486-fs-id1640010\"> <\/span><\/p>\n<p><span id=\"m44486-fs-id2984818\"> <\/span>DNA double helix does not have which of the following?<\/p>\n<div class=\"orderedlist\"><span id=\"m44486-fs-id2701000\"> <\/span><\/p>\n<ol class=\"orderedlist\" type=\"a\">\n<li class=\"listitem\">\n<p>antiparallel configuration<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>complementary base pairing<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>major and minor grooves<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>uracil<\/p>\n<\/li>\n<\/ol>\n<\/div>\n<\/div>\n<div id=\"m44486-fs-id1728094\" class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44486-fs-id2709296\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44486-fs-id1466731\"> <\/span>D<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div id=\"m44486-fs-id2688539\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44486-fs-id2904571\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">7.<\/span><\/a><\/span><\/div>\n<div class=\"body\">&lt;!&#8211;calling informal.object&#8211;&gt;<\/p>\n<div class=\"problem\"><span id=\"m44486-fs-id662862\"> <\/span><\/p>\n<p><span id=\"m44486-fs-id2681297\"> <\/span>In eukaryotes, what is the DNA wrapped around?<\/p>\n<div class=\"orderedlist\"><span id=\"m44486-fs-id3070802\"> <\/span><\/p>\n<ol class=\"orderedlist\" type=\"a\">\n<li class=\"listitem\">\n<p>single-stranded binding proteins<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>sliding clamp<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>polymerase<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>histones<\/p>\n<\/li>\n<\/ol>\n<\/div>\n<\/div>\n<div id=\"m44486-fs-id2904571\" class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44486-fs-id2688539\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44486-fs-id2569081\"> <\/span>D<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"section\">\n<div class=\"title\"><a href=\"#m44487\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.3<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Basics of DNA Replication<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<div id=\"m44487-fs-id2956539\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44487-fs-id1396004\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">10.<\/span><\/a><\/span><\/div>\n<div class=\"body\">&lt;!&#8211;calling informal.object&#8211;&gt;<\/p>\n<div class=\"problem\"><span id=\"m44487-fs-id1439092\"> <\/span><\/p>\n<p><span id=\"m44487-fs-id1561237\"> <\/span>Meselson and Stahl&#8217;s experiments proved that DNA replicates by which mode?<\/p>\n<div class=\"orderedlist\"><span id=\"m44487-fs-id2199309\"> <\/span><\/p>\n<ol class=\"orderedlist\" type=\"a\">\n<li class=\"listitem\">\n<p>conservative<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>semi-conservative<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>dispersive<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>none of the above<\/p>\n<\/li>\n<\/ol>\n<\/div>\n<\/div>\n<div id=\"m44487-fs-id1396004\" class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44487-fs-id2956539\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44487-fs-id1262008\"> <\/span>B<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div id=\"m44487-fs-id2300016\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44487-fs-id2581969\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">11.<\/span><\/a><\/span><\/div>\n<div class=\"body\">&lt;!&#8211;calling informal.object&#8211;&gt;<\/p>\n<div class=\"problem\"><span id=\"m44487-fs-id1812902\"> <\/span><\/p>\n<p><span id=\"m44487-fs-id2089930\"> <\/span>If the sequence of the 5&#8242;-3&#8242; strand is AATGCTAC, then the complementary sequence has the following sequence:<\/p>\n<div class=\"orderedlist\"><span id=\"m44487-fs-id2334300\"> <\/span><\/p>\n<ol class=\"orderedlist\" type=\"a\">\n<li class=\"listitem\">\n<p>3&#8242;-AATGCTAC-5&#8242;<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>3&#8242;-CATCGTAA-5&#8242;<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>3&#8242;-TTACGATG-5&#8242;<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>3&#8242;-GTAGCATT-5&#8242;<\/p>\n<\/li>\n<\/ol>\n<\/div>\n<\/div>\n<div id=\"m44487-fs-id2581969\" class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44487-fs-id2300016\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44487-fs-id2022386\"> <\/span>C<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"section\">\n<div class=\"title\"><a href=\"#m44488\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.4<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Replication in Prokaryotes<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<div id=\"m44488-fs-id1341900\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44488-fs-id2345394\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">14.<\/span><\/a><\/span><\/div>\n<div class=\"body\">&lt;!&#8211;calling informal.object&#8211;&gt;<\/p>\n<div class=\"problem\"><span id=\"m44488-fs-id1519179\"> <\/span><\/p>\n<p><span id=\"m44488-fs-id2329090\"> <\/span>Which of the following components is not involved during the formation of the replication fork?<\/p>\n<div class=\"orderedlist\"><span id=\"m44488-fs-id1602896\"> <\/span><\/p>\n<ol class=\"orderedlist\" type=\"a\">\n<li class=\"listitem\">\n<p>single-strand binding proteins<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>helicase<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>origin of replication<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>ligase<\/p>\n<\/li>\n<\/ol>\n<\/div>\n<\/div>\n<div id=\"m44488-fs-id2345394\" class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44488-fs-id1341900\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44488-fs-id2643307\"> <\/span>D<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div id=\"m44488-fs-id2075108\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44488-fs-id1910465\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">15.<\/span><\/a><\/span><\/div>\n<div class=\"body\">&lt;!&#8211;calling informal.object&#8211;&gt;<\/p>\n<div class=\"problem\"><span id=\"m44488-fs-id1396394\"> <\/span><\/p>\n<p><span id=\"m44488-fs-id2138308\"> <\/span>Which of the following does the enzyme primase synthesize?<\/p>\n<div class=\"orderedlist\"><span id=\"m44488-fs-id2228365\"> <\/span><\/p>\n<ol class=\"orderedlist\" type=\"a\">\n<li class=\"listitem\">\n<p>DNA primer<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>RNA primer<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>Okazaki fragments<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>phosphodiester linkage<\/p>\n<\/li>\n<\/ol>\n<\/div>\n<\/div>\n<div id=\"m44488-fs-id1910465\" class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44488-fs-id2075108\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44488-fs-id2010183\"> <\/span>B<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div id=\"m44488-fs-id1406784\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44488-fs-id1512007\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">16.<\/span><\/a><\/span><\/div>\n<div class=\"body\">&lt;!&#8211;calling informal.object&#8211;&gt;<\/p>\n<div class=\"problem\"><span id=\"m44488-fs-id2019618\"> <\/span><\/p>\n<p><span id=\"m44488-fs-id1798381\"> <\/span>In which direction does DNA replication take place?<\/p>\n<div class=\"orderedlist\"><span id=\"m44488-fs-id3241387\"> <\/span><\/p>\n<ol class=\"orderedlist\" type=\"a\">\n<li class=\"listitem\">\n<p>5&#8242;-3&#8242;<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>3&#8242;-5&#8242;<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>5&#8242;<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>3&#8242;<\/p>\n<\/li>\n<\/ol>\n<\/div>\n<\/div>\n<div id=\"m44488-fs-id1512007\" class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44488-fs-id1406784\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44488-fs-id2979133\"> <\/span>A<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"section\">\n<div class=\"title\"><a href=\"#m44517\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.5<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Replication in Eukaryotes<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<div id=\"m44517-fs-id2739491\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44517-fs-id2075482\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">22.<\/span><\/a><\/span><\/div>\n<div class=\"body\">&lt;!&#8211;calling informal.object&#8211;&gt;<\/p>\n<div class=\"problem\"><span id=\"m44517-fs-id1631701\"> <\/span><\/p>\n<p><span id=\"m44517-fs-id2024527\"> <\/span>The ends of the linear chromosomes are maintained by<\/p>\n<div class=\"orderedlist\"><span id=\"m44517-fs-id3000420\"> <\/span><\/p>\n<ol class=\"orderedlist\" type=\"a\">\n<li class=\"listitem\">\n<p>helicase<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>primase<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>DNA pol<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>telomerase<\/p>\n<\/li>\n<\/ol>\n<\/div>\n<\/div>\n<div id=\"m44517-fs-id2075482\" class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44517-fs-id2739491\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44517-fs-id2314747\"> <\/span>D<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"section\">\n<div class=\"title\"><a href=\"#m44513\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.6<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Repair<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<div id=\"m44513-fs-id1951731\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44513-fs-id2750351\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">25.<\/span><\/a><\/span><\/div>\n<div class=\"body\">&lt;!&#8211;calling informal.object&#8211;&gt;<\/p>\n<div class=\"problem\"><span id=\"m44513-fs-id1477381\"> <\/span><\/p>\n<p><span id=\"m44513-fs-id1685167\"> <\/span>During proofreading, which of the following enzymes reads the DNA?<\/p>\n<div class=\"orderedlist\"><span id=\"m44513-fs-id2781180\"> <\/span><\/p>\n<ol class=\"orderedlist\" type=\"a\">\n<li class=\"listitem\">\n<p>primase<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>topoisomerase<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>DNA pol<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>helicase<\/p>\n<\/li>\n<\/ol>\n<\/div>\n<\/div>\n<div id=\"m44513-fs-id2750351\" class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44513-fs-id1951731\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44513-fs-id1477929\"> <\/span>C<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div id=\"m44513-fs-id1414909\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44513-fs-id1837280\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">26.<\/span><\/a><\/span><\/div>\n<div class=\"body\">&lt;!&#8211;calling informal.object&#8211;&gt;<\/p>\n<div class=\"problem\"><span id=\"m44513-fs-id2415145\"> <\/span><\/p>\n<p><span id=\"m44513-fs-id2073382\"> <\/span>The initial mechanism for repairing nucleotide errors in DNA is ________.<\/p>\n<div class=\"orderedlist\"><span id=\"m44513-fs-id1794075\"> <\/span><\/p>\n<ol class=\"orderedlist\" type=\"a\">\n<li class=\"listitem\">\n<p>mismatch repair<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>DNA polymerase proofreading<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>nucleotide excision repair<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>thymine dimers<\/p>\n<\/li>\n<\/ol>\n<\/div>\n<\/div>\n<div id=\"m44513-fs-id1837280\" class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44513-fs-id1414909\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44513-fs-id2051151\"> <\/span>B<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<p>&lt;!&#8211;CNX: Start Area: &#8220;Free Response&#8221;&#8211;&gt;<\/p>\n<div class=\"cnx-eoc free-response\">\n<div class=\"title\"><span>Free Response<\/span><\/div>\n<div class=\"section empty\">\n<div class=\"title\"><a href=\"#m44484\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Introduction<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<div class=\"section\">\n<div class=\"title\"><a href=\"#m44485\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.1<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Historical Basis of Modern Understanding<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<div id=\"m44485-fs-id1426300\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44485-fs-id2100648\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">3.<\/span><\/a><\/span><\/div>\n<div class=\"body\">&lt;!&#8211;calling informal.object&#8211;&gt;<\/p>\n<div class=\"problem\"><span id=\"m44485-fs-id2334828\"> <\/span><\/p>\n<p><span id=\"m44485-fs-id2739498\"> <\/span>Explain Griffith&#8217;s transformation experiments. What did he conclude from them?<\/p>\n<\/div>\n<div id=\"m44485-fs-id2100648\" class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44485-fs-id1426300\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44485-fs-id2168285\"> <\/span>Live R cells acquired genetic information from the heat-killed S cells that \u201ctransformed\u201d the R cells into S cells.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div id=\"m44485-fs-id2763427\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44485-fs-id2137450\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">4.<\/span><\/a><\/span><\/div>\n<div class=\"body\">&lt;!&#8211;calling informal.object&#8211;&gt;<\/p>\n<div class=\"problem\"><span id=\"m44485-fs-id1760961\"> <\/span><\/p>\n<p><span id=\"m44485-fs-id2926691\"> <\/span>Why were radioactive sulfur and phosphorous used to label bacteriophage in Hershey and Chase&#8217;s experiments?<\/p>\n<\/div>\n<div id=\"m44485-fs-id2137450\" class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44485-fs-id2763427\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44485-fs-id2571119\"> <\/span>Sulfur is an element found in proteins and phosphorus is a component of nucleic acids.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"section\">\n<div class=\"title\"><a href=\"#m44486\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.2<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Structure and Sequencing<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<div id=\"m44486-fs-id1286460\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44486-fs-id2274570\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">8.<\/span><\/a><\/span><\/div>\n<div class=\"body\">&lt;!&#8211;calling informal.object&#8211;&gt;<\/p>\n<div class=\"problem\"><span id=\"m44486-fs-id1986198\"> <\/span><\/p>\n<p><span id=\"m44486-fs-id1704961\"> <\/span>Provide a brief summary of the Sanger sequencing method.<\/p>\n<\/div>\n<div id=\"m44486-fs-id2274570\" class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44486-fs-id1286460\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44486-fs-id2196933\"> <\/span>The template DNA strand is mixed with a DNA polymerase, a primer, the 4 deoxynucleotides, and a limiting concentration of 4 dideoxynucleotides. DNA polymerase synthesizes a strand complementary to the template. Incorporation of ddNTPs at different locations results in DNA fragments that have terminated at every possible base in the template. These fragments are separated by gel electrophoresis and visualized by a laser detector to determine the sequence of bases.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div id=\"m44486-fs-id2926746\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44486-fs-id1569099\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">9.<\/span><\/a><\/span><\/div>\n<div class=\"body\">&lt;!&#8211;calling informal.object&#8211;&gt;<\/p>\n<div class=\"problem\"><span id=\"m44486-fs-id1479286\"> <\/span><\/p>\n<p><span id=\"m44486-fs-id2914790\"> <\/span>Describe the structure and complementary base pairing of DNA.<\/p>\n<\/div>\n<div id=\"m44486-fs-id1569099\" class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44486-fs-id2926746\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44486-fs-id2150246\"> <\/span>DNA has two strands in anti-parallel orientation. The sugar-phosphate linkages form a backbone on the outside, and the bases are paired on the inside: A with T, and G with C, like rungs on a spiral ladder.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"section\">\n<div class=\"title\"><a href=\"#m44487\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.3<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Basics of DNA Replication<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<div id=\"m44487-fs-id1958775\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44487-fs-id1384287\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">12.<\/span><\/a><\/span><\/div>\n<div class=\"body\">&lt;!&#8211;calling informal.object&#8211;&gt;<\/p>\n<div class=\"problem\"><span id=\"m44487-fs-id2025461\"> <\/span><\/p>\n<p><span id=\"m44487-fs-id2072379\"> <\/span>How did the scientific community learn that DNA replication takes place in a semi-conservative fashion?<\/p>\n<\/div>\n<div id=\"m44487-fs-id1384287\" class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44487-fs-id1958775\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44487-fs-id1478330\"> <\/span>Meselson\u2019s experiments with <span class=\"emphasis\"><em>E. coli <\/em><\/span>grown in <sup>15<\/sup>N deduced this finding.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"section\">\n<div class=\"title\"><a href=\"#m44488\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.4<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Replication in Prokaryotes<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<div id=\"m44488-fs-id1286460\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44488-fs-id2936597\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">17.<\/span><\/a><\/span><\/div>\n<div class=\"body\">&lt;!&#8211;calling informal.object&#8211;&gt;<\/p>\n<div class=\"problem\"><span id=\"m44488-fs-id1441996\"> <\/span><\/p>\n<p><span id=\"m44488-fs-id2198448\"> <\/span>DNA replication is bidirectional and discontinuous; explain your understanding of those concepts.<\/p>\n<\/div>\n<div id=\"m44488-fs-id2936597\" class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44488-fs-id1286460\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44488-fs-id1268735\"> <\/span>At an origin of replication, two replication forks are formed that are extended in two directions. On the lagging strand, Okazaki fragments are formed in a discontinuous manner.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div id=\"m44488-fs-id1805432\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44488-fs-id2114708\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">18.<\/span><\/a><\/span><\/div>\n<div class=\"body\">&lt;!&#8211;calling informal.object&#8211;&gt;<\/p>\n<div class=\"problem\"><span id=\"m44488-fs-id1569099\"> <\/span><\/p>\n<p><span id=\"m44488-fs-id2257887\"> <\/span>What are Okazaki fragments and how they are formed?<\/p>\n<\/div>\n<div id=\"m44488-fs-id2114708\" class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44488-fs-id1805432\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44488-fs-id2336863\"> <\/span>Short DNA fragments are formed on the lagging strand synthesized in a direction away from the replication fork. These are synthesized by DNA pol.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div id=\"m44488-fs-id1720501\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44488-fs-id3165297\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">19.<\/span><\/a><\/span><\/div>\n<div class=\"body\">&lt;!&#8211;calling informal.object&#8211;&gt;<\/p>\n<div class=\"problem\"><span id=\"m44488-fs-id2228028\"> <\/span><\/p>\n<p><span id=\"m44488-fs-id1778374\"> <\/span>If the rate of replication in a particular prokaryote is 900 nucleotides per second, how long would it take 1.2 million base pair genomes to make two copies?<\/p>\n<\/div>\n<div id=\"m44488-fs-id3165297\" class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44488-fs-id1720501\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44488-fs-id2279649\"> <\/span>1333 seconds or 22.2 minutes.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div id=\"m44488-fs-id2126300\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44488-fs-id1286063\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">20.<\/span><\/a><\/span><\/div>\n<div class=\"body\">&lt;!&#8211;calling informal.object&#8211;&gt;<\/p>\n<div class=\"problem\"><span id=\"m44488-fs-id671101\"> <\/span><\/p>\n<p><span id=\"m44488-fs-id1986681\"> <\/span>Explain the events taking place at the replication fork. If the gene for helicase is mutated, what part of replication will be affected?<\/p>\n<\/div>\n<div id=\"m44488-fs-id1286063\" class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44488-fs-id2126300\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44488-fs-id1436147\"> <\/span>At the replication fork, the events taking place are helicase action, binding of single-strand binding proteins, primer synthesis, and synthesis of new strands. If there is a mutated helicase gene, the replication fork will not be extended.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div id=\"m44488-fs-id1403064\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44488-fs-id1986827\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">21.<\/span><\/a><\/span><\/div>\n<div class=\"body\">&lt;!&#8211;calling informal.object&#8211;&gt;<\/p>\n<div class=\"problem\"><span id=\"m44488-fs-id2115858\"> <\/span><\/p>\n<p><span id=\"m44488-fs-id1387702\"> <\/span>What is the role of a primer in DNA replication? What would happen if you forgot to add a primer in a tube containing the reaction mix for a DNA sequencing reaction?<\/p>\n<\/div>\n<div id=\"m44488-fs-id1986827\" class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44488-fs-id1403064\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44488-fs-id2385726\"> <\/span>Primer provides a 3&#8242;-OH group for DNA pol to start adding nucleotides. There would be no reaction in the tube without a primer, and no bands would be visible on the electrophoresis.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"section\">\n<div class=\"title\"><a href=\"#m44517\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.5<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Replication in Eukaryotes<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<div id=\"m44517-fs-id2896348\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44517-fs-id2746188\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">23.<\/span><\/a><\/span><\/div>\n<div class=\"body\">&lt;!&#8211;calling informal.object&#8211;&gt;<\/p>\n<div class=\"problem\"><span id=\"m44517-fs-id2167973\"> <\/span><\/p>\n<p><span id=\"m44517-fs-id2694648\"> <\/span>How do the linear chromosomes in eukaryotes ensure that its ends are replicated completely?<\/p>\n<\/div>\n<div id=\"m44517-fs-id2746188\" class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44517-fs-id2896348\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44517-fs-id2190591\"> <\/span>Telomerase has an inbuilt RNA template that extends the 3&#8242; end, so primer is synthesized and extended. Thus, the ends are protected.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"section\">\n<div class=\"title\"><a href=\"#m44513\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">14.6<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">DNA Repair<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<div id=\"m44513-fs-id2008893\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44513-fs-id1385923\"><span class=\"cnx-gentext-exercise cnx-gentext-autogenerated\">Exercise <\/span><span class=\"cnx-gentext-exercise cnx-gentext-n\">27.<\/span><\/a><\/span><\/div>\n<div class=\"body\">&lt;!&#8211;calling informal.object&#8211;&gt;<\/p>\n<div class=\"problem\"><span id=\"m44513-fs-id2763212\"> <\/span><\/p>\n<p><span id=\"m44513-fs-id3044550\"> <\/span>What is the consequence of mutation of a mismatch repair enzyme? How will this affect the function of a gene?<\/p>\n<\/div>\n<div id=\"m44513-fs-id1385923\" class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44513-fs-id2008893\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44513-fs-id1712102\"> <\/span>Mutations are not repaired, as in the case of xeroderma pigmentosa. Gene function may be affected or it may not be expressed.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"cnx-eoc cnx-solutions\">\n<div class=\"title\">Solutions<\/div>\n<p>&lt;!&#8211;CNX: Start Area: &#8220;Art Connections&#8221;&#8211;&gt;<\/p>\n<div class=\"solution\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44486-fs-idp2462496\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\"><a class=\"xref target-figure\" href=\"ch14.html#m44486-fig-ch14_02_06\" title=\"Figure&#xa0;14.10.&#xa0;\">Figure\u00a014.10<\/a> Compartmentalization enables a eukaryotic cell to divide processes into discrete steps so it can build more complex protein and RNA products. But there is an advantage to having a single compartment as well: RNA and protein synthesis occurs much more quickly in a prokaryotic cell.<\/div>\n<\/div>\n<div class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44488-fs-idm104376352\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span> <\/span><a class=\"xref target-figure\" href=\"ch14.html#m44488-fig-ch14_04_01\" title=\"Figure&#xa0;14.14.&#xa0;\">Figure\u00a014.14<\/a> DNA ligase, as this enzyme joins together Okazaki fragments.<\/p>\n<\/div>\n<\/div>\n<div class=\"solution\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44513-fs-idp163052304\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\"><a class=\"xref target-figure\" href=\"ch14.html#m44513-fig-ch14_06_05\" title=\"Figure&#xa0;14.21.&#xa0;\">Figure\u00a014.21<\/a> If three nucleotides are added, one additional amino acid will be incorporated into the protein chain, but the reading frame wont shift.<\/div>\n<\/div>\n<p>&lt;!&#8211;CNX: Start Area: &#8220;Multiple Choice&#8221;&#8211;&gt;<\/p>\n<div class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44485-fs-id2897046\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span> <\/span>C<\/p>\n<\/div>\n<\/div>\n<div class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44485-fs-id1435268\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span> <\/span>D<\/p>\n<\/div>\n<\/div>\n<div class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44486-fs-id2709296\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span> <\/span>D<\/p>\n<\/div>\n<\/div>\n<div class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44486-fs-id2688539\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span> <\/span>D<\/p>\n<\/div>\n<\/div>\n<div class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44487-fs-id2956539\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span> <\/span>B<\/p>\n<\/div>\n<\/div>\n<div class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44487-fs-id2300016\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span> <\/span>C<\/p>\n<\/div>\n<\/div>\n<div class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44488-fs-id1341900\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span> <\/span>D<\/p>\n<\/div>\n<\/div>\n<div class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44488-fs-id2075108\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span> <\/span>B<\/p>\n<\/div>\n<\/div>\n<div class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44488-fs-id1406784\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span> <\/span>A<\/p>\n<\/div>\n<\/div>\n<div class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44517-fs-id2739491\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span> <\/span>D<\/p>\n<\/div>\n<\/div>\n<div class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44513-fs-id1951731\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span> <\/span>C<\/p>\n<\/div>\n<\/div>\n<div class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44513-fs-id1414909\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span> <\/span>B<\/p>\n<\/div>\n<\/div>\n<p>&lt;!&#8211;CNX: Start Area: &#8220;Free Response&#8221;&#8211;&gt;<\/p>\n<div class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44485-fs-id1426300\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span> <\/span>Live R cells acquired genetic information from the heat-killed S cells that \u201ctransformed\u201d the R cells into S cells.<\/p>\n<\/div>\n<\/div>\n<div class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44485-fs-id2763427\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span> <\/span>Sulfur is an element found in proteins and phosphorus is a component of nucleic acids.<\/p>\n<\/div>\n<\/div>\n<div class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44486-fs-id1286460\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span> <\/span>The template DNA strand is mixed with a DNA polymerase, a primer, the 4 deoxynucleotides, and a limiting concentration of 4 dideoxynucleotides. DNA polymerase synthesizes a strand complementary to the template. Incorporation of ddNTPs at different locations results in DNA fragments that have terminated at every possible base in the template. These fragments are separated by gel electrophoresis and visualized by a laser detector to determine the sequence of bases.<\/p>\n<\/div>\n<\/div>\n<div class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44486-fs-id2926746\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span> <\/span>DNA has two strands in anti-parallel orientation. The sugar-phosphate linkages form a backbone on the outside, and the bases are paired on the inside: A with T, and G with C, like rungs on a spiral ladder.<\/p>\n<\/div>\n<\/div>\n<div class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44487-fs-id1958775\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span> <\/span>Meselson\u2019s experiments with <span class=\"emphasis\"><em>E. coli <\/em><\/span>grown in <sup>15<\/sup>N deduced this finding.<\/p>\n<\/div>\n<\/div>\n<div class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44488-fs-id1286460\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span> <\/span>At an origin of replication, two replication forks are formed that are extended in two directions. On the lagging strand, Okazaki fragments are formed in a discontinuous manner.<\/p>\n<\/div>\n<\/div>\n<div class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44488-fs-id1805432\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span> <\/span>Short DNA fragments are formed on the lagging strand synthesized in a direction away from the replication fork. These are synthesized by DNA pol.<\/p>\n<\/div>\n<\/div>\n<div class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44488-fs-id1720501\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span> <\/span>1333 seconds or 22.2 minutes.<\/p>\n<\/div>\n<\/div>\n<div class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44488-fs-id2126300\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span> <\/span>At the replication fork, the events taking place are helicase action, binding of single-strand binding proteins, primer synthesis, and synthesis of new strands. If there is a mutated helicase gene, the replication fork will not be extended.<\/p>\n<\/div>\n<\/div>\n<div class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44488-fs-id1403064\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span> <\/span>Primer provides a 3&#8242;-OH group for DNA pol to start adding nucleotides. There would be no reaction in the tube without a primer, and no bands would be visible on the electrophoresis.<\/p>\n<\/div>\n<\/div>\n<div class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44517-fs-id2896348\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span> <\/span>Telomerase has an inbuilt RNA template that extends the 3&#8242; end, so primer is synthesized and extended. Thus, the ends are protected.<\/p>\n<\/div>\n<\/div>\n<div class=\"solution labeled\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch14.html#m44513-fs-id2008893\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span> <\/span>Mutations are not repaired, as in the case of xeroderma pigmentosa. Gene function may be affected or it may not be expressed.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n","protected":false},"author":17,"menu_order":16,"template":"","meta":{"_candela_citation":"[]","CANDELA_OUTCOMES_GUID":"","pb_show_title":"on","pb_short_title":"","pb_subtitle":"","pb_authors":[],"pb_section_license":""},"chapter-type":[],"contributor":[],"license":[],"class_list":["post-473","chapter","type-chapter","status-publish","hentry"],"part":21,"_links":{"self":[{"href":"https:\/\/courses.lumenlearning.com\/umd-publichealthbio\/wp-json\/pressbooks\/v2\/chapters\/473","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/courses.lumenlearning.com\/umd-publichealthbio\/wp-json\/pressbooks\/v2\/chapters"}],"about":[{"href":"https:\/\/courses.lumenlearning.com\/umd-publichealthbio\/wp-json\/wp\/v2\/types\/chapter"}],"author":[{"embeddable":true,"href":"https:\/\/courses.lumenlearning.com\/umd-publichealthbio\/wp-json\/wp\/v2\/users\/17"}],"version-history":[{"count":1,"href":"https:\/\/courses.lumenlearning.com\/umd-publichealthbio\/wp-json\/pressbooks\/v2\/chapters\/473\/revisions"}],"predecessor-version":[{"id":519,"href":"https:\/\/courses.lumenlearning.com\/umd-publichealthbio\/wp-json\/pressbooks\/v2\/chapters\/473\/revisions\/519"}],"part":[{"href":"https:\/\/courses.lumenlearning.com\/umd-publichealthbio\/wp-json\/pressbooks\/v2\/parts\/21"}],"metadata":[{"href":"https:\/\/courses.lumenlearning.com\/umd-publichealthbio\/wp-json\/pressbooks\/v2\/chapters\/473\/metadata\/"}],"wp:attachment":[{"href":"https:\/\/courses.lumenlearning.com\/umd-publichealthbio\/wp-json\/wp\/v2\/media?parent=473"}],"wp:term":[{"taxonomy":"chapter-type","embeddable":true,"href":"https:\/\/courses.lumenlearning.com\/umd-publichealthbio\/wp-json\/pressbooks\/v2\/chapter-type?post=473"},{"taxonomy":"contributor","embeddable":true,"href":"https:\/\/courses.lumenlearning.com\/umd-publichealthbio\/wp-json\/wp\/v2\/contributor?post=473"},{"taxonomy":"license","embeddable":true,"href":"https:\/\/courses.lumenlearning.com\/umd-publichealthbio\/wp-json\/wp\/v2\/license?post=473"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}