Chemistry 321; Biology 321; BIMO 321

Biochemistry I

Structure and Function of Biological Molecules

SYLLABUS - FALL 2016

SYLLABUS

Assignments for the lecture material are in the text generally called “Lehninger” by Nelson and Cox, Principles of Biochemistry, 6th edition, Freeman, New York, 2013

I.            The Foundations of Biochemistry (chapter 1)
                        Cellular foundations
                        Chemical foundations
                        Genetic foundations
                        Evolutionary foundations

II.            Water, The Biological Solvent (chapter 2)
                        Structure of water
                        Interactions in aqueous solutions
                        Ionization of water, pH, and pK
                        Acids, bases, buffers, and the Henderson-Hasselbalch equation

III.            Bioenergetics
                        Physical foundations of biochemistry (chapter 1, pp. 20-28)
                        Bioenergetics and thermodynamics (chapter 13, pp. 505-517)

IV.            Amino Acids, Peptides, and Proteins (chapter 3)
                        Amino acid structures
                        Acidic and basic properties
                        Stereochemistry of amino acids
                        Reactions of the amino acid functional groups

                        Protein function - structural proteins; enzymes; transport and storage; muscle contraction and motility;immunoproteins; regulatory and receptor proteins
                        Protein purification
                        Proteins can be purified and characterized by using:
                                    Solubility
                                    Chromatography
                                    Electrophoresis
                                    Ultracentrifugation
                                    Specific interactions
                                    Mass spectrometry
                        Amino acid composition/sequence of proteins
                        Protein Evolution

V.            Proteins - Three-Dimensional Structure (chapter 4)
                        The nature of the peptide bond
                        Secondary structure - a-helix, b-pleated sheet, and b-bends
                        Analysis and prediction of secondary structure
                        Supersecondary structures
                        Tertiary structure and the presence of motifs and domains
                        Subunit interaction and quaternary structure
                        Forces that determine protein conformation
                        Protein folding and stability

VI.            Protein Conformation, Dynamics and Function (chapter 5, pp. 158-178)
                        Myoglobin and Hemoglobin
                                    Structure
                                    Mechanism of oxygen binding and transport
                                    Ligand binding
                                    Factors that influence oxygen binding
                        Immunoglobulins
                                    Structure and function of antibodies
                                    Antigen-antibody binding

VII.            Enzymes – Kinetics and Catalysis (chapter 6)
                        Enzyme specificity/cofactors and coenzymes
                        Mechanism of action - acid-base catalysis; covalent catalysis; metal ion catalysis; electrostatic catalysis; catalysis through proximity and orientation effects; and  catalysis by preferential transition state binding
                        Active sites
                        The mechanism of specific enzymes
                                    Serine proteases - chymotrypsin, trypsin, and elastase
                                    Lysozyme
                        Digestive enzymes and coagulation factors
                        Chemical kinetics
                        Enzyme kinetics
                                    Michaelis-Menten kinetic analysis - equilibrium
                                    Briggs-Haldane kinetic analysis - steady state
                        Enzyme inhibition
                                    Irreversible
                                    Competitive
                                    Noncompetitive
                                    Uncompetitive
                        Multisubstrate enzyme kinetics
                        Regulation of Enzyme Activity
                        Allosteric regulation
                        Reversible covalent modification
                        Enzyme stimulation and inhibition by control proteins

VIII.            Nucleic Acids (chapter 8 and 24)
                        Nucleotide - structure and function
                        Basic nucleic acid composition and structure
                        Nucleic acid sequencing
                        Recombinant DNA technology
                        DNA
                                    DNA helix
                                    Forces stabilizing nucleic acid structures
                        RNA
                                    Structure
                        Fractionation and characterization of nucleic acids
                        Nucleic acid-protein interactions
                        DNA supercoiling and topoisomerase
                        Higher orders of nucleic acid structure

IX.            DNA Based Information Technologies (chapter 9)
                        DNA Cloning
                        From Genes to Genomes
                        From Genomes to Proteomes

X.            DNA Replication, Repair, and Recombination (chapter 25)
                        Replication
                                    Mechanism of action of DNA polymerase
                        Repair
                                    Direct repair
                                    Excision repair
                                    SOS response and recombination repair
                        Recombination

XI.            The Flow of Genetic Information (chapter 26 and 27)
                        Transcription (chapter 26)
                                    Mechanism of action of RNA polymerase
                        Posttranscriptional processing of RNA
                        Self-splicing RNA

                        Translation (chapter 27)
                        The genetic code
                        Transfer RNA
                        Ribosome
                        Polypeptide synthesis

See the Course Description.