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Content Category 5D: Structure, function, and reactivity of biologically-relevant molecules

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The structure of biological molecules forms the basis of their chemical reactions including oligomerization and polymerization. Unique aspects of each type of biological molecule dictate their role in living systems, whether providing structure or information storage, or serving as fuel and catalysts. 

The content in this category covers the structure, function, and reactivity of biologically-relevant molecules including the mechanistic considerations that dictate their modes of reactivity. 

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
Nucleotides and Nucleic Acids (OC, BC, BIO)*
  • Nucleotides and nucleosides: composition
    • Sugar phosphate backbone
    • Pyrimidine, purine residues
  • Deoxyribonucleic acid: DNA; double helix
  • Chemistry (OC, BC)
  • Other functions (OC, BC)
  • Ch. 4 DNA, RNA and the Flow of Genetic Information, pp. 114-124
  • Ch. 33 The Structure of Informational Macromolecule: DNA and RNA, pp. 673-690
  • Ch. 3 Nucleotides, Nucleic Acids, and Genetic Information, pp. 42-79
  • Ch. 2 Chemical Composition of the Body, pp. 52-54
  • Ch. 2 The Chemical Basis of Life, pp. 77-79
  • Ch. 10 The Nature of the Gene and the Genome, pp. 373-377, 382-387
  • Ch. 18 Techniques in Cell and Molecular Biology, pp. 721-722
  • Ch. 1.3E, pp. 43-45
  • Ch. 9.1-9.8, pp. 1-38
Amino Acids, Peptides, Proteins (OC, BC)*
  • Amino acids: description
    • Absolute configuration at the α position
    • Dipolar ions
    • Classification
      • Acidic or basic
      • Hydrophilic or hydrophobic
    • Synthesis of α-amino acids (OC)
      • Strecker Synthesis
      • Gabriel Synthesis
  • Peptides and proteins: reactions
    • Sulfur linkage for cysteine and cystine
    • Peptide linkage: polypeptides and proteins
    • Hydrolysis
  • General Principles
    • 1° structure of proteins
    • 2° structure of proteins
    • 3° structure of proteins
    • Isoelectric point
  • Ch. 2 Protein Composition and Structure, pp. 29-64
  • Ch. 3 Amino Acids, pp. 37-45
  • Ch. 4 Protein Three-Dimensional Structure, pp. 49-68
  • Ch. 4 Amino Acids, pp. 80-96
  • Ch. 2 Chemical Composition of the Body, pp. 45-52
  • Ch. 2 The Chemical Basis of Life, pp. 58-70
  • Ch. 1.3D, pp. 41-43
  • Ch. 11.1-11.7, pp. 95-124
  • Ch. 15.6, pp 309-316
The Three-Dimensional Protein Structure (BC)
  • Conformational stability
    • Hydrophobic interactions
    • Solvation layer (entropy)
  • 4° structure
  • Denaturing and folding
  • Ch. 2 Protein Composition and Structure, pp. 52-62
  • Ch. 4 Protein Three-Dimensional Structure, pp. 62-67
  • Ch. 6 Proteins: Three-Dimensional Structure, pp. 131-179
  • Ch. 2 Chemical Composition of the Body, pp. 45-52
  • Ch. 2 The Chemical Basis of Life, pp. 48-70
 NA NA
Nonenzymatic Protein Function (BC)
  • Binding
  • Immune system
  • Motor
  • Ch. 7 Hemoglobin, pp. 207-227
  • Ch. 35 Immune System, pp. 1119-1145
  • Ch. 36 Molecular Motors, pp. 1151-1168
  • Ch. 9 Hemoglobin, an Allosteric Protein, pp. 161-173
 NA
  • Ch. 7 Protein Function: Myoglobin and Hemoglobin, Muscle Contraction and Antibodies, pp. 180-220
  • Ch. 2 Chemical Composition of the Body, pp. 45-52
  • 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
 NA NA
Lipids (BC, OC)*
  • Types
    • Storage
      • Triacyl glycerols
      • Free fatty acids: saponification
    • Structural
      • Phospholipids and phosphatids
      • Sphingolipids
      • Waxes
    • Signals/cofactors
      • Fat-soluble vitamins
      • Steroids
      • Prostaglandins
  • Ch. 12 Lipids and Cell Membranes, pp. 373-380
  • Ch. 26 The Biosynthesis of Membrane Lipids and Steroids, pp. 849-883
  • Ch. 29 Lipid Synthesis: Storage Lipids, Phospholipids and Cholesterol, pp. 577-601
  • Ch. 9 Lipids and Biological Membranes, pp. 245-292
  • Ch. 2 Chemical Composition of the Body, pp. 40-45
  • Ch. 4 Metabolism, pp. 126-127
  • Ch. 2 The Chemical Basis of Life, pp. 46-49
  • Ch. 4 The Structure and Function of the Plasma Membrane, pp. 118-122
  • Ch. 1.3A, pp. 35-39
  • Ch. 11.6, pp. 116-121
Carbohydrates (OC)*
  • Description
    • Nomenclature and classification, common names
    • Absolute configuration
    • Cyclic structure and conformations of hexoses
    • Epimers and anomers
  • Hydrolysis of the glycoside linkage
  • Keto-enol tautomerism of monosaccharides
  • Disaccharides (BC)
  • Polysaccharides (BC)
  • Ch. 11 Carbohydrates, pp. 341-365
  • Ch. 10 Carbohydrates, pp. 181-201
  • Ch. 8 Carbohydrates, pp. 221-245
  • Ch. 2 Chemical Composition of the Body, pp. 36-40
  • Ch. 2 The Chemical Basis of Life, pp. 41-46
  • Ch. 1.3C, pp. 39-43
  • Ch. 3.2 pp. 137-146
  • Ch. 3.6, pp. 161-168
  • Ch. 3.8, pp. 171-173
  • Ch. 10.1-10.3, pp. 53-71
  • Ch. 12.2 A-B, pp. 153-157
Phenols (OC, BC)
  • Oxidation and reduction (e.g., hydroquinones, ubiquinones: biological 2e- redox centers)
 NA NA NA
  • Ch.14 Introduction to Metabolism: Section 3. Oxidation-Reduction Reactions, pp. 461-466
 NA NA NA
  • Ch. 15.1-15.4, pp. 278-307
Polycyclic and Heterocyclic Aromatic Compounds (OC, BC)
  • Biological aromatic heterocycles
 NA NA NA
  • Ch. 3 Nucleotides, Nucleic Acids and Genetic Information: Section 1. Nucleotides, pp. 43
 NA NA NA NA