AP Biology Biochemistry Notes

1. Nucleic Acids,
Proteins, and Enzymes
3

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. Chapter 3 Opening Question
How does an understanding of proteins
and enzymes help to explain how
aspirin works?

4. 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

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

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

7. Figure 3.1 Nucleotides Have Three Components

8. 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.

9. Figure 3.2 Linking Nucleotides Together

10. Concept 3.1 Nucleic Acids Are Informational Macromolecules
Oligonucleotides have about 20 monomers, and
include small RNA molecules important for
DNA replication and gene expression.
DNA and RNA are polynucleotides, the longest
polymers in the living world.

11. Table 3.1 Distinguishing RNA from DNA

12. 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)

13. 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.

14. 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.

15. Figure 3.3 RNA (Part 1)

16. Figure 3.3 RNA (Part 2)

17. 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.

18. Figure 3.4 DNA (Part 1)

19. Figure 3.4 DNA (Part 2)

20. 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.

21. 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′.

22. 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.

23. Figure 3.5 DNA Replication and Transcription

24. 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.

25. 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

26. 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

27. 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.

28. 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.

29. Table 3.2 The Twenty Amino Acids in Proteins (Part 1)

30. Table 3.2 The Twenty Amino Acids in Proteins (Part 2)

31. Table 3.2 The Twenty Amino Acids in Proteins (Part 3)

32. Table 3.2 The Twenty Amino Acids in Proteins (Part 4)

33. 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.

34. Concept 3.2 Proteins Are Polymers with Important Structural and
Metabolic Roles
Oligopeptides or peptides—short polymers of 20
or fewer amino acids (some hormones and
signaling molecules)
Polypeptides or proteins range in size from
insulin, which has 51 amino acids, to huge
molecules such as the muscle protein titin, with
34,350 amino acids.

35. 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.

36. Figure 3.6 Formation of a Peptide Linkage

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

38. 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

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

40. 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.

41. 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

42. Figure 3.8 Noncovalent Interactions between Proteins and Other Molecules

43. Figure 3.9 The Structure of a Protein

44. 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.

45. Figure 3.10 Primary Structure Specifies Tertiary Structure (Part 1)

46. Figure 3.10 Primary Structure Specifies Tertiary Structure (Part 2)

47. Concept 3.2 Proteins Are Polymers with Important Structural and
Metabolic Roles
Quaternary structure—two or more polypeptide
chains (subunits) bind together by hydrophobic
and ionic interactions, and hydrogen bonds.
These weak interactions allow small changes
that aid in the protein’s function.

48. Figure 3.7 E The Four Levels of Protein Structure

49. 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

50. 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).

51. 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.

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

53. Figure 3.11 Activation Energy Initiates Reactions (Part 2)

54. 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!

55. Figure 3.12 Enzymes Lower the Energy Barrier

56. 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.

57. Figure 3.13 Enzyme Action

58. 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.
PEESSE +→→+

59. 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.

60. Concept 3.3 Some Proteins Act as Enzymes to Speed up
Biochemical Reactions
• Substrate orientation—substrates are brought
together so that bonds can form.
• Adding chemical groups—R groups may be
directly involved in the reaction.

61. Concept 3.3 Some Proteins Act as Enzymes to Speed up
Biochemical Reactions
Binding of substrate to enzyme is like a baseball
in a catcher’s mitt. The enzyme changes shape
to make the binding tight—“induced fit.”

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

63. 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.

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

65. 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 the
enzyme becomes saturated.
Saturated—all enzyme molecules are bound to
substrate molecules.

66. Figure 3.15 Catalyzed Reactions Reach a Maximum Rate

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

68. 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.

69. 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.

70. 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.

71. 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.

72. Figure 3.16 Irreversible Inhibition

73. 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.

74. Figure 3.17 Reversible Inhibition (Part 1)

75. Figure 3.17 Reversible Inhibition (Part 2)

76. 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.

77. Figure 3.18 Allosteric Regulation of Enzyme Activity

78. 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.

79. 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.

80. Figure 3.19 Feedback Inhibition of Metabolic Pathways

81. 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.

82. 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.

83. 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.

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

85. 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.

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

87. Concept 3.4 Regulation of Metabolism Occurs by Regulation of
Enzymes
Isozymes catalyze the same reaction but have
different composition and physical properties.
Isozymes may have different optimal
temperatures or pH, allowing an organism to
adapt to changes in its environment.

88. Answer to Opening Question
Aspirin binds to and inhibits the enzyme
cyclooxygenase.
Cyclooxygenase catalyzes the commitment step
for metabolic pathways that produce:
Prostaglandins—involved in inflammation and
pain
Thromboxanes—stimulate blood clotting and
constriction of blood vessels

89. Figure 3.21 Aspirin: An Enzyme Inhibitor

90. Answer to Opening Question
Aspirin binds at the active site of
cyclooxygenase and transfers an acetyl group
to a serine residue.
Serine becomes more hydrophobic, which
changes the shape of the active site and
makes it inaccessible to the substrate.

91. Figure 3.22 Inhibition by Covalent Modification (Part 1)

92. Figure 3.22 Inhibition by Covalent Modification (Part 2)