Organic Compounds

Carbohydrate Molecules

Carbohydrates are essential macromolecules that are classified into three subtypes: monosaccharides, disaccharides, and polysaccharides.

Learning Objectives

Describe the structure of mono-, di-, and poly-saccharides

Key Takeaways

Key Points

  • Monosaccharides are simple sugars made up of three to seven carbons, and they can exist as a linear chain or as ring-shaped molecules.
  • Glucose, galactose, and fructose are monosaccharide isomers, which means they all have the same chemical formula but differ structurally and chemically.
  • Disaccharides form when two monosaccharides undergo a dehydration reaction (a condensation reaction); they are held together by a covalent bond.
  • Sucrose (table sugar) is the most common disaccharide, which is composed of the monomers glucose and fructose.
  • A polysaccharide is a long chain of monosaccharides linked by glycosidic bonds; the chain may be branched or unbranched and can contain many types of monosaccharides.

Key Terms

  • isomer: Any of two or more compounds with the same molecular formula but with different structure.
  • dehydration reaction: A chemical reaction in which two molecules are covalently linked in a reaction that generates H2O as a second product.
  • biopolymer: Any macromolecule of a living organism that is formed from the polymerization of smaller entities; a polymer that occurs in a living organism or results from life.

Carbohydrates can be represented by the stoichiometric formula (CH2O)n, where n is the number of carbons in the molecule. Therefore, the ratio of carbon to hydrogen to oxygen is 1:2:1 in carbohydrate molecules. The origin of the term “carbohydrate” is based on its components: carbon (“carbo”) and water (“hydrate”). Carbohydrates are classified into three subtypes: monosaccharides, disaccharides, and polysaccharides.

Monosaccharides

Monosaccharides (mono- = “one”; sacchar- = “sweet”) are simple sugars. In monosaccharides, the number of carbons usually ranges from three to seven. If the sugar has an aldehyde group (the functional group with the structure R-CHO), it is known as an aldose, and if it has a ketone group (the functional group with the structure RC(=O)R’), it is known as a ketose. Depending on the number of carbons in the sugar, they also may be known as trioses (three carbons), pentoses (five carbons), and or hexoses (six carbons). Monosaccharides can exist as a linear chain or as ring-shaped molecules; in aqueous solutions they are usually found in ring forms.

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Monosaccharides: Monosaccharides are classified based on the position of their carbonyl group and the number of carbons in the backbone. Aldoses have a carbonyl group (indicated in green) at the end of the carbon chain, and ketoses have a carbonyl group in the middle of the carbon chain. Trioses, pentoses, and hexoses have three, five, and six carbon backbones, respectively.

Common Monosaccharides

Glucose (C6H12O6) is a common monosaccharide and an important source of energy. During cellular respiration, energy is released from glucose and that energy is used to help make adenosine triphosphate (ATP). Plants synthesize glucose using carbon dioxide and water, and glucose, in turn, is used for energy requirements for the plant.

Galactose (a milk sugar) and fructose (found in fruit) are other common monosaccharides. Although glucose, galactose, and fructose all have the same chemical formula (C6H12O6), they differ structurally and stereochemically. This makes them different molecules despite sharing the same atoms in the same proportions, and they are all isomers of one another, or isomeric monosaccharides. Glucose and galactose are aldoses, and fructose is a ketose.

Disaccharides

Disaccharides (di- = “two”) form when two monosaccharides undergo a dehydration reaction (also known as a condensation reaction or dehydration synthesis). During this process, the hydroxyl group of one monosaccharide combines with the hydrogen of another monosaccharide, releasing a molecule of water and forming a covalent bond. A covalent bond formed between a carbohydrate molecule and another molecule (in this case, between two monosaccharides) is known as a glycosidic bond. Glycosidic bonds (also called glycosidic linkages) can be of the alpha or the beta type.

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Disaccharides: Sucrose is formed when a monomer of glucose and a monomer of fructose are joined in a dehydration reaction to form a glycosidic bond. In the process, a water molecule is lost. By convention, the carbon atoms in a monosaccharide are numbered from the terminal carbon closest to the carbonyl group. In sucrose, a glycosidic linkage is formed between carbon 1 in glucose and carbon 2 in fructose.

Common Disaccharides

Common disaccharides include lactose, maltose, and sucrose. Lactose is a disaccharide consisting of the monomers glucose and galactose. It is found naturally in milk. Maltose, or malt sugar, is a disaccharide formed by a dehydration reaction between two glucose molecules. The most common disaccharide is sucrose, or table sugar, which is composed of the monomers glucose and fructose.

Polysaccharides

A long chain of monosaccharides linked by glycosidic bonds is known as a polysaccharide (poly- = “many”). The chain may be branched or unbranched, and it may contain different types of monosaccharides. Starch, glycogen, cellulose, and chitin are primary examples of polysaccharides.

Plants are able to synthesize glucose, and the excess glucose is stored as starch in different plant parts, including roots and seeds. Starch is the stored form of sugars in plants and is made up of glucose monomers that are joined by α1-4 or 1-6 glycosidic bonds. The starch in the seeds provides food for the embryo as it germinates while the starch that is consumed by humans is broken down by enzymes into smaller molecules, such as maltose and glucose. The cells can then absorb the glucose.

Common Polysaccharides

Glycogen is the storage form of glucose in humans and other vertebrates. It is made up of monomers of glucose. Glycogen is the animal equivalent of starch and is a highly branched molecule usually stored in liver and muscle cells. Whenever blood glucose levels decrease, glycogen is broken down to release glucose in a process known as glycogenolysis.

Cellulose is the most abundant natural biopolymer. The cell wall of plants is mostly made of cellulose and provides structural support to the cell. Cellulose is made up of glucose monomers that are linked by β 1-4 glycosidic bonds. Every other glucose monomer in cellulose is flipped over, and the monomers are packed tightly as extended long chains. This gives cellulose its rigidity and high tensile strength—which is so important to plant cells.

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Polysaccharides: In cellulose, glucose monomers are linked in unbranched chains by β 1-4 glycosidic linkages. Because of the way the glucose subunits are joined, every glucose monomer is flipped relative to the next one resulting in a linear, fibrous structure.

Carbohydrate Function

Carbohydrates serve various functions in different animals. Arthropods have an outer skeleton, the exoskeleton, which protects their internal body parts. This exoskeleton is made of chitin, which is a polysaccharide-containing nitrogen. It is made of repeating units of N-acetyl-β-d-glucosamine, a modified sugar. Chitin is also a major component of fungal cell walls.

Lipid Molecules

Fats and oils, which may be saturated or unsaturated, can be unhealthy but also serve important functions for plants and animals.

Learning Objectives

Differentiate between saturated and unsaturated fatty acids

Key Takeaways

Key Points

  • Fats provide energy, insulation, and storage of fatty acids for many organisms.
  • Fats may be saturated (having single bonds) or unsaturated (having double bonds).
  • Unsaturated fats may be cis (hydrogens in same plane) or trans (hydrogens in two different planes).
  • Olive oil, a monounsaturated fat, has a single double bond whereas canola oil, a polyunsaturated fat, has more than one double bond.
  • Omega-3 fatty acid and omega-6 fatty acid are essential for human biological processes, but they must be ingested in the diet because they cannot be synthesized.

Key Terms

  • hydrogenation: The chemical reaction of hydrogen with another substance, especially with an unsaturated organic compound, and usually under the influence of temperature, pressure and catalysts.
  • ester: Compound most often formed by the condensation of an alcohol and an acid, by removing water. It contains the functional group carbon-oxygen double bond joined via carbon to another oxygen atom.
  • carboxyl: A univalent functional group consisting of a carbonyl and a hydroxyl functional group (-CO.OH); characteristic of carboxylic acids.

Fats have important functions, and many vitamins are fat soluble. Fats serve as a long-term storage form of fatty acids and act as a source of energy. They also provide insulation for the body.

Glycerol and Fatty Acids

A fat molecule consists of two main components: glycerol and fatty acids. Glycerol is an alcohol with three carbons, five hydrogens, and three hydroxyl (OH) groups. Fatty acids have a long chain of hydrocarbons with a carboxyl group attached and may have 4-36 carbons; however, most of them have 12-18. In a fat molecule, the fatty acids are attached to each of the three carbons of the glycerol molecule with an ester bond through the oxygen atom. During the ester bond formation, three molecules are released. Since fats consist of three fatty acids and a glycerol, they are also called triacylglycerols or triglycerides.

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Triacylglycerols: Triacylglycerol is formed by the joining of three fatty acids to a glycerol backbone in a dehydration reaction. Three molecules of water are released in the process.

Saturated vs. Unsaturated Fatty Acids

Fatty acids may be saturated or unsaturated. In a fatty acid chain, if there are only single bonds between neighboring carbons in the hydrocarbon chain, the fatty acid is said to be saturated. Saturated fatty acids are saturated with hydrogen since single bonds increase the number of hydrogens on each carbon. Stearic acid and palmitic acid, which are commonly found in meat, are examples of saturated fats.

When the hydrocarbon chain contains a double bond, the fatty acid is said to be unsaturated. Oleic acid is an example of an unsaturated fatty acid. Most unsaturated fats are liquid at room temperature and are called oils. If there is only one double bond in the molecule, then it is known as a monounsaturated fat; e.g. olive oil. If there is more than one double bond, then it is known as a polyunsaturated fat; e.g. canola oil. Unsaturated fats help to lower blood cholesterol levels whereas saturated fats contribute to plaque formation in the arteries.

Unsaturated fats or oils are usually of plant origin and contain cis unsaturated fatty acids. Cis and trans indicate the configuration of the molecule around the double bond. If hydrogens are present in the same plane, it is referred to as a cis fat; if the hydrogen atoms are on two different planes, it is referred to as a trans fat. The cis double bond causes a bend or a “kink” that prevents the fatty acids from packing tightly, keeping them liquid at room temperature.

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Fatty Acids: Saturated fatty acids have hydrocarbon chains connected by single bonds only. Unsaturated fatty acids have one or more double bonds. Each double bond may be in a cis or trans configuration. In the cis configuration, both hydrogens are on the same side of the hydrocarbon chain. In the trans configuration, the hydrogens are on opposite sides. A cis double bond causes a kink in the chain.

Trans Fats

In the food industry, oils are artificially hydrogenated to make them semi-solid and of a consistency desirable for many processed food products. During this hydrogenation process, gas is bubbled through oils to solidify them, and the double bonds of the cis-conformation in the hydrocarbon chain may be converted to double bonds in the trans-conformation.

Margarine, some types of peanut butter, and shortening are examples of artificially-hydrogenated trans fats. Recent studies have shown that an increase in trans fats in the human diet may lead to an increase in levels of low-density lipoproteins (LDL), or “bad” cholesterol, which in turn may lead to plaque deposition in the arteries, resulting in heart disease. Many fast food restaurants have recently banned the use of trans fats, and food labels are required to display the trans fat content.

Essential Fatty Acids

Essential fatty acids are fatty acids required for biological processes, but not synthesized by the human body. Consequently, they have to be supplemented through ingestion via the diet and are nutritionally very important. Omega-3 fatty acid, or alpha-linoleic acid (ALA), falls into this category and is one of only two fatty acids known to be essential for humans (the other being omega-6 fatty acid, or linoleic acid). These polyunsaturated fatty acids are called omega-3 because the third carbon from the end of the hydrocarbon chain is connected to its neighboring carbon by a double bond. Salmon, trout, and tuna are good sources of omega-3 fatty acids.

Research indicates that omega-3 fatty acids reduce the risk of sudden death from heart attacks, reduce triglycerides in the blood, lower blood pressure, and prevent thrombosis by inhibiting blood clotting. They also reduce inflammation and may help reduce the risk of some cancers in animals.

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Omega Fatty Acids: Alpha-linolenic acid is an example of an omega-3 fatty acid. It has three cis double bonds and, as a result, a curved shape. For clarity, the carbons are not shown. Each singly bonded carbon has two hydrogens associated with it, also not shown.

DNA and RNA

DNA and RNA are nucleic acids that carry out cellular processes, especially the regulation and expression of genes.

Learning Objectives

Describe the structure of nucleic acids and the types of molecules that contain them

Key Takeaways

Key Points

  • The two main types of nucleic acids are DNA and RNA.
  • Both DNA and RNA are made from nucleotides, each containing a five-carbon sugar backbone, a phosphate group, and a nitrogen base.
  • DNA provides the code for the cell ‘s activities, while RNA converts that code into proteins to carry out cellular functions.
  • The sequence of nitrogen bases (A, T, C, G) in DNA is what forms an organism’s traits.
  • The nitrogen bases A and T (or U in RNA) always go together and C and G always go together, forming the 5′-3′ phosphodiester linkage found in the nucleic acid molecules.

Key Terms

  • nucleotide: the monomer comprising DNA or RNA molecules; consists of a nitrogenous heterocyclic base that can be a purine or pyrimidine, a five-carbon pentose sugar, and a phosphate group
  • genome: the cell’s complete genetic information packaged as a double-stranded DNA molecule
  • monomer: A relatively small molecule which can be covalently bonded to other monomers to form a polymer.

Types of Nucleic Acids

The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material found in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is found in the nucleus of eukaryotes and in the chloroplasts and mitochondria. In prokaryotes, the DNA is not enclosed in a membranous envelope, but rather free-floating within the cytoplasm.

The entire genetic content of a cell is known as its genome and the study of genomes is genomics. In eukaryotic cells, but not in prokaryotes, DNA forms a complex with histone proteins to form chromatin, the substance of eukaryotic chromosomes. A chromosome may contain tens of thousands of genes. Many genes contain the information to make protein products; other genes code for RNA products. DNA controls all of the cellular activities by turning the genes “on” or “off. ”

The other type of nucleic acid, RNA, is mostly involved in protein synthesis. In eukaryotes, the DNA molecules never leave the nucleus but instead use an intermediary to communicate with the rest of the cell. This intermediary is the messenger RNA (mRNA). Other types of RNA—like rRNA, tRNA, and microRNA—are involved in protein synthesis and its regulation.

Nucleotides

DNA and RNA are made up of monomers known as nucleotides. The nucleotides combine with each other to form a polynucleotide: DNA or RNA. Each nucleotide is made up of three components:

  1. a nitrogenous base
  2. a pentose (five-carbon) sugar
  3. a phosphate group

Each nitrogenous base in a nucleotide is attached to a sugar molecule, which is attached to one or more phosphate groups.

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DNA and RNA: A nucleotide is made up of three components: a nitrogenous base, a pentose sugar, and one or more phosphate groups. Carbon residues in the pentose are numbered 1′ through 5′ (the prime distinguishes these residues from those in the base, which are numbered without using a prime notation). The base is attached to the 1′ position of the ribose, and the phosphate is attached to the 5′ position. When a polynucleotide is formed, the 5′ phosphate of the incoming nucleotide attaches to the 3′ hydroxyl group at the end of the growing chain. Two types of pentose are found in nucleotides, deoxyribose (found in DNA) and ribose (found in RNA). Deoxyribose is similar in structure to ribose, but it has an H instead of an OH at the 2′ position. Bases can be divided into two categories: purines and pyrimidines. Purines have a double ring structure, and pyrimidines have a single ring.

Nitrogenous Base

The nitrogenous bases are organic molecules and are so named because they contain carbon and nitrogen. They are bases because they contain an amino group that has the potential of binding an extra hydrogen, and thus, decreasing the hydrogen ion concentration in its environment, making it more basic. Each nucleotide in DNA contains one of four possible nitrogenous bases: adenine (A), guanine (G) cytosine (C), and thymine (T).

Adenine and guanine are classified as purines. The primary structure of a purine consists of two carbon-nitrogen rings. Cytosine, thymine, and uracil are classified as pyrimidines which have a single carbon-nitrogen ring as their primary structure. Each of these basic carbon-nitrogen rings has different functional groups attached to it. In molecular biology shorthand, the nitrogenous bases are simply known by their symbols A, T, G, C, and U. DNA contains A, T, G, and C whereas RNA contains A, U, G, and C.

Five-Carbon Sugar

The pentose sugar in DNA is deoxyribose and in RNA it is ribose. The difference between the sugars is the presence of the hydroxyl group on the second carbon of the ribose and hydrogen on the second carbon of the deoxyribose. The carbon atoms of the sugar molecule are numbered as 1′, 2′, 3′, 4′, and 5′ (1′ is read as “one prime”).

Phosphate Group

The phosphate residue is attached to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms a 5′3′ phosphodiester linkage. The phosphodiester linkage is not formed by simple dehydration reaction like the other linkages connecting monomers in macromolecules: its formation involves the removal of two phosphate groups. A polynucleotide may have thousands of such phosphodiester linkages.

Amino Acids

An amino acid contains an amino group, a carboxyl group, and an R group, and it combines with other amino acids to form polypeptide chains.

Learning Objectives

Describe the structure of an amino acid and the features that confer its specific properties

Key Takeaways

Key Points

  • Each amino acid contains a central C atom, an amino group (NH2), a carboxyl group (COOH), and a specific R group.
  • The R group determines the characteristics (size, polarity, and pH) for each type of amino acid.
  • Peptide bonds form between the carboxyl group of one amino acid and the amino group of another through dehydration synthesis.
  • A chain of amino acids is a polypeptide.

Key Terms

  • amino acid: Any of 20 naturally occurring α-amino acids (having the amino, and carboxylic acid groups on the same carbon atom), and a variety of side chains, that combine, via peptide bonds, to form proteins.
  • R group: The R group is a side chain specific to each amino acid that confers particular chemical properties to that amino acid.
  • polypeptide: Any polymer of (same or different) amino acids joined via peptide bonds.

Structure of an Amino Acid

Amino acids are the monomers that make up proteins. Each amino acid has the same fundamental structure, which consists of a central carbon atom, also known as the alpha (α) carbon, bonded to an amino group (NH2), a carboxyl group (COOH), and to a hydrogen atom. In the aqueous environment of the cell, the both the amino group and the carboxyl group are ionized under physiological conditions, and so have the structures -NH3+ and -COO, respectively. Every amino acid also has another atom or group of atoms bonded to the central atom known as the R group. This R group, or side chain, gives each amino acid proteins specific characteristics, including size, polarity, and pH.

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Amino acid structure: Amino acids have a central asymmetric carbon to which an amino group, a carboxyl group, a hydrogen atom, and a side chain (R group) are attached. This amino acid is unionized, but if it were placed in water at pH 7, its amino group would pick up another hydrogen and a positive charge, and the hydroxyl in its carboxyl group would lose and a hydrogen and gain a negative charge.

Types of Amino Acids

The name “amino acid” is derived from the amino group and carboxyl-acid-group in their basic structure. There are 21 amino acids present in proteins, each with a specific R group or side chain. Ten of these are considered essential amino acids in humans because the human body cannot produce them and they must be obtained from the diet. All organisms have different essential amino acids based on their physiology.

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Types of amino acids: There are 21 common amino acids commonly found in proteins, each with a different R group (variant group) that determines its chemical nature. The 21st amino acid, not shown here, is selenocysteine, with an R group of -CH2-SeH.

Characteristics of Amino Acids

Which categories of amino acid would you expect to find on the surface of a soluble protein, and which would you expect to find in the interior? What distribution of amino acids would you expect to find in a protein embedded in a lipid bilayer?

The chemical composition of the side chain determines the characteristics of the amino acid. Amino acids such as valine, methionine, and alanine are nonpolar (hydrophobic), while amino acids such as serine, threonine, and cysteine are polar (hydrophilic). The side chains of lysine and arginine are positively charged so these amino acids are also known as basic (high pH) amino acids. Proline is an exception to the standard structure of an amino acid because its R group is linked to the amino group, forming a ring-like structure.

Amino acids are represented by a single upper case letter or a three-letter abbreviation. For example, valine is known by the letter V or the three-letter symbol val.

Peptide Bonds

The sequence and the number of amino acids ultimately determine the protein’s shape, size, and function. Each amino acid is attached to another amino acid by a covalent bond, known as a peptide bond. When two amino acids are covalently attached by a peptide bond, the carboxyl group of one amino acid and the amino group of the incoming amino acid combine and release a molecule of water. Any reaction that combines two monomers in a reaction that generates H2O as one of the products is known as a dehydration reaction, so peptide bond formation is an example of a dehydration reaction.

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Peptide bond formation: Peptide bond formation is a dehydration synthesis reaction. The carboxyl group of one amino acid is linked to the amino group of the incoming amino acid. In the process, a molecule of water is released.

Polypeptide Chains

The resulting chain of amino acids is called a polypeptide chain. Each polypeptide has a free amino group at one end. This end is called the N terminal, or the amino terminal, and the other end has a free carboxyl group, also known as the C or carboxyl terminal. When reading or reporting the amino acid sequence of a protein or polypeptide, the convention is to use the N-to-C direction. That is, the first amino acid in the sequence is assumed to the be one at the N terminal and the last amino acid is assumed to be the one at the C terminal.

Although the terms polypeptide and protein are sometimes used interchangeably, a polypeptide is technically any polymer of amino acids, whereas the term protein is used for a polypeptide or polypeptides that have folded properly, combined with any additional components needed for proper functioning, and is now functional.

Types and Functions of Proteins

Proteins perform many essential physiological functions, including catalyzing biochemical reactions.

Learning Objectives

Differentiate among the types and functions of proteins

Key Takeaways

Key Points

  • Proteins are essential for the main physiological processes of life and perform functions in every system of the human body.
  • A protein’s shape determines its function.
  • Proteins are composed of amino acid subunits that form polypeptide chains.
  • Enzymes catalyze biochemical reactions by speeding up chemical reactions, and can either break down their substrate or build larger molecules from their substrate.
  • The shape of an enzyme’s active site matches the shape of the substrate.
  • Hormones are a type of protein used for cell signaling and communication.

Key Terms

  • amino acid: Any of 20 naturally occurring α-amino acids (having the amino, and carboxylic acid groups on the same carbon atom), and a variety of side chains, that combine, via peptide bonds, to form proteins.
  • polypeptide: Any polymer of (same or different) amino acids joined via peptide bonds.
  • catalyze: To accelerate a process.

Types and Functions of Proteins

Proteins perform essential functions throughout the systems of the human body. These long chains of amino acids are critically important for:

  • catalyzing chemical reactions
  • synthesizing and repairing DNA
  • transporting materials across the cell
  • receiving and sending chemical signals
  • responding to stimuli
  • providing structural support

Proteins (a polymer) are macromolecules composed of amino acid subunits (the monomers ). These amino acids are covalently attached to one another to form long linear chains called polypeptides, which then fold into a specific three-dimensional shape. Sometimes these folded polypeptide chains are functional by themselves. Other times they combine with additional polypeptide chains to form the final protein structure. Sometimes non-polypeptide groups are also required in the final protein. For instance, the blood protein hemogobin is made up of four polypeptide chains, each of which also contains a heme molecule, which is ring structure with an iron atom in its center.

Proteins have different shapes and molecular weights, depending on the amino acid sequence. For example, hemoglobin is a globular protein, which means it folds into a compact globe-like structure, but collagen, found in our skin, is a fibrous protein, which means it folds into a long extended fiber-like chain. You probably look similar to your family members because you share similar proteins, but you look different from strangers because the proteins in your eyes, hair, and the rest of your body are different.

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Human Hemoglobin: Structure of human hemoglobin. The proteins’ α and β subunits are in red and blue, and the iron-containing heme groups in green. From the protein data base.

Because form determines function, any slight change to a protein’s shape may cause the protein to become dysfunctional. Small changes in the amino acid sequence of a protein can cause devastating genetic diseases such as Huntington’s disease or sickle cell anemia.

Enzymes

Enzymes are proteins that catalyze biochemical reactions, which otherwise would not take place. These enzymes are essential for chemical processes like digestion and cellular metabolism. Without enzymes, most physiological processes would proceed so slowly (or not at all) that life could not exist.

Because form determines function, each enzyme is specific to its substrates. The substrates are the reactants that undergo the chemical reaction catalyzed by the enzyme. The location where substrates bind to or interact with the enzyme is known as the active site, because that is the site where the chemistry occurs. When the substrate binds to its active site at the enzyme, the enzyme may help in its breakdown, rearrangement, or synthesis. By placing the substrate into a specific shape and microenvironment in the active site, the enzyme encourages the chemical reaction to occur. There are two basic classes of enzymes:

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Enzyme reaction: A catabolic enzyme reaction showing the substrate matching the exact shape of the active site.

  • Catabolic enzymes: enzymes that break down their substrate
  • Anabolic enzymes: enzymes that build more complex molecules from their substrates

Enzymes are essential for digestion: the process of breaking larger food molecules down into subunits small enough to diffuse through a cell membrane and to be used by the cell. These enzymes include amylase, which catalyzes the digestion carbohydrates in the mouth and small intestine; pepsin, which catalyzes the digestion of proteins in the stomach; lipase, which catalyzes reactions need to emulsify fats in the small intestine; and trypsin, which catalyzes the further digestion of proteins in the small intestine.

Enzymes are also essential for biosynthesis: the process of making new, complex molecules from the smaller subunits that are provided to or generated by the cell. These biosynthetic enzymes include DNA Polymerase, which catalyzes the synthesis of new strands of the genetic material before cell division; fatty acid synthetase, which the synthesis of new fatty acids for fat or membrane lipid formation; and components of the ribosome, which catalyzes the formation of new polypeptides from amino acid monomers.

Hormones

Some proteins function as chemical-signaling molecules called hormones. These proteins are secreted by endocrine cells that act to control or regulate specific physiological processes, which include growth, development, metabolism, and reproduction. For example, insulin is a protein hormone that helps to regulate blood glucose levels. Other proteins act as receptors to detect the concentrations of chemicals and send signals to respond. Some types of hormones, such as estrogen and testosterone, are lipid steroids, not proteins.

Other Protein Functions

Proteins perform essential functions throughout the systems of the human body. In the respiratory system, hemoglobin (composed of four protein subunits) transports oxygen for use in cellular metabolism. Additional proteins in the blood plasma and lymph carry nutrients and metabolic waste products throughout the body. The proteins actin and tubulin form cellular structures, while keratin forms the structural support for the dead cells that become fingernails and hair. Antibodies, also called immunoglobins, help recognize and destroy foreign pathogens in the immune system. Actin and myosin allow muscles to contract, while albumin nourishes the early development of an embryo or a seedling.

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Tubulin: The structural protein tubulin stained red in mouse cells.

ATP: Adenosine Triphosphate

Cells couple the exergonic reaction of ATP hydrolysis with endergonic reactions to harness the energy within the bonds of ATP.

Learning Objectives

Explain the role of ATP as the currency of cellular energy

Key Takeaways

Key Points

  • Adenosine triphosphate is composed of the nitrogenous base adenine, the five-carbon sugar ribose, and three phosphate groups.
  • ATP is hydrolyzed to ADP in the reaction ATP+H2O→ADP+Pi+ free energy; the calculated ∆G for the hydrolysis of 1 mole of ATP is -57 kJ/mol.
  • ADP is combined with a phosphate to form ATP in the reaction ADP+Pi+free energy→ATP+H2O.
  • The energy released from the hydrolysis of ATP into ADP is used to perform cellular work, usually by coupling the exergonic reaction of ATP hydrolysis with endergonic reactions.
  • Sodium-potassium pumps use the energy derived from exergonic ATP hydrolysis to pump sodium and potassium ions across the cell membrane while phosphorylation drives the endergonic reaction.

Key Terms

  • energy coupling: Energy coupling occurs when the energy produced by one reaction or system is used to drive another reaction or system.
  • endergonic: Describing a reaction that absorbs (heat) energy from its environment.
  • exergonic: Describing a reaction that releases energy (heat) into its environment.
  • free energy: Gibbs free energy is a thermodynamic potential that measures the useful or process-initiating work obtainable from a thermodynamic system at a constant temperature and pressure (isothermal, isobaric).
  • hydrolysis: A chemical process of decomposition involving the splitting of a bond by the addition of water.

ATP: Adenosine Triphosphate

Adenosine triphosphate (ATP) is the energy currency for cellular processes. ATP provides the energy for both energy-consuming endergonic reactions and energy-releasing exergonic reactions, which require a small input of activation energy. When the chemical bonds within ATP are broken, energy is released and can be harnessed for cellular work. The more bonds in a molecule, the more potential energy it contains. Because the bond in ATP is so easily broken and reformed, ATP is like a rechargeable battery that powers cellular process ranging from DNA replication to protein synthesis.

Molecular Structure

Adenosine triphosphate (ATP) is comprised of the molecule adenosine bound to three phosphate groups. Adenosine is a nucleoside consisting of the nitrogenous base adenine and the five-carbon sugar ribose. The three phosphate groups, in order of closest to furthest from the ribose sugar, are labeled alpha, beta, and gamma. Together, these chemical groups constitute an energy powerhouse. The two bonds between the phosphates are equal high-energy bonds (phosphoanhydride bonds) that, when broken, release sufficient energy to power a variety of cellular reactions and processes. The bond between the beta and gamma phosphate is considered “high-energy” because when the bond breaks, the products [adenosine diphosphate (ADP) and one inorganic phosphate group (Pi)] have a lower free energy than the reactants (ATP and a water molecule). ATP breakdown into ADP and Pi is called hydrolysis because it consumes a water molecule (hydro-, meaning “water”, and lysis, meaning “separation”).

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Adenosine Triphosphate (ATP): ATP is the primary energy currency of the cell. It has an adenosine backbone with three phosphate groups attached.

ATP Hydrolysis and Synthesis

ATP is hydrolyzed into ADP in the following reaction:

ATP+H2O→ADP+Pi+free energy

Like most chemical reactions, the hydrolysis of ATP to ADP is reversible. The reverse reaction combines ADP + Pi to regenerate ATP from ADP. Since ATP hydrolysis releases energy, ATP synthesis must require an input of free energy.

ADP is combined with a phosphate to form ATP in the following reaction:

ADP+Pi+free energy→ATP+H2O

ATP and Energy Coupling

Exactly how much free energy (∆G) is released with the hydrolysis of ATP, and how is that free energy used to do cellular work? The calculated ∆G for the hydrolysis of one mole of ATP into ADP and Pi is −7.3 kcal/mole (−30.5 kJ/mol). However, this is only true under standard conditions, and the ∆G for the hydrolysis of one mole of ATP in a living cell is almost double the value at standard conditions: 14 kcal/mol (−57 kJ/mol).

ATP is a highly unstable molecule. Unless quickly used to perform work, ATP spontaneously dissociates into ADP + Pi, and the free energy released during this process is lost as heat. To harness the energy within the bonds of ATP, cells use a strategy called energy coupling.

Energy Coupling in Sodium-Potassium Pumps

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Energy Coupling: Sodium-potassium pumps use the energy derived from exergonic ATP hydrolysis to pump sodium and potassium ions across the cell membrane.

Cells couple the exergonic reaction of ATP hydrolysis with the endergonic reactions of cellular processes. For example, transmembrane ion pumps in nerve cells use the energy from ATP to pump ions across the cell membrane and generate an action potential. The sodium-potassium pump (Na+/K+ pump) drives sodium out of the cell and potassium into the cell. When ATP is hydrolyzed, it transfers its gamma phosphate to the pump protein in a process called phosphorylation. The Na+/K+ pump gains the free energy and undergoes a conformational change, allowing it to release three Na+ to the outside of the cell. Two extracellular K+ ions bind to the protein, causing the protein to change shape again and discharge the phosphate. By donating free energy to the Na+/K+ pump, phosphorylation drives the endergonic reaction.

Energy Coupling in Metabolism

During cellular metabolic reactions, or the synthesis and breakdown of nutrients, certain molecules must be altered slightly in their conformation to become substrates for the next step in the reaction series. In the very first steps of cellular respiration, glucose is broken down through the process of glycolysis. ATP is required for the phosphorylation of glucose, creating a high-energy but unstable intermediate. This phosphorylation reaction causes a conformational change that allows enzymes to convert the phosphorylated glucose molecule to the phosphorylated sugar fructose. Fructose is a necessary intermediate for glycolysis to move forward. In this example, the exergonic reaction of ATP hydrolysis is coupled with the endergonic reaction of converting glucose for use in the metabolic pathway.