{"id":498,"date":"2016-08-19T15:59:25","date_gmt":"2016-08-19T15:59:25","guid":{"rendered":"https:\/\/courses.lumenlearning.com\/umd-publichealthbio\/?post_type=chapter&#038;p=498"},"modified":"2016-08-19T15:59:26","modified_gmt":"2016-08-19T15:59:26","slug":"chapter-15-genes-and-proteins","status":"publish","type":"chapter","link":"https:\/\/courses.lumenlearning.com\/umd-publichealthbio\/chapter\/chapter-15-genes-and-proteins\/","title":{"raw":"Chapter\u00a015.\u00a0Genes and Proteins","rendered":"Chapter\u00a015.\u00a0Genes and Proteins"},"content":{"raw":"<div class=\"chapter\" title=\"Chapter&#xA0;15.&#xA0;Genes and Proteins\" id=\"id508530\"><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\">15<\/span><span class=\"cnx-gentext-chapter cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-chapter cnx-gentext-t\">Genes and Proteins<\/span><\/h1><\/div><\/div><\/div><div class=\"introduction\" id=\"m44518\"><div id=\"m44518-fig-ch15_00_00\" class=\"figure splash\" title=\"Figure&#xA0;15.1.&#xA0;\"><div class=\"body\"><div class=\"mediaobject\"><span id=\"m44518-fs-id1796314\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155741\/Figure_15_00_01.jpg\" width=\"500\" alt=\"Molecular models show a DNA double helix that is packed in a chromosome in Part a, and two proteins are shown in Parts b and c.\"\/><\/div><\/div><div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">15.1<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"\/><\/div><div class=\"caption\">Genes, which are carried on (a) chromosomes, are linearly organized instructions for making the RNA and protein molecules that are necessary for all of processes of life. The (b) interleukin-2 protein and (c) alpha-2u-globulin protein are just two examples of the array of different molecular structures that are encoded by genes. (credit \u201cchromosome: National Human Genome Research Institute; credit \u201cinterleukin-2\u201d: Ramin Herati\/Created from PDB 1M47 and rendered with Pymol; credit \u201calpha-2u-globulin\u201d: Darren Logan\/rendered with AISMIG)<\/div><\/div><h3 class=\"title\"><span>Introduction<sup><a href=\"co03.html#book-attribution-m44518\">*<\/a><\/sup><\/span><\/h3><p><span id=\"m44518-fs-id1728094\"> <\/span>Since the rediscovery of Mendel\u2019s work in 1900, the definition of the gene has progressed from an abstract unit of heredity to a tangible molecular entity capable of replication, expression, and mutation (<a class=\"xref target-figure\" href=\"ch15.html#m44518-fig-ch15_00_00\" title=\"Figure&#xA0;15.1.&#xA0;\">Figure\u00a015.1<\/a>). Genes are composed of DNA and are linearly arranged on chromosomes. Genes specify the sequences of amino acids, which are the building blocks of proteins. In turn, proteins are responsible for orchestrating nearly every function of the cell. Both genes and the proteins they encode are absolutely essential to life as we know it.<\/p><\/div><div xml:lang=\"en\" class=\"section module\" title=\"15.1.&#xA0;The Genetic Code\"><div class=\"titlepage\"><div><div><h2 id=\"m44522\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.1<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">The Genetic Code<sup><a href=\"co03.html#book-attribution-m44522\">*<\/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 \u201ccentral dogma\u201d of protein synthesis<\/p><\/li><li class=\"listitem\"><p>Describe the genetic code and how the nucleotide sequence prescribes the amino acid and the protein sequence<\/p><\/li><\/ul><\/div><\/div><\/div><\/div><div class=\"toc\"><ul><li class=\"toc-section\"><a href=\"#m44522-fs-id2013510\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">The Central Dogma: DNA Encodes RNA; RNA Encodes Protein<\/span><\/a><ul><li class=\"toc-section\"><a href=\"#m44522-fs-id2000981\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">The Genetic Code Is Degenerate and Universal<\/span><\/a><\/li><\/ul><\/li><\/ul><\/div><p><span id=\"m44522-fs-id2750556\"> <\/span>The cellular process of transcription generates messenger RNA (mRNA), a mobile molecular copy of one or more genes with an alphabet of A, C, G, and uracil (U). Translation of the mRNA template converts nucleotide-based genetic information into a protein product. Protein sequences consist of 20 commonly occurring amino acids; therefore, it can be said that the protein alphabet consists of 20 letters (<a class=\"xref target-figure\" href=\"ch15.html#m44522-fig-ch15_01_01\" title=\"Figure&#xA0;15.2.&#xA0;\">Figure\u00a015.2<\/a>). Each amino acid is defined by a three-nucleotide sequence called the triplet codon. Different amino acids have different chemistries (such as acidic versus basic, or polar and nonpolar) and different structural constraints. Variation in amino acid sequence gives rise to enormous variation in protein structure and function.<\/p><div id=\"m44522-fig-ch15_01_01\" class=\"figure\" title=\"Figure&#xA0;15.2.&#xA0;\"><div class=\"body\"><div class=\"mediaobject\"><span id=\"m44522-fs-id1695436\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155744\/Figure_15_01_01.jpg\" width=\"500\" alt=\"Structures of the twenty amino acids are given. Six amino acids&#x2014;glycine, alanine, valine, leucine, methionine, and isoleucine&#x2014;are non-polar and aliphatic, meaning they do not have a ring. Six amino acids&#x2014;serine, threonine, cysteine, proline, asparagine, and glutamate&#x2014;are polar but uncharged. Three amino acids&#x2014;lysine, arginine, and histidine&#x2014;are positively charged. Two amino acids, glutamate and aspartate, are negatively charged. Three amino acids&#x2014;phenylalanine, tyrosine, and tryptophan&#x2014;are nonpolar and aromatic.\"\/><\/div><\/div><div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">15.2<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"\/><\/div><div class=\"caption\">Structures of the 20 amino acids found in proteins are shown. Each amino acid is composed of an amino group (<span class=\"token\">\n \n  NH<sub>3<\/sub><sup>+<\/sup><\/span>), a carboxyl group (COO<sup>-<\/sup>), and a side chain (blue). The side chain may be nonpolar, polar, or charged, as well as large or small. It is the variety of amino acid side chains that gives rise to the incredible variation of protein structure and function.<\/div><\/div><div class=\"section\" title=\"The Central Dogma: DNA Encodes RNA; RNA Encodes Protein\"><div class=\"titlepage\"><div><div><h3 id=\"m44522-fs-id2013510\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">The Central Dogma: DNA Encodes RNA; RNA Encodes Protein<\/span><\/span><\/h3><\/div><\/div><\/div><p><span id=\"m44522-fs-id2155314\"> <\/span>The flow of genetic information in cells from DNA to mRNA to protein is described by the <em class=\"glossterm\"><span id=\"m44522-autoid-cnx2dbk-id1618570\"> <\/span>Central Dogma<\/em><a id=\"id509242\" class=\"indexterm\"> (<\/a><a class=\"xref target-figure\" href=\"ch15.html#m44522-fig-ch15_01_02\" title=\"Figure&#xA0;15.3.&#xA0;\">Figure\u00a015.3<\/a>), which states that genes specify the sequence of mRNAs, which in turn specify the sequence of proteins. The decoding of one molecule to another is performed by specific proteins and RNAs. Because the information stored in DNA is so central to cellular function, it makes intuitive sense that the cell would make mRNA copies of this information for protein synthesis, while keeping the DNA itself intact and protected. The copying of DNA to RNA is relatively straightforward, with one nucleotide being added to the mRNA strand for every nucleotide read in the DNA strand. The translation to protein is a bit more complex because three mRNA nucleotides correspond to one amino acid in the polypeptide sequence. However, the translation to protein is still systematic and <em class=\"glossterm\"><span id=\"m44522-autoid-cnx2dbk-id1618587\"> <\/span>colinear<\/em><a id=\"id509278\" class=\"indexterm\">, such that nucleotides 1 to 3 correspond to amino acid 1, nucleotides 4 to 6 correspond to amino acid 2, and so on.<\/a><\/p><div id=\"m44522-fig-ch15_01_02\" class=\"figure\" title=\"Figure&#xA0;15.3.&#xA0;\"><div class=\"body\"><div class=\"mediaobject\"><span id=\"m44522-fs-id2681268\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155747\/Figure_15_01_02.jpg\" width=\"280\" alt=\"To make a protein, genetic information encoded by the DNA must be transcribed onto an mRNA molecule. The RNA is then processed by splicing to remove exons and by the addition of a 5' cap and a poly-A tail. A ribosome then reads the sequence on the mRNA, and uses this information to string amino acids into a protein.\"\/><\/div><\/div><div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">15.3<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"\/><\/div><div class=\"caption\">Instructions on DNA are transcribed onto messenger RNA. Ribosomes are able to read the genetic information inscribed on a strand of messenger RNA and use this information to string amino acids together into a protein.<\/div><\/div><div class=\"section\" title=\"The Genetic Code Is Degenerate and Universal\"><div class=\"titlepage\"><div><div><h4 id=\"m44522-fs-id2000981\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">The Genetic Code Is Degenerate and Universal<\/span><\/span><\/h4><\/div><\/div><\/div><p><span id=\"m44522-fs-id1290387\"> <\/span>Given the different numbers of \u201cletters\u201d in the mRNA and protein \u201calphabets,\u201d scientists theorized that combinations of nucleotides corresponded to single amino acids. Nucleotide doublets would not be sufficient to specify every amino acid because there are only 16 possible two-nucleotide combinations (4<sup>2<\/sup>). In contrast, there are 64 possible nucleotide triplets (4<sup>3<\/sup>), which is far more than the number of amino acids. Scientists theorized that amino acids were encoded by nucleotide triplets and that the genetic code was <em class=\"glossterm\"><span id=\"m44522-autoid-cnx2dbk-id1617190\"> <\/span>degenerate<\/em><a id=\"id509355\" class=\"indexterm\">. In other words, a given amino acid could be encoded by more than one nucleotide triplet. This was later confirmed experimentally; Francis Crick and Sydney Brenner used the chemical mutagen proflavin to insert one, two, or three nucleotides into the gene of a virus. When one or two nucleotides were inserted, protein synthesis was completely abolished. When three nucleotides were inserted, the protein was synthesized and functional. This demonstrated that three nucleotides specify each amino acid. These nucleotide triplets are called <em class=\"glossterm\"><span id=\"m44522-autoid-cnx2dbk-id1617198\"> <\/span>codons<\/em><\/a><a id=\"id509373\" class=\"indexterm\">. The insertion of one or two nucleotides completely changed the triplet <em class=\"glossterm\"><span id=\"m44522-autoid-cnx2dbk-id1617202\"> <\/span>reading frame<\/em><\/a><a id=\"id509387\" class=\"indexterm\">, thereby altering the message for every subsequent amino acid (<\/a><a class=\"xref target-figure\" href=\"ch15.html#m44522-fig-ch15_01_05\" title=\"Figure&#xA0;15.5.&#xA0;\">Figure\u00a015.5<\/a>). Though insertion of three nucleotides caused an extra amino acid to be inserted during translation, the integrity of the rest of the protein was maintained.<\/p><p><span id=\"m44522-fs-id1565817\"> <\/span>Scientists painstakingly solved the genetic code by translating synthetic mRNAs in vitro and sequencing the proteins they specified (<a class=\"xref target-figure\" href=\"ch15.html#m44522-fig-ch15_01_04\" title=\"Figure&#xA0;15.4.&#xA0;\">Figure\u00a015.4<\/a>).<\/p><div id=\"m44522-fig-ch15_01_04\" class=\"figure\" title=\"Figure&#xA0;15.4.&#xA0;\"><div class=\"body\"><div class=\"mediaobject\"><span id=\"m44522-fs-id2989543\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155749\/Figure_15_01_04.jpg\" width=\"300\" alt=\"Figure shows all 64 codons. Sixty-two of these code for amino acids, and three are stop codons.\"\/><\/div><\/div><div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">15.4<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"\/><\/div><div class=\"caption\">This figure shows the genetic code for translating each nucleotide triplet in mRNA into an amino acid or a termination signal in a nascent protein. (credit: modification of work by NIH)<\/div><\/div><p><span id=\"m44522-fs-id1634383\"> <\/span>In addition to instructing the addition of a specific amino acid to a polypeptide chain, three of the 64 codons terminate protein synthesis and release the polypeptide from the translation machinery. These triplets are called <em class=\"glossterm\"><span id=\"m44522-autoid-cnx2dbk-id1629280\"> <\/span>nonsense codons<\/em><a id=\"id509470\" class=\"indexterm\">, or stop codons. Another codon, AUG, also has a special function. In addition to specifying the amino acid methionine, it also serves as the start codon to initiate translation. The reading frame for translation is set by the AUG start codon near the 5' end of the mRNA.<\/a><\/p><p><span id=\"m44522-fs-id913366\"> <\/span>The genetic code is universal. With a few exceptions, virtually all species use the same genetic code for protein synthesis. Conservation of codons means that a purified mRNA encoding the globin protein in horses could be transferred to a tulip cell, and the tulip would synthesize horse globin. That there is only one genetic code is powerful evidence that all of life on Earth shares a common origin, especially considering that there are about 10<sup>84<\/sup> possible combinations of 20 amino acids and 64 triplet codons.<\/p><div id=\"m44522-fs-id2739380\" 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=\"m44522-fs-id1712352\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155752\/create_protein.png\" width=\"120\" alt=\"QR Code representing a URL\"\/><\/div><p><span id=\"m44522-fs-id1965995\"> <\/span>Transcribe a gene and translate it to protein using complementary pairing and the genetic code at this <a class=\"link\" href=\"http:\/\/openstaxcollege.org\/l\/create_protein\" target=\"\"> site<\/a>.<\/p><\/div><\/div><div id=\"m44522-fig-ch15_01_05\" class=\"figure\" title=\"Figure&#xA0;15.5.&#xA0;\"><div class=\"body\"><div class=\"mediaobject\"><span id=\"m44522-fs-id2339630\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155753\/Figure_15_01_05.jpg\" width=\"350\" alt=\"Illustration shows a frameshift mutation in which the reading frame is altered by the deletion of two amino acids.\"\/><\/div><\/div><div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">15.5<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"\/><\/div><div class=\"caption\">The deletion of two nucleotides shifts the reading frame of an mRNA and changes the entire protein message, creating a nonfunctional protein or terminating protein synthesis altogether.<\/div><\/div><p><span id=\"m44522-fs-id1288651\"> <\/span>Degeneracy is believed to be a cellular mechanism to reduce the negative impact of random mutations. Codons that specify the same amino acid typically only differ by one nucleotide. In addition, amino acids with chemically similar side chains are encoded by similar codons. This nuance of the genetic code ensures that a single-nucleotide substitution mutation might either specify the same amino acid but have no effect or specify a similar amino acid, preventing the protein from being rendered completely nonfunctional.<\/p><\/div><div id=\"m44522-fs-id1796872\" class=\"note scientific\"><div class=\"title\"><span class=\"cnx-gentext-tip-t\">Scientific Method Connection<\/span><\/div><div class=\"body\"><p title=\"Which Has More DNA: A Kiwi or a Strawberry?\"><span id=\"m44522-eip-id1169982614662\"> <\/span><\/p><div class=\"title\"><b>Which Has More DNA: A Kiwi or a Strawberry?<\/b><\/div><div id=\"m44522-fig-ch15_01_03\" class=\"figure\" title=\"Figure&#xA0;15.6.&#xA0;\"><div class=\"body\"><div class=\"mediaobject\"><span id=\"m44522-fs-id3051050\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155756\/Figure_15_01_03.jpg\" width=\"450\" alt=\"Photographs show a thin slice of a green kiwi fruit and a bowl of strawberries.\"\/><\/div><\/div><div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">15.6<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"\/><\/div><div class=\"caption\">Do you think that a kiwi or a strawberry has more DNA per fruit? (credit \u201ckiwi\u201d: \"Kelbv\"\/Flickr; credit: \u201cstrawberry\u201d: Alisdair McDiarmid)<\/div><\/div><p><span id=\"m44522-eip-id2896007\"> <\/span><span class=\"bold\"><strong>Question<\/strong><\/span>: Would a kiwifruit and strawberry that are approximately the same size (<a class=\"xref target-figure\" href=\"ch15.html#m44522-fig-ch15_01_03\" title=\"Figure&#xA0;15.6.&#xA0;\">Figure\u00a015.6<\/a>) also have approximately the same amount of DNA?<\/p><p><span id=\"m44522-eip-id1416267\"> <\/span><span class=\"bold\"><strong>Background<\/strong><\/span>: Genes are carried on chromosomes and are made of DNA. All mammals are diploid, meaning they have two copies of each chromosome. However, not all plants are diploid. The common strawberry is octoploid (8<span class=\"emphasis\"><em>n<\/em><\/span>) and the cultivated kiwi is hexaploid (6<span class=\"emphasis\"><em>n<\/em><\/span>). Research the total number of chromosomes in the cells of each of these fruits and think about how this might correspond to the amount of DNA in these fruits\u2019 cell nuclei. Read about the technique of DNA isolation to understand how each step in the isolation protocol helps liberate and precipitate DNA.<\/p><p><span id=\"m44522-eip-id1407858\"> <\/span><span class=\"bold\"><strong>Hypothesis<\/strong><\/span>: Hypothesize whether you would be able to detect a difference in DNA quantity from similarly sized strawberries and kiwis. Which fruit do you think would yield more DNA?<\/p><p><span id=\"m44522-eip-id2117311\"> <\/span><span class=\"bold\"><strong>Test your hypothesis<\/strong><\/span>: Isolate the DNA from a strawberry and a kiwi that are similarly sized. Perform the experiment in at least triplicate for each fruit.<\/p><div class=\"orderedlist\"><span id=\"m44522-eip-716\"> <\/span><ol class=\"orderedlist\" type=\"1\"><li class=\"listitem\"><p>Prepare a bottle of DNA extraction buffer from 900 mL water, 50 mL dish detergent, and two teaspoons of table salt. Mix by inversion (cap it and turn it upside down a few times).<\/p><\/li><li class=\"listitem\"><p>Grind a strawberry and a kiwifruit by hand in a plastic bag, or using a mortar and pestle, or with a metal bowl and the end of a blunt instrument. Grind for at least two minutes per fruit.<\/p><\/li><li class=\"listitem\"><p>Add 10 mL of the DNA extraction buffer to each fruit, and mix well for at least one minute.<\/p><\/li><li class=\"listitem\"><p>Remove cellular debris by filtering each fruit mixture through cheesecloth or porous cloth and into a funnel placed in a test tube or an appropriate container.<\/p><\/li><li class=\"listitem\"><p>Pour ice-cold ethanol or isopropanol (rubbing alcohol) into the test tube. You should observe white, precipitated DNA.<\/p><\/li><li class=\"listitem\"><p>Gather the DNA from each fruit by winding it around separate glass rods.<\/p><\/li><\/ol><\/div><p><span id=\"m44522-eip-id2024898\"> <\/span>\n<span class=\"bold\"><strong>Record your observations<\/strong><\/span>: Because you are not quantitatively measuring DNA volume, you can record for each trial whether the two fruits produced the same or different amounts of DNA as observed by eye. If one or the other fruit produced noticeably more DNA, record this as well. Determine whether your observations are consistent with several pieces of each fruit.<\/p><p><span id=\"m44522-eip-id1463552\"> <\/span><span class=\"bold\"><strong>Analyze your data<\/strong><\/span>: Did you notice an obvious difference in the amount of DNA produced by each fruit? Were your results reproducible?<\/p><p><span id=\"m44522-eip-id1458204\"> <\/span><span class=\"bold\"><strong>Draw a conclusion<\/strong><\/span>: Given what you know about the number of chromosomes in each fruit, can you conclude that chromosome number necessarily correlates to DNA amount? Can you identify any drawbacks to this procedure? If you had access to a laboratory, how could you standardize your comparison and make it more quantitative?<\/p><\/div><\/div><\/div><\/div><div xml:lang=\"en\" class=\"section module\" title=\"15.2.&#xA0;Prokaryotic Transcription\"><div class=\"titlepage\"><div><div><h2 id=\"m44523\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.2<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Prokaryotic Transcription<sup><a href=\"co03.html#book-attribution-m44523\">*<\/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>List the different steps in prokaryotic transcription<\/p><\/li><li class=\"listitem\"><p>Discuss the role of promoters in prokaryotic transcription<\/p><\/li><li class=\"listitem\"><p>Describe how and when transcription is terminated<\/p><\/li><\/ul><\/div><\/div><\/div><\/div><div class=\"toc\"><ul><li class=\"toc-section\"><a href=\"#m44523-fs-id2899946\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">Initiation of Transcription in Prokaryotes<\/span><\/a><ul><li class=\"toc-section\"><a href=\"#m44523-fs-id2016560\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">Prokaryotic RNA Polymerase<\/span><\/a><\/li><li class=\"toc-section\"><a href=\"#m44523-fs-id653506\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">Prokaryotic Promoters<\/span><\/a><\/li><\/ul><\/li><li class=\"toc-section\"><a href=\"#m44523-fs-id1298841\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">Elongation and Termination in Prokaryotes<\/span><\/a><\/li><li class=\"toc-section\"><a href=\"#m44523-fs-id1318146\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">Prokaryotic Termination Signals<\/span><\/a><\/li><\/ul><\/div><p><span id=\"m44523-fs-id1468209\"> <\/span>The prokaryotes, which include bacteria and archaea, are mostly single-celled organisms that, by definition, lack membrane-bound nuclei and other organelles. A bacterial chromosome is a covalently\nclosed circle that, unlike eukaryotic chromosomes, is not organized around histone proteins. The central region of the cell in which prokaryotic DNA resides is called the nucleoid. In addition, prokaryotes often have abundant <em class=\"glossterm\"><span id=\"m44523-autoid-cnx2dbk-id1409887\"> <\/span>plasmids<\/em><a id=\"id510286\" class=\"indexterm\">, which are shorter circular DNA molecules that may only contain one or a few genes. Plasmids can be transferred independently of the bacterial chromosome during cell division and often carry traits such as antibiotic resistance.<\/a><\/p><p><span id=\"m44523-fs-id671101\"> <\/span>Transcription in prokaryotes (and in eukaryotes) requires the DNA double helix to partially unwind in the region of mRNA synthesis. The region of unwinding is called a <em class=\"glossterm\"><span id=\"m44523-autoid-cnx2dbk-id1409898\"> <\/span>transcription bubble.<\/em><a id=\"id510309\" class=\"indexterm\"> Transcription always proceeds from the same DNA strand for each gene, which is called the <em class=\"glossterm\"><span id=\"m44523-autoid-cnx2dbk-id1409903\"> <\/span>template strand<\/em><\/a><a id=\"id510323\" class=\"indexterm\">. The mRNA product is complementary to the template strand and is almost identical to the other DNA strand, called the <em class=\"glossterm\"><span id=\"m44523-autoid-cnx2dbk-id1409907\"> <\/span>nontemplate strand<\/em><\/a><a id=\"id510338\" class=\"indexterm\">. The only difference is that in mRNA, all of the T nucleotides are replaced with U nucleotides. In an RNA double helix, A can bind U via two hydrogen bonds, just as in A\u2013T pairing in a DNA double helix.<\/a><\/p><p><span id=\"m44523-fs-id1520179\"> <\/span>The nucleotide pair in the DNA double helix that corresponds to the site from which the first 5' mRNA nucleotide is transcribed is called the +1 site, or the <em class=\"glossterm\"><span id=\"m44523-autoid-cnx2dbk-id1463886\"> <\/span>initiation site<\/em><a id=\"id510363\" class=\"indexterm\">. Nucleotides preceding the initiation site are given negative numbers and are designated <em class=\"glossterm\"><span id=\"m44523-autoid-cnx2dbk-id1463891\"> <\/span>upstream<\/em><\/a><a id=\"id510377\" class=\"indexterm\">. Conversely, nucleotides following the initiation site are denoted with \u201c+\u201d numbering and are called <em class=\"glossterm\"><span id=\"m44523-autoid-cnx2dbk-id1463895\"> <\/span>downstream<\/em><\/a><a id=\"id510392\" class=\"indexterm\"> nucleotides.<\/a><\/p><div class=\"section\" title=\"Initiation of Transcription in Prokaryotes\"><div class=\"titlepage\"><div><div><h3 id=\"m44523-fs-id2899946\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">Initiation of Transcription in Prokaryotes<\/span><\/span><\/h3><\/div><\/div><\/div><p><span id=\"m44523-fs-id2321141\"> <\/span>Prokaryotes do not have membrane-enclosed nuclei. Therefore, the processes of transcription, translation, and mRNA degradation can all occur simultaneously. The intracellular level of a bacterial protein can quickly be amplified by multiple transcription and translation events occurring concurrently on the same DNA template. Prokaryotic transcription often covers more than one gene and produces polycistronic mRNAs that specify more than one protein.<\/p><p><span id=\"m44523-fs-id2117424\"> <\/span>Our discussion here will exemplify transcription by describing this process in <span class=\"emphasis\"><em>Escherichia coli<\/em><\/span>, a well-studied bacterial species. Although some differences exist between transcription in <span class=\"emphasis\"><em>E. coli<\/em><\/span> and transcription in archaea, an understanding of <span class=\"emphasis\"><em>E. coli <\/em><\/span>transcription can be applied to virtually all bacterial species.<\/p><div class=\"section\" title=\"Prokaryotic RNA Polymerase\"><div class=\"titlepage\"><div><div><h4 id=\"m44523-fs-id2016560\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">Prokaryotic RNA Polymerase<\/span><\/span><\/h4><\/div><\/div><\/div><p><span id=\"m44523-fs-id1694517\"> <\/span>Prokaryotes use the same RNA polymerase to transcribe all of their genes. In <span class=\"emphasis\"><em>E. coli<\/em><\/span>, the polymerase is composed of five polypeptide subunits, two of which are identical. Four of these subunits, denoted <span class=\"emphasis\"><em>\u03b1<\/em><\/span>, <span class=\"emphasis\"><em>\u03b1<\/em><\/span>, <span class=\"emphasis\"><em>\u03b2<\/em><\/span>, and <span class=\"emphasis\"><em>\u03b2<\/em><\/span>' comprise the polymerase <em class=\"glossterm\"><span id=\"m44523-autoid-cnx2dbk-id1631940\"> <\/span>core enzyme<\/em><a id=\"id510499\" class=\"indexterm\">. These subunits assemble every time a gene is transcribed, and they disassemble once transcription is complete. Each subunit has a unique role; the two <span class=\"emphasis\"><em>\u03b1<\/em><\/span>-subunits are necessary to assemble the polymerase on the DNA; the <span class=\"emphasis\"><em>\u03b2<\/em><\/span>-subunit binds to the ribonucleoside triphosphate that will become part of the nascent \u201crecently born\u201d mRNA molecule; and the <span class=\"emphasis\"><em>\u03b2<\/em><\/span>' binds the DNA template strand. The fifth subunit, <span class=\"emphasis\"><em>\u03c3<\/em><\/span>, is involved only in transcription initiation. It confers transcriptional specificity such that the polymerase begins to synthesize mRNA from an appropriate initiation site. Without <span class=\"emphasis\"><em>\u03c3<\/em><\/span>, the core enzyme would transcribe from random sites and would produce mRNA molecules that specified protein gibberish. The polymerase comprised of all five subunits is called the <em class=\"glossterm\"><span id=\"m44523-autoid-cnx2dbk-id1631978\"> <\/span>holoenzyme<\/em><\/a><a id=\"id510548\" class=\"indexterm\">.<\/a><\/p><\/div><div class=\"section\" title=\"Prokaryotic Promoters\"><div class=\"titlepage\"><div><div><h4 id=\"m44523-fs-id653506\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">Prokaryotic Promoters<\/span><\/span><\/h4><\/div><\/div><\/div><p><span id=\"m44523-fs-id1236812\"> <\/span>A <em class=\"glossterm\"><span id=\"m44523-autoid-cnx2dbk-id1617903\"> <\/span>promoter<\/em><a id=\"id510578\" class=\"indexterm\"> is a DNA sequence onto which the transcription machinery binds and initiates transcription. In most cases, promoters exist upstream of the genes they regulate. The specific sequence of a promoter is very important because it determines whether the corresponding gene is transcribed all the time, some of the time, or infrequently. Although promoters vary among prokaryotic genomes, a few elements are conserved. At the -10 and -35 regions upstream of the initiation site, there are two promoter <em class=\"glossterm\"><span id=\"m44523-autoid-cnx2dbk-id1617912\"> <\/span>consensus<\/em><\/a><a id=\"id510596\" class=\"indexterm\"> sequences, or regions that are similar across all promoters and across various bacterial species (<\/a><a class=\"xref target-figure\" href=\"ch15.html#m44523-fig-ch15_02_01\" title=\"Figure&#xA0;15.7.&#xA0;\">Figure\u00a015.7<\/a>). The -10 consensus sequence, called the -10 region, is TATAAT. The -35 sequence, TTGACA, is recognized and bound by <span class=\"emphasis\"><em>\u03c3<\/em><\/span>. Once this interaction is made, the subunits of the core enzyme bind to the site. The A\u2013T-rich -10 region facilitates unwinding of the DNA template, and several phosphodiester bonds are made. The transcription initiation phase ends with the production of abortive transcripts, which are polymers of approximately 10 nucleotides that are made and released.<\/p><div id=\"m44523-fig-ch15_02_01\" class=\"figure\" title=\"Figure&#xA0;15.7.&#xA0;\"><div class=\"body\"><div class=\"mediaobject\"><span id=\"m44523-fs-id1482493\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155758\/Figure_15_02_01.jpg\" width=\"350\" alt=\"Illustration shows the &#x3C3; subunit of RNA polymerase bound to two consensus sequences that are 10 and 35 bases upstream of the transcription start site. RNA polymerase is bound to &#x3C3;.\"\/><\/div><\/div><div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">15.7<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"\/><\/div><div class=\"caption\">The <span class=\"emphasis\"><em>\u03c3<\/em><\/span> subunit of prokaryotic RNA polymerase recognizes consensus sequences found in the promoter region upstream of the transcription start sight. The <span class=\"emphasis\"><em>\u03c3<\/em><\/span> subunit dissociates from the polymerase after transcription has been initiated.<\/div><\/div><div id=\"m44523-fs-id889157\" 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=\"m44523-fs-id2217094\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155800\/transcription.png\" width=\"120\" alt=\"QR Code representing a URL\"\/><\/div><p><span id=\"m44523-fs-id1292460\"> <\/span>View this <a class=\"link\" href=\"http:\/\/openstaxcollege.org\/l\/transcription\" target=\"\">MolecularMovies animation<\/a> to see the first part of transcription and the base sequence repetition of the TATA box.<\/p><\/div><\/div><\/div><\/div><div class=\"section\" title=\"Elongation and Termination in Prokaryotes\"><div class=\"titlepage\"><div><div><h3 id=\"m44523-fs-id1298841\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">Elongation and Termination in Prokaryotes<\/span><\/span><\/h3><\/div><\/div><\/div><p><span id=\"m44523-fs-id3319239\"> <\/span>The transcription elongation phase begins with the release of the <span class=\"emphasis\"><em>\u03c3<\/em><\/span> subunit from the polymerase. The dissociation of <span class=\"emphasis\"><em>\u03c3<\/em><\/span> allows the core enzyme to proceed along the DNA template, synthesizing mRNA in the 5' to 3' direction at a rate of approximately 40 nucleotides per second. As elongation proceeds, the DNA is continuously unwound ahead of the core enzyme and rewound behind it (<a class=\"xref target-figure\" href=\"ch15.html#m44523-fig-ch15_02_02\" title=\"Figure&#xA0;15.8.&#xA0;\">Figure\u00a015.8<\/a>). The base pairing between DNA and RNA is not stable enough to maintain the stability of the mRNA synthesis components. Instead, the RNA polymerase acts as a stable linker between the DNA template and the nascent RNA strands to ensure that elongation is not interrupted prematurely.<\/p><div id=\"m44523-fig-ch15_02_02\" class=\"figure\" title=\"Figure&#xA0;15.8.&#xA0;\"><div class=\"body\"><div class=\"mediaobject\"><span id=\"m44523-fs-id3014452\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155802\/Figure_15_02_02.jpg\" width=\"425\" alt=\"Illustration shows RNA synthesis by RNA polymerase. The RNA strand is synthesized in the 5' to 3' direction.\"\/><\/div><\/div><div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">15.8<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"\/><\/div><div class=\"caption\">During elongation, the prokaryotic RNA polymerase tracks along the DNA template, synthesizes mRNA in the 5' to 3' direction, and unwinds and rewinds the DNA as it is read.<\/div><\/div><\/div><div class=\"section\" title=\"Prokaryotic Termination Signals\"><div class=\"titlepage\"><div><div><h3 id=\"m44523-fs-id1318146\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">Prokaryotic Termination Signals<\/span><\/span><\/h3><\/div><\/div><\/div><p><span id=\"m44523-fs-id1403735\"> <\/span>Once a gene is transcribed, the prokaryotic polymerase needs to be instructed to dissociate from the DNA template and liberate the newly made mRNA. Depending on the gene being transcribed, there are two kinds of termination signals. One is protein-based and the other is RNA-based. <em class=\"glossterm\"><span id=\"m44523-autoid-cnx2dbk-id1615324\"> <\/span>Rho-dependent termination<\/em><a id=\"id510831\" class=\"indexterm\"> is controlled by the rho protein, which tracks along behind the polymerase on the growing mRNA chain. Near the end of the gene, the polymerase encounters a run of G nucleotides on the DNA template and it stalls. As a result, the rho protein collides with the polymerase. The interaction with rho releases the mRNA from the transcription bubble.<\/a><\/p><p><span id=\"m44523-fs-id2629848\"> <\/span><em class=\"glossterm\"><span id=\"m44523-autoid-cnx2dbk-id1615335\"> <\/span>Rho-independent termination<\/em><a id=\"id510854\" class=\"indexterm\"> is controlled by specific sequences in the DNA template strand. As the polymerase nears the end of the gene being transcribed, it encounters a region rich in C\u2013G nucleotides. The mRNA folds back on itself, and the complementary C\u2013G nucleotides bind together. The result is a stable <em class=\"glossterm\"><span id=\"m44523-autoid-cnx2dbk-id1615341\"> <\/span>hairpin<\/em><\/a><a id=\"id510871\" class=\"indexterm\"> that causes the polymerase to stall as soon as it begins to transcribe a region rich in A\u2013T nucleotides. The complementary U\u2013A region of the mRNA transcript forms only a weak interaction with the template DNA. This, coupled with the stalled polymerase, induces enough instability for the core enzyme to break away and liberate the new mRNA transcript.<\/a><\/p><p><span id=\"m44523-fs-id2114520\"> <\/span>Upon termination, the process of transcription is complete. By the time termination occurs, the prokaryotic transcript would already have been used to begin synthesis of numerous copies of the encoded protein because these processes can occur concurrently. The unification of transcription, translation, and even mRNA degradation is possible because all of these processes occur in the same 5' to 3' direction, and because there is no membranous compartmentalization in the prokaryotic cell (<a class=\"xref target-figure\" href=\"ch15.html#m44523-fig-ch15_02_03\" title=\"Figure&#xA0;15.9.&#xA0;\">Figure\u00a015.9<\/a>). In contrast, the presence of a nucleus in eukaryotic cells precludes simultaneous transcription and translation.<\/p><div id=\"m44523-fig-ch15_02_03\" class=\"figure\" title=\"Figure&#xA0;15.9.&#xA0;\"><div class=\"body\"><div class=\"mediaobject\"><span id=\"m44523-fs-id1260172\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155804\/Figure_15_02_03.jpg\" width=\"350\" alt=\"Illustration shows multiple mRNAs transcribed off one gene. Ribosomes attach to the mRNA before transcription is complete and begin to make protein.\"\/><\/div><\/div><div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">15.9<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"\/><\/div><div class=\"caption\">Multiple polymerases can transcribe a single bacterial gene while numerous ribosomes concurrently translate the mRNA transcripts into polypeptides. In this way, a specific protein can rapidly reach a high concentration in the bacterial cell.<\/div><\/div><div id=\"m44523-fs-id2626015\" 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=\"m44523-fs-id2608514\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155807\/transcription2.png\" width=\"120\" alt=\"QR Code representing a URL\"\/><\/div><p><span id=\"m44523-fs-id2701078\"> <\/span>Visit this <a class=\"link\" href=\"http:\/\/openstaxcollege.org\/l\/transcription2\" target=\"\"> BioStudio animation<\/a> to see the process of prokaryotic transcription.<\/p><\/div><\/div><\/div><\/div><div xml:lang=\"en\" class=\"section module\" title=\"15.3.&#xA0;Eukaryotic Transcription\"><div class=\"titlepage\"><div><div><h2 id=\"m44524\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.3<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Eukaryotic Transcription<sup><a href=\"co03.html#book-attribution-m44524\">*<\/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>List the steps in eukaryotic transcription<\/p><\/li><li class=\"listitem\"><p>Discuss the role of RNA polymerases in transcription<\/p><\/li><li class=\"listitem\"><p>Compare and contrast the three RNA polymerases<\/p><\/li><li class=\"listitem\"><p>Explain the significance of transcription factors<\/p><\/li><\/ul><\/div><\/div><\/div><\/div><div class=\"toc\"><ul><li class=\"toc-section\"><a href=\"#m44524-fs-id1760576\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">Initiation of Transcription in Eukaryotes<\/span><\/a><ul><li class=\"toc-section\"><a href=\"#m44524-fs-id3688592\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">The Three Eukaryotic RNA Polymerases<\/span><\/a><\/li><li class=\"toc-section\"><a href=\"#m44524-fs-id1951192\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">Structure of an RNA Polymerase II Promoter<\/span><\/a><\/li><li class=\"toc-section\"><a href=\"#m44524-fs-id1894765\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">Transcription Factors for RNA Polymerase II<\/span><\/a><\/li><li class=\"toc-section\"><a href=\"#m44524-fs-id1836540\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">Promoter Structures for RNA Polymerases I and III<\/span><\/a><\/li><\/ul><\/li><li class=\"toc-section\"><a href=\"#m44524-fs-id2896654\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">Eukaryotic Elongation and Termination<\/span><\/a><\/li><\/ul><\/div><p><span id=\"m44524-fs-id2026267\"> <\/span>Prokaryotes and eukaryotes perform fundamentally the same process of transcription, with a few key differences. The most important difference between prokaryotes and eukaryotes is the latter\u2019s membrane-bound nucleus and organelles. With the genes bound in a nucleus, the eukaryotic cell must be able to transport its mRNA to the cytoplasm and must protect its mRNA from degrading before it is translated. Eukaryotes also employ three different polymerases that each transcribe a different subset of genes. Eukaryotic mRNAs are usually monogenic, meaning that they specify a single protein.<\/p><div class=\"section\" title=\"Initiation of Transcription in Eukaryotes\"><div class=\"titlepage\"><div><div><h3 id=\"m44524-fs-id1760576\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">Initiation of Transcription in Eukaryotes<\/span><\/span><\/h3><\/div><\/div><\/div><p><span id=\"m44524-fs-id2862612\"> <\/span>Unlike the prokaryotic polymerase that can bind to a DNA template on its own, eukaryotes require several other proteins, called transcription factors, to first bind to the promoter region and then help recruit the appropriate polymerase.<\/p><div class=\"section\" title=\"The Three Eukaryotic RNA Polymerases\"><div class=\"titlepage\"><div><div><h4 id=\"m44524-fs-id3688592\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">The Three Eukaryotic RNA Polymerases<\/span><\/span><\/h4><\/div><\/div><\/div><p><span id=\"m44524-fs-id3043156\"> <\/span>The features of eukaryotic mRNA synthesis are markedly more complex those of prokaryotes. Instead of a single polymerase comprising five subunits, the eukaryotes have three polymerases that are each made up of 10 subunits or more. Each eukaryotic polymerase also requires a distinct set of transcription factors to bring it to the DNA template.<\/p><p><span id=\"m44524-fs-id2074568\"> <\/span>RNA polymerase I is located in the nucleolus, a specialized nuclear substructure in which ribosomal RNA (rRNA) is transcribed, processed, and assembled into ribosomes (<a class=\"xref target-table\" href=\"ch15.html#m44524-tab-ch15_03_01\" title=\"Table&#xA0;15.1.&#xA0;\">Table\u00a015.1<\/a>). The rRNA molecules are considered structural RNAs because they have a cellular role but are not translated into protein. The rRNAs are components of the ribosome and are essential to the process of translation. RNA polymerase I synthesizes all of the rRNAs except for the 5S rRNA molecule. The \u201cS\u201d designation applies to \u201cSvedberg\u201d units, a nonadditive value that characterizes the speed at which a particle sediments during centrifugation.<\/p><div class=\"table\" id=\"m44524-tab-ch15_03_01\"><table cellpadding=\"0\" summary=\"table x.x\" 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\">15.1. <\/span><\/caption><thead valign=\"bottom\"><tr><th colspan=\"4\" style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">Locations, Products, and Sensitivities of the Three Eukaryotic RNA Polymerases<\/th><\/tr><tr><th style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: center !important;\">RNA Polymerase<\/th><th style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: center !important;\">Cellular Compartment<\/th><th style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: center !important;\">Product of Transcription<\/th><th style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: center !important;\">\u03b1-Amanitin Sensitivity<\/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: center !important;\">I<\/td><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">Nucleolus<\/td><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">All rRNAs except 5S rRNA<\/td><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">Insensitive<\/td><\/tr><tr><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: center !important;\">II<\/td><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">Nucleus<\/td><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">All protein-coding nuclear pre-mRNAs<\/td><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">Extremely sensitive<\/td><\/tr><tr><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 0 !important; text-align: center !important;\">III<\/td><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 0 !important; text-align: left !important;\">Nucleus<\/td><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 0 !important; text-align: left !important;\">5S rRNA, tRNAs, and small nuclear RNAs<\/td><td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 0 !important; text-align: left !important;\">Moderately sensitive<\/td><\/tr><\/tbody><\/table><\/div><p><span id=\"m44524-fs-id2694589\"> <\/span>RNA polymerase II is located in the nucleus and synthesizes all protein-coding nuclear pre-mRNAs. Eukaryotic pre-mRNAs undergo extensive processing after transcription but before translation. For clarity, this module\u2019s discussion of transcription and translation in eukaryotes will use the term \u201cmRNAs\u201d to describe only the mature, processed molecules that are ready to be translated. RNA polymerase II is responsible for transcribing the overwhelming majority of eukaryotic genes.<\/p><p><span id=\"m44524-fs-id2014161\"> <\/span>RNA polymerase III is also located in the nucleus. This polymerase transcribes a variety of structural RNAs that includes the 5S pre-rRNA, transfer pre-RNAs (pre-tRNAs), and <em class=\"glossterm\"><span id=\"m44524-autoid-cnx2dbk-id1599710\"> <\/span>small nuclear <\/em><a id=\"id511693\" class=\"indexterm\">pre-<em class=\"glossterm\"><span id=\"m44524-autoid-cnx2dbk-id1237683\"> <\/span>RNAs<\/em><\/a><a id=\"id511706\" class=\"indexterm\">. The tRNAs have a critical role in translation; they serve as the adaptor molecules between the mRNA template and the growing polypeptide chain. Small nuclear RNAs have a variety of functions, including \u201csplicing\u201d pre-mRNAs and regulating transcription factors.<\/a><\/p><p><span id=\"m44524-fs-id2583722\"> <\/span>A scientist characterizing a new gene can determine which polymerase transcribes it by testing whether the gene is expressed in the presence of a particular mushroom poison, \u03b1-amanitin (<a class=\"xref target-table\" href=\"ch15.html#m44524-tab-ch15_03_01\" title=\"Table&#xA0;15.1.&#xA0;\">Table\u00a015.1<\/a>). Interestingly, \u03b1-amanitin produced by <span class=\"emphasis\"><em>Amanita phalloides<\/em><\/span>, the Death Cap mushroom, affects the three polymerases very differently. RNA polymerase I is completely insensitive to \u03b1-amanitin, meaning that the polymerase can transcribe DNA in vitro in the presence of this poison. In contrast, RNA polymerase II is extremely sensitive to \u03b1-amanitin, and RNA polymerase III is moderately sensitive. Knowing the transcribing polymerase can clue a researcher into the general function of the gene being studied. Because RNA polymerase II transcribes the vast majority of genes, we will focus on this polymerase in our subsequent discussions about eukaryotic transcription factors and promoters.<\/p><\/div><div class=\"section\" title=\"Structure of an RNA Polymerase II Promoter\"><div class=\"titlepage\"><div><div><h4 id=\"m44524-fs-id1951192\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">Structure of an RNA Polymerase II Promoter<\/span><\/span><\/h4><\/div><\/div><\/div><p><span id=\"m44524-fs-id2196807\"> <\/span>Eukaryotic promoters are much larger and more complex than prokaryotic promoters, but both have a TATA box. For example, in the mouse thymidine kinase gene, the TATA box is located at approximately -30 relative to the initiation (+1) site (<a class=\"xref target-figure\" href=\"ch15.html#m44524-fig-ch15_03_01\" title=\"Figure&#xA0;15.10.&#xA0;\">Figure\u00a015.10<\/a>). For this gene, the exact TATA box sequence is TATAAAA, as read in the 5' to 3' direction on the nontemplate strand. This sequence is not identical to the <span class=\"emphasis\"><em>E. coli<\/em><\/span> TATA box, but it conserves the A\u2013T rich element. The thermostability of A\u2013T bonds is low and this helps the DNA template to locally unwind in preparation for transcription.<\/p><div id=\"m44524-fig-ch15_03_01\" class=\"figure\" title=\"Figure&#xA0;15.10.&#xA0;\"><div class=\"body\"><div class=\"mediaobject\"><span id=\"m44524-fs-id2574107\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155808\/Figure_15_03_01.jpg\" width=\"280\" alt=\"Illustration shows a series of transcription factors binding to the promoter, which is upstream of the gene. After all of the transcription factors are bound, RNA polymerase binds as well.\"\/><\/div><\/div><div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">15.10<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"\/><\/div><div class=\"caption\">A generalized promoter of a gene transcribed by RNA polymerase II is shown. Transcription factors recognize the promoter. RNA polymerase II then binds and forms the transcription initiation complex.<\/div><\/div><div id=\"m44524-fs-id1461234\" class=\"note art-connection\"><div class=\"title\"><span class=\"cnx-gentext-tip-t\">Art Connection<\/span><\/div><div class=\"body\"><p><span id=\"m44524-fs-idm74169728\"> <\/span><\/p><div id=\"m44524-fig-ch15_03_02\" class=\"figure\" title=\"Figure&#xA0;15.11.&#xA0;\"><div class=\"body\"><span class=\"inlinemediaobject\"><span id=\"m44524-fs-id2278509\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155810\/Figure_15_03_02.png\" width=\"320\" alt=\"An illustration shows that before RNA processing, there is a primary RNA transcript including five boxes labeled, left to right, as exon 1, intron, exon 2, intron, and exon 3. After RNA processing, there is a spliced RNA with these parts, left to right: a 5' cap, a 5' untranslated region, exon 1, exon 2, exon 3, a 3' untranslated region, and a poly-a tail.\"\/><\/span><\/div><div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">15.11<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"\/><\/div><div class=\"caption\">Eukaryotic mRNA contains introns that must be spliced out. A 5' cap and 3' poly-A tail are also added.<\/div><\/div><p><span id=\"m44524-fs-id2000672\"> <\/span>A scientist splices a eukaryotic promoter in front of a bacterial gene and inserts the gene in a bacterial chromosome. Would you expect the bacteria to transcribe the gene?<\/p><\/div><\/div><p><span id=\"m44524-fs-id1807694\"> <\/span>The mouse genome includes one gene and two pseudogenes for cytoplasmic thymidine kinase. Pseudogenes are genes that have lost their protein-coding ability or are no longer expressed by the cell. These pseudogenes are copied from mRNA and incorporated into the chromosome. For example, the mouse thymidine kinase promoter also has a conserved <em class=\"glossterm\"><span id=\"m44524-autoid-cnx2dbk-id1589613\"> <\/span>CAAT box<\/em><a id=\"id511900\" class=\"indexterm\"> (GGCCAATCT) at approximately -80. This sequence is essential and is involved in binding transcription factors. Further upstream of the TATA box, eukaryotic promoters may also contain one or more <em class=\"glossterm\"><span id=\"m44524-autoid-cnx2dbk-id1589619\"> <\/span>GC-rich boxes<\/em><\/a><a id=\"id511916\" class=\"indexterm\"> (GGCG) or <em class=\"glossterm\"><span id=\"m44524-autoid-cnx2dbk-id1601449\"> <\/span>octamer boxes<\/em><\/a><a id=\"id511929\" class=\"indexterm\"> (ATTTGCAT). These elements bind cellular factors that increase the efficiency of transcription initiation and are often identified in more \u201cactive\u201d genes that are constantly being expressed by the cell.<\/a><\/p><\/div><div class=\"section\" title=\"Transcription Factors for RNA Polymerase II\"><div class=\"titlepage\"><div><div><h4 id=\"m44524-fs-id1894765\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">Transcription Factors for RNA Polymerase II<\/span><\/span><\/h4><\/div><\/div><\/div><p><span id=\"m44524-fs-id1977416\"> <\/span>The complexity of eukaryotic transcription does not end with the polymerases and promoters. An army of basal transcription factors, enhancers, and silencers also help to regulate the frequency with which pre-mRNA is synthesized from a gene. Enhancers and silencers affect the efficiency of transcription but are not necessary for transcription to proceed. Basal transcription factors are crucial in the formation of a <em class=\"glossterm\"><span id=\"m44524-autoid-cnx2dbk-id1601475\"> <\/span>preinitiation complex<\/em><a id=\"id511966\" class=\"indexterm\"> on the DNA template that subsequently recruits RNA polymerase II for transcription initiation.<\/a><\/p><p><span id=\"m44524-fs-id2334805\"> <\/span>The names of the basal transcription factors begin with \u201cTFII\u201d (this is the transcription factor for RNA polymerase II) and are specified with the letters A\u2013J. The transcription factors systematically fall into place on the DNA template, with each one further stabilizing the preinitiation complex and contributing to the recruitment of RNA polymerase II.<\/p><p><span id=\"m44524-fs-id1720501\"> <\/span>The processes of bringing RNA polymerases I and III to the DNA template involve slightly less complex collections of transcription factors, but the general theme is the same. Eukaryotic transcription is a tightly regulated process that requires a variety of proteins to interact with each other and with the DNA strand. Although the process of transcription in eukaryotes involves a greater metabolic investment than in prokaryotes, it ensures that the cell transcribes precisely the pre-mRNAs that it needs for protein synthesis.<\/p><div id=\"m44524-fs-id2016560\" class=\"note evolution\"><div class=\"title\"><span class=\"cnx-gentext-tip-t\">Evolution Connection<\/span><\/div><div class=\"body\"><p title=\"The Evolution of Promoters\"><span id=\"m44524-fs-id1479424\"> <\/span><\/p><div class=\"title\"><b>The Evolution of Promoters<\/b><\/div><p title=\"The Evolution of Promoters\">The evolution of genes may be a familiar concept. Mutations can occur in genes during DNA replication, and the result may or may not be beneficial to the cell. By altering an enzyme, structural protein, or some other factor, the process of mutation can transform functions or physical features. However, eukaryotic promoters and other gene regulatory sequences may evolve as well. For instance, consider a gene that, over many generations, becomes more valuable to the cell. Maybe the gene encodes a structural protein that the cell needs to synthesize in abundance for a certain function. If this is the case, it would be beneficial to the cell for that gene\u2019s promoter to recruit transcription factors more efficiently and increase gene expression.<\/p><p><span id=\"m44524-fs-id2694641\"> <\/span>Scientists examining the evolution of promoter sequences have reported varying results. In part, this is because it is difficult to infer exactly where a eukaryotic promoter begins and ends. Some promoters occur within genes; others are located very far upstream, or even downstream, of the genes they are regulating. However, when researchers limited their examination to human core promoter sequences that were defined experimentally as sequences that bind the preinitiation complex, they found that promoters evolve even faster than protein-coding genes.<\/p><p><span id=\"m44524-fs-id1448131\"> <\/span>It is still unclear how promoter evolution might correspond to the evolution of humans or other higher organisms. However, the evolution of a promoter to effectively make more or less of a given gene product is an intriguing alternative to the evolution of the genes themselves.<sup><sup>[<a id=\"m44524-fs-idm20771056\" href=\"#ftn.m44524-fs-idm20771056\" class=\"footnote\">13<\/a>]<\/sup><\/sup><\/p><\/div><\/div><\/div><div class=\"section\" title=\"Promoter Structures for RNA Polymerases I and III\"><div class=\"titlepage\"><div><div><h4 id=\"m44524-fs-id1836540\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">Promoter Structures for RNA Polymerases I and III<\/span><\/span><\/h4><\/div><\/div><\/div><p><span id=\"m44524-fs-id2279649\"> <\/span>In eukaryotes, the conserved promoter elements differ for genes transcribed by RNA polymerases I, II, and III. RNA polymerase I transcribes genes that have two GC-rich promoter sequences in the -45 to +20 region. These sequences alone are sufficient for transcription initiation to occur, but promoters with additional sequences in the region from -180 to -105 upstream of the initiation site will further enhance initiation. Genes that are transcribed by RNA polymerase III have upstream promoters or promoters that occur within the genes themselves.<\/p><\/div><\/div><div class=\"section\" title=\"Eukaryotic Elongation and Termination\"><div class=\"titlepage\"><div><div><h3 id=\"m44524-fs-id2896654\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">Eukaryotic Elongation and Termination<\/span><\/span><\/h3><\/div><\/div><\/div><p><span id=\"m44524-fs-id1613052\"> <\/span>Following the formation of the preinitiation complex, the polymerase is released from the other transcription factors, and elongation is allowed to proceed as it does in prokaryotes with the polymerase synthesizing pre-mRNA in the 5' to 3' direction. As discussed previously, RNA polymerase II transcribes the major share of eukaryotic genes, so this section will focus on how this polymerase accomplishes elongation and termination.<\/p><p><span id=\"m44524-fs-id3053365\"> <\/span>Although the enzymatic process of elongation is essentially the same in eukaryotes and prokaryotes, the DNA template is more complex. When eukaryotic cells are not dividing, their genes exist as a diffuse mass of DNA and proteins called chromatin. The DNA is tightly packaged around charged histone proteins at repeated intervals. These DNA\u2013histone complexes, collectively called nucleosomes, are regularly spaced and include 146 nucleotides of DNA wound around eight histones like thread around a spool.<\/p><p><span id=\"m44524-fs-id1910636\"> <\/span>For polynucleotide synthesis to occur, the transcription machinery needs to move histones out of the way every time it encounters a nucleosome. This is accomplished by a special protein complex called <em class=\"glossterm\"><span id=\"m44524-autoid-cnx2dbk-id1280665\"> <\/span>FACT<\/em><a id=\"id512137\" class=\"indexterm\">, which stands for \u201cfacilitates chromatin transcription.\u201d This complex pulls histones away from the DNA template as the polymerase moves along it. Once the pre-mRNA is synthesized, the FACT complex replaces the histones to recreate the nucleosomes.<\/a><\/p><p><span id=\"m44524-fs-id1360285\"> <\/span>The termination of transcription is different for the different polymerases. Unlike in prokaryotes, elongation by RNA polymerase II in eukaryotes takes place 1,000\u20132,000 nucleotides beyond the end of the gene being transcribed. This pre-mRNA tail is subsequently removed by cleavage during mRNA processing. On the other hand, RNA polymerases I and III require termination signals. Genes transcribed by RNA polymerase I contain a specific 18-nucleotide sequence that is recognized by a termination protein. The process of termination in RNA polymerase III involves an mRNA hairpin similar to rho-independent termination of transcription in prokaryotes.<\/p><\/div><\/div><div xml:lang=\"en\" class=\"section module\" title=\"15.4.&#xA0;RNA Processing in Eukaryotes\"><div class=\"titlepage\"><div><div><h2 id=\"m44532\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.4<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">RNA Processing in Eukaryotes<sup><a href=\"co03.html#book-attribution-m44532\">*<\/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 different steps in RNA processing<\/p><\/li><li class=\"listitem\"><p>Understand the significance of exons, introns, and splicing<\/p><\/li><li class=\"listitem\"><p>Explain how tRNAs and rRNAs are processed<\/p><\/li><\/ul><\/div><\/div><\/div><\/div><div class=\"toc\"><ul><li class=\"toc-section\"><a href=\"#m44532-fs-id1983488\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">mRNA Processing<\/span><\/a><ul><li class=\"toc-section\"><a href=\"#m44532-fs-id2349302\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">5' Capping<\/span><\/a><\/li><li class=\"toc-section\"><a href=\"#m44532-fs-id1422041\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">3' Poly-A Tail<\/span><\/a><\/li><li class=\"toc-section\"><a href=\"#m44532-fs-id2195071\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">Pre-mRNA Splicing<\/span><\/a><\/li><\/ul><\/li><li class=\"toc-section\"><a href=\"#m44532-fs-id1650543\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">Processing of tRNAs and rRNAs<\/span><\/a><\/li><\/ul><\/div><p><span id=\"m44532-fs-id2263546\"> <\/span>After transcription, eukaryotic pre-mRNAs must undergo several processing steps before they can be translated. Eukaryotic (and prokaryotic) tRNAs and rRNAs also undergo processing before they can function as components in the protein synthesis machinery.<\/p><div class=\"section\" title=\"mRNA Processing\"><div class=\"titlepage\"><div><div><h3 id=\"m44532-fs-id1983488\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">mRNA Processing<\/span><\/span><\/h3><\/div><\/div><\/div><p><span id=\"m44532-fs-id2186668\"> <\/span>The eukaryotic pre-mRNA undergoes extensive processing before it is ready to be translated. The additional steps involved in eukaryotic mRNA maturation create a molecule with a much longer half-life than a prokaryotic mRNA. Eukaryotic mRNAs last for several hours, whereas the typical <span class=\"emphasis\"><em>E. coli<\/em><\/span> mRNA lasts no more than five seconds.<\/p><p><span id=\"m44532-fs-id2262076\"> <\/span>Pre-mRNAs are first coated in RNA-stabilizing proteins; these protect the pre-mRNA from degradation while it is processed and exported out of the nucleus. The three most important steps of pre-mRNA processing are the addition of stabilizing and signaling factors at the 5' and 3' ends of the molecule, and the removal of intervening sequences that do not specify the appropriate amino acids. In rare cases, the mRNA transcript can be \u201cedited\u201d after it is transcribed.<\/p><div id=\"m44532-fs-id2863005\" class=\"note evolution\"><div class=\"title\"><span class=\"cnx-gentext-tip-t\">Evolution Connection<\/span><\/div><div class=\"body\"><p title=\"RNA Editing in Trypanosomes\"><span id=\"m44532-fs-id2655263\"> <\/span><\/p><div class=\"title\"><b>RNA Editing in Trypanosomes<\/b><\/div><p title=\"RNA Editing in Trypanosomes\">The trypanosomes are a group of protozoa that include the pathogen <span class=\"emphasis\"><em>Trypanosoma brucei<\/em><\/span>, which causes sleeping sickness in humans (<a class=\"xref target-figure\" href=\"ch15.html#m44532-fig-ch15_04_01\" title=\"Figure&#xA0;15.12.&#xA0;\">Figure\u00a015.12<\/a>). Trypanosomes, and virtually all other eukaryotes, have organelles called mitochondria that supply the cell with chemical energy. Mitochondria are organelles that express their own DNA and are believed to be the remnants of a symbiotic relationship between a eukaryote and an engulfed prokaryote.  The mitochondrial DNA of trypanosomes exhibit an interesting exception to The Central Dogma: their pre-mRNAs do not have the correct information to specify a functional protein. Usually, this is because the mRNA is missing several U nucleotides. The cell performs an additional RNA processing step called <em class=\"glossterm\"><span id=\"m44532-autoid-cnx2dbk-id1622607\"> <\/span>RNA editing<\/em><a id=\"id512661\" class=\"indexterm\"> to remedy this.<\/a><\/p><div id=\"m44532-fig-ch15_04_01\" class=\"figure\" title=\"Figure&#xA0;15.12.&#xA0;\"><div class=\"body\"><div class=\"mediaobject\"><span id=\"m44532-fs-id2595588\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155812\/Figure_15_04_01.jpg\" width=\"250\" alt=\"Micrograph shows T. brucei, which has a u-shaped cell body and a long tail.\"\/><\/div><\/div><div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">15.12<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"\/><\/div><div class=\"caption\"><span class=\"emphasis\"><em>Trypanosoma brucei<\/em><\/span> is the causative agent of sleeping sickness in humans. The mRNAs of this pathogen must be modified by the addition of nucleotides before protein synthesis can occur. (credit: modification of work by Torsten Ochsenreiter)<\/div><\/div><p><span id=\"m44532-fs-id1288287\"> <\/span>Other genes in the mitochondrial genome encode 40- to 80-nucleotide guide RNAs. One or more of these molecules interacts by complementary base pairing with some of the nucleotides in the pre-mRNA transcript. However, the guide RNA has more A nucleotides than the pre-mRNA has U nucleotides to bind with. In these regions, the guide RNA loops out. The 3' ends of guide RNAs have a long poly-U tail, and these U bases are inserted in regions of the pre-mRNA transcript at which the guide RNAs are looped. This process is entirely mediated by RNA molecules. That is, guide RNAs\u2014rather than proteins\u2014serve as the catalysts in RNA editing.<\/p><p><span id=\"m44532-fs-id2300063\"> <\/span>RNA editing is not just a phenomenon of trypanosomes. In the mitochondria of some plants, almost all pre-mRNAs are edited. RNA editing has also been identified in mammals such as rats, rabbits, and even humans. What could be the evolutionary reason for this additional step in pre-mRNA processing? One possibility is that the mitochondria, being remnants of ancient prokaryotes, have an equally ancient RNA-based method for regulating gene expression. In support of this hypothesis, edits made to pre-mRNAs differ depending on cellular conditions. Although speculative, the process of RNA editing may be a holdover from a primordial time when RNA molecules, instead of proteins, were responsible for catalyzing reactions.<\/p><\/div><\/div><div class=\"section\" title=\"5' Capping\"><div class=\"titlepage\"><div><div><h4 id=\"m44532-fs-id2349302\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">5' Capping<\/span><\/span><\/h4><\/div><\/div><\/div><p><span id=\"m44532-fs-id2196807\"> <\/span>While the pre-mRNA is still being synthesized, a <em class=\"glossterm\"><span id=\"m44532-autoid-cnx2dbk-id1377856\"> <\/span>7-methylguanosine cap<\/em><a id=\"id512757\" class=\"indexterm\"> is added to the 5' end of the growing transcript by a phosphate linkage. This moiety (functional group) protects the nascent mRNA from degradation. In addition, factors involved in protein synthesis recognize the cap to help initiate translation by ribosomes.<\/a><\/p><\/div><div class=\"section\" title=\"3' Poly-A Tail\"><div class=\"titlepage\"><div><div><h4 id=\"m44532-fs-id1422041\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">3' Poly-A Tail<\/span><\/span><\/h4><\/div><\/div><\/div><p><span id=\"m44532-fs-id2229067\"> <\/span>Once elongation is complete, the pre-mRNA is cleaved by an endonuclease between an AAUAAA consensus sequence and a GU-rich sequence, leaving the AAUAAA sequence on the pre-mRNA. An enzyme called poly-A polymerase then adds a string of approximately 200 A residues, called the <em class=\"glossterm\"><span id=\"m44532-autoid-cnx2dbk-id1644985\"> <\/span>poly-A tail<\/em><a id=\"id512792\" class=\"indexterm\">. This modification further protects the pre-mRNA from degradation and signals the export of the cellular factors that the transcript needs to the cytoplasm.<\/a><\/p><\/div><div class=\"section\" title=\"Pre-mRNA Splicing\"><div class=\"titlepage\"><div><div><h4 id=\"m44532-fs-id2195071\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">Pre-mRNA Splicing<\/span><\/span><\/h4><\/div><\/div><\/div><p><span id=\"m44532-fs-id2914078\"> <\/span>Eukaryotic genes are composed of <em class=\"glossterm\"><span id=\"m44532-autoid-cnx2dbk-id1645010\"> <\/span>exons<\/em><a id=\"id512824\" class=\"indexterm\">, which correspond to protein-coding sequences (<span class=\"emphasis\"><em>ex-<\/em><\/span>on signifies that they are <span class=\"emphasis\"><em>ex<\/em><\/span>pressed), and <span class=\"emphasis\"><em>int<\/em><\/span>ervening sequences called <em class=\"glossterm\"><span id=\"m44532-autoid-cnx2dbk-id1682669\"> <\/span>introns<\/em><\/a><a id=\"id512855\" class=\"indexterm\"> (<span class=\"emphasis\"><em>int-<\/em><\/span>ron denotes their <span class=\"emphasis\"><em>int<\/em><\/span>ervening role), which may be involved in gene regulation but are removed from the pre-mRNA during processing. Intron sequences in mRNA do not encode functional proteins.<\/a><\/p><p><span id=\"m44532-fs-id2098378\"> <\/span>The discovery of introns came as a surprise to researchers in the 1970s who expected that pre-mRNAs would specify protein sequences without further processing, as they had observed in prokaryotes. The genes of higher eukaryotes very often contain one or more introns. These regions may correspond to regulatory sequences; however, the biological significance of having many introns or having very long introns in a gene is unclear. It is possible that introns slow down gene expression because it takes longer to transcribe pre-mRNAs with lots of introns. Alternatively, introns may be nonfunctional sequence remnants left over from the fusion of ancient genes throughout evolution. This is supported by the fact that separate exons often encode separate protein subunits or domains. For the most part, the sequences of introns can be mutated without ultimately affecting the protein product.<\/p><p><span id=\"m44532-fs-id2117424\"> <\/span>All of a pre-mRNA\u2019s introns must be completely and precisely removed before protein synthesis. If the process errs by even a single nucleotide, the reading frame of the rejoined exons would shift, and the resulting protein would be dysfunctional. The process of removing introns and reconnecting exons is called <em class=\"glossterm\"><span id=\"m44532-autoid-cnx2dbk-id1682705\"> <\/span>splicing<\/em><a id=\"id512909\" class=\"indexterm\"> (<\/a><a class=\"xref target-figure\" href=\"ch15.html#m44532-fig-ch15_04_02\" title=\"Figure&#xA0;15.13.&#xA0;\">Figure\u00a015.13<\/a>). Introns are removed and degraded while the pre-mRNA is still in the nucleus. Splicing occurs by a sequence-specific mechanism that ensures introns will be removed and exons rejoined with the accuracy and precision of a single nucleotide. The splicing of pre-mRNAs is conducted by complexes of proteins and RNA molecules called spliceosomes.<\/p><div id=\"m44532-fs-id2937179\" class=\"note art-connection\"><div class=\"title\"><span class=\"cnx-gentext-tip-t\">Art Connection<\/span><\/div><div class=\"body\"><p><span id=\"m44532-fs-idp68937344\"> <\/span><\/p><div id=\"m44532-fig-ch15_04_02\" class=\"figure\" title=\"Figure&#xA0;15.13.&#xA0;\"><div class=\"body\"><span class=\"inlinemediaobject\"><span id=\"m44532-fs-id1480619\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155814\/Figure_15_04_02.png\" width=\"280\" alt=\"Illustration shows a spliceosome bound to mRNA. An intron is wrapped around snRNPs associated with the spliceosome. When the splice is complete, the exons on either side of the intron are fused together, and the intron forms a ring structure.\"\/><\/span><\/div><div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">15.13<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"\/><\/div><div class=\"caption\">Pre-mRNA splicing involves the precise removal of introns from the primary RNA transcript. The splicing process is catalyzed by protein complexes called spliceosomes that are composed of proteins and RNA molecules called snRNAs. Spliceosomes recognize sequences at the 5' and 3' end of the intron.<\/div><\/div><p><span id=\"m44532-fs-id1864575\"> <\/span>Errors in splicing are implicated in cancers and other human diseases. What kinds of mutations might lead to splicing errors? Think of different possible outcomes if splicing errors occur.<\/p><\/div><\/div><p><span id=\"m44532-fs-id2000672\"> <\/span>Note that more than 70 individual introns can be present, and each has to undergo the process of splicing\u2014in addition to 5' capping and the addition of a poly-A tail\u2014just to generate a single, translatable mRNA molecule.<\/p><div id=\"m44532-fs-id2010314\" 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=\"m44532-fs-id1436147\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155816\/RNA_splicing.png\" width=\"120\" alt=\"QR Code representing a URL\"\/><\/div><p><span id=\"m44532-fs-id1425631\"> <\/span>See how introns are removed during RNA splicing <a class=\"link\" href=\"http:\/\/openstaxcollege.org\/l\/RNA_splicing\" target=\"\">at this website<\/a>.<\/p><\/div><\/div><\/div><\/div><div class=\"section\" title=\"Processing of tRNAs and rRNAs\"><div class=\"titlepage\"><div><div><h3 id=\"m44532-fs-id1650543\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">Processing of tRNAs and rRNAs<\/span><\/span><\/h3><\/div><\/div><\/div><p><span id=\"m44532-fs-id2644904\"> <\/span>The tRNAs and rRNAs are structural molecules that have roles in protein synthesis; however, these RNAs are not themselves translated. Pre-rRNAs are transcribed, processed, and assembled into ribosomes in the nucleolus. Pre-tRNAs are transcribed and processed in the nucleus and then released into the cytoplasm where they are linked to free amino acids for protein synthesis.<\/p><p><span id=\"m44532-fs-id2595368\"> <\/span>Most of the tRNAs and rRNAs in eukaryotes and prokaryotes are first transcribed as a long precursor molecule that spans multiple rRNAs or tRNAs. Enzymes then cleave the precursors into subunits corresponding to each structural RNA. Some of the bases of pre-rRNAs are methylated; that is, a \u2013CH<sub>3<\/sub> moiety (methyl functional group) is added for stability. Pre-tRNA molecules also undergo methylation. As with pre-mRNAs, subunit excision occurs in eukaryotic pre-RNAs destined to become tRNAs or rRNAs.<\/p><p><span id=\"m44532-fs-id1450254\"> <\/span>Mature rRNAs make up approximately 50 percent of each ribosome. Some of a ribosome\u2019s RNA molecules are purely structural, whereas others have catalytic or binding activities. Mature tRNAs take on a three-dimensional structure through intramolecular hydrogen bonding to position the amino acid binding site at one end and the <em class=\"glossterm\"><span id=\"m44532-autoid-cnx2dbk-id1578066\"> <\/span>anticodon<\/em><a id=\"id513117\" class=\"indexterm\"> at the other end (<\/a><a class=\"xref target-figure\" href=\"ch15.html#m44532-fig-ch15_04_03\" title=\"Figure&#xA0;15.14.&#xA0;\">Figure\u00a015.14<\/a>). The anticodon is a three-nucleotide sequence in a tRNA that interacts with an mRNA codon through complementary base pairing.<\/p><div id=\"m44532-fig-ch15_04_03\" class=\"figure\" title=\"Figure&#xA0;15.14.&#xA0;\"><div class=\"body\"><div class=\"mediaobject\"><span id=\"m44532-fs-id1440481\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155819\/Figure_15_04_03.jpg\" width=\"300\" alt=\"The molecular model of phenylalanine tRNA is L-shaped. At one end is the anticodon AAG. At the other end is the attachment site for the amino acid phenylalanine\"\/><\/div><\/div><div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">15.14<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"\/><\/div><div class=\"caption\">This is a space-filling model of a tRNA molecule that adds the amino acid phenylalanine to a growing polypeptide chain. The anticodon AAG binds the Codon UUC on the mRNA. The amino acid phenylalanine is attached to the other end of the tRNA.<\/div><\/div><\/div><\/div><div xml:lang=\"en\" class=\"section module\" title=\"15.5.&#xA0;Ribosomes and Protein Synthesis\"><div class=\"titlepage\"><div><div><h2 id=\"m44529\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.5<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Ribosomes and Protein Synthesis<sup><a href=\"co03.html#book-attribution-m44529\">*<\/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 different steps in protein synthesis<\/p><\/li><li class=\"listitem\"><p>Discuss the role of ribosomes in protein synthesis<\/p><\/li><\/ul><\/div><\/div><\/div><\/div><div class=\"toc\"><ul><li class=\"toc-section\"><a href=\"#m44529-fs-id2009587\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">The Protein Synthesis Machinery<\/span><\/a><ul><li class=\"toc-section\"><a href=\"#m44529-fs-id1425631\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">Ribosomes<\/span><\/a><\/li><li class=\"toc-section\"><a href=\"#m44529-fs-id2897379\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">tRNAs<\/span><\/a><\/li><li class=\"toc-section\"><a href=\"#m44529-fs-id1461234\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">Aminoacyl tRNA Synthetases<\/span><\/a><\/li><\/ul><\/li><li class=\"toc-section\"><a href=\"#m44529-fs-id1986668\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">The Mechanism of Protein Synthesis<\/span><\/a><ul><li class=\"toc-section\"><a href=\"#m44529-fs-id2321391\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">Initiation of Translation<\/span><\/a><\/li><li class=\"toc-section\"><a href=\"#m44529-fs-id2217094\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">Translation, Elongation, and Termination<\/span><\/a><\/li><\/ul><\/li><li class=\"toc-section\"><a href=\"#m44529-fs-id2762763\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">Protein Folding, Modification, and Targeting<\/span><\/a><\/li><\/ul><\/div><p><span id=\"m44529-fs-id2195690\"> <\/span>The synthesis of proteins consumes more of a cell\u2019s energy than any other metabolic process. In turn, proteins account for more mass than any other component of living organisms (with the exception of water), and proteins perform virtually every function of a cell. The process of translation, or protein synthesis, involves the decoding of an mRNA message into a polypeptide product. Amino acids are covalently strung together by interlinking peptide bonds in lengths ranging from approximately 50 amino acid residues to more than 1,000. Each individual amino acid has an amino group (NH<sub>2<\/sub>) and a carboxyl (COOH) group. Polypeptides are formed when the amino group of one amino acid forms an amide (i.e., peptide) bond with the carboxyl group of another amino acid (<a class=\"xref target-figure\" href=\"ch15.html#m44529-fig-ch15_05_01\" title=\"Figure&#xA0;15.15.&#xA0;\">Figure\u00a015.15<\/a>). This reaction is catalyzed by ribosomes and generates one water molecule.<\/p><div id=\"m44529-fig-ch15_05_01\" class=\"figure\" title=\"Figure&#xA0;15.15.&#xA0;\"><div class=\"body\"><div class=\"mediaobject\"><span id=\"m44529-fs-id1236580\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155821\/Figure_15_05_01.jpg\" width=\"280\" alt=\"Illustration shows two amino acids side-by-side. Each amino acid has an amino group, a carboxyl group, and a side chain labeled R or R'. Upon formation of a peptide bond, the amino group is joined to the carboxyl group. A water molecule is released in the process.\"\/><\/div><\/div><div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">15.15<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"\/><\/div><div class=\"caption\">A peptide bond links the carboxyl end of one amino acid with the amino end of another, expelling one water molecule. For simplicity in this image, only the functional groups involved in the peptide bond are shown. The R and R' designations refer to the rest of each amino acid structure.<\/div><\/div><div class=\"section\" title=\"The Protein Synthesis Machinery\"><div class=\"titlepage\"><div><div><h3 id=\"m44529-fs-id2009587\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">The Protein Synthesis Machinery<\/span><\/span><\/h3><\/div><\/div><\/div><p><span id=\"m44529-fs-id2739564\"> <\/span>In addition to the mRNA template, many molecules and macromolecules contribute to the process of translation. The composition of each component may vary across species; for instance, ribosomes may consist of different numbers of rRNAs and polypeptides depending on the organism. However, the general structures and functions of the protein synthesis machinery are comparable from bacteria to human cells. Translation requires the input of an mRNA template, ribosomes, tRNAs, and various enzymatic factors.<\/p><div id=\"m44529-fs-id2046909\" 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=\"m44529-fs-id2890478\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155823\/prokary_protein.png\" width=\"120\" alt=\"QR Code representing a URL\"\/><\/div><p><span id=\"m44529-fs-id2694589\"> <\/span>Click through the steps of this <a class=\"link\" href=\"http:\/\/openstaxcollege.org\/l\/prokary_protein\" target=\"\">PBS interactive<\/a> to see protein synthesis in action.<\/p><\/div><\/div><div class=\"section\" title=\"Ribosomes\"><div class=\"titlepage\"><div><div><h4 id=\"m44529-fs-id1425631\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">Ribosomes<\/span><\/span><\/h4><\/div><\/div><\/div><p><span id=\"m44529-fs-id1769427\"> <\/span>Even before an mRNA is translated, a cell must invest energy to build each of its ribosomes. In <span class=\"emphasis\"><em>E. coli<\/em><\/span>, there are  between 10,000 and 70,000  ribosomes present in each cell at any given time. A ribosome is a complex macromolecule composed of structural and catalytic rRNAs, and many distinct polypeptides. In eukaryotes, the nucleolus is completely specialized for the synthesis and assembly of rRNAs.<\/p><p><span id=\"m44529-fs-id2000981\"> <\/span>Ribosomes exist in the cytoplasm in prokaryotes and in the cytoplasm and rough endoplasmic reticulum in eukaryotes. Mitochondria and chloroplasts also have their own ribosomes in the matrix and stroma, which look more similar to prokaryotic ribosomes (and have similar drug sensitivities) than the ribosomes just outside their outer membranes in the cytoplasm.  Ribosomes dissociate into large and small subunits when they are not synthesizing proteins and reassociate during the initiation of translation. In <span class=\"emphasis\"><em>E. coli<\/em><\/span>, the small subunit is described as 30S, and the large subunit is 50S, for a total of 70S (recall that Svedberg units are not additive). Mammalian ribosomes have a small 40S subunit and a large 60S subunit, for a total of 80S. The small subunit is responsible for binding the mRNA template, whereas the large subunit sequentially binds tRNAs. Each mRNA molecule is simultaneously translated by many ribosomes, all synthesizing protein in the same direction: reading the mRNA from 5' to 3' and synthesizing the polypeptide from the N terminus to the C terminus. The complete mRNA\/poly-ribosome structure is called a <em class=\"glossterm\"><span id=\"m44529-autoid-cnx2dbk-id1591612\"> <\/span>polysome<\/em><a id=\"id513761\" class=\"indexterm\">.<\/a><\/p><\/div><div class=\"section\" title=\"tRNAs\"><div class=\"titlepage\"><div><div><h4 id=\"m44529-fs-id2897379\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">tRNAs<\/span><\/span><\/h4><\/div><\/div><\/div><p><span id=\"m44529-fs-id1613052\"> <\/span>The tRNAs are structural RNA molecules that were transcribed from genes by RNA polymerase III. Depending on the species, 40 to 60 types of tRNAs exist in the cytoplasm. Serving as adaptors, specific tRNAs bind to sequences on the mRNA template and add the corresponding amino acid to the polypeptide chain. Therefore, tRNAs are the molecules that actually \u201ctranslate\u201d the language of RNA into the language of proteins.<\/p><p><span id=\"m44529-fs-id2853827\"> <\/span>Of the 64 possible mRNA codons\u2014or triplet combinations of A, U, G, and C\u2014three specify the termination of protein synthesis and 61 specify the addition of amino acids to the polypeptide chain. Of these 61, one codon (AUG) also encodes the initiation of translation. Each tRNA anticodon can base pair with one of the mRNA codons and add an amino acid or terminate translation, according to the genetic code. For instance, if the sequence CUA occurred on an mRNA template in the proper reading frame, it would bind a tRNA expressing the complementary sequence, GAU, which would be linked to the amino acid leucine.<\/p><p><span id=\"m44529-fs-id3063554\"> <\/span>As the adaptor molecules of translation, it is surprising that tRNAs can fit so much specificity into such a small package. Consider that tRNAs need to interact with three factors:  1) they must be recognized by the correct aminoacyl synthetase (see below); 2) they must be recognized by ribosomes; and 3) they must bind to the correct sequence in mRNA.<\/p><\/div><div class=\"section\" title=\"Aminoacyl tRNA Synthetases\"><div class=\"titlepage\"><div><div><h4 id=\"m44529-fs-id1461234\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">Aminoacyl tRNA Synthetases<\/span><\/span><\/h4><\/div><\/div><\/div><p><span id=\"m44529-fs-id1720501\"> <\/span>The process of pre-tRNA synthesis by RNA polymerase III only creates the RNA portion of the adaptor molecule. The corresponding amino acid must be added later, once the tRNA is processed and exported to the cytoplasm. Through the process of tRNA \u201ccharging,\u201d each tRNA molecule is linked to its correct amino acid by a group of enzymes called <em class=\"glossterm\"><span id=\"m44529-autoid-cnx2dbk-id1237710\"> <\/span>aminoacyl tRNA synthetases<\/em><a id=\"id513846\" class=\"indexterm\">. At least one type of aminoacyl tRNA synthetase exists for each of the 20 amino acids; the exact number of aminoacyl tRNA synthetases varies by species. These enzymes first bind and hydrolyze ATP to catalyze a high-energy bond between an amino acid and adenosine monophosphate (AMP); a pyrophosphate molecule is expelled in this reaction. The activated amino acid is then transferred to the tRNA, and AMP is released.<\/a><\/p><\/div><\/div><div class=\"section\" title=\"The Mechanism of Protein Synthesis\"><div class=\"titlepage\"><div><div><h3 id=\"m44529-fs-id1986668\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">The Mechanism of Protein Synthesis<\/span><\/span><\/h3><\/div><\/div><\/div><p><span id=\"m44529-fs-id2334597\"> <\/span>As with mRNA synthesis, protein synthesis can be divided into three phases: initiation, elongation, and termination. The process of translation is similar in prokaryotes and eukaryotes. Here we\u2019ll explore how translation occurs in <span class=\"emphasis\"><em>E. coli<\/em><\/span>, a representative prokaryote, and specify any differences between prokaryotic and eukaryotic translation.<\/p><div class=\"section\" title=\"Initiation of Translation\"><div class=\"titlepage\"><div><div><h4 id=\"m44529-fs-id2321391\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">Initiation of Translation<\/span><\/span><\/h4><\/div><\/div><\/div><p><span id=\"m44529-fs-id1240070\"> <\/span>Protein synthesis begins with the formation of an initiation complex. In <span class=\"emphasis\"><em>E. coli<\/em><\/span>, this complex involves the small 30S ribosome, the mRNA template, three initiation factors (IFs; IF-1, IF-2, and IF-3), and a special <em class=\"glossterm\"><span id=\"m44529-autoid-cnx2dbk-id1276479\"> <\/span>initiator tRNA<\/em><a id=\"id513915\" class=\"indexterm\">, called <span class=\"inlinemediaobject\"><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155825\/autogen-svg2png-00013.png\" style=\"width:; height:; vertical-align:-5.2783999999999995pt;\" alt=\"image\"\/><\/span>. The initiator tRNA interacts with the <em class=\"glossterm\"><span id=\"m44529-autoid-cnx2dbk-id1624879\"> <\/span>start codon<\/em><\/a><a id=\"id514135\" class=\"indexterm\"> AUG (or rarely, GUG), links to a formylated methionine called fMet, and can also bind IF-2. Formylated methionine is inserted by <span class=\"inlinemediaobject\"><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155825\/autogen-svg2png-00021.png\" style=\"width:; height:; vertical-align:-5.278400000000001pt;\" alt=\"image\"\/><\/span> at the beginning of every polypeptide chain synthesized by <span class=\"emphasis\"><em>E. coli<\/em><\/span>, but it is usually clipped off after translation is complete. When an in-frame AUG is encountered during translation elongation, a non-formylated methionine is inserted by a regular Met-tRNA<sup>Met<\/sup>.<\/a><\/p><p><span id=\"m44529-fs-id2936033\"> <\/span>In <span class=\"emphasis\"><em>E. coli<\/em><\/span> mRNA, a sequence upstream of the first AUG codon, called the <em class=\"glossterm\"><span id=\"m44529-autoid-cnx2dbk-id1401010\"> <\/span>Shine-Dalgarno sequence<\/em><a id=\"id514455\" class=\"indexterm\"> (AGGAGG), interacts with the rRNA molecules that compose the ribosome. This interaction anchors the 30S ribosomal subunit at the correct location on the mRNA template. Guanosine triphosphate (GTP), which is a purine nucleotide triphosphate, acts as an energy source during translation\u2014both at the start of elongation and during the ribosome\u2019s translocation.<\/a><\/p><p><span id=\"m44529-fs-id2334805\"> <\/span>In eukaryotes, a similar initiation complex forms, comprising mRNA, the 40S small ribosomal subunit, IFs, and nucleoside triphosphates (GTP and ATP). The charged initiator tRNA, called Met-tRNA<sub>i<\/sub>, does not bind fMet in eukaryotes, but is distinct from other Met-tRNAs in that it can bind IFs.<\/p><p><span id=\"m44529-fs-id3053365\"> <\/span>Instead of depositing at the Shine-Dalgarno sequence, the eukaryotic initiation complex recognizes the 7-methylguanosine cap at the 5' end of the mRNA. A cap-binding protein (CBP) and several other IFs assist the movement of the ribosome to the 5' cap. Once at the cap, the initiation complex tracks along the mRNA in the 5' to 3' direction, searching for the AUG start codon. Many eukaryotic mRNAs are translated from the first AUG, but this is not always the case. According to <em class=\"glossterm\"><span id=\"m44529-autoid-cnx2dbk-id1401038\"> <\/span>Kozak\u2019s rules<\/em><a id=\"id514498\" class=\"indexterm\">, the nucleotides around the AUG indicate whether it is the correct start codon. Kozak\u2019s rules state that the following consensus sequence must appear around the AUG of vertebrate genes: 5'-gccRccAUGG-3'. The R (for purine) indicates a site that can be either A or G, but cannot be C or U. Essentially, the closer the sequence is to this consensus, the higher the efficiency of translation.<\/a><\/p><p><span id=\"m44529-fs-id2682290\"> <\/span>Once the appropriate AUG is identified, the other proteins and CBP dissociate, and the 60S subunit binds to the complex of Met-tRNA<sub>i<\/sub>, mRNA, and the 40S subunit. This step completes the initiation of translation in eukaryotes.<\/p><\/div><div class=\"section\" title=\"Translation, Elongation, and Termination\"><div class=\"titlepage\"><div><div><h4 id=\"m44529-fs-id2217094\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">Translation, Elongation, and Termination<\/span><\/span><\/h4><\/div><\/div><\/div><p><span id=\"m44529-fs-id2013469\"> <\/span>In prokaryotes and eukaryotes, the basics of elongation are the same, so we will review elongation from the perspective of <span class=\"emphasis\"><em>E. coli<\/em><\/span>. The 50S ribosomal subunit of <span class=\"emphasis\"><em>E. coli <\/em><\/span>consists of three compartments: the A (aminoacyl) site binds incoming charged aminoacyl tRNAs. The P (peptidyl) site binds charged tRNAs carrying amino acids that have formed peptide bonds with the growing polypeptide chain but have not yet dissociated from their corresponding tRNA. The E (exit) site releases dissociated tRNAs so that they can be recharged with free amino acids. There is one exception to this assembly line of tRNAs: in <span class=\"emphasis\"><em>E. coli<\/em><\/span>, <span class=\"inlinemediaobject\"><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155826\/autogen-svg2png-0003.png\" style=\"width:; height:; vertical-align:-5.278400000000001pt;\" alt=\"image\"\/><\/span> is capable of entering the P site directly without first entering the A site. Similarly, the eukaryotic Met-tRNA<sub>i<\/sub>, with help from other proteins of the initiation complex, binds directly to the P site. In both cases, this creates an initiation complex with a free A site ready to accept the tRNA corresponding to the first codon after the AUG.<\/p><p><span id=\"m44529-fs-id1313555\"> <\/span>During translation elongation, the mRNA template provides specificity. As the ribosome moves along the mRNA, each mRNA codon comes into register, and specific binding with the corresponding charged tRNA anticodon is ensured. If mRNA were not present in the elongation complex, the ribosome would bind tRNAs nonspecifically.<\/p><p><span id=\"m44529-fs-id2608514\"> <\/span>Elongation proceeds with charged tRNAs entering the A site and then shifting to the P site followed by the E site with each single-codon \u201cstep\u201d of the ribosome. Ribosomal steps are induced by conformational changes that advance the ribosome by three bases in the 3' direction. The energy for each step of the ribosome is donated by an elongation factor that hydrolyzes GTP. Peptide bonds form between the amino group of the amino acid attached to the A-site tRNA and the carboxyl group of the amino acid attached to the P-site tRNA. The formation of each peptide bond is catalyzed by <em class=\"glossterm\"><span id=\"m44529-autoid-cnx2dbk-id1423355\"> <\/span>peptidyl transferase<\/em><a id=\"id514886\" class=\"indexterm\">, an RNA-based enzyme that is integrated into the 50S ribosomal subunit. The energy for each peptide bond formation is derived from GTP hydrolysis, which is catalyzed by a separate elongation factor. The amino acid bound to the P-site tRNA is also linked to the growing polypeptide chain. As the ribosome steps across the mRNA, the former P-site tRNA enters the E site, detaches from the amino acid, and is expelled (<\/a><a class=\"xref target-figure\" href=\"ch15.html#m44529-fig-ch15_05_02\" title=\"Figure&#xA0;15.16.&#xA0;\">Figure\u00a015.16<\/a>). Amazingly, the <span class=\"emphasis\"><em>E. coli <\/em><\/span>translation apparatus takes only 0.05 seconds to add each amino acid, meaning that a 200-amino acid protein can be translated in just 10 seconds.<\/p><div id=\"m44529-fs-id1097260\" class=\"note art-connection\"><div class=\"title\"><span class=\"cnx-gentext-tip-t\">Art Connection<\/span><\/div><div class=\"body\"><p><span id=\"m44529-fs-idm66901536\"> <\/span><\/p><div id=\"m44529-fig-ch15_05_02\" class=\"figure\" title=\"Figure&#xA0;15.16.&#xA0;\"><div class=\"body\"><span class=\"inlinemediaobject\"><span id=\"m44529-fs-id1786828\"> <\/span><img src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155827\/Figure_15_05_02.png\" width=\"250\" alt=\"Illustration shows the steps of protein synthesis. First, the initiator tRNA recognizes the sequence AUG on an mRNA that is associated with the small ribosomal subunit. The large subunit then joins the complex. Next, a second tRNA is recruited at the A site. A peptide bond is formed between the first amino acid, which is at the P site, and the second amino acid, which is at the A site. The mRNA then shifts and the first tRNA is moved to the E site, where it dissociates from the ribosome. Another tRNA binds at the A site, and the process is repeated.\"\/><\/span><\/div><div class=\"title\"><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">Figure\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-n\">15.16<\/span><span class=\"cnx-gentext-figure cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-figure cnx-gentext-t\"\/><\/div><div class=\"caption\">Translation begins when an initiator tRNA anticodon recognizes a codon on mRNA. The large ribosomal subunit joins the small subunit, and a second tRNA is recruited. As the mRNA moves relative to the ribosome, the polypeptide chain is formed. Entry of a release factor into the A site terminates translation and the components dissociate.<\/div><\/div><p><span id=\"m44529-fs-id1354131\"> <\/span>Many antibiotics inhibit bacterial protein synthesis. For example, tetracycline blocks the A site on the bacterial ribosome, and chloramphenicol blocks peptidyl transfer. What specific effect would you expect each of these antibiotics to have on protein synthesis?<\/p><p><span id=\"m44529-fs-id2682756\"> <\/span>Tetracycline would directly affect:<\/p><div class=\"orderedlist\"><span id=\"m44529-fs-id1471212\"> <\/span><ol class=\"orderedlist\" type=\"a\"><li class=\"listitem\"><p>tRNA binding to the ribosome<\/p><\/li><li class=\"listitem\"><p>ribosome assembly<\/p><\/li><li class=\"listitem\"><p>growth of the protein chain<\/p><\/li><\/ol><\/div><p><span id=\"m44529-fs-id2114520\"> <\/span>Chloramphenicol would directly affect<\/p><div class=\"orderedlist\"><span id=\"m44529-fs-id1803212\"> <\/span><ol class=\"orderedlist\" type=\"a\"><li class=\"listitem\"><p>tRNA binding to the ribosome<\/p><\/li><li class=\"listitem\"><p>ribosome assembly<\/p><\/li><li class=\"listitem\"><p>growth of the protein chain<\/p><\/li><\/ol><\/div><\/div><\/div><p><span id=\"m44529-fs-id2155698\"> <\/span>Termination of translation occurs when a nonsense codon (UAA, UAG, or UGA) is encountered. Upon aligning with the A site, these nonsense codons are recognized by release factors in prokaryotes and eukaryotes that instruct peptidyl transferase to add a water molecule to the carboxyl end of the P-site amino acid. This reaction forces the P-site amino acid to detach from its tRNA, and the newly made protein is released. The small and large ribosomal subunits dissociate from the mRNA and from each other; they are recruited almost immediately into another translation initiation complex. After many ribosomes have completed translation, the mRNA is degraded so the nucleotides can be reused in another transcription reaction.<\/p><\/div><\/div><div class=\"section\" title=\"Protein Folding, Modification, and Targeting\"><div class=\"titlepage\"><div><div><h3 id=\"m44529-fs-id2762763\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">Protein Folding, Modification, and Targeting<\/span><\/span><\/h3><\/div><\/div><\/div><p><span id=\"m44529-fs-id2979153\"> <\/span>During and after translation, individual amino acids may be chemically modified, signal sequences may be appended, and the new protein \u201cfolds\u201d into a distinct three-dimensional structure as a result of intramolecular interactions. A <em class=\"glossterm\"><span id=\"m44529-autoid-cnx2dbk-id1387490\"> <\/span>signal sequence<\/em><a id=\"id515087\" class=\"indexterm\"> is a short tail of amino acids that directs a protein to a specific cellular compartment. These sequences at the amino end or the carboxyl end of the protein can be thought of as the protein\u2019s \u201ctrain ticket\u201d to its ultimate destination. Other cellular factors recognize each signal sequence and help transport the protein from the cytoplasm to its correct compartment. For instance, a specific sequence at the amino terminus will direct a protein to the mitochondria or chloroplasts (in plants). Once the protein reaches its cellular destination, the signal sequence is usually clipped off.<\/a><\/p><p><span id=\"m44529-fs-id2165193\"> <\/span>Many proteins fold spontaneously, but some proteins require helper molecules, called chaperones, to prevent them from aggregating during the complicated process of folding. Even if a protein is properly specified by its corresponding mRNA, it could take on a completely dysfunctional shape if abnormal temperature or pH conditions prevent it from folding correctly.<\/p><\/div><\/div><div class=\"glossary\" title=\"Glossary\" id=\"id515529\"><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>7-methylguanosine cap<\/dt><dd><p>modification added to the 5' end of pre-mRNAs to protect mRNA from degradation and assist translation<\/p><\/dd><dt>aminoacyl tRNA synthetase<\/dt><dd><p>enzyme that \u201ccharges\u201d tRNA molecules by catalyzing a bond between the tRNA and a corresponding amino acid<\/p><\/dd><dt>anticodon<\/dt><dd><p>three-nucleotide sequence in a tRNA molecule that corresponds to an mRNA codon<\/p><\/dd><dt>CAAT box<\/dt><dd><p>(GGCCAATCT) essential eukaryotic promoter sequence involved in binding transcription factors<\/p><\/dd><dt>Central Dogma<\/dt><dd><p>states that genes specify the sequence of mRNAs, which in turn specify the sequence of proteins<\/p><\/dd><dt>codon<\/dt><dd><p>three consecutive nucleotides in mRNA that specify the insertion of an amino acid or the release of a polypeptide chain during translation<\/p><\/dd><dt>colinear<\/dt><dd><p>in terms of RNA and protein, three \u201cunits\u201d of RNA (nucleotides) specify one \u201cunit\u201d of protein (amino acid) in a consecutive fashion<\/p><\/dd><dt>consensus<\/dt><dd><p>DNA sequence that is used by many species to perform the same or similar functions<\/p><\/dd><dt>core enzyme<\/dt><dd><p>prokaryotic RNA polymerase consisting of <span class=\"emphasis\"><em>\u03b1<\/em><\/span>, <span class=\"emphasis\"><em>\u03b1<\/em><\/span>, <span class=\"emphasis\"><em>\u03b2<\/em><\/span>, and <span class=\"emphasis\"><em>\u03b2<\/em><\/span>' but missing <span class=\"emphasis\"><em>\u03c3<\/em><\/span>; this complex performs elongation<\/p><\/dd><dt>degeneracy<\/dt><dd><p>(of the genetic code) describes that a given amino acid can be encoded by more than one nucleotide triplet; the code is degenerate, but not ambiguous<\/p><\/dd><dt>downstream<\/dt><dd><p>nucleotides following the initiation site in the direction of mRNA transcription; in general, sequences that are toward the 3' end relative to a site on the mRNA<\/p><\/dd><dt>exon<\/dt><dd><p>sequence present in protein-coding mRNA after completion of pre-mRNA splicing<\/p><\/dd><dt>FACT<\/dt><dd><p>complex that \u201cfacilitates chromatin transcription\u201d by disassembling nucleosomes ahead of a transcribing RNA polymerase II and reassembling them after the polymerase passes by<\/p><\/dd><dt>GC-rich box<\/dt><dd><p>(GGCG) nonessential eukaryotic promoter sequence that binds cellular factors to increase the efficiency of transcription; may be present several times in a promoter<\/p><\/dd><dt>hairpin<\/dt><dd><p>structure of RNA when it folds back on itself and forms intramolecular hydrogen bonds between complementary nucleotides<\/p><\/dd><dt>holoenzyme<\/dt><dd><p>prokaryotic RNA polymerase consisting of <span class=\"emphasis\"><em>\u03b1<\/em><\/span>, <span class=\"emphasis\"><em>\u03b1<\/em><\/span>, <span class=\"emphasis\"><em>\u03b2<\/em><\/span>, <span class=\"emphasis\"><em>\u03b2<\/em><\/span>', and <span class=\"emphasis\"><em>\u03c3<\/em><\/span>; this complex is responsible for transcription initiation<\/p><\/dd><dt>initiation site<\/dt><dd><p>nucleotide from which mRNA synthesis proceeds in the 5' to 3' direction; denoted with a \u201c+1\u201d<\/p><\/dd><dt>initiator tRNA<\/dt><dd><p>in prokaryotes, called <span class=\"token\">\n \n  <span class=\"emphasis mathml-mi\"><em>t<\/em><\/span><span class=\"emphasis mathml-mi\"><em>R<\/em><\/span><span class=\"emphasis mathml-mi\"><em>N<\/em><\/span><span class=\"emphasis mathml-mi\"><em>A<\/em><\/span><sub><span class=\"emphasis mathml-mi\"><em>f<\/em><\/span><\/sub><sup><span class=\"bold mathml-mi\"><strong>Met<\/strong><\/span><\/sup><\/span>\n; in eukaryotes, called tRNA<sub>i<\/sub>; a tRNA that interacts with a start codon, binds directly to the ribosome P site, and links to a special methionine to begin a polypeptide chain<\/p><\/dd><dt>intron<\/dt><dd><p>non\u2013protein-coding intervening sequences that are spliced from mRNA during processing<\/p><\/dd><dt>Kozak\u2019s rules<\/dt><dd><p>determines the correct initiation AUG in a eukaryotic mRNA; the following consensus sequence must appear around the AUG: 5\u2019-GCC(<span class=\"bold\"><strong>purine<\/strong><\/span>)CCAUG<span class=\"bold\"><strong>G<\/strong><\/span>-3\u2019; the bolded bases are most important<\/p><\/dd><dt>nonsense codon<\/dt><dd><p>one of the three mRNA codons that specifies termination of translation<\/p><\/dd><dt>nontemplate strand<\/dt><dd><p>strand of DNA that is not used to transcribe mRNA; this strand is identical to the mRNA except that T nucleotides in the DNA are replaced by U nucleotides in the mRNA<\/p><\/dd><dt>Octamer box<\/dt><dd><p>(ATTTGCAT) nonessential eukaryotic promoter sequence that binds cellular factors to increase the efficiency of transcription; may be present several times in a promoter<\/p><\/dd><dt>peptidyl transferase<\/dt><dd><p>RNA-based enzyme that is integrated into the 50S ribosomal subunit and catalyzes the formation of peptide bonds<\/p><\/dd><dt>plasmid<\/dt><dd><p>extrachromosomal, covalently closed, circular DNA molecule that may only contain one or a few genes; common in prokaryotes<\/p><\/dd><dt>poly-A tail<\/dt><dd><p>modification added to the 3' end of pre-mRNAs to protect mRNA from degradation and assist mRNA export from the nucleus<\/p><\/dd><dt>polysome<\/dt><dd><p>mRNA molecule simultaneously being translated by many ribosomes all going in the same direction<\/p><\/dd><dt>preinitiation complex<\/dt><dd><p>cluster of transcription factors and other proteins that recruit RNA polymerase II for transcription of a DNA template<\/p><\/dd><dt>promoter<\/dt><dd><p>DNA sequence to which RNA polymerase and associated factors bind and initiate transcription<\/p><\/dd><dt>RNA editing<\/dt><dd><p>direct alteration of one or more nucleotides in an mRNA that has already been synthesized<\/p><\/dd><dt>Rho-dependent termination<\/dt><dd><p>in prokaryotes, termination of transcription by an interaction between RNA polymerase and the rho protein at a run of G nucleotides on the DNA template<\/p><\/dd><dt>Rho-independent<\/dt><dd><p>termination sequence-dependent termination of prokaryotic mRNA synthesis; caused by hairpin formation in the mRNA that stalls the polymerase<\/p><\/dd><dt>reading frame<\/dt><dd><p>sequence of triplet codons in mRNA that specify a particular protein; a ribosome shift of one or two nucleotides in either direction completely abolishes synthesis of that protein<\/p><\/dd><dt>Shine-Dalgarno sequence<\/dt><dd><p>(AGGAGG); initiates prokaryotic translation by interacting with rRNA molecules comprising the 30S ribosome<\/p><\/dd><dt>signal sequence<\/dt><dd><p>short tail of amino acids that directs a protein to a specific cellular compartment<\/p><\/dd><dt>small nuclear RNA<\/dt><dd><p>molecules synthesized by RNA polymerase III that have a variety of functions, including splicing pre-mRNAs and regulating transcription factors<\/p><\/dd><dt>splicing<\/dt><dd><p>process of removing introns and reconnecting exons in a pre-mRNA<\/p><\/dd><dt>start codon<\/dt><dd><p>AUG (or rarely, GUG) on an mRNA from which translation begins; always specifies methionine<\/p><\/dd><dt>TATA box<\/dt><dd><p>conserved promoter sequence in eukaryotes and prokaryotes that helps to establish the initiation site for transcription<\/p><\/dd><dt>template strand<\/dt><dd><p>strand of DNA that specifies the complementary mRNA molecule<\/p><\/dd><dt>transcription bubble<\/dt><dd><p>region of locally unwound DNA that allows for transcription of mRNA<\/p><\/dd><dt>upstream<\/dt><dd><p>nucleotides preceding the initiation site; in general, sequences toward the 5' end relative to a site on the mRNA<\/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=\"#m44518\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.<\/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=\"#m44522\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.1<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">The Genetic Code<\/span><\/span><\/a><\/div><div class=\"body\"><p><span id=\"m44522-fs-id3086772\"> <\/span>The genetic code refers to the DNA alphabet (A, T, C, G), the RNA alphabet (A, U, C, G), and the polypeptide alphabet (20 amino acids). The Central Dogma describes the flow of genetic information in the cell from genes to mRNA to proteins. Genes are used to make mRNA by the process of transcription; mRNA is used to synthesize proteins by the process of translation. The genetic code is degenerate because 64 triplet codons in mRNA specify only 20 amino acids and three nonsense codons. Almost every species on the planet uses the same genetic code.<\/p><\/div><\/div><div class=\"section\"><div class=\"title\"><a href=\"#m44523\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.2<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Prokaryotic Transcription<\/span><\/span><\/a><\/div><div class=\"body\"><p><span id=\"m44523-fs-id1265785\"> <\/span>In prokaryotes, mRNA synthesis is initiated at a promoter sequence on the DNA template comprising two consensus sequences that recruit RNA polymerase. The prokaryotic polymerase consists of a core enzyme of four protein subunits and a <span class=\"emphasis\"><em>\u03c3<\/em><\/span> protein that assists only with initiation. Elongation synthesizes mRNA in the 5' to 3' direction at a rate of 40 nucleotides per second. Termination liberates the mRNA and occurs either by rho protein interaction or by the formation of an mRNA hairpin.<\/p><\/div><\/div><div class=\"section\"><div class=\"title\"><a href=\"#m44524\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.3<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Eukaryotic Transcription<\/span><\/span><\/a><\/div><div class=\"body\"><p><span id=\"m44524-fs-id1097260\"> <\/span>Transcription in eukaryotes involves one of three types of polymerases, depending on the gene being transcribed. RNA polymerase II transcribes all of the protein-coding genes, whereas RNA polymerase I transcribes rRNA genes, and RNA polymerase III transcribes rRNA, tRNA, and small nuclear RNA genes. The initiation of transcription in eukaryotes involves the binding of several transcription factors to complex promoter sequences that are usually located upstream of the gene being copied. The mRNA is synthesized in the 5' to 3' direction, and the FACT complex moves and reassembles nucleosomes as the polymerase passes by. Whereas RNA polymerases I and III terminate transcription by protein- or RNA hairpin-dependent methods, RNA polymerase II transcribes for 1,000 or more nucleotides beyond the gene template and cleaves the excess during pre-mRNA processing.<\/p><\/div><\/div><div class=\"section\"><div class=\"title\"><a href=\"#m44532\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.4<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">RNA Processing in Eukaryotes<\/span><\/span><\/a><\/div><div class=\"body\"><p><span id=\"m44532-fs-id2270525\"> <\/span>Eukaryotic pre-mRNAs are modified with a 5' methylguanosine cap and a poly-A tail. These structures protect the mature mRNA from degradation and help export it from the nucleus. Pre-mRNAs also undergo splicing, in which introns are removed and exons are reconnected with single-nucleotide accuracy. Only finished mRNAs that have undergone 5' capping, 3' polyadenylation, and intron splicing are exported from the nucleus to the cytoplasm. Pre-rRNAs and pre-tRNAs may be processed by intramolecular cleavage, splicing, methylation, and chemical conversion of nucleotides. Rarely, RNA editing is also performed to insert missing bases after an mRNA has been synthesized.<\/p><\/div><\/div><div class=\"section\"><div class=\"title\"><a href=\"#m44529\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.5<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Ribosomes and Protein Synthesis<\/span><\/span><\/a><\/div><div class=\"body\"><p><span id=\"m44529-fs-id1957598\"> <\/span>The players in translation include the mRNA template, ribosomes, tRNAs, and various enzymatic factors. The small ribosomal subunit forms on the mRNA template either at the Shine-Dalgarno sequence (prokaryotes) or the 5' cap (eukaryotes). Translation begins at the initiating AUG on the mRNA, specifying methionine. The formation of peptide bonds occurs between sequential amino acids specified by the mRNA template according to the genetic code. Charged tRNAs enter the ribosomal A site, and their amino acid bonds with the amino acid at the P site. The entire mRNA is translated in three-nucleotide \u201csteps\u201d of the ribosome. When a nonsense codon is encountered, a release factor binds and dissociates the components and frees the new protein. Folding of the protein occurs during and after translation.<\/p><\/div><\/div><\/div>&lt;!--CNX: Start Area: \"\"--&gt;<div class=\"cnx-eoc art-exercise\"><div class=\"title\"><span\/><\/div><div class=\"section empty\"><div class=\"title\"><a href=\"#m44518\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.<\/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=\"#m44522\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.1<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">The Genetic Code<\/span><\/span><\/a><\/div><div class=\"body\"><div class=\"section empty\"><div class=\"title\"><a href=\"#m44523\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.2<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Prokaryotic Transcription<\/span><\/span><\/a><\/div><div class=\"body\"><div class=\"section\"><div class=\"title\"><a href=\"#m44524\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.3<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Eukaryotic Transcription<\/span><\/span><\/a><\/div><div class=\"body\"><div id=\"m44524-fs-idp79573648\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44524-fs-idm45398016\"><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=\"m44524-fs-idm70130112\"> <\/span>\n<p><span id=\"m44524-fs-idm59081616\"> <\/span><a class=\"xref target-figure\" href=\"ch15.html#m44524-fig-ch15_03_02\" title=\"Figure&#xA0;15.11.&#xA0;\">Figure\u00a015.11<\/a> A scientist splices a eukaryotic promoter in front of a bacterial gene and inserts the gene in a bacterial chromosome. Would you expect the bacteria to transcribe the gene?<\/p>\n<\/div><div id=\"m44524-fs-idm45398016\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch15.html#m44524-fs-idp79573648\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44524-fs-idm11981392\"> <\/span><a class=\"xref target-figure\" href=\"ch15.html#m44524-fig-ch15_03_02\" title=\"Figure&#xA0;15.11.&#xA0;\">Figure\u00a015.11<\/a> No. Prokaryotes use different promoters than eukaryotes.<\/p><\/div><\/div><\/div><\/div><\/div><\/div><div class=\"section\"><div class=\"title\"><a href=\"#m44532\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.4<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">RNA Processing in Eukaryotes<\/span><\/span><\/a><\/div><div class=\"body\"><div id=\"m44532-fs-idp101720928\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44532-fs-idp39733568\"><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=\"m44532-fs-idp95572528\"> <\/span>\n        <p><span id=\"m44532-fs-idm14702160\"> <\/span><a class=\"xref target-figure\" href=\"ch15.html#m44532-fig-ch15_04_02\" title=\"Figure&#xA0;15.13.&#xA0;\">Figure\u00a015.13<\/a> Errors in splicing are implicated in cancers and other human diseases. What kinds of mutations might lead to splicing errors? Think of different possible outcomes if splicing errors occur.<\/p>\n    <\/div><div id=\"m44532-fs-idp39733568\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch15.html#m44532-fs-idp101720928\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44532-fs-idp63298640\"> <\/span><a class=\"xref target-figure\" href=\"ch15.html#m44532-fig-ch15_04_02\" title=\"Figure&#xA0;15.13.&#xA0;\">Figure\u00a015.13<\/a> Mutations in the spliceosome recognition sequence at each end of the intron, or in the proteins and RNAs that make up the spliceosome, may impair splicing. Mutations may also add new spliceosome recognition sites. Splicing errors could lead to introns being retained in spliced RNA, exons being excised, or changes in the location of the splice site.<\/p><\/div><\/div><\/div><\/div><\/div><\/div><div class=\"section\"><div class=\"title\"><a href=\"#m44529\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.5<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Ribosomes and Protein Synthesis<\/span><\/span><\/a><\/div><div class=\"body\"><div id=\"m44529-fs-idp7053584\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44529-fs-idm128656560\"><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=\"m44529-fs-idm67653088\"> <\/span> <p><span id=\"m44529-fs-idp39443152\"> <\/span><a class=\"xref target-figure\" href=\"ch15.html#m44529-fig-ch15_05_02\" title=\"Figure&#xA0;15.16.&#xA0;\">Figure\u00a015.16<\/a> Many antibiotics inhibit bacterial protein synthesis. For example, tetracycline blocks the A site on the bacterial ribosome, and chloramphenicol blocks peptidyl transfer. What specific effect would you expect each of these antibiotics to have on protein synthesis?<\/p>\n        <p><span id=\"m44529-fs-idm20767424\"> <\/span>Tetracycline would directly affect:<\/p>\n        <div class=\"orderedlist\"><span id=\"m44529-fs-idp18488912\"> <\/span><ol class=\"orderedlist\" type=\"a\"><li class=\"listitem\"><p>tRNA binding to the ribosome<\/p><\/li><li class=\"listitem\"><p>ribosome assembly<\/p><\/li><li class=\"listitem\"><p>growth of the protein chain<\/p><\/li><\/ol><\/div>\n        <p><span id=\"m44529-fs-idp62151840\"> <\/span>Chloramphenicol would directly affect<\/p>\n        <div class=\"orderedlist\"><span id=\"m44529-fs-idp128801344\"> <\/span><ol class=\"orderedlist\" type=\"a\"><li class=\"listitem\"><p>tRNA binding to the ribosome<\/p><\/li><li class=\"listitem\"><p>ribosome assembly<\/p><\/li><li class=\"listitem\"><p>growth of the protein chain<\/p><\/li><\/ol><\/div>\n    <\/div><div id=\"m44529-fs-idm128656560\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch15.html#m44529-fs-idp7053584\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44529-fs-idp66684464\"> <\/span><a class=\"xref target-figure\" href=\"ch15.html#m44529-fig-ch15_05_02\" title=\"Figure&#xA0;15.16.&#xA0;\">Figure\u00a015.16<\/a> Tetracycline: a; Chloramphenicol: c.<\/p><\/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=\"#m44518\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.<\/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=\"#m44522\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.1<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">The Genetic Code<\/span><\/span><\/a><\/div><div class=\"body\"><div id=\"m44522-fs-id2024650\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44522-fs-id2682565\"><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=\"m44522-fs-id2567848\"> <\/span><p><span id=\"m44522-fs-id2574085\"> <\/span>The AUC and AUA codons in mRNA both specify isoleucine. What feature of the genetic code explains this?<\/p>\n<div class=\"orderedlist\"><span id=\"m44522-fs-id1812494\"> <\/span><ol class=\"orderedlist\" type=\"a\"><li class=\"listitem\"><p>complementarity<\/p><\/li><li class=\"listitem\"><p>nonsense codons<\/p><\/li><li class=\"listitem\"><p>universality<\/p><\/li><li class=\"listitem\"><p>degeneracy<\/p><\/li><\/ol><\/div>\n<\/div><div id=\"m44522-fs-id2682565\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch15.html#m44522-fs-id2024650\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44522-fs-id1310016\"> <\/span>D<\/p><\/div><\/div><\/div><\/div><div id=\"m44522-fs-id1428699\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44522-fs-id1425193\"><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=\"m44522-fs-id2318009\"> <\/span><p><span id=\"m44522-fs-id2013469\"> <\/span>How many nucleotides are in 12 mRNA codons?<\/p>\n<div class=\"orderedlist\"><span id=\"m44522-fs-id1450423\"> <\/span><ol class=\"orderedlist\" type=\"a\"><li class=\"listitem\"><p>12<\/p><\/li><li class=\"listitem\"><p>24<\/p><\/li><li class=\"listitem\"><p>36<\/p><\/li><li class=\"listitem\"><p>48<\/p><\/li><\/ol><\/div>\n<\/div><div id=\"m44522-fs-id1425193\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch15.html#m44522-fs-id1428699\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44522-fs-id2688570\"> <\/span>C<\/p><\/div><\/div><\/div><\/div><\/div><\/div><div class=\"section\"><div class=\"title\"><a href=\"#m44523\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.2<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Prokaryotic Transcription<\/span><\/span><\/a><\/div><div class=\"body\"><div id=\"m44523-fs-id2914875\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44523-fs-id890335\"><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=\"m44523-fs-id1420578\"> <\/span><p><span id=\"m44523-fs-id1404598\"> <\/span>Which subunit of the <span class=\"emphasis\"><em>E. coli<\/em><\/span> polymerase confers specificity to transcription?<\/p>\n<div class=\"orderedlist\"><span id=\"m44523-fs-id1425193\"> <\/span><ol class=\"orderedlist\" type=\"a\"><li class=\"listitem\"><p><span class=\"emphasis\"><em>\u03b1<\/em><\/span><\/p><\/li><li class=\"listitem\"><p><span class=\"emphasis\"><em>\u03b2<\/em><\/span><\/p><\/li><li class=\"listitem\"><p><span class=\"emphasis\"><em>\u03b2<\/em><\/span>'<\/p><\/li><li class=\"listitem\"><p><span class=\"emphasis\"><em>\u03c3<\/em><\/span><\/p><\/li><\/ol><\/div>\n<\/div><div id=\"m44523-fs-id890335\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch15.html#m44523-fs-id2914875\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44523-fs-id1006438\"> <\/span>D<\/p><\/div><\/div><\/div><\/div><div id=\"m44523-fs-id1313546\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44523-fs-id846953\"><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=\"m44523-fs-id1957391\"> <\/span><p><span id=\"m44523-fs-id1394141\"> <\/span>The -10 and -35 regions of prokaryotic promoters are called consensus sequences because ________.<\/p>\n<div class=\"orderedlist\"><span id=\"m44523-fs-id1704430\"> <\/span><ol class=\"orderedlist\" type=\"a\"><li class=\"listitem\"><p>they are identical in all bacterial species<\/p><\/li><li class=\"listitem\"><p>they are similar in all bacterial species<\/p><\/li><li class=\"listitem\"><p>they exist in all organisms<\/p><\/li><li class=\"listitem\"><p>they have the same function in all organisms<\/p><\/li><\/ol><\/div>\n<\/div><div id=\"m44523-fs-id846953\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch15.html#m44523-fs-id1313546\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44523-fs-id1605467\"> <\/span>B<\/p><\/div><\/div><\/div><\/div><\/div><\/div><div class=\"section\"><div class=\"title\"><a href=\"#m44524\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.3<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Eukaryotic Transcription<\/span><\/span><\/a><\/div><div class=\"body\"><div id=\"m44524-fs-id2062496\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44524-fs-id2155698\"><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=\"m44524-fs-id1236812\"> <\/span><p><span id=\"m44524-fs-id2169822\"> <\/span>Which feature of promoters can be found in both prokaryotes and eukaryotes?<\/p>\n<div class=\"orderedlist\"><span id=\"m44524-fs-id1418272\"> <\/span><ol class=\"orderedlist\" type=\"a\"><li class=\"listitem\"><p>GC box<\/p><\/li><li class=\"listitem\"><p>TATA box<\/p><\/li><li class=\"listitem\"><p>octamer box<\/p><\/li><li class=\"listitem\"><p>-10 and -35 sequences<\/p><\/li><\/ol><\/div>\n<\/div><div id=\"m44524-fs-id2155698\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch15.html#m44524-fs-id2062496\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44524-fs-id1275139\"> <\/span>B<\/p><\/div><\/div><\/div><\/div><div id=\"m44524-fs-id1419233\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44524-fs-id782653\"><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=\"m44524-fs-id2338606\"> <\/span><p><span id=\"m44524-fs-id1447963\"> <\/span>What transcripts will be most affected by low levels of \u03b1-amanitin?<\/p>\n<div class=\"orderedlist\"><span id=\"m44524-fs-id1380375\"> <\/span><ol class=\"orderedlist\" type=\"a\"><li class=\"listitem\"><p>18S and 28S rRNAs<\/p><\/li><li class=\"listitem\"><p>pre-mRNAs<\/p><\/li><li class=\"listitem\"><p>5S rRNAs and tRNAs<\/p><\/li><li class=\"listitem\"><p>other small nuclear RNAs<\/p><\/li><\/ol><\/div>\n<\/div><div id=\"m44524-fs-id782653\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch15.html#m44524-fs-id1419233\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44524-fs-id1461386\"> <\/span>B<\/p><\/div><\/div><\/div><\/div><\/div><\/div><div class=\"section\"><div class=\"title\"><a href=\"#m44532\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.4<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">RNA Processing in Eukaryotes<\/span><\/span><\/a><\/div><div class=\"body\"><div id=\"m44532-fs-id1466731\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44532-fs-id2261966\"><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=\"m44532-fs-id2080887\"> <\/span><p><span id=\"m44532-fs-id2914626\"> <\/span>Which pre-mRNA processing step is important for initiating translation?<\/p>\n<div class=\"orderedlist\"><span id=\"m44532-fs-id1847065\"> <\/span><ol class=\"orderedlist\" type=\"a\"><li class=\"listitem\"><p>poly-A tail<\/p><\/li><li class=\"listitem\"><p>RNA editing<\/p><\/li><li class=\"listitem\"><p>splicing<\/p><\/li><li class=\"listitem\"><p>7-methylguanosine cap<\/p><\/li><\/ol><\/div>\n<\/div><div id=\"m44532-fs-id2261966\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch15.html#m44532-fs-id1466731\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44532-fs-id1986526\"> <\/span>D<\/p><\/div><\/div><\/div><\/div><div id=\"m44532-fs-id1428536\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44532-fs-id1281610\"><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=\"m44532-fs-id1571225\"> <\/span><p><span id=\"m44532-fs-id1419233\"> <\/span>What processing step enhances the stability of pre-tRNAs and pre-rRNAs?<\/p>\n<div class=\"orderedlist\"><span id=\"m44532-fs-id1242629\"> <\/span><ol class=\"orderedlist\" type=\"a\"><li class=\"listitem\"><p>methylation<\/p><\/li><li class=\"listitem\"><p>nucleotide modification<\/p><\/li><li class=\"listitem\"><p>cleavage<\/p><\/li><li class=\"listitem\"><p>splicing<\/p><\/li><\/ol><\/div>\n<\/div><div id=\"m44532-fs-id1281610\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch15.html#m44532-fs-id1428536\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44532-fs-id2344853\"> <\/span>A<\/p><\/div><\/div><\/div><\/div><\/div><\/div><div class=\"section\"><div class=\"title\"><a href=\"#m44529\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.5<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Ribosomes and Protein Synthesis<\/span><\/span><\/a><\/div><div class=\"body\"><div id=\"m44529-fs-id2904762\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44529-fs-id2595784\"><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=\"m44529-fs-id1644930\"> <\/span><p><span id=\"m44529-fs-id1812931\"> <\/span> The RNA components of ribosomes are synthesized in the ________.<\/p>\n<div class=\"orderedlist\"><span id=\"m44529-fs-id1970715\"> <\/span><ol class=\"orderedlist\" type=\"a\"><li class=\"listitem\"><p>cytoplasm<\/p><\/li><li class=\"listitem\"><p>nucleus<\/p><\/li><li class=\"listitem\"><p>nucleolus<\/p><\/li><li class=\"listitem\"><p>endoplasmic reticulum<\/p><\/li><\/ol><\/div>\n<\/div><div id=\"m44529-fs-id2595784\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch15.html#m44529-fs-id2904762\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44529-fs-id1977751\"> <\/span>C<\/p><\/div><\/div><\/div><\/div><div id=\"m44529-fs-id2991759\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44529-fs-id1828761\"><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=\"m44529-fs-id2962890\"> <\/span><p><span id=\"m44529-fs-id2169252\"> <\/span>In any given species, there are at least how many types of aminoacyl tRNA synthetases?<\/p>\n<div class=\"orderedlist\"><span id=\"m44529-fs-id2750159\"> <\/span><ol class=\"orderedlist\" type=\"a\"><li class=\"listitem\"><p>20<\/p><\/li><li class=\"listitem\"><p>40<\/p><\/li><li class=\"listitem\"><p>100<\/p><\/li><li class=\"listitem\"><p>200<\/p><\/li><\/ol><\/div>\n<\/div><div id=\"m44529-fs-id1828761\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch15.html#m44529-fs-id2991759\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44529-fs-id1248186\"> <\/span>A<\/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=\"#m44518\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.<\/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=\"#m44522\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.1<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">The Genetic Code<\/span><\/span><\/a><\/div><div class=\"body\"><div id=\"m44522-fs-id2198100\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44522-fs-id2575162\"><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=\"m44522-fs-id2171449\"> <\/span><p><span id=\"m44522-fs-id2072320\"> <\/span>Imagine if there were 200 commonly occurring amino acids instead of 20. Given what you know about the genetic code, what would be the shortest possible codon length? Explain.<\/p><\/div><div id=\"m44522-fs-id2575162\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch15.html#m44522-fs-id2198100\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44522-fs-id653506\"> <\/span>For 200 commonly occurring amino acids, codons consisting of four types of nucleotides would have to be at least four nucleotides long, because 4<sup>4<\/sup> = 256. There would be much less degeneracy in this case.<\/p><\/div><\/div><\/div><\/div><div id=\"m44522-fs-id889157\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44522-fs-id1280839\"><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=\"m44522-fs-id1449262\"> <\/span><p><span id=\"m44522-fs-id1292460\"> <\/span>Discuss how degeneracy of the genetic code makes cells more robust to mutations.<\/p><\/div><div id=\"m44522-fs-id1280839\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch15.html#m44522-fs-id889157\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44522-fs-id2595443\"> <\/span>Codons that specify the same amino acid typically only differ by one nucleotide. In addition, amino acids with chemically similar side chains are encoded by similar codons. This nuance of the genetic code ensures that a single-nucleotide substitution mutation might either specify the same amino acid and have no effect, or may specify a similar amino acid, preventing the protein from being rendered completely nonfunctional.<\/p><\/div><\/div><\/div><\/div><\/div><\/div><div class=\"section\"><div class=\"title\"><a href=\"#m44523\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.2<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Prokaryotic Transcription<\/span><\/span><\/a><\/div><div class=\"body\"><div id=\"m44523-fs-id1444265\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44523-fs-id1291455\"><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=\"m44523-fs-id1427093\"> <\/span><p><span id=\"m44523-fs-id1414962\"> <\/span>If mRNA is complementary to the DNA template strand and the DNA template strand is complementary to the DNA nontemplate strand, then why are base sequences of mRNA and the DNA nontemplate strand not identical? Could they ever be?<\/p><\/div><div id=\"m44523-fs-id1291455\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch15.html#m44523-fs-id1444265\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44523-fs-id1432929\"> <\/span>DNA is different from RNA in that T nucleotides in DNA are replaced with U nucleotides in RNA. Therefore, they could never be identical in base sequence.<\/p><\/div><\/div><\/div><\/div><div id=\"m44523-fs-id1385377\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44523-fs-id2896656\"><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=\"m44523-fs-id1165423\"> <\/span><p><span id=\"m44523-fs-id889896\"> <\/span>In your own words, describe the difference between rho-dependent and rho-independent termination of transcription in prokaryotes.<\/p><\/div><div id=\"m44523-fs-id2896656\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch15.html#m44523-fs-id1385377\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44523-fs-id1393826\"> <\/span>Rho-dependent termination is controlled by the rho protein, which tracks along behind the polymerase on the growing mRNA chain. Near the end of the gene, the polymerase stalls at a run of G nucleotides on the DNA template. The rho protein collides with the polymerase and releases mRNA from the transcription bubble. Rho-independent termination is controlled by specific sequences in the DNA template strand. As the polymerase nears the end of the gene being transcribed, it encounters a region rich in C\u2013G nucleotides. This creates an mRNA hairpin that causes the polymerase to stall right as it begins to transcribe a region rich in A\u2013T nucleotides. Because A\u2013U bonds are less thermostable, the core enzyme falls away.<\/p><\/div><\/div><\/div><\/div><\/div><\/div><div class=\"section empty\"><div class=\"title\"><a href=\"#m44524\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.3<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Eukaryotic Transcription<\/span><\/span><\/a><\/div><div class=\"body\"><div class=\"section empty\"><div class=\"title\"><a href=\"#m44532\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.4<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">RNA Processing in Eukaryotes<\/span><\/span><\/a><\/div><div class=\"body\"><div class=\"section\"><div class=\"title\"><a href=\"#m44529\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.5<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Ribosomes and Protein Synthesis<\/span><\/span><\/a><\/div><div class=\"body\"><div id=\"m44529-fs-id2200536\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44529-fs-id1720804\"><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=\"m44529-fs-id2023354\"> <\/span><p><span id=\"m44529-fs-id2062496\"> <\/span>Transcribe and translate the following DNA sequence (nontemplate strand): 5'-ATGGCCGGTTATTAAGCA-3'<\/p><\/div><div id=\"m44529-fs-id1720804\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch15.html#m44529-fs-id2200536\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44529-fs-id2626001\"> <\/span>The mRNA would be: 5'-AUGGCCGGUUAUUAAGCA-3'. The protein would be: MAGY. Even though there are six codons, the fifth codon corresponds to a stop, so the sixth codon would not be translated.<\/p><\/div><\/div><\/div><\/div><div id=\"m44529-fs-id2119483\" class=\"exercise\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44529-fs-id2853893\"><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=\"m44529-fs-id2890873\"> <\/span><p><span id=\"m44529-fs-id2318009\"> <\/span>Explain how single nucleotide changes can have vastly different effects on protein function.<\/p><\/div><div id=\"m44529-fs-id2853893\" class=\"solution labeled\">&lt;!--calling formal.object--&gt;<div class=\"title\"><span><span class=\"epub-only pre-text\"> (<\/span><a class=\"solution\" href=\"ch15.html#m44529-fs-id2119483\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span id=\"m44529-fs-id2583976\"> <\/span>Nucleotide changes in the third position of codons may not change the amino acid and would have no effect on the protein. Other nucleotide changes that change important amino acids or create or delete start or stop codons would have severe effects on the amino acid sequence of the protein.<\/p><\/div><\/div><\/div><\/div><\/div><\/div><\/div><div class=\"cnx-eoc cnx-solutions\"><div class=\"title\">Solutions<\/div>&lt;!--CNX: Start Area: \"\"--&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=\"ch15.html#m44524-fs-idp79573648\">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=\"ch15.html#m44524-fig-ch15_03_02\" title=\"Figure&#xA0;15.11.&#xA0;\">Figure\u00a015.11<\/a> No. Prokaryotes use different promoters than eukaryotes.<\/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=\"ch15.html#m44532-fs-idp101720928\">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=\"ch15.html#m44532-fig-ch15_04_02\" title=\"Figure&#xA0;15.13.&#xA0;\">Figure\u00a015.13<\/a> Mutations in the spliceosome recognition sequence at each end of the intron, or in the proteins and RNAs that make up the spliceosome, may impair splicing. Mutations may also add new spliceosome recognition sites. Splicing errors could lead to introns being retained in spliced RNA, exons being excised, or changes in the location of the splice site.<\/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=\"ch15.html#m44529-fs-idp7053584\">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=\"ch15.html#m44529-fig-ch15_05_02\" title=\"Figure&#xA0;15.16.&#xA0;\">Figure\u00a015.16<\/a> Tetracycline: a; Chloramphenicol: c.<\/p><\/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=\"ch15.html#m44522-fs-id2024650\">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=\"ch15.html#m44522-fs-id1428699\">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=\"ch15.html#m44523-fs-id2914875\">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=\"ch15.html#m44523-fs-id1313546\">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=\"ch15.html#m44524-fs-id2062496\">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=\"ch15.html#m44524-fs-id1419233\">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=\"ch15.html#m44532-fs-id1466731\">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=\"ch15.html#m44532-fs-id1428536\">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=\"ch15.html#m44529-fs-id2904762\">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=\"ch15.html#m44529-fs-id2991759\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span> <\/span>A<\/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=\"ch15.html#m44522-fs-id2198100\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span> <\/span>For 200 commonly occurring amino acids, codons consisting of four types of nucleotides would have to be at least four nucleotides long, because 4<sup>4<\/sup> = 256. There would be much less degeneracy in this case.<\/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=\"ch15.html#m44522-fs-id889157\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span> <\/span>Codons that specify the same amino acid typically only differ by one nucleotide. In addition, amino acids with chemically similar side chains are encoded by similar codons. This nuance of the genetic code ensures that a single-nucleotide substitution mutation might either specify the same amino acid and have no effect, or may specify a similar amino acid, preventing the protein from being rendered completely nonfunctional.<\/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=\"ch15.html#m44523-fs-id1444265\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span> <\/span>DNA is different from RNA in that T nucleotides in DNA are replaced with U nucleotides in RNA. Therefore, they could never be identical in base sequence.<\/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=\"ch15.html#m44523-fs-id1385377\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span> <\/span>Rho-dependent termination is controlled by the rho protein, which tracks along behind the polymerase on the growing mRNA chain. Near the end of the gene, the polymerase stalls at a run of G nucleotides on the DNA template. The rho protein collides with the polymerase and releases mRNA from the transcription bubble. Rho-independent termination is controlled by specific sequences in the DNA template strand. As the polymerase nears the end of the gene being transcribed, it encounters a region rich in C\u2013G nucleotides. This creates an mRNA hairpin that causes the polymerase to stall right as it begins to transcribe a region rich in A\u2013T nucleotides. Because A\u2013U bonds are less thermostable, the core enzyme falls away.<\/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=\"ch15.html#m44529-fs-id2200536\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span> <\/span>The mRNA would be: 5'-AUGGCCGGUUAUUAAGCA-3'. The protein would be: MAGY. Even though there are six codons, the fifth codon corresponds to a stop, so the sixth codon would not be translated.<\/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=\"ch15.html#m44529-fs-id2119483\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div><div class=\"body\"><p><span> <\/span>Nucleotide changes in the third position of codons may not change the amino acid and would have no effect on the protein. Other nucleotide changes that change important amino acids or create or delete start or stop codons would have severe effects on the amino acid sequence of the protein.<\/p><\/div><\/div><\/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;15.&#xa0;Genes and Proteins\" id=\"id508530\">\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\">15<\/span><span class=\"cnx-gentext-chapter cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-chapter cnx-gentext-t\">Genes and Proteins<\/span><\/h1>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"introduction\" id=\"m44518\">\n<div id=\"m44518-fig-ch15_00_00\" class=\"figure splash\" title=\"Figure&#xa0;15.1.&#xa0;\">\n<div class=\"body\">\n<div class=\"mediaobject\"><span id=\"m44518-fs-id1796314\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155741\/Figure_15_00_01.jpg\" width=\"500\" alt=\"Molecular models show a DNA double helix that is packed in a chromosome in Part a, and two proteins are shown in Parts b and c.\" \/><\/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\">15.1<\/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\">Genes, which are carried on (a) chromosomes, are linearly organized instructions for making the RNA and protein molecules that are necessary for all of processes of life. The (b) interleukin-2 protein and (c) alpha-2u-globulin protein are just two examples of the array of different molecular structures that are encoded by genes. (credit \u201cchromosome: National Human Genome Research Institute; credit \u201cinterleukin-2\u201d: Ramin Herati\/Created from PDB 1M47 and rendered with Pymol; credit \u201calpha-2u-globulin\u201d: Darren Logan\/rendered with AISMIG)<\/div>\n<\/div>\n<h3 class=\"title\"><span>Introduction<sup><a href=\"co03.html#book-attribution-m44518\">*<\/a><\/sup><\/span><\/h3>\n<p><span id=\"m44518-fs-id1728094\"> <\/span>Since the rediscovery of Mendel\u2019s work in 1900, the definition of the gene has progressed from an abstract unit of heredity to a tangible molecular entity capable of replication, expression, and mutation (<a class=\"xref target-figure\" href=\"ch15.html#m44518-fig-ch15_00_00\" title=\"Figure&#xa0;15.1.&#xa0;\">Figure\u00a015.1<\/a>). Genes are composed of DNA and are linearly arranged on chromosomes. Genes specify the sequences of amino acids, which are the building blocks of proteins. In turn, proteins are responsible for orchestrating nearly every function of the cell. Both genes and the proteins they encode are absolutely essential to life as we know it.<\/p>\n<\/div>\n<div xml:lang=\"en\" class=\"section module\" title=\"15.1.&#xa0;The Genetic Code\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h2 id=\"m44522\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.1<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">The Genetic Code<sup><a href=\"co03.html#book-attribution-m44522\">*<\/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 \u201ccentral dogma\u201d of protein synthesis<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>Describe the genetic code and how the nucleotide sequence prescribes the amino acid and the protein sequence<\/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=\"#m44522-fs-id2013510\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">The Central Dogma: DNA Encodes RNA; RNA Encodes Protein<\/span><\/a>\n<ul>\n<li class=\"toc-section\"><a href=\"#m44522-fs-id2000981\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">The Genetic Code Is Degenerate and Universal<\/span><\/a><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/div>\n<p><span id=\"m44522-fs-id2750556\"> <\/span>The cellular process of transcription generates messenger RNA (mRNA), a mobile molecular copy of one or more genes with an alphabet of A, C, G, and uracil (U). Translation of the mRNA template converts nucleotide-based genetic information into a protein product. Protein sequences consist of 20 commonly occurring amino acids; therefore, it can be said that the protein alphabet consists of 20 letters (<a class=\"xref target-figure\" href=\"ch15.html#m44522-fig-ch15_01_01\" title=\"Figure&#xa0;15.2.&#xa0;\">Figure\u00a015.2<\/a>). Each amino acid is defined by a three-nucleotide sequence called the triplet codon. Different amino acids have different chemistries (such as acidic versus basic, or polar and nonpolar) and different structural constraints. Variation in amino acid sequence gives rise to enormous variation in protein structure and function.<\/p>\n<div id=\"m44522-fig-ch15_01_01\" class=\"figure\" title=\"Figure&#xa0;15.2.&#xa0;\">\n<div class=\"body\">\n<div class=\"mediaobject\"><span id=\"m44522-fs-id1695436\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155744\/Figure_15_01_01.jpg\" width=\"500\" alt=\"Structures of the twenty amino acids are given. Six amino acids&#x2014;glycine, alanine, valine, leucine, methionine, and isoleucine&#x2014;are non-polar and aliphatic, meaning they do not have a ring. Six amino acids&#x2014;serine, threonine, cysteine, proline, asparagine, and glutamate&#x2014;are polar but uncharged. Three amino acids&#x2014;lysine, arginine, and histidine&#x2014;are positively charged. Two amino acids, glutamate and aspartate, are negatively charged. Three amino acids&#x2014;phenylalanine, tyrosine, and tryptophan&#x2014;are nonpolar and aromatic.\" \/><\/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\">15.2<\/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\">Structures of the 20 amino acids found in proteins are shown. Each amino acid is composed of an amino group (<span class=\"token\"><\/p>\n<p>  NH<sub>3<\/sub><sup>+<\/sup><\/span>), a carboxyl group (COO<sup>&#8211;<\/sup>), and a side chain (blue). The side chain may be nonpolar, polar, or charged, as well as large or small. It is the variety of amino acid side chains that gives rise to the incredible variation of protein structure and function.<\/div>\n<\/div>\n<div class=\"section\" title=\"The Central Dogma: DNA Encodes RNA; RNA Encodes Protein\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h3 id=\"m44522-fs-id2013510\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">The Central Dogma: DNA Encodes RNA; RNA Encodes Protein<\/span><\/span><\/h3>\n<\/div>\n<\/div>\n<\/div>\n<p><span id=\"m44522-fs-id2155314\"> <\/span>The flow of genetic information in cells from DNA to mRNA to protein is described by the <em class=\"glossterm\"><span id=\"m44522-autoid-cnx2dbk-id1618570\"> <\/span>Central Dogma<\/em><a id=\"id509242\" class=\"indexterm\"> (<\/a><a class=\"xref target-figure\" href=\"ch15.html#m44522-fig-ch15_01_02\" title=\"Figure&#xa0;15.3.&#xa0;\">Figure\u00a015.3<\/a>), which states that genes specify the sequence of mRNAs, which in turn specify the sequence of proteins. The decoding of one molecule to another is performed by specific proteins and RNAs. Because the information stored in DNA is so central to cellular function, it makes intuitive sense that the cell would make mRNA copies of this information for protein synthesis, while keeping the DNA itself intact and protected. The copying of DNA to RNA is relatively straightforward, with one nucleotide being added to the mRNA strand for every nucleotide read in the DNA strand. The translation to protein is a bit more complex because three mRNA nucleotides correspond to one amino acid in the polypeptide sequence. However, the translation to protein is still systematic and <em class=\"glossterm\"><span id=\"m44522-autoid-cnx2dbk-id1618587\"> <\/span>colinear<\/em><a id=\"id509278\" class=\"indexterm\">, such that nucleotides 1 to 3 correspond to amino acid 1, nucleotides 4 to 6 correspond to amino acid 2, and so on.<\/a><\/p>\n<div id=\"m44522-fig-ch15_01_02\" class=\"figure\" title=\"Figure&#xa0;15.3.&#xa0;\">\n<div class=\"body\">\n<div class=\"mediaobject\"><span id=\"m44522-fs-id2681268\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155747\/Figure_15_01_02.jpg\" width=\"280\" alt=\"To make a protein, genetic information encoded by the DNA must be transcribed onto an mRNA molecule. The RNA is then processed by splicing to remove exons and by the addition of a 5' cap and a poly-A tail. A ribosome then reads the sequence on the mRNA, and uses this information to string amino acids into a protein.\" \/><\/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\">15.3<\/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\">Instructions on DNA are transcribed onto messenger RNA. Ribosomes are able to read the genetic information inscribed on a strand of messenger RNA and use this information to string amino acids together into a protein.<\/div>\n<\/div>\n<div class=\"section\" title=\"The Genetic Code Is Degenerate and Universal\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h4 id=\"m44522-fs-id2000981\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">The Genetic Code Is Degenerate and Universal<\/span><\/span><\/h4>\n<\/div>\n<\/div>\n<\/div>\n<p><span id=\"m44522-fs-id1290387\"> <\/span>Given the different numbers of \u201cletters\u201d in the mRNA and protein \u201calphabets,\u201d scientists theorized that combinations of nucleotides corresponded to single amino acids. Nucleotide doublets would not be sufficient to specify every amino acid because there are only 16 possible two-nucleotide combinations (4<sup>2<\/sup>). In contrast, there are 64 possible nucleotide triplets (4<sup>3<\/sup>), which is far more than the number of amino acids. Scientists theorized that amino acids were encoded by nucleotide triplets and that the genetic code was <em class=\"glossterm\"><span id=\"m44522-autoid-cnx2dbk-id1617190\"> <\/span>degenerate<\/em><a id=\"id509355\" class=\"indexterm\">. In other words, a given amino acid could be encoded by more than one nucleotide triplet. This was later confirmed experimentally; Francis Crick and Sydney Brenner used the chemical mutagen proflavin to insert one, two, or three nucleotides into the gene of a virus. When one or two nucleotides were inserted, protein synthesis was completely abolished. When three nucleotides were inserted, the protein was synthesized and functional. This demonstrated that three nucleotides specify each amino acid. These nucleotide triplets are called <em class=\"glossterm\"><span id=\"m44522-autoid-cnx2dbk-id1617198\"> <\/span>codons<\/em><\/a><a id=\"id509373\" class=\"indexterm\">. The insertion of one or two nucleotides completely changed the triplet <em class=\"glossterm\"><span id=\"m44522-autoid-cnx2dbk-id1617202\"> <\/span>reading frame<\/em><\/a><a id=\"id509387\" class=\"indexterm\">, thereby altering the message for every subsequent amino acid (<\/a><a class=\"xref target-figure\" href=\"ch15.html#m44522-fig-ch15_01_05\" title=\"Figure&#xa0;15.5.&#xa0;\">Figure\u00a015.5<\/a>). Though insertion of three nucleotides caused an extra amino acid to be inserted during translation, the integrity of the rest of the protein was maintained.<\/p>\n<p><span id=\"m44522-fs-id1565817\"> <\/span>Scientists painstakingly solved the genetic code by translating synthetic mRNAs in vitro and sequencing the proteins they specified (<a class=\"xref target-figure\" href=\"ch15.html#m44522-fig-ch15_01_04\" title=\"Figure&#xa0;15.4.&#xa0;\">Figure\u00a015.4<\/a>).<\/p>\n<div id=\"m44522-fig-ch15_01_04\" class=\"figure\" title=\"Figure&#xa0;15.4.&#xa0;\">\n<div class=\"body\">\n<div class=\"mediaobject\"><span id=\"m44522-fs-id2989543\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155749\/Figure_15_01_04.jpg\" width=\"300\" alt=\"Figure shows all 64 codons. Sixty-two of these code for amino acids, and three are stop codons.\" \/><\/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\">15.4<\/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\">This figure shows the genetic code for translating each nucleotide triplet in mRNA into an amino acid or a termination signal in a nascent protein. (credit: modification of work by NIH)<\/div>\n<\/div>\n<p><span id=\"m44522-fs-id1634383\"> <\/span>In addition to instructing the addition of a specific amino acid to a polypeptide chain, three of the 64 codons terminate protein synthesis and release the polypeptide from the translation machinery. These triplets are called <em class=\"glossterm\"><span id=\"m44522-autoid-cnx2dbk-id1629280\"> <\/span>nonsense codons<\/em><a id=\"id509470\" class=\"indexterm\">, or stop codons. Another codon, AUG, also has a special function. In addition to specifying the amino acid methionine, it also serves as the start codon to initiate translation. The reading frame for translation is set by the AUG start codon near the 5&#8242; end of the mRNA.<\/a><\/p>\n<p><span id=\"m44522-fs-id913366\"> <\/span>The genetic code is universal. With a few exceptions, virtually all species use the same genetic code for protein synthesis. Conservation of codons means that a purified mRNA encoding the globin protein in horses could be transferred to a tulip cell, and the tulip would synthesize horse globin. That there is only one genetic code is powerful evidence that all of life on Earth shares a common origin, especially considering that there are about 10<sup>84<\/sup> possible combinations of 20 amino acids and 64 triplet codons.<\/p>\n<div id=\"m44522-fs-id2739380\" 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=\"m44522-fs-id1712352\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155752\/create_protein.png\" width=\"120\" alt=\"QR Code representing a URL\" \/><\/div>\n<p><span id=\"m44522-fs-id1965995\"> <\/span>Transcribe a gene and translate it to protein using complementary pairing and the genetic code at this <a class=\"link\" href=\"http:\/\/openstaxcollege.org\/l\/create_protein\" target=\"\"> site<\/a>.<\/p>\n<\/div>\n<\/div>\n<div id=\"m44522-fig-ch15_01_05\" class=\"figure\" title=\"Figure&#xa0;15.5.&#xa0;\">\n<div class=\"body\">\n<div class=\"mediaobject\"><span id=\"m44522-fs-id2339630\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155753\/Figure_15_01_05.jpg\" width=\"350\" alt=\"Illustration shows a frameshift mutation in which the reading frame is altered by the deletion of two amino acids.\" \/><\/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\">15.5<\/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\">The deletion of two nucleotides shifts the reading frame of an mRNA and changes the entire protein message, creating a nonfunctional protein or terminating protein synthesis altogether.<\/div>\n<\/div>\n<p><span id=\"m44522-fs-id1288651\"> <\/span>Degeneracy is believed to be a cellular mechanism to reduce the negative impact of random mutations. Codons that specify the same amino acid typically only differ by one nucleotide. In addition, amino acids with chemically similar side chains are encoded by similar codons. This nuance of the genetic code ensures that a single-nucleotide substitution mutation might either specify the same amino acid but have no effect or specify a similar amino acid, preventing the protein from being rendered completely nonfunctional.<\/p>\n<\/div>\n<div id=\"m44522-fs-id1796872\" class=\"note scientific\">\n<div class=\"title\"><span class=\"cnx-gentext-tip-t\">Scientific Method Connection<\/span><\/div>\n<div class=\"body\">\n<p title=\"Which Has More DNA: A Kiwi or a Strawberry?\"><span id=\"m44522-eip-id1169982614662\"> <\/span><\/p>\n<div class=\"title\"><b>Which Has More DNA: A Kiwi or a Strawberry?<\/b><\/div>\n<div id=\"m44522-fig-ch15_01_03\" class=\"figure\" title=\"Figure&#xa0;15.6.&#xa0;\">\n<div class=\"body\">\n<div class=\"mediaobject\"><span id=\"m44522-fs-id3051050\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155756\/Figure_15_01_03.jpg\" width=\"450\" alt=\"Photographs show a thin slice of a green kiwi fruit and a bowl of strawberries.\" \/><\/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\">15.6<\/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\">Do you think that a kiwi or a strawberry has more DNA per fruit? (credit \u201ckiwi\u201d: &#8220;Kelbv&#8221;\/Flickr; credit: \u201cstrawberry\u201d: Alisdair McDiarmid)<\/div>\n<\/div>\n<p><span id=\"m44522-eip-id2896007\"> <\/span><span class=\"bold\"><strong>Question<\/strong><\/span>: Would a kiwifruit and strawberry that are approximately the same size (<a class=\"xref target-figure\" href=\"ch15.html#m44522-fig-ch15_01_03\" title=\"Figure&#xa0;15.6.&#xa0;\">Figure\u00a015.6<\/a>) also have approximately the same amount of DNA?<\/p>\n<p><span id=\"m44522-eip-id1416267\"> <\/span><span class=\"bold\"><strong>Background<\/strong><\/span>: Genes are carried on chromosomes and are made of DNA. All mammals are diploid, meaning they have two copies of each chromosome. However, not all plants are diploid. The common strawberry is octoploid (8<span class=\"emphasis\"><em>n<\/em><\/span>) and the cultivated kiwi is hexaploid (6<span class=\"emphasis\"><em>n<\/em><\/span>). Research the total number of chromosomes in the cells of each of these fruits and think about how this might correspond to the amount of DNA in these fruits\u2019 cell nuclei. Read about the technique of DNA isolation to understand how each step in the isolation protocol helps liberate and precipitate DNA.<\/p>\n<p><span id=\"m44522-eip-id1407858\"> <\/span><span class=\"bold\"><strong>Hypothesis<\/strong><\/span>: Hypothesize whether you would be able to detect a difference in DNA quantity from similarly sized strawberries and kiwis. Which fruit do you think would yield more DNA?<\/p>\n<p><span id=\"m44522-eip-id2117311\"> <\/span><span class=\"bold\"><strong>Test your hypothesis<\/strong><\/span>: Isolate the DNA from a strawberry and a kiwi that are similarly sized. Perform the experiment in at least triplicate for each fruit.<\/p>\n<div class=\"orderedlist\"><span id=\"m44522-eip-716\"> <\/span><\/p>\n<ol class=\"orderedlist\" type=\"1\">\n<li class=\"listitem\">\n<p>Prepare a bottle of DNA extraction buffer from 900 mL water, 50 mL dish detergent, and two teaspoons of table salt. Mix by inversion (cap it and turn it upside down a few times).<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>Grind a strawberry and a kiwifruit by hand in a plastic bag, or using a mortar and pestle, or with a metal bowl and the end of a blunt instrument. Grind for at least two minutes per fruit.<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>Add 10 mL of the DNA extraction buffer to each fruit, and mix well for at least one minute.<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>Remove cellular debris by filtering each fruit mixture through cheesecloth or porous cloth and into a funnel placed in a test tube or an appropriate container.<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>Pour ice-cold ethanol or isopropanol (rubbing alcohol) into the test tube. You should observe white, precipitated DNA.<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>Gather the DNA from each fruit by winding it around separate glass rods.<\/p>\n<\/li>\n<\/ol>\n<\/div>\n<p><span id=\"m44522-eip-id2024898\"> <\/span><br \/>\n<span class=\"bold\"><strong>Record your observations<\/strong><\/span>: Because you are not quantitatively measuring DNA volume, you can record for each trial whether the two fruits produced the same or different amounts of DNA as observed by eye. If one or the other fruit produced noticeably more DNA, record this as well. Determine whether your observations are consistent with several pieces of each fruit.<\/p>\n<p><span id=\"m44522-eip-id1463552\"> <\/span><span class=\"bold\"><strong>Analyze your data<\/strong><\/span>: Did you notice an obvious difference in the amount of DNA produced by each fruit? Were your results reproducible?<\/p>\n<p><span id=\"m44522-eip-id1458204\"> <\/span><span class=\"bold\"><strong>Draw a conclusion<\/strong><\/span>: Given what you know about the number of chromosomes in each fruit, can you conclude that chromosome number necessarily correlates to DNA amount? Can you identify any drawbacks to this procedure? If you had access to a laboratory, how could you standardize your comparison and make it more quantitative?<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div xml:lang=\"en\" class=\"section module\" title=\"15.2.&#xa0;Prokaryotic Transcription\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h2 id=\"m44523\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.2<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Prokaryotic Transcription<sup><a href=\"co03.html#book-attribution-m44523\">*<\/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>List the different steps in prokaryotic transcription<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>Discuss the role of promoters in prokaryotic transcription<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>Describe how and when transcription is terminated<\/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=\"#m44523-fs-id2899946\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">Initiation of Transcription in Prokaryotes<\/span><\/a>\n<ul>\n<li class=\"toc-section\"><a href=\"#m44523-fs-id2016560\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">Prokaryotic RNA Polymerase<\/span><\/a><\/li>\n<li class=\"toc-section\"><a href=\"#m44523-fs-id653506\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">Prokaryotic Promoters<\/span><\/a><\/li>\n<\/ul>\n<\/li>\n<li class=\"toc-section\"><a href=\"#m44523-fs-id1298841\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">Elongation and Termination in Prokaryotes<\/span><\/a><\/li>\n<li class=\"toc-section\"><a href=\"#m44523-fs-id1318146\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">Prokaryotic Termination Signals<\/span><\/a><\/li>\n<\/ul>\n<\/div>\n<p><span id=\"m44523-fs-id1468209\"> <\/span>The prokaryotes, which include bacteria and archaea, are mostly single-celled organisms that, by definition, lack membrane-bound nuclei and other organelles. A bacterial chromosome is a covalently<br \/>\nclosed circle that, unlike eukaryotic chromosomes, is not organized around histone proteins. The central region of the cell in which prokaryotic DNA resides is called the nucleoid. In addition, prokaryotes often have abundant <em class=\"glossterm\"><span id=\"m44523-autoid-cnx2dbk-id1409887\"> <\/span>plasmids<\/em><a id=\"id510286\" class=\"indexterm\">, which are shorter circular DNA molecules that may only contain one or a few genes. Plasmids can be transferred independently of the bacterial chromosome during cell division and often carry traits such as antibiotic resistance.<\/a><\/p>\n<p><span id=\"m44523-fs-id671101\"> <\/span>Transcription in prokaryotes (and in eukaryotes) requires the DNA double helix to partially unwind in the region of mRNA synthesis. The region of unwinding is called a <em class=\"glossterm\"><span id=\"m44523-autoid-cnx2dbk-id1409898\"> <\/span>transcription bubble.<\/em><a id=\"id510309\" class=\"indexterm\"> Transcription always proceeds from the same DNA strand for each gene, which is called the <em class=\"glossterm\"><span id=\"m44523-autoid-cnx2dbk-id1409903\"> <\/span>template strand<\/em><\/a><a id=\"id510323\" class=\"indexterm\">. The mRNA product is complementary to the template strand and is almost identical to the other DNA strand, called the <em class=\"glossterm\"><span id=\"m44523-autoid-cnx2dbk-id1409907\"> <\/span>nontemplate strand<\/em><\/a><a id=\"id510338\" class=\"indexterm\">. The only difference is that in mRNA, all of the T nucleotides are replaced with U nucleotides. In an RNA double helix, A can bind U via two hydrogen bonds, just as in A\u2013T pairing in a DNA double helix.<\/a><\/p>\n<p><span id=\"m44523-fs-id1520179\"> <\/span>The nucleotide pair in the DNA double helix that corresponds to the site from which the first 5&#8242; mRNA nucleotide is transcribed is called the +1 site, or the <em class=\"glossterm\"><span id=\"m44523-autoid-cnx2dbk-id1463886\"> <\/span>initiation site<\/em><a id=\"id510363\" class=\"indexterm\">. Nucleotides preceding the initiation site are given negative numbers and are designated <em class=\"glossterm\"><span id=\"m44523-autoid-cnx2dbk-id1463891\"> <\/span>upstream<\/em><\/a><a id=\"id510377\" class=\"indexterm\">. Conversely, nucleotides following the initiation site are denoted with \u201c+\u201d numbering and are called <em class=\"glossterm\"><span id=\"m44523-autoid-cnx2dbk-id1463895\"> <\/span>downstream<\/em><\/a><a id=\"id510392\" class=\"indexterm\"> nucleotides.<\/a><\/p>\n<div class=\"section\" title=\"Initiation of Transcription in Prokaryotes\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h3 id=\"m44523-fs-id2899946\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">Initiation of Transcription in Prokaryotes<\/span><\/span><\/h3>\n<\/div>\n<\/div>\n<\/div>\n<p><span id=\"m44523-fs-id2321141\"> <\/span>Prokaryotes do not have membrane-enclosed nuclei. Therefore, the processes of transcription, translation, and mRNA degradation can all occur simultaneously. The intracellular level of a bacterial protein can quickly be amplified by multiple transcription and translation events occurring concurrently on the same DNA template. Prokaryotic transcription often covers more than one gene and produces polycistronic mRNAs that specify more than one protein.<\/p>\n<p><span id=\"m44523-fs-id2117424\"> <\/span>Our discussion here will exemplify transcription by describing this process in <span class=\"emphasis\"><em>Escherichia coli<\/em><\/span>, a well-studied bacterial species. Although some differences exist between transcription in <span class=\"emphasis\"><em>E. coli<\/em><\/span> and transcription in archaea, an understanding of <span class=\"emphasis\"><em>E. coli <\/em><\/span>transcription can be applied to virtually all bacterial species.<\/p>\n<div class=\"section\" title=\"Prokaryotic RNA Polymerase\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h4 id=\"m44523-fs-id2016560\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">Prokaryotic RNA Polymerase<\/span><\/span><\/h4>\n<\/div>\n<\/div>\n<\/div>\n<p><span id=\"m44523-fs-id1694517\"> <\/span>Prokaryotes use the same RNA polymerase to transcribe all of their genes. In <span class=\"emphasis\"><em>E. coli<\/em><\/span>, the polymerase is composed of five polypeptide subunits, two of which are identical. Four of these subunits, denoted <span class=\"emphasis\"><em>\u03b1<\/em><\/span>, <span class=\"emphasis\"><em>\u03b1<\/em><\/span>, <span class=\"emphasis\"><em>\u03b2<\/em><\/span>, and <span class=\"emphasis\"><em>\u03b2<\/em><\/span>&#8216; comprise the polymerase <em class=\"glossterm\"><span id=\"m44523-autoid-cnx2dbk-id1631940\"> <\/span>core enzyme<\/em><a id=\"id510499\" class=\"indexterm\">. These subunits assemble every time a gene is transcribed, and they disassemble once transcription is complete. Each subunit has a unique role; the two <span class=\"emphasis\"><em>\u03b1<\/em><\/span>-subunits are necessary to assemble the polymerase on the DNA; the <span class=\"emphasis\"><em>\u03b2<\/em><\/span>-subunit binds to the ribonucleoside triphosphate that will become part of the nascent \u201crecently born\u201d mRNA molecule; and the <span class=\"emphasis\"><em>\u03b2<\/em><\/span>&#8216; binds the DNA template strand. The fifth subunit, <span class=\"emphasis\"><em>\u03c3<\/em><\/span>, is involved only in transcription initiation. It confers transcriptional specificity such that the polymerase begins to synthesize mRNA from an appropriate initiation site. Without <span class=\"emphasis\"><em>\u03c3<\/em><\/span>, the core enzyme would transcribe from random sites and would produce mRNA molecules that specified protein gibberish. The polymerase comprised of all five subunits is called the <em class=\"glossterm\"><span id=\"m44523-autoid-cnx2dbk-id1631978\"> <\/span>holoenzyme<\/em><\/a><a id=\"id510548\" class=\"indexterm\">.<\/a><\/p>\n<\/div>\n<div class=\"section\" title=\"Prokaryotic Promoters\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h4 id=\"m44523-fs-id653506\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">Prokaryotic Promoters<\/span><\/span><\/h4>\n<\/div>\n<\/div>\n<\/div>\n<p><span id=\"m44523-fs-id1236812\"> <\/span>A <em class=\"glossterm\"><span id=\"m44523-autoid-cnx2dbk-id1617903\"> <\/span>promoter<\/em><a id=\"id510578\" class=\"indexterm\"> is a DNA sequence onto which the transcription machinery binds and initiates transcription. In most cases, promoters exist upstream of the genes they regulate. The specific sequence of a promoter is very important because it determines whether the corresponding gene is transcribed all the time, some of the time, or infrequently. Although promoters vary among prokaryotic genomes, a few elements are conserved. At the -10 and -35 regions upstream of the initiation site, there are two promoter <em class=\"glossterm\"><span id=\"m44523-autoid-cnx2dbk-id1617912\"> <\/span>consensus<\/em><\/a><a id=\"id510596\" class=\"indexterm\"> sequences, or regions that are similar across all promoters and across various bacterial species (<\/a><a class=\"xref target-figure\" href=\"ch15.html#m44523-fig-ch15_02_01\" title=\"Figure&#xa0;15.7.&#xa0;\">Figure\u00a015.7<\/a>). The -10 consensus sequence, called the -10 region, is TATAAT. The -35 sequence, TTGACA, is recognized and bound by <span class=\"emphasis\"><em>\u03c3<\/em><\/span>. Once this interaction is made, the subunits of the core enzyme bind to the site. The A\u2013T-rich -10 region facilitates unwinding of the DNA template, and several phosphodiester bonds are made. The transcription initiation phase ends with the production of abortive transcripts, which are polymers of approximately 10 nucleotides that are made and released.<\/p>\n<div id=\"m44523-fig-ch15_02_01\" class=\"figure\" title=\"Figure&#xa0;15.7.&#xa0;\">\n<div class=\"body\">\n<div class=\"mediaobject\"><span id=\"m44523-fs-id1482493\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155758\/Figure_15_02_01.jpg\" width=\"350\" alt=\"Illustration shows the &#x3c3; subunit of RNA polymerase bound to two consensus sequences that are 10 and 35 bases upstream of the transcription start site. RNA polymerase is bound to &#x3c3;.\" \/><\/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\">15.7<\/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\">The <span class=\"emphasis\"><em>\u03c3<\/em><\/span> subunit of prokaryotic RNA polymerase recognizes consensus sequences found in the promoter region upstream of the transcription start sight. The <span class=\"emphasis\"><em>\u03c3<\/em><\/span> subunit dissociates from the polymerase after transcription has been initiated.<\/div>\n<\/div>\n<div id=\"m44523-fs-id889157\" 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=\"m44523-fs-id2217094\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155800\/transcription.png\" width=\"120\" alt=\"QR Code representing a URL\" \/><\/div>\n<p><span id=\"m44523-fs-id1292460\"> <\/span>View this <a class=\"link\" href=\"http:\/\/openstaxcollege.org\/l\/transcription\" target=\"\">MolecularMovies animation<\/a> to see the first part of transcription and the base sequence repetition of the TATA box.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"section\" title=\"Elongation and Termination in Prokaryotes\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h3 id=\"m44523-fs-id1298841\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">Elongation and Termination in Prokaryotes<\/span><\/span><\/h3>\n<\/div>\n<\/div>\n<\/div>\n<p><span id=\"m44523-fs-id3319239\"> <\/span>The transcription elongation phase begins with the release of the <span class=\"emphasis\"><em>\u03c3<\/em><\/span> subunit from the polymerase. The dissociation of <span class=\"emphasis\"><em>\u03c3<\/em><\/span> allows the core enzyme to proceed along the DNA template, synthesizing mRNA in the 5&#8242; to 3&#8242; direction at a rate of approximately 40 nucleotides per second. As elongation proceeds, the DNA is continuously unwound ahead of the core enzyme and rewound behind it (<a class=\"xref target-figure\" href=\"ch15.html#m44523-fig-ch15_02_02\" title=\"Figure&#xa0;15.8.&#xa0;\">Figure\u00a015.8<\/a>). The base pairing between DNA and RNA is not stable enough to maintain the stability of the mRNA synthesis components. Instead, the RNA polymerase acts as a stable linker between the DNA template and the nascent RNA strands to ensure that elongation is not interrupted prematurely.<\/p>\n<div id=\"m44523-fig-ch15_02_02\" class=\"figure\" title=\"Figure&#xa0;15.8.&#xa0;\">\n<div class=\"body\">\n<div class=\"mediaobject\"><span id=\"m44523-fs-id3014452\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155802\/Figure_15_02_02.jpg\" width=\"425\" alt=\"Illustration shows RNA synthesis by RNA polymerase. The RNA strand is synthesized in the 5' to 3' direction.\" \/><\/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\">15.8<\/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\">During elongation, the prokaryotic RNA polymerase tracks along the DNA template, synthesizes mRNA in the 5&#8242; to 3&#8242; direction, and unwinds and rewinds the DNA as it is read.<\/div>\n<\/div>\n<\/div>\n<div class=\"section\" title=\"Prokaryotic Termination Signals\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h3 id=\"m44523-fs-id1318146\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">Prokaryotic Termination Signals<\/span><\/span><\/h3>\n<\/div>\n<\/div>\n<\/div>\n<p><span id=\"m44523-fs-id1403735\"> <\/span>Once a gene is transcribed, the prokaryotic polymerase needs to be instructed to dissociate from the DNA template and liberate the newly made mRNA. Depending on the gene being transcribed, there are two kinds of termination signals. One is protein-based and the other is RNA-based. <em class=\"glossterm\"><span id=\"m44523-autoid-cnx2dbk-id1615324\"> <\/span>Rho-dependent termination<\/em><a id=\"id510831\" class=\"indexterm\"> is controlled by the rho protein, which tracks along behind the polymerase on the growing mRNA chain. Near the end of the gene, the polymerase encounters a run of G nucleotides on the DNA template and it stalls. As a result, the rho protein collides with the polymerase. The interaction with rho releases the mRNA from the transcription bubble.<\/a><\/p>\n<p><span id=\"m44523-fs-id2629848\"> <\/span><em class=\"glossterm\"><span id=\"m44523-autoid-cnx2dbk-id1615335\"> <\/span>Rho-independent termination<\/em><a id=\"id510854\" class=\"indexterm\"> is controlled by specific sequences in the DNA template strand. As the polymerase nears the end of the gene being transcribed, it encounters a region rich in C\u2013G nucleotides. The mRNA folds back on itself, and the complementary C\u2013G nucleotides bind together. The result is a stable <em class=\"glossterm\"><span id=\"m44523-autoid-cnx2dbk-id1615341\"> <\/span>hairpin<\/em><\/a><a id=\"id510871\" class=\"indexterm\"> that causes the polymerase to stall as soon as it begins to transcribe a region rich in A\u2013T nucleotides. The complementary U\u2013A region of the mRNA transcript forms only a weak interaction with the template DNA. This, coupled with the stalled polymerase, induces enough instability for the core enzyme to break away and liberate the new mRNA transcript.<\/a><\/p>\n<p><span id=\"m44523-fs-id2114520\"> <\/span>Upon termination, the process of transcription is complete. By the time termination occurs, the prokaryotic transcript would already have been used to begin synthesis of numerous copies of the encoded protein because these processes can occur concurrently. The unification of transcription, translation, and even mRNA degradation is possible because all of these processes occur in the same 5&#8242; to 3&#8242; direction, and because there is no membranous compartmentalization in the prokaryotic cell (<a class=\"xref target-figure\" href=\"ch15.html#m44523-fig-ch15_02_03\" title=\"Figure&#xa0;15.9.&#xa0;\">Figure\u00a015.9<\/a>). In contrast, the presence of a nucleus in eukaryotic cells precludes simultaneous transcription and translation.<\/p>\n<div id=\"m44523-fig-ch15_02_03\" class=\"figure\" title=\"Figure&#xa0;15.9.&#xa0;\">\n<div class=\"body\">\n<div class=\"mediaobject\"><span id=\"m44523-fs-id1260172\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155804\/Figure_15_02_03.jpg\" width=\"350\" alt=\"Illustration shows multiple mRNAs transcribed off one gene. Ribosomes attach to the mRNA before transcription is complete and begin to make protein.\" \/><\/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\">15.9<\/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\">Multiple polymerases can transcribe a single bacterial gene while numerous ribosomes concurrently translate the mRNA transcripts into polypeptides. In this way, a specific protein can rapidly reach a high concentration in the bacterial cell.<\/div>\n<\/div>\n<div id=\"m44523-fs-id2626015\" 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=\"m44523-fs-id2608514\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155807\/transcription2.png\" width=\"120\" alt=\"QR Code representing a URL\" \/><\/div>\n<p><span id=\"m44523-fs-id2701078\"> <\/span>Visit this <a class=\"link\" href=\"http:\/\/openstaxcollege.org\/l\/transcription2\" target=\"\"> BioStudio animation<\/a> to see the process of prokaryotic transcription.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div xml:lang=\"en\" class=\"section module\" title=\"15.3.&#xa0;Eukaryotic Transcription\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h2 id=\"m44524\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.3<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Eukaryotic Transcription<sup><a href=\"co03.html#book-attribution-m44524\">*<\/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>List the steps in eukaryotic transcription<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>Discuss the role of RNA polymerases in transcription<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>Compare and contrast the three RNA polymerases<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>Explain the significance of transcription factors<\/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=\"#m44524-fs-id1760576\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">Initiation of Transcription in Eukaryotes<\/span><\/a>\n<ul>\n<li class=\"toc-section\"><a href=\"#m44524-fs-id3688592\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">The Three Eukaryotic RNA Polymerases<\/span><\/a><\/li>\n<li class=\"toc-section\"><a href=\"#m44524-fs-id1951192\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">Structure of an RNA Polymerase II Promoter<\/span><\/a><\/li>\n<li class=\"toc-section\"><a href=\"#m44524-fs-id1894765\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">Transcription Factors for RNA Polymerase II<\/span><\/a><\/li>\n<li class=\"toc-section\"><a href=\"#m44524-fs-id1836540\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">Promoter Structures for RNA Polymerases I and III<\/span><\/a><\/li>\n<\/ul>\n<\/li>\n<li class=\"toc-section\"><a href=\"#m44524-fs-id2896654\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">Eukaryotic Elongation and Termination<\/span><\/a><\/li>\n<\/ul>\n<\/div>\n<p><span id=\"m44524-fs-id2026267\"> <\/span>Prokaryotes and eukaryotes perform fundamentally the same process of transcription, with a few key differences. The most important difference between prokaryotes and eukaryotes is the latter\u2019s membrane-bound nucleus and organelles. With the genes bound in a nucleus, the eukaryotic cell must be able to transport its mRNA to the cytoplasm and must protect its mRNA from degrading before it is translated. Eukaryotes also employ three different polymerases that each transcribe a different subset of genes. Eukaryotic mRNAs are usually monogenic, meaning that they specify a single protein.<\/p>\n<div class=\"section\" title=\"Initiation of Transcription in Eukaryotes\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h3 id=\"m44524-fs-id1760576\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">Initiation of Transcription in Eukaryotes<\/span><\/span><\/h3>\n<\/div>\n<\/div>\n<\/div>\n<p><span id=\"m44524-fs-id2862612\"> <\/span>Unlike the prokaryotic polymerase that can bind to a DNA template on its own, eukaryotes require several other proteins, called transcription factors, to first bind to the promoter region and then help recruit the appropriate polymerase.<\/p>\n<div class=\"section\" title=\"The Three Eukaryotic RNA Polymerases\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h4 id=\"m44524-fs-id3688592\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">The Three Eukaryotic RNA Polymerases<\/span><\/span><\/h4>\n<\/div>\n<\/div>\n<\/div>\n<p><span id=\"m44524-fs-id3043156\"> <\/span>The features of eukaryotic mRNA synthesis are markedly more complex those of prokaryotes. Instead of a single polymerase comprising five subunits, the eukaryotes have three polymerases that are each made up of 10 subunits or more. Each eukaryotic polymerase also requires a distinct set of transcription factors to bring it to the DNA template.<\/p>\n<p><span id=\"m44524-fs-id2074568\"> <\/span>RNA polymerase I is located in the nucleolus, a specialized nuclear substructure in which ribosomal RNA (rRNA) is transcribed, processed, and assembled into ribosomes (<a class=\"xref target-table\" href=\"ch15.html#m44524-tab-ch15_03_01\" title=\"Table&#xa0;15.1.&#xa0;\">Table\u00a015.1<\/a>). The rRNA molecules are considered structural RNAs because they have a cellular role but are not translated into protein. The rRNAs are components of the ribosome and are essential to the process of translation. RNA polymerase I synthesizes all of the rRNAs except for the 5S rRNA molecule. The \u201cS\u201d designation applies to \u201cSvedberg\u201d units, a nonadditive value that characterizes the speed at which a particle sediments during centrifugation.<\/p>\n<div class=\"table\" id=\"m44524-tab-ch15_03_01\">\n<table cellpadding=\"0\" summary=\"table x.x\" 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\">15.1. <\/span><\/caption>\n<thead valign=\"bottom\">\n<tr>\n<th colspan=\"4\" style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">Locations, Products, and Sensitivities of the Three Eukaryotic RNA Polymerases<\/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: center !important;\">RNA Polymerase<\/th>\n<th style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: center !important;\">Cellular Compartment<\/th>\n<th style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: center !important;\">Product of Transcription<\/th>\n<th style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: center !important;\">\u03b1-Amanitin Sensitivity<\/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: center !important;\">I<\/td>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">Nucleolus<\/td>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">All rRNAs except 5S rRNA<\/td>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">Insensitive<\/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: center !important;\">II<\/td>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">Nucleus<\/td>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 1px solid; text-align: left !important;\">All protein-coding nuclear pre-mRNAs<\/td>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 1px solid; text-align: left !important;\">Extremely sensitive<\/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: center !important;\">III<\/td>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 0 !important; text-align: left !important;\">Nucleus<\/td>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 1px solid; border-bottom: 0 !important; text-align: left !important;\">5S rRNA, tRNAs, and small nuclear RNAs<\/td>\n<td style=\"border-left: 0 !important; border-top: 0 !important; border-right: 0 !important; border-bottom: 0 !important; text-align: left !important;\">Moderately sensitive<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n<p><span id=\"m44524-fs-id2694589\"> <\/span>RNA polymerase II is located in the nucleus and synthesizes all protein-coding nuclear pre-mRNAs. Eukaryotic pre-mRNAs undergo extensive processing after transcription but before translation. For clarity, this module\u2019s discussion of transcription and translation in eukaryotes will use the term \u201cmRNAs\u201d to describe only the mature, processed molecules that are ready to be translated. RNA polymerase II is responsible for transcribing the overwhelming majority of eukaryotic genes.<\/p>\n<p><span id=\"m44524-fs-id2014161\"> <\/span>RNA polymerase III is also located in the nucleus. This polymerase transcribes a variety of structural RNAs that includes the 5S pre-rRNA, transfer pre-RNAs (pre-tRNAs), and <em class=\"glossterm\"><span id=\"m44524-autoid-cnx2dbk-id1599710\"> <\/span>small nuclear <\/em><a id=\"id511693\" class=\"indexterm\">pre-<em class=\"glossterm\"><span id=\"m44524-autoid-cnx2dbk-id1237683\"> <\/span>RNAs<\/em><\/a><a id=\"id511706\" class=\"indexterm\">. The tRNAs have a critical role in translation; they serve as the adaptor molecules between the mRNA template and the growing polypeptide chain. Small nuclear RNAs have a variety of functions, including \u201csplicing\u201d pre-mRNAs and regulating transcription factors.<\/a><\/p>\n<p><span id=\"m44524-fs-id2583722\"> <\/span>A scientist characterizing a new gene can determine which polymerase transcribes it by testing whether the gene is expressed in the presence of a particular mushroom poison, \u03b1-amanitin (<a class=\"xref target-table\" href=\"ch15.html#m44524-tab-ch15_03_01\" title=\"Table&#xa0;15.1.&#xa0;\">Table\u00a015.1<\/a>). Interestingly, \u03b1-amanitin produced by <span class=\"emphasis\"><em>Amanita phalloides<\/em><\/span>, the Death Cap mushroom, affects the three polymerases very differently. RNA polymerase I is completely insensitive to \u03b1-amanitin, meaning that the polymerase can transcribe DNA in vitro in the presence of this poison. In contrast, RNA polymerase II is extremely sensitive to \u03b1-amanitin, and RNA polymerase III is moderately sensitive. Knowing the transcribing polymerase can clue a researcher into the general function of the gene being studied. Because RNA polymerase II transcribes the vast majority of genes, we will focus on this polymerase in our subsequent discussions about eukaryotic transcription factors and promoters.<\/p>\n<\/div>\n<div class=\"section\" title=\"Structure of an RNA Polymerase II Promoter\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h4 id=\"m44524-fs-id1951192\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">Structure of an RNA Polymerase II Promoter<\/span><\/span><\/h4>\n<\/div>\n<\/div>\n<\/div>\n<p><span id=\"m44524-fs-id2196807\"> <\/span>Eukaryotic promoters are much larger and more complex than prokaryotic promoters, but both have a TATA box. For example, in the mouse thymidine kinase gene, the TATA box is located at approximately -30 relative to the initiation (+1) site (<a class=\"xref target-figure\" href=\"ch15.html#m44524-fig-ch15_03_01\" title=\"Figure&#xa0;15.10.&#xa0;\">Figure\u00a015.10<\/a>). For this gene, the exact TATA box sequence is TATAAAA, as read in the 5&#8242; to 3&#8242; direction on the nontemplate strand. This sequence is not identical to the <span class=\"emphasis\"><em>E. coli<\/em><\/span> TATA box, but it conserves the A\u2013T rich element. The thermostability of A\u2013T bonds is low and this helps the DNA template to locally unwind in preparation for transcription.<\/p>\n<div id=\"m44524-fig-ch15_03_01\" class=\"figure\" title=\"Figure&#xa0;15.10.&#xa0;\">\n<div class=\"body\">\n<div class=\"mediaobject\"><span id=\"m44524-fs-id2574107\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155808\/Figure_15_03_01.jpg\" width=\"280\" alt=\"Illustration shows a series of transcription factors binding to the promoter, which is upstream of the gene. After all of the transcription factors are bound, RNA polymerase binds as well.\" \/><\/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\">15.10<\/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 generalized promoter of a gene transcribed by RNA polymerase II is shown. Transcription factors recognize the promoter. RNA polymerase II then binds and forms the transcription initiation complex.<\/div>\n<\/div>\n<div id=\"m44524-fs-id1461234\" 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=\"m44524-fs-idm74169728\"> <\/span><\/p>\n<div id=\"m44524-fig-ch15_03_02\" class=\"figure\" title=\"Figure&#xa0;15.11.&#xa0;\">\n<div class=\"body\"><span class=\"inlinemediaobject\"><span id=\"m44524-fs-id2278509\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155810\/Figure_15_03_02.png\" width=\"320\" alt=\"An illustration shows that before RNA processing, there is a primary RNA transcript including five boxes labeled, left to right, as exon 1, intron, exon 2, intron, and exon 3. After RNA processing, there is a spliced RNA with these parts, left to right: a 5' cap, a 5' untranslated region, exon 1, exon 2, exon 3, a 3' untranslated region, and a poly-a tail.\" \/><\/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\">15.11<\/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\">Eukaryotic mRNA contains introns that must be spliced out. A 5&#8242; cap and 3&#8242; poly-A tail are also added.<\/div>\n<\/div>\n<p><span id=\"m44524-fs-id2000672\"> <\/span>A scientist splices a eukaryotic promoter in front of a bacterial gene and inserts the gene in a bacterial chromosome. Would you expect the bacteria to transcribe the gene?<\/p>\n<\/div>\n<\/div>\n<p><span id=\"m44524-fs-id1807694\"> <\/span>The mouse genome includes one gene and two pseudogenes for cytoplasmic thymidine kinase. Pseudogenes are genes that have lost their protein-coding ability or are no longer expressed by the cell. These pseudogenes are copied from mRNA and incorporated into the chromosome. For example, the mouse thymidine kinase promoter also has a conserved <em class=\"glossterm\"><span id=\"m44524-autoid-cnx2dbk-id1589613\"> <\/span>CAAT box<\/em><a id=\"id511900\" class=\"indexterm\"> (GGCCAATCT) at approximately -80. This sequence is essential and is involved in binding transcription factors. Further upstream of the TATA box, eukaryotic promoters may also contain one or more <em class=\"glossterm\"><span id=\"m44524-autoid-cnx2dbk-id1589619\"> <\/span>GC-rich boxes<\/em><\/a><a id=\"id511916\" class=\"indexterm\"> (GGCG) or <em class=\"glossterm\"><span id=\"m44524-autoid-cnx2dbk-id1601449\"> <\/span>octamer boxes<\/em><\/a><a id=\"id511929\" class=\"indexterm\"> (ATTTGCAT). These elements bind cellular factors that increase the efficiency of transcription initiation and are often identified in more \u201cactive\u201d genes that are constantly being expressed by the cell.<\/a><\/p>\n<\/div>\n<div class=\"section\" title=\"Transcription Factors for RNA Polymerase II\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h4 id=\"m44524-fs-id1894765\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">Transcription Factors for RNA Polymerase II<\/span><\/span><\/h4>\n<\/div>\n<\/div>\n<\/div>\n<p><span id=\"m44524-fs-id1977416\"> <\/span>The complexity of eukaryotic transcription does not end with the polymerases and promoters. An army of basal transcription factors, enhancers, and silencers also help to regulate the frequency with which pre-mRNA is synthesized from a gene. Enhancers and silencers affect the efficiency of transcription but are not necessary for transcription to proceed. Basal transcription factors are crucial in the formation of a <em class=\"glossterm\"><span id=\"m44524-autoid-cnx2dbk-id1601475\"> <\/span>preinitiation complex<\/em><a id=\"id511966\" class=\"indexterm\"> on the DNA template that subsequently recruits RNA polymerase II for transcription initiation.<\/a><\/p>\n<p><span id=\"m44524-fs-id2334805\"> <\/span>The names of the basal transcription factors begin with \u201cTFII\u201d (this is the transcription factor for RNA polymerase II) and are specified with the letters A\u2013J. The transcription factors systematically fall into place on the DNA template, with each one further stabilizing the preinitiation complex and contributing to the recruitment of RNA polymerase II.<\/p>\n<p><span id=\"m44524-fs-id1720501\"> <\/span>The processes of bringing RNA polymerases I and III to the DNA template involve slightly less complex collections of transcription factors, but the general theme is the same. Eukaryotic transcription is a tightly regulated process that requires a variety of proteins to interact with each other and with the DNA strand. Although the process of transcription in eukaryotes involves a greater metabolic investment than in prokaryotes, it ensures that the cell transcribes precisely the pre-mRNAs that it needs for protein synthesis.<\/p>\n<div id=\"m44524-fs-id2016560\" class=\"note evolution\">\n<div class=\"title\"><span class=\"cnx-gentext-tip-t\">Evolution Connection<\/span><\/div>\n<div class=\"body\">\n<p title=\"The Evolution of Promoters\"><span id=\"m44524-fs-id1479424\"> <\/span><\/p>\n<div class=\"title\"><b>The Evolution of Promoters<\/b><\/div>\n<p title=\"The Evolution of Promoters\">The evolution of genes may be a familiar concept. Mutations can occur in genes during DNA replication, and the result may or may not be beneficial to the cell. By altering an enzyme, structural protein, or some other factor, the process of mutation can transform functions or physical features. However, eukaryotic promoters and other gene regulatory sequences may evolve as well. For instance, consider a gene that, over many generations, becomes more valuable to the cell. Maybe the gene encodes a structural protein that the cell needs to synthesize in abundance for a certain function. If this is the case, it would be beneficial to the cell for that gene\u2019s promoter to recruit transcription factors more efficiently and increase gene expression.<\/p>\n<p><span id=\"m44524-fs-id2694641\"> <\/span>Scientists examining the evolution of promoter sequences have reported varying results. In part, this is because it is difficult to infer exactly where a eukaryotic promoter begins and ends. Some promoters occur within genes; others are located very far upstream, or even downstream, of the genes they are regulating. However, when researchers limited their examination to human core promoter sequences that were defined experimentally as sequences that bind the preinitiation complex, they found that promoters evolve even faster than protein-coding genes.<\/p>\n<p><span id=\"m44524-fs-id1448131\"> <\/span>It is still unclear how promoter evolution might correspond to the evolution of humans or other higher organisms. However, the evolution of a promoter to effectively make more or less of a given gene product is an intriguing alternative to the evolution of the genes themselves.<sup><sup>[<a id=\"m44524-fs-idm20771056\" href=\"#ftn.m44524-fs-idm20771056\" class=\"footnote\">13<\/a>]<\/sup><\/sup><\/p>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"section\" title=\"Promoter Structures for RNA Polymerases I and III\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h4 id=\"m44524-fs-id1836540\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">Promoter Structures for RNA Polymerases I and III<\/span><\/span><\/h4>\n<\/div>\n<\/div>\n<\/div>\n<p><span id=\"m44524-fs-id2279649\"> <\/span>In eukaryotes, the conserved promoter elements differ for genes transcribed by RNA polymerases I, II, and III. RNA polymerase I transcribes genes that have two GC-rich promoter sequences in the -45 to +20 region. These sequences alone are sufficient for transcription initiation to occur, but promoters with additional sequences in the region from -180 to -105 upstream of the initiation site will further enhance initiation. Genes that are transcribed by RNA polymerase III have upstream promoters or promoters that occur within the genes themselves.<\/p>\n<\/div>\n<\/div>\n<div class=\"section\" title=\"Eukaryotic Elongation and Termination\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h3 id=\"m44524-fs-id2896654\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">Eukaryotic Elongation and Termination<\/span><\/span><\/h3>\n<\/div>\n<\/div>\n<\/div>\n<p><span id=\"m44524-fs-id1613052\"> <\/span>Following the formation of the preinitiation complex, the polymerase is released from the other transcription factors, and elongation is allowed to proceed as it does in prokaryotes with the polymerase synthesizing pre-mRNA in the 5&#8242; to 3&#8242; direction. As discussed previously, RNA polymerase II transcribes the major share of eukaryotic genes, so this section will focus on how this polymerase accomplishes elongation and termination.<\/p>\n<p><span id=\"m44524-fs-id3053365\"> <\/span>Although the enzymatic process of elongation is essentially the same in eukaryotes and prokaryotes, the DNA template is more complex. When eukaryotic cells are not dividing, their genes exist as a diffuse mass of DNA and proteins called chromatin. The DNA is tightly packaged around charged histone proteins at repeated intervals. These DNA\u2013histone complexes, collectively called nucleosomes, are regularly spaced and include 146 nucleotides of DNA wound around eight histones like thread around a spool.<\/p>\n<p><span id=\"m44524-fs-id1910636\"> <\/span>For polynucleotide synthesis to occur, the transcription machinery needs to move histones out of the way every time it encounters a nucleosome. This is accomplished by a special protein complex called <em class=\"glossterm\"><span id=\"m44524-autoid-cnx2dbk-id1280665\"> <\/span>FACT<\/em><a id=\"id512137\" class=\"indexterm\">, which stands for \u201cfacilitates chromatin transcription.\u201d This complex pulls histones away from the DNA template as the polymerase moves along it. Once the pre-mRNA is synthesized, the FACT complex replaces the histones to recreate the nucleosomes.<\/a><\/p>\n<p><span id=\"m44524-fs-id1360285\"> <\/span>The termination of transcription is different for the different polymerases. Unlike in prokaryotes, elongation by RNA polymerase II in eukaryotes takes place 1,000\u20132,000 nucleotides beyond the end of the gene being transcribed. This pre-mRNA tail is subsequently removed by cleavage during mRNA processing. On the other hand, RNA polymerases I and III require termination signals. Genes transcribed by RNA polymerase I contain a specific 18-nucleotide sequence that is recognized by a termination protein. The process of termination in RNA polymerase III involves an mRNA hairpin similar to rho-independent termination of transcription in prokaryotes.<\/p>\n<\/div>\n<\/div>\n<div xml:lang=\"en\" class=\"section module\" title=\"15.4.&#xa0;RNA Processing in Eukaryotes\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h2 id=\"m44532\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.4<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">RNA Processing in Eukaryotes<sup><a href=\"co03.html#book-attribution-m44532\">*<\/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 different steps in RNA processing<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>Understand the significance of exons, introns, and splicing<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>Explain how tRNAs and rRNAs are processed<\/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=\"#m44532-fs-id1983488\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">mRNA Processing<\/span><\/a>\n<ul>\n<li class=\"toc-section\"><a href=\"#m44532-fs-id2349302\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">5&#8242; Capping<\/span><\/a><\/li>\n<li class=\"toc-section\"><a href=\"#m44532-fs-id1422041\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">3&#8242; Poly-A Tail<\/span><\/a><\/li>\n<li class=\"toc-section\"><a href=\"#m44532-fs-id2195071\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">Pre-mRNA Splicing<\/span><\/a><\/li>\n<\/ul>\n<\/li>\n<li class=\"toc-section\"><a href=\"#m44532-fs-id1650543\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">Processing of tRNAs and rRNAs<\/span><\/a><\/li>\n<\/ul>\n<\/div>\n<p><span id=\"m44532-fs-id2263546\"> <\/span>After transcription, eukaryotic pre-mRNAs must undergo several processing steps before they can be translated. Eukaryotic (and prokaryotic) tRNAs and rRNAs also undergo processing before they can function as components in the protein synthesis machinery.<\/p>\n<div class=\"section\" title=\"mRNA Processing\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h3 id=\"m44532-fs-id1983488\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">mRNA Processing<\/span><\/span><\/h3>\n<\/div>\n<\/div>\n<\/div>\n<p><span id=\"m44532-fs-id2186668\"> <\/span>The eukaryotic pre-mRNA undergoes extensive processing before it is ready to be translated. The additional steps involved in eukaryotic mRNA maturation create a molecule with a much longer half-life than a prokaryotic mRNA. Eukaryotic mRNAs last for several hours, whereas the typical <span class=\"emphasis\"><em>E. coli<\/em><\/span> mRNA lasts no more than five seconds.<\/p>\n<p><span id=\"m44532-fs-id2262076\"> <\/span>Pre-mRNAs are first coated in RNA-stabilizing proteins; these protect the pre-mRNA from degradation while it is processed and exported out of the nucleus. The three most important steps of pre-mRNA processing are the addition of stabilizing and signaling factors at the 5&#8242; and 3&#8242; ends of the molecule, and the removal of intervening sequences that do not specify the appropriate amino acids. In rare cases, the mRNA transcript can be \u201cedited\u201d after it is transcribed.<\/p>\n<div id=\"m44532-fs-id2863005\" class=\"note evolution\">\n<div class=\"title\"><span class=\"cnx-gentext-tip-t\">Evolution Connection<\/span><\/div>\n<div class=\"body\">\n<p title=\"RNA Editing in Trypanosomes\"><span id=\"m44532-fs-id2655263\"> <\/span><\/p>\n<div class=\"title\"><b>RNA Editing in Trypanosomes<\/b><\/div>\n<p title=\"RNA Editing in Trypanosomes\">The trypanosomes are a group of protozoa that include the pathogen <span class=\"emphasis\"><em>Trypanosoma brucei<\/em><\/span>, which causes sleeping sickness in humans (<a class=\"xref target-figure\" href=\"ch15.html#m44532-fig-ch15_04_01\" title=\"Figure&#xa0;15.12.&#xa0;\">Figure\u00a015.12<\/a>). Trypanosomes, and virtually all other eukaryotes, have organelles called mitochondria that supply the cell with chemical energy. Mitochondria are organelles that express their own DNA and are believed to be the remnants of a symbiotic relationship between a eukaryote and an engulfed prokaryote.  The mitochondrial DNA of trypanosomes exhibit an interesting exception to The Central Dogma: their pre-mRNAs do not have the correct information to specify a functional protein. Usually, this is because the mRNA is missing several U nucleotides. The cell performs an additional RNA processing step called <em class=\"glossterm\"><span id=\"m44532-autoid-cnx2dbk-id1622607\"> <\/span>RNA editing<\/em><a id=\"id512661\" class=\"indexterm\"> to remedy this.<\/a><\/p>\n<div id=\"m44532-fig-ch15_04_01\" class=\"figure\" title=\"Figure&#xa0;15.12.&#xa0;\">\n<div class=\"body\">\n<div class=\"mediaobject\"><span id=\"m44532-fs-id2595588\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155812\/Figure_15_04_01.jpg\" width=\"250\" alt=\"Micrograph shows T. brucei, which has a u-shaped cell body and a long tail.\" \/><\/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\">15.12<\/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\"><span class=\"emphasis\"><em>Trypanosoma brucei<\/em><\/span> is the causative agent of sleeping sickness in humans. The mRNAs of this pathogen must be modified by the addition of nucleotides before protein synthesis can occur. (credit: modification of work by Torsten Ochsenreiter)<\/div>\n<\/div>\n<p><span id=\"m44532-fs-id1288287\"> <\/span>Other genes in the mitochondrial genome encode 40- to 80-nucleotide guide RNAs. One or more of these molecules interacts by complementary base pairing with some of the nucleotides in the pre-mRNA transcript. However, the guide RNA has more A nucleotides than the pre-mRNA has U nucleotides to bind with. In these regions, the guide RNA loops out. The 3&#8242; ends of guide RNAs have a long poly-U tail, and these U bases are inserted in regions of the pre-mRNA transcript at which the guide RNAs are looped. This process is entirely mediated by RNA molecules. That is, guide RNAs\u2014rather than proteins\u2014serve as the catalysts in RNA editing.<\/p>\n<p><span id=\"m44532-fs-id2300063\"> <\/span>RNA editing is not just a phenomenon of trypanosomes. In the mitochondria of some plants, almost all pre-mRNAs are edited. RNA editing has also been identified in mammals such as rats, rabbits, and even humans. What could be the evolutionary reason for this additional step in pre-mRNA processing? One possibility is that the mitochondria, being remnants of ancient prokaryotes, have an equally ancient RNA-based method for regulating gene expression. In support of this hypothesis, edits made to pre-mRNAs differ depending on cellular conditions. Although speculative, the process of RNA editing may be a holdover from a primordial time when RNA molecules, instead of proteins, were responsible for catalyzing reactions.<\/p>\n<\/div>\n<\/div>\n<div class=\"section\" title=\"5' Capping\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h4 id=\"m44532-fs-id2349302\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">5&#8242; Capping<\/span><\/span><\/h4>\n<\/div>\n<\/div>\n<\/div>\n<p><span id=\"m44532-fs-id2196807\"> <\/span>While the pre-mRNA is still being synthesized, a <em class=\"glossterm\"><span id=\"m44532-autoid-cnx2dbk-id1377856\"> <\/span>7-methylguanosine cap<\/em><a id=\"id512757\" class=\"indexterm\"> is added to the 5&#8242; end of the growing transcript by a phosphate linkage. This moiety (functional group) protects the nascent mRNA from degradation. In addition, factors involved in protein synthesis recognize the cap to help initiate translation by ribosomes.<\/a><\/p>\n<\/div>\n<div class=\"section\" title=\"3' Poly-A Tail\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h4 id=\"m44532-fs-id1422041\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">3&#8242; Poly-A Tail<\/span><\/span><\/h4>\n<\/div>\n<\/div>\n<\/div>\n<p><span id=\"m44532-fs-id2229067\"> <\/span>Once elongation is complete, the pre-mRNA is cleaved by an endonuclease between an AAUAAA consensus sequence and a GU-rich sequence, leaving the AAUAAA sequence on the pre-mRNA. An enzyme called poly-A polymerase then adds a string of approximately 200 A residues, called the <em class=\"glossterm\"><span id=\"m44532-autoid-cnx2dbk-id1644985\"> <\/span>poly-A tail<\/em><a id=\"id512792\" class=\"indexterm\">. This modification further protects the pre-mRNA from degradation and signals the export of the cellular factors that the transcript needs to the cytoplasm.<\/a><\/p>\n<\/div>\n<div class=\"section\" title=\"Pre-mRNA Splicing\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h4 id=\"m44532-fs-id2195071\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">Pre-mRNA Splicing<\/span><\/span><\/h4>\n<\/div>\n<\/div>\n<\/div>\n<p><span id=\"m44532-fs-id2914078\"> <\/span>Eukaryotic genes are composed of <em class=\"glossterm\"><span id=\"m44532-autoid-cnx2dbk-id1645010\"> <\/span>exons<\/em><a id=\"id512824\" class=\"indexterm\">, which correspond to protein-coding sequences (<span class=\"emphasis\"><em>ex-<\/em><\/span>on signifies that they are <span class=\"emphasis\"><em>ex<\/em><\/span>pressed), and <span class=\"emphasis\"><em>int<\/em><\/span>ervening sequences called <em class=\"glossterm\"><span id=\"m44532-autoid-cnx2dbk-id1682669\"> <\/span>introns<\/em><\/a><a id=\"id512855\" class=\"indexterm\"> (<span class=\"emphasis\"><em>int-<\/em><\/span>ron denotes their <span class=\"emphasis\"><em>int<\/em><\/span>ervening role), which may be involved in gene regulation but are removed from the pre-mRNA during processing. Intron sequences in mRNA do not encode functional proteins.<\/a><\/p>\n<p><span id=\"m44532-fs-id2098378\"> <\/span>The discovery of introns came as a surprise to researchers in the 1970s who expected that pre-mRNAs would specify protein sequences without further processing, as they had observed in prokaryotes. The genes of higher eukaryotes very often contain one or more introns. These regions may correspond to regulatory sequences; however, the biological significance of having many introns or having very long introns in a gene is unclear. It is possible that introns slow down gene expression because it takes longer to transcribe pre-mRNAs with lots of introns. Alternatively, introns may be nonfunctional sequence remnants left over from the fusion of ancient genes throughout evolution. This is supported by the fact that separate exons often encode separate protein subunits or domains. For the most part, the sequences of introns can be mutated without ultimately affecting the protein product.<\/p>\n<p><span id=\"m44532-fs-id2117424\"> <\/span>All of a pre-mRNA\u2019s introns must be completely and precisely removed before protein synthesis. If the process errs by even a single nucleotide, the reading frame of the rejoined exons would shift, and the resulting protein would be dysfunctional. The process of removing introns and reconnecting exons is called <em class=\"glossterm\"><span id=\"m44532-autoid-cnx2dbk-id1682705\"> <\/span>splicing<\/em><a id=\"id512909\" class=\"indexterm\"> (<\/a><a class=\"xref target-figure\" href=\"ch15.html#m44532-fig-ch15_04_02\" title=\"Figure&#xa0;15.13.&#xa0;\">Figure\u00a015.13<\/a>). Introns are removed and degraded while the pre-mRNA is still in the nucleus. Splicing occurs by a sequence-specific mechanism that ensures introns will be removed and exons rejoined with the accuracy and precision of a single nucleotide. The splicing of pre-mRNAs is conducted by complexes of proteins and RNA molecules called spliceosomes.<\/p>\n<div id=\"m44532-fs-id2937179\" 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=\"m44532-fs-idp68937344\"> <\/span><\/p>\n<div id=\"m44532-fig-ch15_04_02\" class=\"figure\" title=\"Figure&#xa0;15.13.&#xa0;\">\n<div class=\"body\"><span class=\"inlinemediaobject\"><span id=\"m44532-fs-id1480619\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155814\/Figure_15_04_02.png\" width=\"280\" alt=\"Illustration shows a spliceosome bound to mRNA. An intron is wrapped around snRNPs associated with the spliceosome. When the splice is complete, the exons on either side of the intron are fused together, and the intron forms a ring structure.\" \/><\/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\">15.13<\/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\">Pre-mRNA splicing involves the precise removal of introns from the primary RNA transcript. The splicing process is catalyzed by protein complexes called spliceosomes that are composed of proteins and RNA molecules called snRNAs. Spliceosomes recognize sequences at the 5&#8242; and 3&#8242; end of the intron.<\/div>\n<\/div>\n<p><span id=\"m44532-fs-id1864575\"> <\/span>Errors in splicing are implicated in cancers and other human diseases. What kinds of mutations might lead to splicing errors? Think of different possible outcomes if splicing errors occur.<\/p>\n<\/div>\n<\/div>\n<p><span id=\"m44532-fs-id2000672\"> <\/span>Note that more than 70 individual introns can be present, and each has to undergo the process of splicing\u2014in addition to 5&#8242; capping and the addition of a poly-A tail\u2014just to generate a single, translatable mRNA molecule.<\/p>\n<div id=\"m44532-fs-id2010314\" 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=\"m44532-fs-id1436147\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155816\/RNA_splicing.png\" width=\"120\" alt=\"QR Code representing a URL\" \/><\/div>\n<p><span id=\"m44532-fs-id1425631\"> <\/span>See how introns are removed during RNA splicing <a class=\"link\" href=\"http:\/\/openstaxcollege.org\/l\/RNA_splicing\" target=\"\">at this website<\/a>.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"section\" title=\"Processing of tRNAs and rRNAs\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h3 id=\"m44532-fs-id1650543\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">Processing of tRNAs and rRNAs<\/span><\/span><\/h3>\n<\/div>\n<\/div>\n<\/div>\n<p><span id=\"m44532-fs-id2644904\"> <\/span>The tRNAs and rRNAs are structural molecules that have roles in protein synthesis; however, these RNAs are not themselves translated. Pre-rRNAs are transcribed, processed, and assembled into ribosomes in the nucleolus. Pre-tRNAs are transcribed and processed in the nucleus and then released into the cytoplasm where they are linked to free amino acids for protein synthesis.<\/p>\n<p><span id=\"m44532-fs-id2595368\"> <\/span>Most of the tRNAs and rRNAs in eukaryotes and prokaryotes are first transcribed as a long precursor molecule that spans multiple rRNAs or tRNAs. Enzymes then cleave the precursors into subunits corresponding to each structural RNA. Some of the bases of pre-rRNAs are methylated; that is, a \u2013CH<sub>3<\/sub> moiety (methyl functional group) is added for stability. Pre-tRNA molecules also undergo methylation. As with pre-mRNAs, subunit excision occurs in eukaryotic pre-RNAs destined to become tRNAs or rRNAs.<\/p>\n<p><span id=\"m44532-fs-id1450254\"> <\/span>Mature rRNAs make up approximately 50 percent of each ribosome. Some of a ribosome\u2019s RNA molecules are purely structural, whereas others have catalytic or binding activities. Mature tRNAs take on a three-dimensional structure through intramolecular hydrogen bonding to position the amino acid binding site at one end and the <em class=\"glossterm\"><span id=\"m44532-autoid-cnx2dbk-id1578066\"> <\/span>anticodon<\/em><a id=\"id513117\" class=\"indexterm\"> at the other end (<\/a><a class=\"xref target-figure\" href=\"ch15.html#m44532-fig-ch15_04_03\" title=\"Figure&#xa0;15.14.&#xa0;\">Figure\u00a015.14<\/a>). The anticodon is a three-nucleotide sequence in a tRNA that interacts with an mRNA codon through complementary base pairing.<\/p>\n<div id=\"m44532-fig-ch15_04_03\" class=\"figure\" title=\"Figure&#xa0;15.14.&#xa0;\">\n<div class=\"body\">\n<div class=\"mediaobject\"><span id=\"m44532-fs-id1440481\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155819\/Figure_15_04_03.jpg\" width=\"300\" alt=\"The molecular model of phenylalanine tRNA is L-shaped. At one end is the anticodon AAG. At the other end is the attachment site for the amino acid phenylalanine\" \/><\/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\">15.14<\/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\">This is a space-filling model of a tRNA molecule that adds the amino acid phenylalanine to a growing polypeptide chain. The anticodon AAG binds the Codon UUC on the mRNA. The amino acid phenylalanine is attached to the other end of the tRNA.<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div xml:lang=\"en\" class=\"section module\" title=\"15.5.&#xa0;Ribosomes and Protein Synthesis\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h2 id=\"m44529\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.5<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Ribosomes and Protein Synthesis<sup><a href=\"co03.html#book-attribution-m44529\">*<\/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 different steps in protein synthesis<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>Discuss the role of ribosomes in protein synthesis<\/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=\"#m44529-fs-id2009587\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">The Protein Synthesis Machinery<\/span><\/a>\n<ul>\n<li class=\"toc-section\"><a href=\"#m44529-fs-id1425631\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">Ribosomes<\/span><\/a><\/li>\n<li class=\"toc-section\"><a href=\"#m44529-fs-id2897379\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">tRNAs<\/span><\/a><\/li>\n<li class=\"toc-section\"><a href=\"#m44529-fs-id1461234\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">Aminoacyl tRNA Synthetases<\/span><\/a><\/li>\n<\/ul>\n<\/li>\n<li class=\"toc-section\"><a href=\"#m44529-fs-id1986668\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">The Mechanism of Protein Synthesis<\/span><\/a>\n<ul>\n<li class=\"toc-section\"><a href=\"#m44529-fs-id2321391\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">Initiation of Translation<\/span><\/a><\/li>\n<li class=\"toc-section\"><a href=\"#m44529-fs-id2217094\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">Translation, Elongation, and Termination<\/span><\/a><\/li>\n<\/ul>\n<\/li>\n<li class=\"toc-section\"><a href=\"#m44529-fs-id2762763\" class=\"target-section\"><span class=\"cnx-gentext-section cnx-gentext-t\">Protein Folding, Modification, and Targeting<\/span><\/a><\/li>\n<\/ul>\n<\/div>\n<p><span id=\"m44529-fs-id2195690\"> <\/span>The synthesis of proteins consumes more of a cell\u2019s energy than any other metabolic process. In turn, proteins account for more mass than any other component of living organisms (with the exception of water), and proteins perform virtually every function of a cell. The process of translation, or protein synthesis, involves the decoding of an mRNA message into a polypeptide product. Amino acids are covalently strung together by interlinking peptide bonds in lengths ranging from approximately 50 amino acid residues to more than 1,000. Each individual amino acid has an amino group (NH<sub>2<\/sub>) and a carboxyl (COOH) group. Polypeptides are formed when the amino group of one amino acid forms an amide (i.e., peptide) bond with the carboxyl group of another amino acid (<a class=\"xref target-figure\" href=\"ch15.html#m44529-fig-ch15_05_01\" title=\"Figure&#xa0;15.15.&#xa0;\">Figure\u00a015.15<\/a>). This reaction is catalyzed by ribosomes and generates one water molecule.<\/p>\n<div id=\"m44529-fig-ch15_05_01\" class=\"figure\" title=\"Figure&#xa0;15.15.&#xa0;\">\n<div class=\"body\">\n<div class=\"mediaobject\"><span id=\"m44529-fs-id1236580\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155821\/Figure_15_05_01.jpg\" width=\"280\" alt=\"Illustration shows two amino acids side-by-side. Each amino acid has an amino group, a carboxyl group, and a side chain labeled R or R'. Upon formation of a peptide bond, the amino group is joined to the carboxyl group. A water molecule is released in the process.\" \/><\/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\">15.15<\/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\">A peptide bond links the carboxyl end of one amino acid with the amino end of another, expelling one water molecule. For simplicity in this image, only the functional groups involved in the peptide bond are shown. The R and R&#8217; designations refer to the rest of each amino acid structure.<\/div>\n<\/div>\n<div class=\"section\" title=\"The Protein Synthesis Machinery\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h3 id=\"m44529-fs-id2009587\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">The Protein Synthesis Machinery<\/span><\/span><\/h3>\n<\/div>\n<\/div>\n<\/div>\n<p><span id=\"m44529-fs-id2739564\"> <\/span>In addition to the mRNA template, many molecules and macromolecules contribute to the process of translation. The composition of each component may vary across species; for instance, ribosomes may consist of different numbers of rRNAs and polypeptides depending on the organism. However, the general structures and functions of the protein synthesis machinery are comparable from bacteria to human cells. Translation requires the input of an mRNA template, ribosomes, tRNAs, and various enzymatic factors.<\/p>\n<div id=\"m44529-fs-id2046909\" 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=\"m44529-fs-id2890478\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155823\/prokary_protein.png\" width=\"120\" alt=\"QR Code representing a URL\" \/><\/div>\n<p><span id=\"m44529-fs-id2694589\"> <\/span>Click through the steps of this <a class=\"link\" href=\"http:\/\/openstaxcollege.org\/l\/prokary_protein\" target=\"\">PBS interactive<\/a> to see protein synthesis in action.<\/p>\n<\/div>\n<\/div>\n<div class=\"section\" title=\"Ribosomes\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h4 id=\"m44529-fs-id1425631\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">Ribosomes<\/span><\/span><\/h4>\n<\/div>\n<\/div>\n<\/div>\n<p><span id=\"m44529-fs-id1769427\"> <\/span>Even before an mRNA is translated, a cell must invest energy to build each of its ribosomes. In <span class=\"emphasis\"><em>E. coli<\/em><\/span>, there are  between 10,000 and 70,000  ribosomes present in each cell at any given time. A ribosome is a complex macromolecule composed of structural and catalytic rRNAs, and many distinct polypeptides. In eukaryotes, the nucleolus is completely specialized for the synthesis and assembly of rRNAs.<\/p>\n<p><span id=\"m44529-fs-id2000981\"> <\/span>Ribosomes exist in the cytoplasm in prokaryotes and in the cytoplasm and rough endoplasmic reticulum in eukaryotes. Mitochondria and chloroplasts also have their own ribosomes in the matrix and stroma, which look more similar to prokaryotic ribosomes (and have similar drug sensitivities) than the ribosomes just outside their outer membranes in the cytoplasm.  Ribosomes dissociate into large and small subunits when they are not synthesizing proteins and reassociate during the initiation of translation. In <span class=\"emphasis\"><em>E. coli<\/em><\/span>, the small subunit is described as 30S, and the large subunit is 50S, for a total of 70S (recall that Svedberg units are not additive). Mammalian ribosomes have a small 40S subunit and a large 60S subunit, for a total of 80S. The small subunit is responsible for binding the mRNA template, whereas the large subunit sequentially binds tRNAs. Each mRNA molecule is simultaneously translated by many ribosomes, all synthesizing protein in the same direction: reading the mRNA from 5&#8242; to 3&#8242; and synthesizing the polypeptide from the N terminus to the C terminus. The complete mRNA\/poly-ribosome structure is called a <em class=\"glossterm\"><span id=\"m44529-autoid-cnx2dbk-id1591612\"> <\/span>polysome<\/em><a id=\"id513761\" class=\"indexterm\">.<\/a><\/p>\n<\/div>\n<div class=\"section\" title=\"tRNAs\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h4 id=\"m44529-fs-id2897379\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">tRNAs<\/span><\/span><\/h4>\n<\/div>\n<\/div>\n<\/div>\n<p><span id=\"m44529-fs-id1613052\"> <\/span>The tRNAs are structural RNA molecules that were transcribed from genes by RNA polymerase III. Depending on the species, 40 to 60 types of tRNAs exist in the cytoplasm. Serving as adaptors, specific tRNAs bind to sequences on the mRNA template and add the corresponding amino acid to the polypeptide chain. Therefore, tRNAs are the molecules that actually \u201ctranslate\u201d the language of RNA into the language of proteins.<\/p>\n<p><span id=\"m44529-fs-id2853827\"> <\/span>Of the 64 possible mRNA codons\u2014or triplet combinations of A, U, G, and C\u2014three specify the termination of protein synthesis and 61 specify the addition of amino acids to the polypeptide chain. Of these 61, one codon (AUG) also encodes the initiation of translation. Each tRNA anticodon can base pair with one of the mRNA codons and add an amino acid or terminate translation, according to the genetic code. For instance, if the sequence CUA occurred on an mRNA template in the proper reading frame, it would bind a tRNA expressing the complementary sequence, GAU, which would be linked to the amino acid leucine.<\/p>\n<p><span id=\"m44529-fs-id3063554\"> <\/span>As the adaptor molecules of translation, it is surprising that tRNAs can fit so much specificity into such a small package. Consider that tRNAs need to interact with three factors:  1) they must be recognized by the correct aminoacyl synthetase (see below); 2) they must be recognized by ribosomes; and 3) they must bind to the correct sequence in mRNA.<\/p>\n<\/div>\n<div class=\"section\" title=\"Aminoacyl tRNA Synthetases\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h4 id=\"m44529-fs-id1461234\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">Aminoacyl tRNA Synthetases<\/span><\/span><\/h4>\n<\/div>\n<\/div>\n<\/div>\n<p><span id=\"m44529-fs-id1720501\"> <\/span>The process of pre-tRNA synthesis by RNA polymerase III only creates the RNA portion of the adaptor molecule. The corresponding amino acid must be added later, once the tRNA is processed and exported to the cytoplasm. Through the process of tRNA \u201ccharging,\u201d each tRNA molecule is linked to its correct amino acid by a group of enzymes called <em class=\"glossterm\"><span id=\"m44529-autoid-cnx2dbk-id1237710\"> <\/span>aminoacyl tRNA synthetases<\/em><a id=\"id513846\" class=\"indexterm\">. At least one type of aminoacyl tRNA synthetase exists for each of the 20 amino acids; the exact number of aminoacyl tRNA synthetases varies by species. These enzymes first bind and hydrolyze ATP to catalyze a high-energy bond between an amino acid and adenosine monophosphate (AMP); a pyrophosphate molecule is expelled in this reaction. The activated amino acid is then transferred to the tRNA, and AMP is released.<\/a><\/p>\n<\/div>\n<\/div>\n<div class=\"section\" title=\"The Mechanism of Protein Synthesis\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h3 id=\"m44529-fs-id1986668\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">The Mechanism of Protein Synthesis<\/span><\/span><\/h3>\n<\/div>\n<\/div>\n<\/div>\n<p><span id=\"m44529-fs-id2334597\"> <\/span>As with mRNA synthesis, protein synthesis can be divided into three phases: initiation, elongation, and termination. The process of translation is similar in prokaryotes and eukaryotes. Here we\u2019ll explore how translation occurs in <span class=\"emphasis\"><em>E. coli<\/em><\/span>, a representative prokaryote, and specify any differences between prokaryotic and eukaryotic translation.<\/p>\n<div class=\"section\" title=\"Initiation of Translation\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h4 id=\"m44529-fs-id2321391\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">Initiation of Translation<\/span><\/span><\/h4>\n<\/div>\n<\/div>\n<\/div>\n<p><span id=\"m44529-fs-id1240070\"> <\/span>Protein synthesis begins with the formation of an initiation complex. In <span class=\"emphasis\"><em>E. coli<\/em><\/span>, this complex involves the small 30S ribosome, the mRNA template, three initiation factors (IFs; IF-1, IF-2, and IF-3), and a special <em class=\"glossterm\"><span id=\"m44529-autoid-cnx2dbk-id1276479\"> <\/span>initiator tRNA<\/em><a id=\"id513915\" class=\"indexterm\">, called <span class=\"inlinemediaobject\"><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155825\/autogen-svg2png-00013.png\" style=\"width:; height:; vertical-align:-5.2783999999999995pt;\" alt=\"image\" \/><\/span>. The initiator tRNA interacts with the <em class=\"glossterm\"><span id=\"m44529-autoid-cnx2dbk-id1624879\"> <\/span>start codon<\/em><\/a><a id=\"id514135\" class=\"indexterm\"> AUG (or rarely, GUG), links to a formylated methionine called fMet, and can also bind IF-2. Formylated methionine is inserted by <span class=\"inlinemediaobject\"><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155825\/autogen-svg2png-00021.png\" style=\"width:; height:; vertical-align:-5.278400000000001pt;\" alt=\"image\" \/><\/span> at the beginning of every polypeptide chain synthesized by <span class=\"emphasis\"><em>E. coli<\/em><\/span>, but it is usually clipped off after translation is complete. When an in-frame AUG is encountered during translation elongation, a non-formylated methionine is inserted by a regular Met-tRNA<sup>Met<\/sup>.<\/a><\/p>\n<p><span id=\"m44529-fs-id2936033\"> <\/span>In <span class=\"emphasis\"><em>E. coli<\/em><\/span> mRNA, a sequence upstream of the first AUG codon, called the <em class=\"glossterm\"><span id=\"m44529-autoid-cnx2dbk-id1401010\"> <\/span>Shine-Dalgarno sequence<\/em><a id=\"id514455\" class=\"indexterm\"> (AGGAGG), interacts with the rRNA molecules that compose the ribosome. This interaction anchors the 30S ribosomal subunit at the correct location on the mRNA template. Guanosine triphosphate (GTP), which is a purine nucleotide triphosphate, acts as an energy source during translation\u2014both at the start of elongation and during the ribosome\u2019s translocation.<\/a><\/p>\n<p><span id=\"m44529-fs-id2334805\"> <\/span>In eukaryotes, a similar initiation complex forms, comprising mRNA, the 40S small ribosomal subunit, IFs, and nucleoside triphosphates (GTP and ATP). The charged initiator tRNA, called Met-tRNA<sub>i<\/sub>, does not bind fMet in eukaryotes, but is distinct from other Met-tRNAs in that it can bind IFs.<\/p>\n<p><span id=\"m44529-fs-id3053365\"> <\/span>Instead of depositing at the Shine-Dalgarno sequence, the eukaryotic initiation complex recognizes the 7-methylguanosine cap at the 5&#8242; end of the mRNA. A cap-binding protein (CBP) and several other IFs assist the movement of the ribosome to the 5&#8242; cap. Once at the cap, the initiation complex tracks along the mRNA in the 5&#8242; to 3&#8242; direction, searching for the AUG start codon. Many eukaryotic mRNAs are translated from the first AUG, but this is not always the case. According to <em class=\"glossterm\"><span id=\"m44529-autoid-cnx2dbk-id1401038\"> <\/span>Kozak\u2019s rules<\/em><a id=\"id514498\" class=\"indexterm\">, the nucleotides around the AUG indicate whether it is the correct start codon. Kozak\u2019s rules state that the following consensus sequence must appear around the AUG of vertebrate genes: 5&#8242;-gccRccAUGG-3&#8242;. The R (for purine) indicates a site that can be either A or G, but cannot be C or U. Essentially, the closer the sequence is to this consensus, the higher the efficiency of translation.<\/a><\/p>\n<p><span id=\"m44529-fs-id2682290\"> <\/span>Once the appropriate AUG is identified, the other proteins and CBP dissociate, and the 60S subunit binds to the complex of Met-tRNA<sub>i<\/sub>, mRNA, and the 40S subunit. This step completes the initiation of translation in eukaryotes.<\/p>\n<\/div>\n<div class=\"section\" title=\"Translation, Elongation, and Termination\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h4 id=\"m44529-fs-id2217094\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">Translation, Elongation, and Termination<\/span><\/span><\/h4>\n<\/div>\n<\/div>\n<\/div>\n<p><span id=\"m44529-fs-id2013469\"> <\/span>In prokaryotes and eukaryotes, the basics of elongation are the same, so we will review elongation from the perspective of <span class=\"emphasis\"><em>E. coli<\/em><\/span>. The 50S ribosomal subunit of <span class=\"emphasis\"><em>E. coli <\/em><\/span>consists of three compartments: the A (aminoacyl) site binds incoming charged aminoacyl tRNAs. The P (peptidyl) site binds charged tRNAs carrying amino acids that have formed peptide bonds with the growing polypeptide chain but have not yet dissociated from their corresponding tRNA. The E (exit) site releases dissociated tRNAs so that they can be recharged with free amino acids. There is one exception to this assembly line of tRNAs: in <span class=\"emphasis\"><em>E. coli<\/em><\/span>, <span class=\"inlinemediaobject\"><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155826\/autogen-svg2png-0003.png\" style=\"width:; height:; vertical-align:-5.278400000000001pt;\" alt=\"image\" \/><\/span> is capable of entering the P site directly without first entering the A site. Similarly, the eukaryotic Met-tRNA<sub>i<\/sub>, with help from other proteins of the initiation complex, binds directly to the P site. In both cases, this creates an initiation complex with a free A site ready to accept the tRNA corresponding to the first codon after the AUG.<\/p>\n<p><span id=\"m44529-fs-id1313555\"> <\/span>During translation elongation, the mRNA template provides specificity. As the ribosome moves along the mRNA, each mRNA codon comes into register, and specific binding with the corresponding charged tRNA anticodon is ensured. If mRNA were not present in the elongation complex, the ribosome would bind tRNAs nonspecifically.<\/p>\n<p><span id=\"m44529-fs-id2608514\"> <\/span>Elongation proceeds with charged tRNAs entering the A site and then shifting to the P site followed by the E site with each single-codon \u201cstep\u201d of the ribosome. Ribosomal steps are induced by conformational changes that advance the ribosome by three bases in the 3&#8242; direction. The energy for each step of the ribosome is donated by an elongation factor that hydrolyzes GTP. Peptide bonds form between the amino group of the amino acid attached to the A-site tRNA and the carboxyl group of the amino acid attached to the P-site tRNA. The formation of each peptide bond is catalyzed by <em class=\"glossterm\"><span id=\"m44529-autoid-cnx2dbk-id1423355\"> <\/span>peptidyl transferase<\/em><a id=\"id514886\" class=\"indexterm\">, an RNA-based enzyme that is integrated into the 50S ribosomal subunit. The energy for each peptide bond formation is derived from GTP hydrolysis, which is catalyzed by a separate elongation factor. The amino acid bound to the P-site tRNA is also linked to the growing polypeptide chain. As the ribosome steps across the mRNA, the former P-site tRNA enters the E site, detaches from the amino acid, and is expelled (<\/a><a class=\"xref target-figure\" href=\"ch15.html#m44529-fig-ch15_05_02\" title=\"Figure&#xa0;15.16.&#xa0;\">Figure\u00a015.16<\/a>). Amazingly, the <span class=\"emphasis\"><em>E. coli <\/em><\/span>translation apparatus takes only 0.05 seconds to add each amino acid, meaning that a 200-amino acid protein can be translated in just 10 seconds.<\/p>\n<div id=\"m44529-fs-id1097260\" 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=\"m44529-fs-idm66901536\"> <\/span><\/p>\n<div id=\"m44529-fig-ch15_05_02\" class=\"figure\" title=\"Figure&#xa0;15.16.&#xa0;\">\n<div class=\"body\"><span class=\"inlinemediaobject\"><span id=\"m44529-fs-id1786828\"> <\/span><img decoding=\"async\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/511\/2016\/08\/19155827\/Figure_15_05_02.png\" width=\"250\" alt=\"Illustration shows the steps of protein synthesis. First, the initiator tRNA recognizes the sequence AUG on an mRNA that is associated with the small ribosomal subunit. The large subunit then joins the complex. Next, a second tRNA is recruited at the A site. A peptide bond is formed between the first amino acid, which is at the P site, and the second amino acid, which is at the A site. The mRNA then shifts and the first tRNA is moved to the E site, where it dissociates from the ribosome. Another tRNA binds at the A site, and the process is repeated.\" \/><\/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\">15.16<\/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\">Translation begins when an initiator tRNA anticodon recognizes a codon on mRNA. The large ribosomal subunit joins the small subunit, and a second tRNA is recruited. As the mRNA moves relative to the ribosome, the polypeptide chain is formed. Entry of a release factor into the A site terminates translation and the components dissociate.<\/div>\n<\/div>\n<p><span id=\"m44529-fs-id1354131\"> <\/span>Many antibiotics inhibit bacterial protein synthesis. For example, tetracycline blocks the A site on the bacterial ribosome, and chloramphenicol blocks peptidyl transfer. What specific effect would you expect each of these antibiotics to have on protein synthesis?<\/p>\n<p><span id=\"m44529-fs-id2682756\"> <\/span>Tetracycline would directly affect:<\/p>\n<div class=\"orderedlist\"><span id=\"m44529-fs-id1471212\"> <\/span><\/p>\n<ol class=\"orderedlist\" type=\"a\">\n<li class=\"listitem\">\n<p>tRNA binding to the ribosome<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>ribosome assembly<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>growth of the protein chain<\/p>\n<\/li>\n<\/ol>\n<\/div>\n<p><span id=\"m44529-fs-id2114520\"> <\/span>Chloramphenicol would directly affect<\/p>\n<div class=\"orderedlist\"><span id=\"m44529-fs-id1803212\"> <\/span><\/p>\n<ol class=\"orderedlist\" type=\"a\">\n<li class=\"listitem\">\n<p>tRNA binding to the ribosome<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>ribosome assembly<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>growth of the protein chain<\/p>\n<\/li>\n<\/ol>\n<\/div>\n<\/div>\n<\/div>\n<p><span id=\"m44529-fs-id2155698\"> <\/span>Termination of translation occurs when a nonsense codon (UAA, UAG, or UGA) is encountered. Upon aligning with the A site, these nonsense codons are recognized by release factors in prokaryotes and eukaryotes that instruct peptidyl transferase to add a water molecule to the carboxyl end of the P-site amino acid. This reaction forces the P-site amino acid to detach from its tRNA, and the newly made protein is released. The small and large ribosomal subunits dissociate from the mRNA and from each other; they are recruited almost immediately into another translation initiation complex. After many ribosomes have completed translation, the mRNA is degraded so the nucleotides can be reused in another transcription reaction.<\/p>\n<\/div>\n<\/div>\n<div class=\"section\" title=\"Protein Folding, Modification, and Targeting\">\n<div class=\"titlepage\">\n<div>\n<div>\n<h3 id=\"m44529-fs-id2762763\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-t\">Protein Folding, Modification, and Targeting<\/span><\/span><\/h3>\n<\/div>\n<\/div>\n<\/div>\n<p><span id=\"m44529-fs-id2979153\"> <\/span>During and after translation, individual amino acids may be chemically modified, signal sequences may be appended, and the new protein \u201cfolds\u201d into a distinct three-dimensional structure as a result of intramolecular interactions. A <em class=\"glossterm\"><span id=\"m44529-autoid-cnx2dbk-id1387490\"> <\/span>signal sequence<\/em><a id=\"id515087\" class=\"indexterm\"> is a short tail of amino acids that directs a protein to a specific cellular compartment. These sequences at the amino end or the carboxyl end of the protein can be thought of as the protein\u2019s \u201ctrain ticket\u201d to its ultimate destination. Other cellular factors recognize each signal sequence and help transport the protein from the cytoplasm to its correct compartment. For instance, a specific sequence at the amino terminus will direct a protein to the mitochondria or chloroplasts (in plants). Once the protein reaches its cellular destination, the signal sequence is usually clipped off.<\/a><\/p>\n<p><span id=\"m44529-fs-id2165193\"> <\/span>Many proteins fold spontaneously, but some proteins require helper molecules, called chaperones, to prevent them from aggregating during the complicated process of folding. Even if a protein is properly specified by its corresponding mRNA, it could take on a completely dysfunctional shape if abnormal temperature or pH conditions prevent it from folding correctly.<\/p>\n<\/div>\n<\/div>\n<div class=\"glossary\" title=\"Glossary\" id=\"id515529\">\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>7-methylguanosine cap<\/dt>\n<dd>\n<p>modification added to the 5&#8242; end of pre-mRNAs to protect mRNA from degradation and assist translation<\/p>\n<\/dd>\n<dt>aminoacyl tRNA synthetase<\/dt>\n<dd>\n<p>enzyme that \u201ccharges\u201d tRNA molecules by catalyzing a bond between the tRNA and a corresponding amino acid<\/p>\n<\/dd>\n<dt>anticodon<\/dt>\n<dd>\n<p>three-nucleotide sequence in a tRNA molecule that corresponds to an mRNA codon<\/p>\n<\/dd>\n<dt>CAAT box<\/dt>\n<dd>\n<p>(GGCCAATCT) essential eukaryotic promoter sequence involved in binding transcription factors<\/p>\n<\/dd>\n<dt>Central Dogma<\/dt>\n<dd>\n<p>states that genes specify the sequence of mRNAs, which in turn specify the sequence of proteins<\/p>\n<\/dd>\n<dt>codon<\/dt>\n<dd>\n<p>three consecutive nucleotides in mRNA that specify the insertion of an amino acid or the release of a polypeptide chain during translation<\/p>\n<\/dd>\n<dt>colinear<\/dt>\n<dd>\n<p>in terms of RNA and protein, three \u201cunits\u201d of RNA (nucleotides) specify one \u201cunit\u201d of protein (amino acid) in a consecutive fashion<\/p>\n<\/dd>\n<dt>consensus<\/dt>\n<dd>\n<p>DNA sequence that is used by many species to perform the same or similar functions<\/p>\n<\/dd>\n<dt>core enzyme<\/dt>\n<dd>\n<p>prokaryotic RNA polymerase consisting of <span class=\"emphasis\"><em>\u03b1<\/em><\/span>, <span class=\"emphasis\"><em>\u03b1<\/em><\/span>, <span class=\"emphasis\"><em>\u03b2<\/em><\/span>, and <span class=\"emphasis\"><em>\u03b2<\/em><\/span>&#8216; but missing <span class=\"emphasis\"><em>\u03c3<\/em><\/span>; this complex performs elongation<\/p>\n<\/dd>\n<dt>degeneracy<\/dt>\n<dd>\n<p>(of the genetic code) describes that a given amino acid can be encoded by more than one nucleotide triplet; the code is degenerate, but not ambiguous<\/p>\n<\/dd>\n<dt>downstream<\/dt>\n<dd>\n<p>nucleotides following the initiation site in the direction of mRNA transcription; in general, sequences that are toward the 3&#8242; end relative to a site on the mRNA<\/p>\n<\/dd>\n<dt>exon<\/dt>\n<dd>\n<p>sequence present in protein-coding mRNA after completion of pre-mRNA splicing<\/p>\n<\/dd>\n<dt>FACT<\/dt>\n<dd>\n<p>complex that \u201cfacilitates chromatin transcription\u201d by disassembling nucleosomes ahead of a transcribing RNA polymerase II and reassembling them after the polymerase passes by<\/p>\n<\/dd>\n<dt>GC-rich box<\/dt>\n<dd>\n<p>(GGCG) nonessential eukaryotic promoter sequence that binds cellular factors to increase the efficiency of transcription; may be present several times in a promoter<\/p>\n<\/dd>\n<dt>hairpin<\/dt>\n<dd>\n<p>structure of RNA when it folds back on itself and forms intramolecular hydrogen bonds between complementary nucleotides<\/p>\n<\/dd>\n<dt>holoenzyme<\/dt>\n<dd>\n<p>prokaryotic RNA polymerase consisting of <span class=\"emphasis\"><em>\u03b1<\/em><\/span>, <span class=\"emphasis\"><em>\u03b1<\/em><\/span>, <span class=\"emphasis\"><em>\u03b2<\/em><\/span>, <span class=\"emphasis\"><em>\u03b2<\/em><\/span>&#8216;, and <span class=\"emphasis\"><em>\u03c3<\/em><\/span>; this complex is responsible for transcription initiation<\/p>\n<\/dd>\n<dt>initiation site<\/dt>\n<dd>\n<p>nucleotide from which mRNA synthesis proceeds in the 5&#8242; to 3&#8242; direction; denoted with a \u201c+1\u201d<\/p>\n<\/dd>\n<dt>initiator tRNA<\/dt>\n<dd>\n<p>in prokaryotes, called <span class=\"token\"><\/p>\n<p>  <span class=\"emphasis mathml-mi\"><em>t<\/em><\/span><span class=\"emphasis mathml-mi\"><em>R<\/em><\/span><span class=\"emphasis mathml-mi\"><em>N<\/em><\/span><span class=\"emphasis mathml-mi\"><em>A<\/em><\/span><sub><span class=\"emphasis mathml-mi\"><em>f<\/em><\/span><\/sub><sup><span class=\"bold mathml-mi\"><strong>Met<\/strong><\/span><\/sup><\/span><br \/>\n; in eukaryotes, called tRNA<sub>i<\/sub>; a tRNA that interacts with a start codon, binds directly to the ribosome P site, and links to a special methionine to begin a polypeptide chain<\/p>\n<\/dd>\n<dt>intron<\/dt>\n<dd>\n<p>non\u2013protein-coding intervening sequences that are spliced from mRNA during processing<\/p>\n<\/dd>\n<dt>Kozak\u2019s rules<\/dt>\n<dd>\n<p>determines the correct initiation AUG in a eukaryotic mRNA; the following consensus sequence must appear around the AUG: 5\u2019-GCC(<span class=\"bold\"><strong>purine<\/strong><\/span>)CCAUG<span class=\"bold\"><strong>G<\/strong><\/span>-3\u2019; the bolded bases are most important<\/p>\n<\/dd>\n<dt>nonsense codon<\/dt>\n<dd>\n<p>one of the three mRNA codons that specifies termination of translation<\/p>\n<\/dd>\n<dt>nontemplate strand<\/dt>\n<dd>\n<p>strand of DNA that is not used to transcribe mRNA; this strand is identical to the mRNA except that T nucleotides in the DNA are replaced by U nucleotides in the mRNA<\/p>\n<\/dd>\n<dt>Octamer box<\/dt>\n<dd>\n<p>(ATTTGCAT) nonessential eukaryotic promoter sequence that binds cellular factors to increase the efficiency of transcription; may be present several times in a promoter<\/p>\n<\/dd>\n<dt>peptidyl transferase<\/dt>\n<dd>\n<p>RNA-based enzyme that is integrated into the 50S ribosomal subunit and catalyzes the formation of peptide bonds<\/p>\n<\/dd>\n<dt>plasmid<\/dt>\n<dd>\n<p>extrachromosomal, covalently closed, circular DNA molecule that may only contain one or a few genes; common in prokaryotes<\/p>\n<\/dd>\n<dt>poly-A tail<\/dt>\n<dd>\n<p>modification added to the 3&#8242; end of pre-mRNAs to protect mRNA from degradation and assist mRNA export from the nucleus<\/p>\n<\/dd>\n<dt>polysome<\/dt>\n<dd>\n<p>mRNA molecule simultaneously being translated by many ribosomes all going in the same direction<\/p>\n<\/dd>\n<dt>preinitiation complex<\/dt>\n<dd>\n<p>cluster of transcription factors and other proteins that recruit RNA polymerase II for transcription of a DNA template<\/p>\n<\/dd>\n<dt>promoter<\/dt>\n<dd>\n<p>DNA sequence to which RNA polymerase and associated factors bind and initiate transcription<\/p>\n<\/dd>\n<dt>RNA editing<\/dt>\n<dd>\n<p>direct alteration of one or more nucleotides in an mRNA that has already been synthesized<\/p>\n<\/dd>\n<dt>Rho-dependent termination<\/dt>\n<dd>\n<p>in prokaryotes, termination of transcription by an interaction between RNA polymerase and the rho protein at a run of G nucleotides on the DNA template<\/p>\n<\/dd>\n<dt>Rho-independent<\/dt>\n<dd>\n<p>termination sequence-dependent termination of prokaryotic mRNA synthesis; caused by hairpin formation in the mRNA that stalls the polymerase<\/p>\n<\/dd>\n<dt>reading frame<\/dt>\n<dd>\n<p>sequence of triplet codons in mRNA that specify a particular protein; a ribosome shift of one or two nucleotides in either direction completely abolishes synthesis of that protein<\/p>\n<\/dd>\n<dt>Shine-Dalgarno sequence<\/dt>\n<dd>\n<p>(AGGAGG); initiates prokaryotic translation by interacting with rRNA molecules comprising the 30S ribosome<\/p>\n<\/dd>\n<dt>signal sequence<\/dt>\n<dd>\n<p>short tail of amino acids that directs a protein to a specific cellular compartment<\/p>\n<\/dd>\n<dt>small nuclear RNA<\/dt>\n<dd>\n<p>molecules synthesized by RNA polymerase III that have a variety of functions, including splicing pre-mRNAs and regulating transcription factors<\/p>\n<\/dd>\n<dt>splicing<\/dt>\n<dd>\n<p>process of removing introns and reconnecting exons in a pre-mRNA<\/p>\n<\/dd>\n<dt>start codon<\/dt>\n<dd>\n<p>AUG (or rarely, GUG) on an mRNA from which translation begins; always specifies methionine<\/p>\n<\/dd>\n<dt>TATA box<\/dt>\n<dd>\n<p>conserved promoter sequence in eukaryotes and prokaryotes that helps to establish the initiation site for transcription<\/p>\n<\/dd>\n<dt>template strand<\/dt>\n<dd>\n<p>strand of DNA that specifies the complementary mRNA molecule<\/p>\n<\/dd>\n<dt>transcription bubble<\/dt>\n<dd>\n<p>region of locally unwound DNA that allows for transcription of mRNA<\/p>\n<\/dd>\n<dt>upstream<\/dt>\n<dd>\n<p>nucleotides preceding the initiation site; in general, sequences toward the 5&#8242; end relative to a site on the mRNA<\/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=\"#m44518\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.<\/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=\"#m44522\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.1<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">The Genetic Code<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<p><span id=\"m44522-fs-id3086772\"> <\/span>The genetic code refers to the DNA alphabet (A, T, C, G), the RNA alphabet (A, U, C, G), and the polypeptide alphabet (20 amino acids). The Central Dogma describes the flow of genetic information in the cell from genes to mRNA to proteins. Genes are used to make mRNA by the process of transcription; mRNA is used to synthesize proteins by the process of translation. The genetic code is degenerate because 64 triplet codons in mRNA specify only 20 amino acids and three nonsense codons. Almost every species on the planet uses the same genetic code.<\/p>\n<\/div>\n<\/div>\n<div class=\"section\">\n<div class=\"title\"><a href=\"#m44523\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.2<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Prokaryotic Transcription<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<p><span id=\"m44523-fs-id1265785\"> <\/span>In prokaryotes, mRNA synthesis is initiated at a promoter sequence on the DNA template comprising two consensus sequences that recruit RNA polymerase. The prokaryotic polymerase consists of a core enzyme of four protein subunits and a <span class=\"emphasis\"><em>\u03c3<\/em><\/span> protein that assists only with initiation. Elongation synthesizes mRNA in the 5&#8242; to 3&#8242; direction at a rate of 40 nucleotides per second. Termination liberates the mRNA and occurs either by rho protein interaction or by the formation of an mRNA hairpin.<\/p>\n<\/div>\n<\/div>\n<div class=\"section\">\n<div class=\"title\"><a href=\"#m44524\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.3<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Eukaryotic Transcription<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<p><span id=\"m44524-fs-id1097260\"> <\/span>Transcription in eukaryotes involves one of three types of polymerases, depending on the gene being transcribed. RNA polymerase II transcribes all of the protein-coding genes, whereas RNA polymerase I transcribes rRNA genes, and RNA polymerase III transcribes rRNA, tRNA, and small nuclear RNA genes. The initiation of transcription in eukaryotes involves the binding of several transcription factors to complex promoter sequences that are usually located upstream of the gene being copied. The mRNA is synthesized in the 5&#8242; to 3&#8242; direction, and the FACT complex moves and reassembles nucleosomes as the polymerase passes by. Whereas RNA polymerases I and III terminate transcription by protein- or RNA hairpin-dependent methods, RNA polymerase II transcribes for 1,000 or more nucleotides beyond the gene template and cleaves the excess during pre-mRNA processing.<\/p>\n<\/div>\n<\/div>\n<div class=\"section\">\n<div class=\"title\"><a href=\"#m44532\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.4<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">RNA Processing in Eukaryotes<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<p><span id=\"m44532-fs-id2270525\"> <\/span>Eukaryotic pre-mRNAs are modified with a 5&#8242; methylguanosine cap and a poly-A tail. These structures protect the mature mRNA from degradation and help export it from the nucleus. Pre-mRNAs also undergo splicing, in which introns are removed and exons are reconnected with single-nucleotide accuracy. Only finished mRNAs that have undergone 5&#8242; capping, 3&#8242; polyadenylation, and intron splicing are exported from the nucleus to the cytoplasm. Pre-rRNAs and pre-tRNAs may be processed by intramolecular cleavage, splicing, methylation, and chemical conversion of nucleotides. Rarely, RNA editing is also performed to insert missing bases after an mRNA has been synthesized.<\/p>\n<\/div>\n<\/div>\n<div class=\"section\">\n<div class=\"title\"><a href=\"#m44529\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.5<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Ribosomes and Protein Synthesis<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<p><span id=\"m44529-fs-id1957598\"> <\/span>The players in translation include the mRNA template, ribosomes, tRNAs, and various enzymatic factors. The small ribosomal subunit forms on the mRNA template either at the Shine-Dalgarno sequence (prokaryotes) or the 5&#8242; cap (eukaryotes). Translation begins at the initiating AUG on the mRNA, specifying methionine. The formation of peptide bonds occurs between sequential amino acids specified by the mRNA template according to the genetic code. Charged tRNAs enter the ribosomal A site, and their amino acid bonds with the amino acid at the P site. The entire mRNA is translated in three-nucleotide \u201csteps\u201d of the ribosome. When a nonsense codon is encountered, a release factor binds and dissociates the components and frees the new protein. Folding of the protein occurs during and after translation.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<p>&lt;!&#8211;CNX: Start Area: &#8220;&#8221;&#8211;&gt;<\/p>\n<div class=\"cnx-eoc art-exercise\">\n<div class=\"title\"><span><\/span><\/div>\n<div class=\"section empty\">\n<div class=\"title\"><a href=\"#m44518\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.<\/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=\"#m44522\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.1<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">The Genetic Code<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<div class=\"section empty\">\n<div class=\"title\"><a href=\"#m44523\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.2<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Prokaryotic Transcription<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<div class=\"section\">\n<div class=\"title\"><a href=\"#m44524\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.3<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Eukaryotic Transcription<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<div id=\"m44524-fs-idp79573648\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44524-fs-idm45398016\"><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=\"m44524-fs-idm70130112\"> <\/span><\/p>\n<p><span id=\"m44524-fs-idm59081616\"> <\/span><a class=\"xref target-figure\" href=\"ch15.html#m44524-fig-ch15_03_02\" title=\"Figure&#xa0;15.11.&#xa0;\">Figure\u00a015.11<\/a> A scientist splices a eukaryotic promoter in front of a bacterial gene and inserts the gene in a bacterial chromosome. Would you expect the bacteria to transcribe the gene?<\/p>\n<\/div>\n<div id=\"m44524-fs-idm45398016\" 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=\"ch15.html#m44524-fs-idp79573648\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44524-fs-idm11981392\"> <\/span><a class=\"xref target-figure\" href=\"ch15.html#m44524-fig-ch15_03_02\" title=\"Figure&#xa0;15.11.&#xa0;\">Figure\u00a015.11<\/a> No. Prokaryotes use different promoters than eukaryotes.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"section\">\n<div class=\"title\"><a href=\"#m44532\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.4<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">RNA Processing in Eukaryotes<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<div id=\"m44532-fs-idp101720928\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44532-fs-idp39733568\"><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=\"m44532-fs-idp95572528\"> <\/span><\/p>\n<p><span id=\"m44532-fs-idm14702160\"> <\/span><a class=\"xref target-figure\" href=\"ch15.html#m44532-fig-ch15_04_02\" title=\"Figure&#xa0;15.13.&#xa0;\">Figure\u00a015.13<\/a> Errors in splicing are implicated in cancers and other human diseases. What kinds of mutations might lead to splicing errors? Think of different possible outcomes if splicing errors occur.<\/p>\n<\/p><\/div>\n<div id=\"m44532-fs-idp39733568\" 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=\"ch15.html#m44532-fs-idp101720928\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44532-fs-idp63298640\"> <\/span><a class=\"xref target-figure\" href=\"ch15.html#m44532-fig-ch15_04_02\" title=\"Figure&#xa0;15.13.&#xa0;\">Figure\u00a015.13<\/a> Mutations in the spliceosome recognition sequence at each end of the intron, or in the proteins and RNAs that make up the spliceosome, may impair splicing. Mutations may also add new spliceosome recognition sites. Splicing errors could lead to introns being retained in spliced RNA, exons being excised, or changes in the location of the splice site.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"section\">\n<div class=\"title\"><a href=\"#m44529\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.5<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Ribosomes and Protein Synthesis<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<div id=\"m44529-fs-idp7053584\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44529-fs-idm128656560\"><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=\"m44529-fs-idm67653088\"> <\/span> <\/p>\n<p><span id=\"m44529-fs-idp39443152\"> <\/span><a class=\"xref target-figure\" href=\"ch15.html#m44529-fig-ch15_05_02\" title=\"Figure&#xa0;15.16.&#xa0;\">Figure\u00a015.16<\/a> Many antibiotics inhibit bacterial protein synthesis. For example, tetracycline blocks the A site on the bacterial ribosome, and chloramphenicol blocks peptidyl transfer. What specific effect would you expect each of these antibiotics to have on protein synthesis?<\/p>\n<p><span id=\"m44529-fs-idm20767424\"> <\/span>Tetracycline would directly affect:<\/p>\n<div class=\"orderedlist\"><span id=\"m44529-fs-idp18488912\"> <\/span><\/p>\n<ol class=\"orderedlist\" type=\"a\">\n<li class=\"listitem\">\n<p>tRNA binding to the ribosome<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>ribosome assembly<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>growth of the protein chain<\/p>\n<\/li>\n<\/ol>\n<\/div>\n<p><span id=\"m44529-fs-idp62151840\"> <\/span>Chloramphenicol would directly affect<\/p>\n<div class=\"orderedlist\"><span id=\"m44529-fs-idp128801344\"> <\/span><\/p>\n<ol class=\"orderedlist\" type=\"a\">\n<li class=\"listitem\">\n<p>tRNA binding to the ribosome<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>ribosome assembly<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>growth of the protein chain<\/p>\n<\/li>\n<\/ol>\n<\/div><\/div>\n<div id=\"m44529-fs-idm128656560\" 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=\"ch15.html#m44529-fs-idp7053584\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44529-fs-idp66684464\"> <\/span><a class=\"xref target-figure\" href=\"ch15.html#m44529-fig-ch15_05_02\" title=\"Figure&#xa0;15.16.&#xa0;\">Figure\u00a015.16<\/a> Tetracycline: a; Chloramphenicol: c.<\/p>\n<\/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=\"#m44518\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.<\/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=\"#m44522\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.1<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">The Genetic Code<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<div id=\"m44522-fs-id2024650\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44522-fs-id2682565\"><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=\"m44522-fs-id2567848\"> <\/span><\/p>\n<p><span id=\"m44522-fs-id2574085\"> <\/span>The AUC and AUA codons in mRNA both specify isoleucine. What feature of the genetic code explains this?<\/p>\n<div class=\"orderedlist\"><span id=\"m44522-fs-id1812494\"> <\/span><\/p>\n<ol class=\"orderedlist\" type=\"a\">\n<li class=\"listitem\">\n<p>complementarity<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>nonsense codons<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>universality<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>degeneracy<\/p>\n<\/li>\n<\/ol>\n<\/div>\n<\/div>\n<div id=\"m44522-fs-id2682565\" 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=\"ch15.html#m44522-fs-id2024650\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44522-fs-id1310016\"> <\/span>D<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div id=\"m44522-fs-id1428699\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44522-fs-id1425193\"><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=\"m44522-fs-id2318009\"> <\/span><\/p>\n<p><span id=\"m44522-fs-id2013469\"> <\/span>How many nucleotides are in 12 mRNA codons?<\/p>\n<div class=\"orderedlist\"><span id=\"m44522-fs-id1450423\"> <\/span><\/p>\n<ol class=\"orderedlist\" type=\"a\">\n<li class=\"listitem\">\n<p>12<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>24<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>36<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>48<\/p>\n<\/li>\n<\/ol>\n<\/div>\n<\/div>\n<div id=\"m44522-fs-id1425193\" 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=\"ch15.html#m44522-fs-id1428699\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44522-fs-id2688570\"> <\/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=\"#m44523\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.2<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Prokaryotic Transcription<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<div id=\"m44523-fs-id2914875\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44523-fs-id890335\"><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=\"m44523-fs-id1420578\"> <\/span><\/p>\n<p><span id=\"m44523-fs-id1404598\"> <\/span>Which subunit of the <span class=\"emphasis\"><em>E. coli<\/em><\/span> polymerase confers specificity to transcription?<\/p>\n<div class=\"orderedlist\"><span id=\"m44523-fs-id1425193\"> <\/span><\/p>\n<ol class=\"orderedlist\" type=\"a\">\n<li class=\"listitem\">\n<p><span class=\"emphasis\"><em>\u03b1<\/em><\/span><\/p>\n<\/li>\n<li class=\"listitem\">\n<p><span class=\"emphasis\"><em>\u03b2<\/em><\/span><\/p>\n<\/li>\n<li class=\"listitem\">\n<p><span class=\"emphasis\"><em>\u03b2<\/em><\/span>&#8216;<\/p>\n<\/li>\n<li class=\"listitem\">\n<p><span class=\"emphasis\"><em>\u03c3<\/em><\/span><\/p>\n<\/li>\n<\/ol>\n<\/div>\n<\/div>\n<div id=\"m44523-fs-id890335\" 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=\"ch15.html#m44523-fs-id2914875\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44523-fs-id1006438\"> <\/span>D<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div id=\"m44523-fs-id1313546\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44523-fs-id846953\"><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=\"m44523-fs-id1957391\"> <\/span><\/p>\n<p><span id=\"m44523-fs-id1394141\"> <\/span>The -10 and -35 regions of prokaryotic promoters are called consensus sequences because ________.<\/p>\n<div class=\"orderedlist\"><span id=\"m44523-fs-id1704430\"> <\/span><\/p>\n<ol class=\"orderedlist\" type=\"a\">\n<li class=\"listitem\">\n<p>they are identical in all bacterial species<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>they are similar in all bacterial species<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>they exist in all organisms<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>they have the same function in all organisms<\/p>\n<\/li>\n<\/ol>\n<\/div>\n<\/div>\n<div id=\"m44523-fs-id846953\" 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=\"ch15.html#m44523-fs-id1313546\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44523-fs-id1605467\"> <\/span>B<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"section\">\n<div class=\"title\"><a href=\"#m44524\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.3<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Eukaryotic Transcription<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<div id=\"m44524-fs-id2062496\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44524-fs-id2155698\"><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=\"m44524-fs-id1236812\"> <\/span><\/p>\n<p><span id=\"m44524-fs-id2169822\"> <\/span>Which feature of promoters can be found in both prokaryotes and eukaryotes?<\/p>\n<div class=\"orderedlist\"><span id=\"m44524-fs-id1418272\"> <\/span><\/p>\n<ol class=\"orderedlist\" type=\"a\">\n<li class=\"listitem\">\n<p>GC box<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>TATA box<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>octamer box<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>-10 and -35 sequences<\/p>\n<\/li>\n<\/ol>\n<\/div>\n<\/div>\n<div id=\"m44524-fs-id2155698\" 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=\"ch15.html#m44524-fs-id2062496\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44524-fs-id1275139\"> <\/span>B<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div id=\"m44524-fs-id1419233\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44524-fs-id782653\"><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=\"m44524-fs-id2338606\"> <\/span><\/p>\n<p><span id=\"m44524-fs-id1447963\"> <\/span>What transcripts will be most affected by low levels of \u03b1-amanitin?<\/p>\n<div class=\"orderedlist\"><span id=\"m44524-fs-id1380375\"> <\/span><\/p>\n<ol class=\"orderedlist\" type=\"a\">\n<li class=\"listitem\">\n<p>18S and 28S rRNAs<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>pre-mRNAs<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>5S rRNAs and tRNAs<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>other small nuclear RNAs<\/p>\n<\/li>\n<\/ol>\n<\/div>\n<\/div>\n<div id=\"m44524-fs-id782653\" 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=\"ch15.html#m44524-fs-id1419233\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44524-fs-id1461386\"> <\/span>B<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"section\">\n<div class=\"title\"><a href=\"#m44532\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.4<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">RNA Processing in Eukaryotes<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<div id=\"m44532-fs-id1466731\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44532-fs-id2261966\"><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=\"m44532-fs-id2080887\"> <\/span><\/p>\n<p><span id=\"m44532-fs-id2914626\"> <\/span>Which pre-mRNA processing step is important for initiating translation?<\/p>\n<div class=\"orderedlist\"><span id=\"m44532-fs-id1847065\"> <\/span><\/p>\n<ol class=\"orderedlist\" type=\"a\">\n<li class=\"listitem\">\n<p>poly-A tail<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>RNA editing<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>splicing<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>7-methylguanosine cap<\/p>\n<\/li>\n<\/ol>\n<\/div>\n<\/div>\n<div id=\"m44532-fs-id2261966\" 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=\"ch15.html#m44532-fs-id1466731\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44532-fs-id1986526\"> <\/span>D<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div id=\"m44532-fs-id1428536\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44532-fs-id1281610\"><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=\"m44532-fs-id1571225\"> <\/span><\/p>\n<p><span id=\"m44532-fs-id1419233\"> <\/span>What processing step enhances the stability of pre-tRNAs and pre-rRNAs?<\/p>\n<div class=\"orderedlist\"><span id=\"m44532-fs-id1242629\"> <\/span><\/p>\n<ol class=\"orderedlist\" type=\"a\">\n<li class=\"listitem\">\n<p>methylation<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>nucleotide modification<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>cleavage<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>splicing<\/p>\n<\/li>\n<\/ol>\n<\/div>\n<\/div>\n<div id=\"m44532-fs-id1281610\" 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=\"ch15.html#m44532-fs-id1428536\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44532-fs-id2344853\"> <\/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=\"#m44529\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.5<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Ribosomes and Protein Synthesis<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<div id=\"m44529-fs-id2904762\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44529-fs-id2595784\"><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=\"m44529-fs-id1644930\"> <\/span><\/p>\n<p><span id=\"m44529-fs-id1812931\"> <\/span> The RNA components of ribosomes are synthesized in the ________.<\/p>\n<div class=\"orderedlist\"><span id=\"m44529-fs-id1970715\"> <\/span><\/p>\n<ol class=\"orderedlist\" type=\"a\">\n<li class=\"listitem\">\n<p>cytoplasm<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>nucleus<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>nucleolus<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>endoplasmic reticulum<\/p>\n<\/li>\n<\/ol>\n<\/div>\n<\/div>\n<div id=\"m44529-fs-id2595784\" 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=\"ch15.html#m44529-fs-id2904762\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44529-fs-id1977751\"> <\/span>C<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div id=\"m44529-fs-id2991759\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44529-fs-id1828761\"><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=\"m44529-fs-id2962890\"> <\/span><\/p>\n<p><span id=\"m44529-fs-id2169252\"> <\/span>In any given species, there are at least how many types of aminoacyl tRNA synthetases?<\/p>\n<div class=\"orderedlist\"><span id=\"m44529-fs-id2750159\"> <\/span><\/p>\n<ol class=\"orderedlist\" type=\"a\">\n<li class=\"listitem\">\n<p>20<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>40<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>100<\/p>\n<\/li>\n<li class=\"listitem\">\n<p>200<\/p>\n<\/li>\n<\/ol>\n<\/div>\n<\/div>\n<div id=\"m44529-fs-id1828761\" 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=\"ch15.html#m44529-fs-id2991759\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44529-fs-id1248186\"> <\/span>A<\/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=\"#m44518\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.<\/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=\"#m44522\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.1<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">The Genetic Code<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<div id=\"m44522-fs-id2198100\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44522-fs-id2575162\"><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=\"m44522-fs-id2171449\"> <\/span><\/p>\n<p><span id=\"m44522-fs-id2072320\"> <\/span>Imagine if there were 200 commonly occurring amino acids instead of 20. Given what you know about the genetic code, what would be the shortest possible codon length? Explain.<\/p>\n<\/div>\n<div id=\"m44522-fs-id2575162\" 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=\"ch15.html#m44522-fs-id2198100\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44522-fs-id653506\"> <\/span>For 200 commonly occurring amino acids, codons consisting of four types of nucleotides would have to be at least four nucleotides long, because 4<sup>4<\/sup> = 256. There would be much less degeneracy in this case.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div id=\"m44522-fs-id889157\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44522-fs-id1280839\"><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=\"m44522-fs-id1449262\"> <\/span><\/p>\n<p><span id=\"m44522-fs-id1292460\"> <\/span>Discuss how degeneracy of the genetic code makes cells more robust to mutations.<\/p>\n<\/div>\n<div id=\"m44522-fs-id1280839\" 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=\"ch15.html#m44522-fs-id889157\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44522-fs-id2595443\"> <\/span>Codons that specify the same amino acid typically only differ by one nucleotide. In addition, amino acids with chemically similar side chains are encoded by similar codons. This nuance of the genetic code ensures that a single-nucleotide substitution mutation might either specify the same amino acid and have no effect, or may specify a similar amino acid, preventing the protein from being rendered completely nonfunctional.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"section\">\n<div class=\"title\"><a href=\"#m44523\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.2<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Prokaryotic Transcription<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<div id=\"m44523-fs-id1444265\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44523-fs-id1291455\"><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=\"m44523-fs-id1427093\"> <\/span><\/p>\n<p><span id=\"m44523-fs-id1414962\"> <\/span>If mRNA is complementary to the DNA template strand and the DNA template strand is complementary to the DNA nontemplate strand, then why are base sequences of mRNA and the DNA nontemplate strand not identical? Could they ever be?<\/p>\n<\/div>\n<div id=\"m44523-fs-id1291455\" 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=\"ch15.html#m44523-fs-id1444265\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44523-fs-id1432929\"> <\/span>DNA is different from RNA in that T nucleotides in DNA are replaced with U nucleotides in RNA. Therefore, they could never be identical in base sequence.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div id=\"m44523-fs-id1385377\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44523-fs-id2896656\"><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=\"m44523-fs-id1165423\"> <\/span><\/p>\n<p><span id=\"m44523-fs-id889896\"> <\/span>In your own words, describe the difference between rho-dependent and rho-independent termination of transcription in prokaryotes.<\/p>\n<\/div>\n<div id=\"m44523-fs-id2896656\" 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=\"ch15.html#m44523-fs-id1385377\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44523-fs-id1393826\"> <\/span>Rho-dependent termination is controlled by the rho protein, which tracks along behind the polymerase on the growing mRNA chain. Near the end of the gene, the polymerase stalls at a run of G nucleotides on the DNA template. The rho protein collides with the polymerase and releases mRNA from the transcription bubble. Rho-independent termination is controlled by specific sequences in the DNA template strand. As the polymerase nears the end of the gene being transcribed, it encounters a region rich in C\u2013G nucleotides. This creates an mRNA hairpin that causes the polymerase to stall right as it begins to transcribe a region rich in A\u2013T nucleotides. Because A\u2013U bonds are less thermostable, the core enzyme falls away.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"section empty\">\n<div class=\"title\"><a href=\"#m44524\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.3<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Eukaryotic Transcription<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<div class=\"section empty\">\n<div class=\"title\"><a href=\"#m44532\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.4<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">RNA Processing in Eukaryotes<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<div class=\"section\">\n<div class=\"title\"><a href=\"#m44529\"><span class=\"cnx-gentext-section cnx-gentext-autogenerated\"><span class=\"cnx-gentext-section cnx-gentext-n\">15.5<\/span><span class=\"cnx-gentext-section cnx-gentext-autogenerated\">.\u00a0<\/span><span class=\"cnx-gentext-section cnx-gentext-t\">Ribosomes and Protein Synthesis<\/span><\/span><\/a><\/div>\n<div class=\"body\">\n<div id=\"m44529-fs-id2200536\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44529-fs-id1720804\"><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=\"m44529-fs-id2023354\"> <\/span><\/p>\n<p><span id=\"m44529-fs-id2062496\"> <\/span>Transcribe and translate the following DNA sequence (nontemplate strand): 5&#8242;-ATGGCCGGTTATTAAGCA-3&#8242;<\/p>\n<\/div>\n<div id=\"m44529-fs-id1720804\" 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=\"ch15.html#m44529-fs-id2200536\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44529-fs-id2626001\"> <\/span>The mRNA would be: 5&#8242;-AUGGCCGGUUAUUAAGCA-3&#8242;. The protein would be: MAGY. Even though there are six codons, the fifth codon corresponds to a stop, so the sixth codon would not be translated.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<div id=\"m44529-fs-id2119483\" class=\"exercise\">&lt;!&#8211;calling formal.object&#8211;&gt;<\/p>\n<div class=\"title\"><span><a class=\"solution-number\" href=\"#m44529-fs-id2853893\"><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=\"m44529-fs-id2890873\"> <\/span><\/p>\n<p><span id=\"m44529-fs-id2318009\"> <\/span>Explain how single nucleotide changes can have vastly different effects on protein function.<\/p>\n<\/div>\n<div id=\"m44529-fs-id2853893\" 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=\"ch15.html#m44529-fs-id2119483\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span id=\"m44529-fs-id2583976\"> <\/span>Nucleotide changes in the third position of codons may not change the amino acid and would have no effect on the protein. Other nucleotide changes that change important amino acids or create or delete start or stop codons would have severe effects on the amino acid sequence of the protein.<\/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;&#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=\"ch15.html#m44524-fs-idp79573648\">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=\"ch15.html#m44524-fig-ch15_03_02\" title=\"Figure&#xa0;15.11.&#xa0;\">Figure\u00a015.11<\/a> No. Prokaryotes use different promoters than eukaryotes.<\/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=\"ch15.html#m44532-fs-idp101720928\">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=\"ch15.html#m44532-fig-ch15_04_02\" title=\"Figure&#xa0;15.13.&#xa0;\">Figure\u00a015.13<\/a> Mutations in the spliceosome recognition sequence at each end of the intron, or in the proteins and RNAs that make up the spliceosome, may impair splicing. Mutations may also add new spliceosome recognition sites. Splicing errors could lead to introns being retained in spliced RNA, exons being excised, or changes in the location of the splice site.<\/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=\"ch15.html#m44529-fs-idp7053584\">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=\"ch15.html#m44529-fig-ch15_05_02\" title=\"Figure&#xa0;15.16.&#xa0;\">Figure\u00a015.16<\/a> Tetracycline: a; Chloramphenicol: c.<\/p>\n<\/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=\"ch15.html#m44522-fs-id2024650\">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=\"ch15.html#m44522-fs-id1428699\">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=\"ch15.html#m44523-fs-id2914875\">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=\"ch15.html#m44523-fs-id1313546\">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=\"ch15.html#m44524-fs-id2062496\">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=\"ch15.html#m44524-fs-id1419233\">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=\"ch15.html#m44532-fs-id1466731\">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=\"ch15.html#m44532-fs-id1428536\">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=\"ch15.html#m44529-fs-id2904762\">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=\"ch15.html#m44529-fs-id2991759\">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<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=\"ch15.html#m44522-fs-id2198100\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span> <\/span>For 200 commonly occurring amino acids, codons consisting of four types of nucleotides would have to be at least four nucleotides long, because 4<sup>4<\/sup> = 256. There would be much less degeneracy in this case.<\/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=\"ch15.html#m44522-fs-id889157\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span> <\/span>Codons that specify the same amino acid typically only differ by one nucleotide. In addition, amino acids with chemically similar side chains are encoded by similar codons. This nuance of the genetic code ensures that a single-nucleotide substitution mutation might either specify the same amino acid and have no effect, or may specify a similar amino acid, preventing the protein from being rendered completely nonfunctional.<\/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=\"ch15.html#m44523-fs-id1444265\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span> <\/span>DNA is different from RNA in that T nucleotides in DNA are replaced with U nucleotides in RNA. Therefore, they could never be identical in base sequence.<\/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=\"ch15.html#m44523-fs-id1385377\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span> <\/span>Rho-dependent termination is controlled by the rho protein, which tracks along behind the polymerase on the growing mRNA chain. Near the end of the gene, the polymerase stalls at a run of G nucleotides on the DNA template. The rho protein collides with the polymerase and releases mRNA from the transcription bubble. Rho-independent termination is controlled by specific sequences in the DNA template strand. As the polymerase nears the end of the gene being transcribed, it encounters a region rich in C\u2013G nucleotides. This creates an mRNA hairpin that causes the polymerase to stall right as it begins to transcribe a region rich in A\u2013T nucleotides. Because A\u2013U bonds are less thermostable, the core enzyme falls away.<\/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=\"ch15.html#m44529-fs-id2200536\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span> <\/span>The mRNA would be: 5&#8242;-AUGGCCGGUUAUUAAGCA-3&#8242;. The protein would be: MAGY. Even though there are six codons, the fifth codon corresponds to a stop, so the sixth codon would not be translated.<\/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=\"ch15.html#m44529-fs-id2119483\">Return to Exercise<\/a><span class=\"epub-only post-text\">)<\/span><\/span><\/div>\n<div class=\"body\">\n<p><span> <\/span>Nucleotide changes in the third position of codons may not change the amino acid and would have no effect on the protein. Other nucleotide changes that change important amino acids or create or delete start or stop codons would have severe effects on the amino acid sequence of the protein.<\/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<\/div>\n<\/div>\n","protected":false},"author":17,"menu_order":17,"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-498","chapter","type-chapter","status-publish","hentry"],"part":21,"_links":{"self":[{"href":"https:\/\/courses.lumenlearning.com\/umd-publichealthbio\/wp-json\/pressbooks\/v2\/chapters\/498","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\/498\/revisions"}],"predecessor-version":[{"id":521,"href":"https:\/\/courses.lumenlearning.com\/umd-publichealthbio\/wp-json\/pressbooks\/v2\/chapters\/498\/revisions\/521"}],"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\/498\/metadata\/"}],"wp:attachment":[{"href":"https:\/\/courses.lumenlearning.com\/umd-publichealthbio\/wp-json\/wp\/v2\/media?parent=498"}],"wp:term":[{"taxonomy":"chapter-type","embeddable":true,"href":"https:\/\/courses.lumenlearning.com\/umd-publichealthbio\/wp-json\/pressbooks\/v2\/chapter-type?post=498"},{"taxonomy":"contributor","embeddable":true,"href":"https:\/\/courses.lumenlearning.com\/umd-publichealthbio\/wp-json\/wp\/v2\/contributor?post=498"},{"taxonomy":"license","embeddable":true,"href":"https:\/\/courses.lumenlearning.com\/umd-publichealthbio\/wp-json\/wp\/v2\/license?post=498"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}