Content Category 1A: Structure and function of proteins and their constituent amino acids

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Macromolecules formed from amino acids adopt well-defined, three-dimensional structures with chemical properties that are responsible for their participation in virtually every process occurring within and between cells. The three-dimensional structure of proteins is a direct consequence of the nature of the covalently-bonded sequence of amino acids, their chemical and physical properties, and the way in which the whole assembly interacts with water.  

Enzymes are proteins that interact in highly regio- and stereo-specific ways with dissolved solutes. They either facilitate the chemical transformation of these solutes or allow for their transport innocuously. Dissolved solutes compete for protein-binding sites, and protein conformational dynamics give rise to mechanisms capable of controlling enzymatic activity. 

The infinite variability of potential amino acid sequences allows for adaptable responses to pathogenic organisms and materials. The rigidity of some amino acid sequences makes them suitable for structural roles in complex living systems. 

Content in this category covers a range of protein behaviors which originate from the unique chemistry of amino acids themselves. Amino acid classifications and protein structural elements are covered. Special emphasis is placed on enzyme catalysis including mechanistic considerations, kinetics, models of enzyme-substrate interaction, and regulation. 

Topic Biochemistry Biochemistry: A Short Course Biology, 2e Fundamentals of Biochemistry Human Physiology Karp’s Cell and Molecular Biology Organic Chemistry With a Biological Emphasis, Vol. 1 Organic Chemistry With a Biological Emphasis, Vol. 2
Amino Acids (BC, OC) Description
  • Absolute configuration at the α position
  • Amino acids as dipolar ions
  • Classifications
    • Acidic or basic
    • Hydrophobic or hydrophilic
Reactions
  • Sulfur linkage: cysteine and cysteine
  • Peptide linkage: polypeptides and proteins
  • Hydrolysis
  • Ch. 2 Proteins: Composition and Structure, pp. 29-42
  • Ch. 3 Amino Acids, pp. 37-45
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  • Ch.4 Amino Acids, pp. 80-96
  • Ch. 2 Chemical Composition of the Body, pp. 45-46
  • Ch. 7 The Nervous System and Neuronal Excitability, pp. 232-234
  • Ch. 21 The Digestive System, p. 775
  • Ch. 22 Metabolic Adaptations, Energy Balance, and Temperature Regulation, pp. 793-795
  • Ch. 2 The Chemical Basis of Life, pp. 48-60
  • Ch. 1.3D, pp. 41-42
  • Ch. 3.3-3.4 pp. 146-158
  • Ch. 15.6, pp. 309-316
  • Ch. 11.1-11.7, pp. 95-124

Protein Structure (BIO, BC, OC)

Structure
  • 1° structure of proteins
  • 2° structure of proteins
  • 3° structure of proteins; role of proline, cystine, hydrophobic bonding
  • 4° structure of proteins (BIO, BC)
Conformational stability
  • Denaturing and folding
  • Hydrophobic interactions
  • Solvation layer (entropy) (BC)
Separation techniques
  • Isoelectric point
  • Electrophoresis
  • Ch. 2 Proteins: Composition and Structure, pp. 42-66
  • Ch. 3 Exploring Proteins and Proteomes, pp. 69-108
  • Ch. 4 Protein Three-Dimensional Structure, pp. 49-68
  • Ch. 5 Techniques in Protein Biochemistry, pp. 76-92
  • Ch. 5 Proteins: Primary Structure, pp. 97-130
  • Ch. 6 Proteins: Three- Dimensional Structure, pp. 131-179
  • Ch. 2 Chemical Composition of the Body, pp. 32, 45-48
  • Ch. 2 The Chemical Basis of Life, pp. 48-70
  • Ch. 18 Techniques in Cell and Molecular Biology pp. 712, 715-716
  • Ch. 2.5C pp. 113 - 115
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Non-Enzymatic Protein Function (BIO, BC)
  • Binding
  • Immune system
  • Motors
  • Ch. 7 Hemoglobin, pp. 207-225
  • Ch. 35 Immune System, pp. 1119-1149 (online chapter)
  • Chapter 36 Molecular Motors, pp. 1151-1168 (online chapter)
  • Ch. 9 Hemoglobin, An Allosteric Protein, pp. 161-173
  • Ch. 7 Protein Function: Myoglobin and Hemoglobin, Muscle Contraction and Antibodies, pp. 180-220
  • Ch. 2 Chemical Composition of the Body, pp. 48-52
  • Ch. 11 Muscle, pp. 382-385
  • Ch. 17 The Immune System, pp. 625-627
  • Ch. 2 The Chemical Basis of Life, pp. 73-76
  • Ch. 7 Interactions Between Cells and Their Environment, pp. 238-241
  • Ch. 9 The Cytoskeleton and Cell Motility, pp. 315-320
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Enzyme Structure and Function (BIO, BC)
  • Function of enzymes in catalyzing biological reactions
  • Enzyme classification by reaction type
  • Reduction of activation energy
  • Substrates and enzyme specificity
  • Active Site Model
  • Induced-fit Model
  • Mechanism of catalysis
    • Cofactors
    • Coenzymes
    • Water-soluble vitamins
  • Effects of local conditions on enzyme activity
  • Ch. 8 Enzymes: Basic Concept and Kinetics, pp. 233-264
  • Ch. 9 Catalytic Strategies, pp. 273-306
  • Ch. 6 Basic Concepts of Enzyme Action, pp. 105-115
  • Ch.11 Enzymatic Catalysis, pp. 322-360
  • Ch. 4 Energy and Metabolism, pp. 102-106
  • Ch. 21 The Digestive System, pp. 762-763
  • Ch. 3 Bioenergetics, Enzymes, and Metabolism, pp. 89-97, 106
  • Ch. 6.1-6.4, pp. 303-324
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Control of Enzyme Activity (BIO, BC)*
  • Kinetics
    • General (catalysis)
    • Michaelis-Menten
    • Cooperativity
  • Feedback regulation
  • Inhibition — types
    • Competitive
    • Noncompetitive
    • Mixed (BC)
    • Uncompetitive (BC)
  • Regulatory enzymes
    • Allosteric enzymes
    • Covalently modified enzymes
    • Zymogen
  • Ch. 8 Enzymes: Basic Concept and Kinetics, pp. 233-264
  • Ch. 10 Regulatory Strategies, pp. 309-335
  • Ch. 7 Kinetics and Regulation, pp. 119-134
  • Ch. 8 Mechanisms and Inhibitor, pp. 143-156
  • Ch. 12 Enzyme Kinetics, Inhibition, and Control, pp. 361-401
  • Ch. 2 Chemical Composition of the Body, pp. 51-52
  • Ch. 4 Energy and Metabolism, pp. 102-106
  • Ch. 3 Bioenergetics, Enzymes, and Metabolism, pp. 97-100, 109-110
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