Chapter 3 Nucleic Acids, Proteins, and Enzymes Key Concepts 3.1 Nucleic Acids Are Informational Macromolecules 3.2 Proteins Are Polymers with Important Structural and Metabolic Roles 3.3 Some Proteins Act as Enzymes to Speed up Biochemical Reactions 3.4 Regulation of Metabolism Occurs by Regulation of Enzymes

Concept 2.2 Atoms Interact and Form Molecules Macromolecules Working with a partner, determine whether each of the compounds described below is a lipid, carbohydrate, nucleic acid, or protein. Compound 1 stores information and has 4 different monomer subunits. Compound 2 is a polymer of monosaccharides. Compound 3 is hydrophobic with monomers interacting through noncovalent forces. Compound 4 is a polymer of amino acids. Discuss with your partner what macromolecules were in the foods you ate last night for dinner. Instructor’s note: The dinner macromolecules can be shared with the class as part of a greater discussion on how the foods we eat are often comprised of all types of macromolecules, for example an avocado has protein, carbohydrates, lipids and nucleic acids, students often forget that cells (plant or animal) have DNA and thus nucleic acids. Answer: Compound 1 is a nucleic acid. Compound 2 is a carbohydrate. Compound 3 is a lipid. Compound 4 is a protein. 2

Concept 3.1 Nucleic Acids Are Informational Macromolecules What are Nucleic acids? - polymers that store, transmit, and express hereditary (genetic) information DNA = deoxyribonucleic acid RNA = ribonucleic acid The monomers are nucleotides.

Concept 3.1 Nucleic Acids Are Informational Macromolecules What are the Bases? Pyrimidines—single rings Purines—double rings What are the Sugars? DNA contains deoxyribose RNA contains ribose

Figure 3.1 Nucleotides Have Three Components Figure 3.1 Nucleotides Have Three Components Nucleotide monomers are the building blocks of DNA and RNA polymers. Nucleotides may have one to three phosphate groups; those in DNA and RNA have one.

Concept 3.1 Nucleic Acids Are Informational Macromolecules What are the three major differences between DNA and RNA? DNA = base pairs are A–T and C–G RNA = base pairs are A–U and C–G DNA = double-stranded RNA = single-stranded DNA = deoxyribose sugar RNA = ribose sugar

Table 3.1

Concept 3.1 Nucleic Acids Are Informational Macromolecules Complementary base pairing:

Figure 3.3 RNA Figure 3.3 RNA (A) RNA is usually a single strand. (B) When a single-stranded RNA folds back on itself, hydrogen bonds between complementary sequences can stabilize it into a three-dimensional shape with distinct surface characteristics.

Concept 3.1 Nucleic Acids Are Informational Macromolecules DNA is usually double stranded. Two polynucleotide strands form a “ladder” that twists into a double helix. Sugar-phosphate groups form the sides of the ladder, the hydrogen-bonded bases form the rungs.

Figure 3.4 DNA Figure 3.4 DNA (A) DNA usually consists of two strands running in opposite directions that are held together by base pairing between purines and pyrimidines opposite one another on the two strands. (B) The two antiparallel strands in a DNA molecule are twisted into a double helix.

Concept 3.1 Nucleic Acids Are Informational Macromolecules The two strands are antiparallel (running in opposite directions), and the double helix is right-handed.

In-Text Art, Chapter 3, p. 40 (2)

Concept 3.1 Nucleic Acids Are Informational Macromolecules What are the two functions of DNA? Replication Information is copied to RNA and used to specify amino acid sequences in proteins.

Concept 3.1 Nucleic Acids Are Informational Macromolecules DNA replication and transcription depend on base pairing: 5′-TCAGCA-3′ 3′-AGTCGT-5′ transcribes to RNA with the sequence 5′-UCAGCA-3′.

Concept 3.1 Nucleic Acids Are Informational Macromolecules What is the Genome? - complete set of DNA in a living organism What are Genes? - DNA sequences that encode specific proteins and are transcribed into RNA

Figure 3.5 DNA Replication and Transcription Figure 3.5 DNA Replication and Transcription DNA is completely replicated during cell reproduction (A), but it is only partially transcribed (B). In transcription, the DNA code is copied to RNA. The sequence of the latter determines the amino acid sequence of a protein. Transcription of the genes for many different proteins is activated at different times and, in multicellular organisms, in different cells of the body.

Concept 3.1 Nucleic Acids Are Informational Macromolecules DNA base sequences reveal evolutionary relationships. Closely related living species should have more similar base sequences than species that are more distantly related.

What are the major functions of proteins? Enzymes—catalytic molecules Concept 3.2 Proteins Are Polymers with Important Structural and Metabolic Roles What are the major functions of proteins? Enzymes—catalytic molecules Defensive proteins (e.g., antibodies) Hormonal and regulatory proteins—control physiological processes Receptor proteins—receive and respond to molecular signals Storage proteins—store amino acids

Concept 3.2 Proteins Are Polymers with Important Structural and Metabolic Roles What are amino acids? Amino and carboxyl functional groups allow them to act as both acid and base.

The R group (side chain) differs in each amino acid. Concept 3.2 Proteins Are Polymers with Important Structural and Metabolic Roles The R group (side chain) differs in each amino acid. How many amino acids occur extensively in the proteins of all organisms? 20

Table 3.2 (Part 1)

Table 3.2 (Part 2)

Table 3.2 (Part 3)

Cysteine side chains can form covalent bonds called disulfide bridges. Concept 3.2 Proteins Are Polymers with Important Structural and Metabolic Roles Cysteine side chains can form covalent bonds called disulfide bridges.

Figure 3.6 Formation of a Peptide Bond Figure 3.6 Formation of a Peptide Bond In living things, the reaction leading to a peptide bond has many intermediate steps, but the reactants and products are the same as those shown in this simplified diagram.

Figure 3.7 The Four Levels of Protein Structure Figure 3.7 The Four Levels of Protein Structure The primary structure (A) of a protein determines what its secondary (B and C), tertiary (D), and quaternary (E) structures will be.

What is the Primary structure of a protein? Concept 3.2 Proteins Are Polymers with Important Structural and Metabolic Roles What is the Primary structure of a protein? - the sequence of amino acids

What is the Secondary structure Concept 3.2 Proteins Are Polymers with Important Structural and Metabolic Roles What is the Secondary structure - regular, repeated spatial patterns in different regions, resulting from hydrogen bonding α (alpha) helix—right-handed coil β (beta) pleated sheet—two or more sequences are extended and aligned

Figure 3.7 The Four Levels of Protein Structure (Part 2) Figure 3.7 The Four Levels of Protein Structure The primary structure (A) of a protein determines what its secondary (B and C), tertiary (D), and quaternary (E) structures will be.

What is the Tertiary structure Concept 3.2 Proteins Are Polymers with Important Structural and Metabolic Roles What is the Tertiary structure - polypeptide chain is bent and folded; results in the definitive 3-D shape

Interactions between R groups determine tertiary structure Concept 3.2 Proteins Are Polymers with Important Structural and Metabolic Roles Interactions between R groups determine tertiary structure

Figure 3.10 Primary Structure Specifies Tertiary Structure (Part 1) Figure 3.10 Primary Structure Specifies Tertiary Structure Using the protein ribonuclease, Christian Anfinsen showed that proteins spontaneously fold into functionally correct three-dimensional configurations.a As long as the primary structure is not disrupted, the information for correct folding (under the right conditions) is retained. [a C. B. Anfinsen et al. 1961. Proceedings of the National Academy of Sciences USA. 47: 1309–1314.]

Figure 3.10 Primary Structure Specifies Tertiary Structure (Part 2) Figure 3.10 Primary Structure Specifies Tertiary Structure Using the protein ribonuclease, Christian Anfinsen showed that proteins spontaneously fold into functionally correct three-dimensional configurations.a As long as the primary structure is not disrupted, the information for correct folding (under the right conditions) is retained. [a C. B. Anfinsen et al. 1961. Proceedings of the National Academy of Sciences USA. 47: 1309–1314.]

What is the Quaternary structure? Concept 3.2 Proteins Are Polymers with Important Structural and Metabolic Roles What is the Quaternary structure? - two or more polypeptide chains (subunits) bind together by hydrophobic and ionic interactions and hydrogen bonds

Figure 3.7 The Four Levels of Protein Structure (Part 3) Figure 3.7 The Four Levels of Protein Structure The primary structure (A) of a protein determines what its secondary (B and C), tertiary (D), and quaternary (E) structures will be.

Nucleic Acids and Proteins

Concept 3.1 Nucleic Acids Are Informational Macromolecules DNA replication and transcription This DNA sequence is one of two strands in a double helix: 5′ - AGCATTGCTAGCGTA - 3′ Write the nucleotide sequence of each of the following, making sure to label the 5′ and 3′ ends of each molecule: The complementary DNA strand The RNA strand transcribed from the above DNA strand The RNA strand transcribed from the complementary DNA strand Answers: 1. 5′ - TCGTAACGATCGCAT- 3′ 2. 5′ - UCGUAACGAUCGCAU- 3′ 3. 5′ - AGCAUUGCUAGCGUA - 3′ 38

Figure 3.11 Protein Structure Can Change Figure 3.11 Protein Structure Can Change Proteins can change their tertiary structure when they bind to other molecules (A) or are modified chemically (B).

No catalyst makes a reaction occur that cannot otherwise occur. Concept 3.3 Some Proteins Act as Enzymes to Speed up Biochemical Reactions What are Catalysts? - substances that speed up the reactions without being permanently altered No catalyst makes a reaction occur that cannot otherwise occur. Most are proteins

What is released in an exergonic reaction? Concept 3.3 Some Proteins Act as Enzymes to Speed up Biochemical Reactions What is released in an exergonic reaction? - free energy (G), the amount of energy in a system that is available to do work What happens if there is no catalyst? The reaction will be very slow because there is an energy barrier between reactants and products. What is the activation energy or Ea? - an input of energy that initiates the reaction, which puts reactants into a transition state

Figure 3.12 Activation Energy Initiates Reactions Figure 3.12 Activation Energy Initiates Reactions (A) In any chemical reaction, an initial stable state must become less stable before change is possible. (B) A ball on a hillside provides a physical analogy to the biochemical principle graphed in A. Although these graphs show an exergonic reaction, activation energy is needed for endergonic reactions as well.

Enzyme Catalysis

Concept 3.3 Some Proteins Act as Enzymes to Speed up Biochemical Reactions Activation energy can come from heat—the molecules have more kinetic energy. Enzymes lower the activation energy by enabling reactants to come together and react more easily. Example: A molecule of sucrose in solution may hydrolyze in about 15 days; with sucrase present, the same reaction occurs in 1 second!

Figure 3.13 Enzymes Lower the Energy Barrier Figure 3.13 Enzymes Lower the Energy Barrier The activation energy (Ea) is lower in an enzyme-catalyzed reaction than in an uncatalyzed reaction, but the free energy released is the same with or without catalysis. A lower activation energy means the reaction will take place at a faster rate.

Figure 3.13 Enzymes Lower the Energy Barrier Figure 3.13 Enzymes Lower the Energy Barrier The activation energy (Ea) is lower in an enzyme-catalyzed reaction than in an uncatalyzed reaction, but the free energy released is the same with or without catalysis. A lower activation energy means the reaction will take place at a faster rate.

What are the substrates? reactants What are the active sites? Concept 3.3 Some Proteins Act as Enzymes to Speed up Biochemical Reactions Enzymes are highly specific—each one catalyzes only one chemical reaction. What are the substrates? reactants What are the active sites? specific sites on the enzyme where the reactants binds

Figure 3.14 Enzyme Action Figure 3.14 Enzyme Action Sucrase catalyzes the hydrolysis of sucrose. After the reaction, the enzyme is unchanged and is ready to accept another substrate molecule.

The enzyme is not changed at the end of the reaction. Concept 3.3 Some Proteins Act as Enzymes to Speed up Biochemical Reactions The enzyme–substrate complex (ES) is held together by hydrogen bonding, electrical attraction, or temporary covalent bonding. The enzyme is not changed at the end of the reaction.

Enzymes use one or more mechanisms to catalyze a reaction: Concept 3.3 Some Proteins Act as Enzymes to Speed up Biochemical Reactions Enzymes use one or more mechanisms to catalyze a reaction: Inducing strain—bonds in the substrate are stretched, putting it in an unstable transition state.

Many enzymes change shape when the substrate binds. Concept 3.3 Some Proteins Act as Enzymes to Speed up Biochemical Reactions Enzyme 3-D structures are so specific that they bind only one or a few related substrates. Many enzymes change shape when the substrate binds. The binding is like a baseball in a catcher’s mitt. The enzyme changes shape to make the binding tight—“induced fit.”

Figure 3.15 Some Enzymes Change Shape When Substrate Binds to Them Figure 3.15 Some Enzymes Change Shape When Substrate Binds to Them Shape changes result in an induced fit between enzyme and substrate, improving the catalytic ability of the enzyme. Induced fit can be observed in the enzyme hexokinase, seen here with and without its substrates, glucose (green) and ATP (yellow).

What are the cofactors that some enzymes require? Metal ions Concept 3.3 Some Proteins Act as Enzymes to Speed up Biochemical Reactions What are the cofactors that some enzymes require? Metal ions Coenzymes add or remove chemical groups from the substrate. Prosthetic groups (nonamino acid groups) permanently bound to their enzymes.

Table 3.3

Rates of catalyzed reactions: Concept 3.3 Some Proteins Act as Enzymes to Speed up Biochemical Reactions Rates of catalyzed reactions: There is usually less enzyme than substrate present, so reaction rate levels off when all enzyme molecules are bound to substrate molecules. The enzyme is said to be saturated.

Figure 3.16 Catalyzed Reactions Reach a Maximum Rate Figure 3.16 Catalyzed Reactions Reach a Maximum Rate Because there is usually less enzyme than substrate present, the reaction rate levels off when the enzyme becomes saturated.

Turnover ranges from 1 to 40 million molecules per second! Concept 3.3 Some Proteins Act as Enzymes to Speed up Biochemical Reactions Maximum reaction rate is used to calculate enzyme efficiency—molecules of substrate converted to product per unit time (turnover). Turnover ranges from 1 to 40 million molecules per second!

Concept 3.4 Regulation of Metabolism Occurs by Regulation of Enzymes Enzyme-catalyzed reactions operate in metabolic pathways. The product of one reaction is a substrate for the next reaction. Each step is catalyzed by a specific enzyme. Cell have hundreds of enzymes that participate in interconnecting metabolic pathways, forming a metabolic system.

Figure 3.17 A Biochemical System Figure 3.17 A Biochemical System The complex interactions of metabolic pathways can be studied using the tools of systems biology. Enzymes are a major element controlling these pathways.

Concept 3.4 Regulation of Metabolism Occurs by Regulation of Enzymes How can cells regulate metabolism? - by controlling the amount of an enzyme - have the ability to turn synthesis of enzymes off or on

Concept 3.4 Regulation of Metabolism Occurs by Regulation of Enzymes What are chemical inhibitors? They bind to enzymes and slow reaction rates. What is irreversible inhibition? Inhibitor covalently binds to a side chain in the active site. The enzyme is permanently inactivated. Some insecticides act in this way.

Figure 3.18 Irreversible Inhibition Figure 3.18 Irreversible Inhibition DIPF forms a stable covalent bond with the amino acid serine at the active site of the enzyme acetylcholinesterase, thus irreversibly disabling the enzyme.

Concept 3.4 Regulation of Metabolism Occurs by Regulation of Enzymes What is reversible inhibition? A competitive inhibitor binds at the active site but no reaction occurs. It competes with the natural substrate. A noncompetitive inhibitor binds at a site distinct from the active site, causing change in enzyme shape and function. It prevents substrate binding or slows the reaction rate. ANIMATED TUTORIAL 3.2 Enzyme Catalysis

Figure 3.19 Reversible Inhibition Figure 3.19 Reversible Inhibition (A) A competitive inhibitor binds temporarily to the active site of an enzyme. (B) A noncompetitive inhibitor binds temporarily to the enzyme at a site away from the active site. In both cases, the enzyme’s function is disabled for only as long as the inhibitor remains bound.

Figure 3.19 Reversible Inhibition Figure 3.19 Reversible Inhibition (A) A competitive inhibitor binds temporarily to the active site of an enzyme. (B) A noncompetitive inhibitor binds temporarily to the enzyme at a site away from the active site. In both cases, the enzyme’s function is disabled for only as long as the inhibitor remains bound.

Concept 3.4 Regulation of Metabolism Occurs by Regulation of Enzymes What is allosteric regulation? - non-substrate molecule binds a site other than the active site (the allosteric site) The enzyme changes shape, which alters the chemical attraction (affinity) of the active site for the substrate. Allosteric regulation can activate or inactivate enzymes.

Enzyme Allosteric Regulation

Figure 3.20 Allosteric Regulation of Enzyme Activity Figure 3.20 Allosteric Regulation of Enzyme Activity (A) Noncovalent binding of a regulator (in this case an activator) can cause an enzyme to change shape and expose an active site. B) Enzymes can also be activated by covalent modification, in this case phosphorylation. Note that allosteric regulation can be negative as well, with the active site becoming hidden.

Concept 3.4 Regulation of Metabolism Occurs by Regulation of Enzymes Protein tertiary structure (and thus function) is very sensitive to the concentration of H+ (pH) in the environment. All enzymes have an optimal pH for activity.

Concept 3.4 Regulation of Metabolism Occurs by Regulation of Enzymes Temperature affects protein structure and enzyme activity: Warming increases rates of chemical reactions, but if temperature is too high, noncovalent bonds can break, inactivating enzymes. All enzymes have an optimal temperature for activity.

Figure 3.22 Enzyme Activity Is Affected by the Environment Figure 3.22 Enzyme Activity Is Affected by the Environment (A) The activity curve for each enzyme peaks at its optimal pH. For example, pepsin is active in the acidic environment of the stomach, whereas chymotrypsin is active in the neutral environment of the small intestine, and arginase is active in a basic environment. (B) Similarly, there is an optimal temperature for each enzyme. At higher temperatures the enzyme becomes denatured and inactive; this explains why the activity curve falls off abruptly at temperatures that are above optimal.