CHEM 737/7370 - Enzymes

Semester: Spring 2021

Professor: J. Honek | Discipline: Biochemistry | Campus: Waterloo


This graduate course will address the underlying principles of enzymatic catalysis (with examples) along with discussion of techniques that are applied to this area. This course will focus on the protein itself and how its structure contributes to catalysis. Subtopics will include protein dynamics, electrostatic potential, active-site geometry and transition state stabilization among other factors that contribute to enzyme catalysis and substrate selectivity. The chemical mechanism of example enzymes as well as general practical techniques in enzymology will also be discussed. Additional topics such as bioconjugation and enzyme applications will be discussed and will depend on the background and areas of interest to students (see Prerequisites)

Prerequisites: Students should have some previous background in biochemistry and organic chemistry at the undergraduate level. If you are uncertain about your background in these areas, please contact me. I especially want to hear from potential students interested in the course and ask them to provide a brief description of their graduate research projects by May 5, 2021 so that I can better tailor the course to address their specific research interests/problems.

Learning Objectives:

The overall learning objective in this course is for a student to be able to propose likely factors that account for an enzyme’s catalytic activity and a likely enzyme chemical mechanism given the structure of the substrate(s) and the product(s). As well, a student should be able to suggest a series of biochemical/chemical experiments that would help to understand a new enzyme and its enzyme mechanism, its isolation and characterization and how to develop a biochemical assay for the enzyme.

Chem730/7370 Lectures begin: May 13


Class notes, review articles and journal articles will be used


Marking scheme: Tentative—dependent upon actual enrolment numbers

Class (online) participation & problem-based discussion with submitted answers after several of the class periods (30%) + oral presentation(s) of assigned research articles (30%) + Final Written Research Proposal (15 pages, single-spaced, includes figures and references, due July 14, 2021; 40%).


Tentative List of Topics:
1. Introduction: information on enzymes (protein structure and four-dimensional representations; resources: text and web-based information including databases (structure and sequence), structural and homology modeling, etc), handling enzymes (isolation, characterization, assays, immobilization and bioconjugation). The above will be a survey with class participation & group analyses of hypothetical scenarios and journal-based research. Input on areas of interest to students is encouraged so the course can better address student research areas.
2. Mechanisms of enzyme rate enhancement including model systems.
a) electrostatic effects
b) hydration/dehydration
c) protein dynamics
d) active-site effects including transition state stabilization and thermodynamics
e) catalytic proficiency
3. Survey of some techniques used in studying enzymes (inhibitors, cryoenzymology, Laue diffraction, spectroscopy, stereochemistry, crystallography, mutagenesis, etc.)
4. Survey of the six EC classes of enzyme and common chemical mechanistic themes. Survey of enzymes utilizing cofactors and post-translationally-produced cofactors
5. Multifunctional and multienzyme complexes/channeling of substrates and intermediates in enzyme catalysis
6. Possible additional topics (time permitting & student interest): Applications of enzymes, catalytic antibodies, ribozymes, DNAzymes, synthetic biology, bionanomaterials, enzymes from various organisms such as psychrophiles/cryophiles, mesophiles, thermophiles, and enzymes used in biomaterials science.


  • Tue: 2:00 pm - 4:20 pm in Remote
  • Thu: 2:00 pm - 4:20 pm in Remote

Office Hours

ESC-246 (office; my office is in my lab: ESC-244A) email: [email protected]