TEXT: Thomas E. Creighton, Proteins: Structures and Molecular Properties, W. H. Freeman and Company, New York (1993).
General Web Resources:
List on BMB Home page
BIOLOGY ON-LINE
GRADING:
Quizzes and Problems (60%)
Mid Term (15%)
Final (25%)
COURSE CONTENTS [Assigned Reading Material and Page Numbers]:
Introduction [handouts]:
Goals of Course
What is Enzymology?
Enzymes are molecular machines.
What are molecules like?
Interesting reading (but not assigned): T. Hager, "Force of
Nature: The Life of Linus Pauling," Simon & Schuster, New York,
1995.. See quotation at the top of page 457.
Web Resources:
An introduction to Enyzmology by David R. Bevan,
Dept. of Biochemistry, Virginia Tech
Assignments:
Describe the Jelly Fish at the Treasure Cove Divers site,
Westfield, NJ. Assume that all of the animals shown
in the picture are the same species and that the diameter
of the largest in view is 10.5 cm.
What other assumptions are you making?
How would your description differ if the only
animal you saw was the largest one?
Essay (5 page limit)
Composition and Structure of Proteins [Chapters 1, 4, 5 and 6]:
Amino Acids, sequence and folding.
What do we know about protein folding?
Torsion angles on the mainchain, phi, psi and omega.
Protein Folding (four classes of structure)
Amino acid side chains
Additivity and Synergy in Protein Structure
Enzymes and other Molecular Machines (R. V. Eck)
What molecules are like (R. V. Eck)
Web Resources:
Tutorial on Protein Structure, J. E. Wampler
Principles of Protein Structure,Birkbeck College.
Assignments:
Take-home problem (Analysis of a Composition)
Methods of Estimating an Enzyme Structure:
De Novo structure prediction from sequence.
Solution structure from NMR measurements.
Solution of X-ray diffraction pattern
Modeling from a close homolog.
Comparing different structures.
Web Resources:
Validation of Macromolecular Crystal Structures, by Lynn F. Ten
Eyck, Chem 215, University of California, San Diego.
Tutorial on NMR Spectroscopy, P. R. Young,
University of Illinois at Chicago
Lecture notes on X-ray Structure Determination, Anthony L. Fink,
UCSC
Assignments:
Quiz #1 (Structure and NMR)
From Protein Science to Enzymology:
The Chronology of Enzymology!
Enzyme Nomenclature.
The Enzyme Assay
Web Resources:
General Principles of Enzyme Assays,
by Wilbur H. Campbell, Michigan Technological University
Assignments:
Quiz #2 (X-ray structure and enzymology)
Chemical and Physical properties of enzymes [Sections 1.5, 7.1.2, 7.3]:
Information from composition and sequence.
Structural Details.
Determining the Molecular Weight
Size and Shape
Solvation
Bound Ions
Time Variation
Enzymes and pH
Mid-term (through Dynamical Behavior)
Enzyme Kinetics: Binding[handouts, selected readings Chapters 4 & 8]:
Irreversible binding and titrations.
One binding site, one:one interactions
Multiple Equivalent, Independent Sites.
Other Multi-site Models and Cooperativity
Assignments:
Take-home problem (Binding Site Analysis)
Quiz #3 (Interactions and Binding)
Enzyme Kinetics: Steady State Kinetics [handouts]:
What defines a kinetic model?
Single substrate/product models.
More about Cleland nomenclature.
Aids to solving rate equations.
Higher order models and cooperativity
Web Resources:
Lecture notes on Inhibition kinetics, Anthony L. Fink,
UCSC: Lecture 14, Lecture 15, Lecture 16
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.
Assignments:
Quiz #4 (Enzyme Catalysis, Basic Principles, Rapid Kinetics)
Take-Home problems (Kinetics Problem Set)
Quiz #5 (Enzyme Kinetics)
Enzyme Kinetics: 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.
Defining an Enzyme Mechanism [Sections 4.4 and 9.2]:
Transition State Theory [Section 9.2.2]
Chemical Catalysis [Section 9.2.
Proximity Effects [Section 4.4]
Web Resources:
The Mechanism of Acetylcholinesterase, on the
ESTHER server.
Lecture notes on Chemical Catalysis, Anthony L. Fink,
UCSC
Techniques for Mechanistic Details:
Methods using Isotopes.
Chemical modifications and labeling.
More uses of substrate analogs.
Protein engineering approaches [Chapters 2 & 3].
Web Resources:
Lecture notes enzyme mechanisms, Anthony L. Fink,
UCSC
Protein Purification [Handouts]
Web Resources:
James Kling's article on Protein Purification,
The Scientist, Vol:11, #14, 14-15, 1997)
Affinity purification of HRP, R. Bateman & J. Evans,
University of Southern Mississippi.
Selecting the Separtation Mode, Waters Corporation,
Milford, MA.
Final Exam (All material covered since Mid-term)
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