BCMB 8010, Advanced Biochemistry and Molecular Biology

TEXT:

R. H. Garret & Charles M. Grisham, BIOCHEMISTRY, Saunders College Publishing,
Harcourt Brace, New York (1999, Second edition) [G&G]

 C. Branden & John Tooze, Introduction to Protein Structure, Garland Publishing, Inc., New York (1991) [B&T]

List on BMB Home page
BIOLOGY ON-LINE

Dr. Wampler's half:                Quizzes and Problems (30%) Mid Term (20%)*
Dr. Moremen's half:                Three tests (including final) (12.5% each), Homework (12.5%)

COURSE CONTENTS [Assigned Reading Material]:
For a lecture schedule Click here

Part 1 John E. Wampler [with readings from Chapters 1-6 & 14-16 of Garret & Grisham]

Introduction [Chapter 1 of G&G]

Coures Goals and Philosophy
Biochemistry is...
The Molecular Scale & Environment.
Enzymes function by...

Water Structure & Properties
What a Water Model tells us.
Water is not your typical solvent.
Is a Hydrogen Bond a Unique form of Non-bonded Interaction?
Water also defines Acids & Bases.

Edward Goo's Lecture Notes on Water

Introduction to Protein Structure
Amino acid properties, mutations and
Protein Folding (four classes of structure)
Amino Acids, sequence and folding.
What do we know about protein folding?
Torsion angles on the mainchain, phi, psi and omega.
Amino acid side chains folding and preferences
Additivity and Synergy in Protein Structure
Introduction to Structural Motifs
Motifs, Motifs, Motifs...

Web Resources:

Tutorial on Protein Structure, J. E. Wampler

Principles of Protein Structure,Birkbeck College.

Link to the Pfam Database of protein domains

The "Complete" Description of the Solution Spieces of a Protein [Appendix to Chapter 5, G&G]

Structural Details.
Determining the Molecular Weight
Size and Shape
Solvation
Bound Ions
Time Variation

Web Resources:

Analytical Ultracentrifugation of Complex Macromolecular Systems by Jeffrey C. Hansen , Jacob Lebowitz, and Borries Demeler

Enzymes and other Molecular Machines (R. V. Eck)
The Enzyme Assay Enzymes and pH
Enzyme Nomenclature.

Web Resources:

"Symbolism and Terminology in Enzyme Kinetics" about Biochemical Nomenclature and related topics.
General Principles of Enzyme Assays, by Wilbur H. Campbell, Michigan Technological University
PROWL- The EC Enzyme Classification Page from Rockefeller University
EC Enzyme, The ENZYME data bank by Amos Bairoch
Enzyme Structures Database by Roman Laskowski and Andrew Wallace
PROCAT-A database of 3D enzyme active site templates by Andrew C. Wallace and Janet M. Thornton

Binding Studies

Irreversible binding and titrations.

One binding site, one:one interactions

Multiple Equivalent, Independent Sites.

Other Multi-site Models and Cooperativity

Steady State Kinetics and the Michaelis Menten Equation

What defines a kinetic model?

Single substrate/product models.

Cleland Nomenclature, reaction schemes and diagrams

Mutliple substrates and effectors

Defining and Analyzing Kinetic Mechanisms

Multisite enzymes

Kinetic Cooperativity and Allosteric Regulation

Transient State Kinetics

Types of experiments.

The typical stopped-flow experiment.

Models that give multi-exponential curves.

Value and use of time resolved spectra.

Intermediate times, the approach to steady-state.

 Web Resources:

Lecture notes on Inhibition kinetics, Anthony L. Fink, UCSC:

Lecture 14

Lecture 15

Lecture 16

On-Line Textbook on Enzyme Kinetics, Department of Biological Sciences, University of Paisley

Kinetics of Multi-Enzyme Systems, Web version of Chapter 10 from Fundamentals of Enzyme Kinetics (Athel Cornish-Bowden, 1995, Portland Press, London).
MIT Tutorial on Enzyme Kinetics, from the MIT Biology Hypertextbook
Experiment on Kinetics of Invertase, N. S. Wang, University of Maryland.

Structural Basis of Enzyme Action and Function

         More on Structural elements: Motifs
            EF hand structures: Calmodulin and Recoverin
            Helix-turn-helix: Cro and repressor
            Zinc Fingers: TFIIIA (Xenopus), gag protein, Glucocorticoid receptor, Gal4 

        More on Structural Elements: Domains
            a-Domain structures: four helix bundle, globin folds, other examples
            a/b Domain structures: Barrels vs. open twisted sheets, prediction of active site positions
            b-structures: antiparallel structures and active site positions

        How do enzymes work: reaction direction vs. rate
            Catalytic mechanisms: 
                Acid-base catalysis
                Covalent catalysis
                Metal ion catalysis
                Electrostatic catalysis
                Proximity and orientation
                Preferential binding of the transition state complex

        Case studies to illustrate catalytic mechanisms:
                General Acid-General Base catalysis: Lysozyme and other glycosidases
                Covalent catalysis: Serine proteases
        Nucleotide binding proteins:
                Hexokinase
                Nicotinamide coenzymes: Dehydrogenases
                Flavin Coenzymes: multiple examples including glutathione reductase

       Other cofactors
               Thiamine Pyrophosphate: decarboxylation: pyruvate decarboxylase
                                                             a-ketol transfers: transketolase
                Pantothenic acid and Coenzyme A: Thioketolase
                Lipoic acid: Pyruvate dehydrogenase 
                Integration of cofactors into catalytic reactions: pyruvate dehydrogenase

Regulation of enzyme activities, control of metabolic pathways

        Mechanisms of regulation of enzyme activities
                Controls of transcript levels
                    Detection of transcript levels: Northern blots, SAGE, Gene chip arrays
                Regulation of enzyme activity:
                    Irreversible covalent modification
                    Reversible covalent modification
                    Cooperativity: Hemoglobin
                    Allosteric regulation: T states and R states
                Use of Allosteric enzymes to regulate metabolite flux: ATCase

       Model systems for Allosteric Control:
                Glycolysis: Phosphofructokinase and allosteric control by ATP, ADP, AMP, and F-2,6-P2
                            Fructose-1,6-P2-ase and allosteric regulation
                            Synthesis and breakdown of F-2,6-P2 by the bifunctional 6PF-2-K/Fru-2,6-P2ase
                            Pyruvate kinase allosteric and covalent regulation
                Hormonal control of glycolysis: coordinate control of multiple enzymes
                Glycogen synthesis and breakdown: 
                            Glycogen breakdown: Glycogen phosphorylase (role of pyridoxal phosphate) 
                                                Glycogen debranching enzyme
                                                Phosphoglucomutase
                            Glycogen synthesis: UDP-glucose pyrophosphorylase
                                                Glycogen synthase
                Hormonal control of glycogen synthesis and breakdown 

        Phosphorylation cascades in Metabolic Control
                Cell permeable vs. impermeable hormones
                Cell surface receptors: 
                            Oligomeric ion channels
                            Seven helix bundle proteins
                            Single transmembrane segment catalytic receptors
                Heterotrimeric G proteins as signal transducers: role of conformation change
                            Heterotrimeric G proteins vs. monomeric G proteins: switch regions
                            Upstream and downstream effectors for G proteins: how do they interact with G proteins 
                Protein kinases in signal transduction pathways:
                            Basic structural fold and evolution of kinase structure
                            Mechanism of kinase activation:
                                    Intrasteric regulation:  PKA regulatory and catalytic subunits
                                                             Ca+2-Calmodulin dependent protein kinases
                                                             PKC regulation by Ca+2 and DAG
                                                             Cyclin dependent kinases: cyclins and phosphorylation control
                            Receptor Tyr kinases: role of oligomerization in activation of the kinase domain
                            SH2 and SH3 domains
                Phosphorylation cascades for cell proliferation signals
 
        Other pathways linked to Glycolysis and gluconeogenesis
                Metabolism of pyruvate through aerobic oxidation vs. anaerobic fermentation
                Pathways for the synthesis of cellular reducing power:
                        Pentose phosphate pathway

       Roles of ATP in metabolism
                Energy currency in the cell
                Central allosteric effector for metabolic control
                Committed steps in metabolic pathways
                Anabolic/Catabolic conversions linked to energy charge