Chemistry 321; Biology 321; BIMO 321
Biochemistry I: Structure and Function of Biological Molecules
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.