General Description: This course will examine enzymes and cofactors from a mechanistic and chemical point of view. Aspects of physical organic chemistry will be introduced to address the chemical mechanisms of enzymes, the biosynthesis of certain natural products, the development of medically important drugs, the generation of new catalysts. Time permitting, students may be exposed to "special topics" that have recently appeared in the literature giving an appreciation for experimental design and the most recent advances. This course builds off of courses 313 and 330. Although not absolutely essential, they are highly recommended prerequisites.
Required Text: An Introduction to Enzyme and Coenzyme Chemistry by Tim Bugg. Supplemental lecture material may be drawn from (i) Biochemistry by Voet & Voet and (ii) The Organic Chemistry of Enzyme Catalyzed Reactions by Richard Silverman. The latter two books are not required but course attendance is highly recommended.
Examinations: There will be EITHER two midterms (20%, 30%) and a final exam (50%), OR one midterm (33%) and a final exam (66%). Grading is on a curve. A higher score on the final will be used to offset poor midterm performance.
Graduate Level: Graduate Students taking this course as 565 will be required to write an original 5-page single-spaced research proposal on a topic in enzymology — please see me as soon as possible to discuss such a topic. For graduate students, the midterm(s) will count 25% respectively with the proposal representing 25% of the grade and the final representing 50%.
Instructor: Dr. David M. Perrin, Assistant Professor.
Office Hours: Monday 2:30-3:30 Rm. A 337 — or by appointment.
Outline:
Intro: Reasons to Study Enzymes - comparison to organic synthesis
Enzyme Structure Overview: catalytic components, cofactors, forces that fold the enzyme and permit catalysis, chemical properties of enzymes. Sections 2.1-2.3 (pp 7-10.5), Sections 2.5-2.8 (pp 12.5-20.5).
Stereo/Regiochemistry: concepts of labelling, stereo/regiospecificity. Sections 3.1 (pp. 25-26), Section 4.4 (pp 53.7 — 59.7).
Types of Catalysis:, nucleophilic, transition state stabilization, acid/base, polarization, chelation. Sections 3.5-3.6 (pp. 33.5-40.4)
Enzyme-Reaction Intermediates: transition states, trapping, exchange, stereochemical inversion. Sections 4.5-4.6 (pp. 59.7-66.5).
Determination of Active Site: affinity labelling: Sections 4.7 (66.5-69.5).
Thermodynamics and Rate Enhancement. Section 3.2 (pp. 27.2-29.2)
Kinetics and Inhibition: Michaelis Menten — Lineweaver-Burk / Eadie-Hofstee / Transition State, Mechanism Based: Section 4.3 (pp. 47.7-53.9)
Hydrolytic Enzymes: peptidases, esterases, lipases, RNaseA, phosphoryl transferase: Section 5.1-5.3 (pp. 73-88.5), reading not covered in class but required 5.4-5.5 (pp. 88.5-95.2).
One-Carbon Transfer Reactions: SAM, THF: Section 5.6 (pp.95.2-96.5) and Section 5.8 (pp. 99.5-102.5)
Enzyme Redox Chemistry: NAD, FAD Baeyer-Villiger, Fe-S clusters, metal-dependent mono/di-oxygenases, a-KG oxygenases - vitamin C: Sections: 6.1-6.4 (pp. 106-120.5), Sections 6.8-6.9 (pp. 126-130.2)
Enzymatic Addition/Elimination Reactions: hydration/dehydration, EPSP synthase: Sections 8.1-8.2 (pp. 170-174), Section 8.4-8.5 (pp. 178.5-182.5).
Carbon-Carbon Bond Formation: aldolases, transketolase, Claisen condensation, fatty acids, polyketides, biotin-carboxylase, TPP: Sections 7.1, 7.2 (pp. 136-152.5, 155.2-157).
Cationic Condensation/Polymerization: geranyl-pyrophosphate synthetase, terpenes, polyene cyclization, taxidiene, Section 7.3 (158-162.4).
Transformation of Amino Acids: PLP dependent reactions, deaminase, transaminase, racemase, b-carbon functionalization: lyase, decarboxylase, glycine degradation, alkaloid biosynthesis Sections 9.1-9.5 (pp. 185-198).
Related Special Topics - Time Permitting
Generation of New Catalysts: molecular imprinting, catalytic antibodies for synthesis
Catalytic Nucleic Acids: DNAzymes for RNA hydrolysis and Diels-Alder Chemistry
Chemienzymatic Synthesis: Aldolases
Combinatorial Enzyme Engineering: virtual macrolide libraries
Peptide (peptide derived) Antibiotics: non-ribosomal polypeptide synthases
Protein auto-Degradation: Asp-isoAsp and carboxy-methyltransferase
Novel Side Chains: new cofactors and fluorescent proteins.
Protein Splicing: intein inhibitors of tyrosine-hydroxylase.