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	3.5 Nucleic Acids	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	3.4 Proteins	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	3.4 Proteins	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	3.3 Lipids	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	3.2 Carbohydrates	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

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