1. Nucleic Acids, Proteins, and Enzymes3
Nucleic Acids, Proteins, and Enzymes

2. 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

3. Concept 3.1 Nucleic Acids Are Informational Macromolecules
Nucleic acids are polymers specialized for storage, transmission, and use of genetic information.
DNA = deoxyribonucleic acid
RNA = ribonucleic acid
Monomers: Nucleotides

4. Concept 3.1 Nucleic Acids Are Informational Macromolecules
Nucleotide: Pentose sugar + N-containing base + phosphate group
Nucleosides: Pentose sugar + N-containing base

5. Concept 3.1 Nucleic Acids Are Informational Macromolecules
Bases:
Pyrimidines—single rings
Purines—double rings
Sugars:
DNA contains deoxyribose
RNA contains ribose

6. Figure 3.1 Nucleotides Have Three Components

7. Concept 3.1 Nucleic Acids Are Informational Macromolecules
Nucleotides bond in condensation reactions to form phosphodiester linkages.
Nucleic acids grow in the 5′ to 3′ direction.

8. Figure 3.2 Linking Nucleotides Together

9. Table 3.1 Distinguishing RNA from DNA

10. Concept 3.1 Nucleic Acids Are Informational Macromolecules
Complementary base pairing:
adenine and thymine always pair (A-T)
cytosine and guanine always pair (C-G)

11. Concept 3.1 Nucleic Acids Are Informational Macromolecules
Base pairs are linked by hydrogen bonds.
There are so many hydrogen bonds in DNA and RNA that they form a fairly strong attraction, but not as strong as covalent bonds.
Thus, base pairs can be separated with only a small amount of energy.
LINK Hydrogen bonds play an essential role in the chemistry of life; see Concept 2.2

12. Concept 3.1 Nucleic Acids Are Informational Macromolecules
RNA is usually single-stranded, but may be folded into 3-D structures, by hydrogen bonding.
Folding occurs by complementary base pairing, so structure is determined by the order of bases.

13. Figure 3.3 RNA (Part 1)

14. Figure 3.3 RNA (Part 2)

15. Concept 3.1 Nucleic Acids Are Informational Macromolecules
DNA—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.
VIDEO 3.1 Deoxyribonucleic acid: A three-dimensional model
VIDEO 3.2 Cell Visualization: The structure of DNA

16. Figure 3.4 DNA (Part 1)

17. Figure 3.4 DNA (Part 2)

18. Concept 3.1 Nucleic Acids Are Informational Macromolecules
DNA is an informational molecule: genetic information is in the sequence of base pairs.
DNA has two functions:
Replication
Gene expression—base sequences are copied to RNA, and specify amino acids sequences in proteins.

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

20. Concept 3.1 Nucleic Acids Are Informational Macromolecules
Genome—complete set of DNA in a living organism
Genes—DNA sequences that encode specific proteins and are transcribed into RNA
Not all genes are transcribed in all cells of an organism.

21. Figure 3.5 DNA Replication and Transcription

22. 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.
Scientists are now able to determine and compare entire genomes of organisms to study evolutionary relationships.
ANIMATED TUTORIAL 3.1 Macromolecules: Nucleic Acids and Proteins
LINK The use of DNA sequences to reconstruct the evolutionary history of life is described in Chapter 16

23. Major functions of proteins: Enzymes—catalytic proteins
Concept 3.2 Proteins Are Polymers with Important Structural and Metabolic Roles
Major functions of proteins:
Enzymes—catalytic proteins
• 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

24. • Structural proteins—physical stability and movement
Concept 3.2 Proteins Are Polymers with Important Structural and Metabolic Roles
• Structural proteins—physical stability and movement
• Transport proteins carry substances (e.g., hemoglobin)
• Genetic regulatory proteins regulate when, how, and to what extent a gene is expressed

25. Protein monomers are amino acids.
Concept 3.2 Proteins Are Polymers with Important Structural and Metabolic Roles
Protein monomers are amino acids.
Amino and carboxylic acid functional groups allow them to act as both acid and base.
The R group differs in each amino acid.

26. They are grouped according to properties conferred by the R groups.
Concept 3.2 Proteins Are Polymers with Important Structural and Metabolic Roles
Only 20 amino acids occur extensively in the proteins of all organisms.
They are grouped according to properties conferred by the R groups.

27. Concept 3.2 Proteins Are Polymers with Important Structural and Metabolic Roles
Cysteine side chains can form covalent bonds— a disulfide bridge, or disulfide bond.

28. Polymerization takes place in the amino to carboxyl direction.
Concept 3.2 Proteins Are Polymers with Important Structural and Metabolic Roles
Amino acids are linked in condensation reactions to form peptide linkages or bonds.
Polymerization takes place in the amino to carboxyl direction.

29. Figure 3.6 Formation of a Peptide Linkage

30. Primary structure of a protein—the sequence of amino acids
Concept 3.2 Proteins Are Polymers with Important Structural and Metabolic Roles
Primary structure of a protein—the sequence of amino acids

31. • α (alpha) helix—right-handed coil
Concept 3.2 Proteins Are Polymers with Important Structural and Metabolic Roles
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 polypeptide chains are extended and aligned

32. Figure 3.7 B, C The Four Levels of Protein Structure

33. Concept 3.2 Proteins Are Polymers with Important Structural and Metabolic Roles
Tertiary structure—polypeptide chain is bent and folded; results in the definitive 3-D shape
The outer surfaces present functional groups that can interact with other molecules.
VIDEO 3.3 Lysozyme: A three-dimensional model

34. 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.
• Disulfide bridges hold a folded polypeptide together
• Hydrogen bonds stabilize folds
Hydrophobic side chains can aggregate
van der Waals interactions between hydrophobic side chains
• Ionic interactions form salt bridges

35. Figure 3.9 The Structure of a Protein

36. Concept 3.2 Proteins Are Polymers with Important Structural and Metabolic Roles
Secondary and tertiary protein structure derive from primary structure.
Denaturing—heat or chemicals are used to disrupt weaker interactions in a protein, destroying secondary and tertiary structure.
The protein can return to normal when cooled— all the information needed to specify the unique shape is contained in the primary structure.

37. High concentrations of polar substances Nonpolar substances
Concept 3.2 Proteins Are Polymers with Important Structural and Metabolic Roles
Factors that can disrupt the interactions that determine protein structure (denaturing):
Temperature
Concentration of H+
High concentrations of polar substances
Nonpolar substances
APPLY THE CONCEPT Proteins are polymers with important structural and metabolic roles

38. No catalyst makes a reaction occur that cannot otherwise occur.
Concept 3.3 Some Proteins Act as Enzymes to Speed up Biochemical Reactions
Living systems depend on reactions that occur spontaneously, but at very slow rates.
Catalysts are substances that speed up reactions without being permanently altered.
No catalyst makes a reaction occur that cannot otherwise occur.
Most biological catalysts are proteins (enzymes); a few are RNA molecules (ribozymes).

39. Concept 3.3 Some Proteins Act as Enzymes to Speed up Biochemical Reactions
In some exergonic reactions there is an energy barrier between reactants and products.
An input of energy (the activation energy or Ea) will put reactants into a transition state.

40. Figure 3.11 Activation Energy Initiates Reactions (Part 1)

41. Concept 3.3 Some Proteins Act as Enzymes to Speed up Biochemical Reactions
Enzymes lower the activation energy—they allow 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!

42. Figure 3.12 Enzymes Lower the Energy Barrier

43. Concept 3.3 Some Proteins Act as Enzymes to Speed up Biochemical Reactions
Enzymes are highly specific—each one catalyzes only one chemical reaction.
Reactants are substrates: they bind to a specific site on the enzyme—the active site.
Specificity results from the exact 3-D shape and chemical properties of the active site.

44. Figure 3.13 Enzyme Action

45. 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.

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

47. Figure 3.14 Some Enzymes Change Shape When Substrate Binds to Them

48. Some enzymes require ions or other molecules in order to function:
Concept 3.3 Some Proteins Act as Enzymes to Speed up Biochemical Reactions
Some enzymes require ions or other molecules in order to function:
Cofactors—inorganic ions
Coenzymes add or remove chemical groups from the substrate. They can participate in many different reactions.
Prosthetic groups (non-amino acid groups) permanently bound to their enzymes.
VIDEO 3.5 Glyceraldehyde 3-phosphate dehydrogenase and coenzyme NAD: A three-dimensional model

49. Table 3.3 Some Examples of Nonprotein “Partners” of Enzymes

50. Concept 3.4 Regulation of Metabolism Occurs by Regulation of Enzymes
Enzyme-catalyzed reactions are part of metabolic pathways—the product of one reaction is a substrate for the next.

51. Concept 3.4 Regulation of Metabolism Occurs by Regulation of Enzymes
Homeostasis—the maintenance of stable internal conditions
Cells can regulate metabolism by controlling the amount of an enzyme.
Cells often have the ability to turn synthesis of enzymes off or on.
LINK The regulation of enzyme synthesis is described in Chapter 11

52. Concept 3.4 Regulation of Metabolism Occurs by Regulation of Enzymes
Chemical inhibitors can bind to enzymes and slow reaction rates.
Natural inhibitors regulate metabolism; artificial inhibitors are used to treat diseases, kill pests, and study enzyme function.

53. Concept 3.4 Regulation of Metabolism Occurs by Regulation of Enzymes
Irreversible inhibition—inhibitor covalently binds to a side chain in the active site. The enzyme is permanently inactivated.

54. Figure 3.16 Irreversible Inhibition

55. Concept 3.4 Regulation of Metabolism Occurs by Regulation of Enzymes
Reversible inhibition (more common in cells):
A competitive inhibitor competes with natural substrate for active site.
A noncompetitive inhibitor binds at a site distinct from the active site—this causes change in enzyme shape and function.
ANIMATED TUTORIAL 3.2 Enzyme Catalysis

56. Figure 3.17 Reversible Inhibition (Part 1)

57. Figure 3.17 Reversible Inhibition (Part 2)

58. Concept 3.4 Regulation of Metabolism Occurs by Regulation of Enzymes
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.
ANIMATED TUTORIAL 3.3 Allosteric Regulation of Enzymes

59. Figure 3.18 Allosteric Regulation of Enzyme Activity

60. Concept 3.4 Regulation of Metabolism Occurs by Regulation of Enzymes
Protein kinases are enzymes that regulate responses to the environment by organisms.
They are subject to allosteric regulation.
The active form regulates the activity of other enzymes, by phosphorylating allosteric or active sites on the other enzymes.
LINK The role of protein kinases in intracellular signaling pathways is described in Chapter 5

61. Concept 3.4 Regulation of Metabolism Occurs by Regulation of Enzymes
Metabolic pathways:
The first reaction is the commitment step—other reactions then happen in sequence.
Feedback inhibition (end-product inhibition)— the final product acts as a noncompetitive inhibitor of the first enzyme, which shuts down the pathway.

62. Concept 3.4 Regulation of Metabolism Occurs by Regulation of Enzymes
pH affects enzyme activity:
Acidic side chains generate H+ and become anions.
Basic side chains attract H+ and become cations.

63. Concept 3.4 Regulation of Metabolism Occurs by Regulation of Enzymes
Example:
glutamic acid—COOH glutamic acid—COO– + H+
The law of mass action—the higher the H+ concentration, the more reaction is driven to the left to the less hydrophilic form.
This can affect enzyme shape and function.

64. 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.

65. Figure 3.20 A Enzyme Activity Is Affected by the Environment

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

67. Figure 3.20 B Enzyme Activity Is Affected by the Environment