Fall 2013

Biochem. I: Course Objectives, Chapters 6, 7, 10

Chapter 6: Enzymes, kinetics, and mechanisms
Good problems for practice from Nelson and Cox, Chapter 6: 7-13 (use excel for 12 and 13), 15, 16 (dont turn in)

Catalysis:
1. Draw a reaction diagram for the conversion of S P, labeling the free energy change for the reaction,
the activation energy, and the effects that a catalyst has on this pathway.
2. Understand in molecular detail the concepts of binding energy and transition state stabilization.
3. Use the Arrhenius equation (would be given to you) to calculate the effect of an enzyme on the rate of a
reaction, given the change in activation energy.
Enzyme kinetics:
1.) Understand the steps taken to derive the Michaelis-Menton Eqn.
2.) Understand the meaning of steady-state approximation and show how it is used as the basis for the
Michaelis-Menton equation.
3.) Be able to represent the Michaelis-Menton constant, Km, in terms of elementary rate constants, and
understand how it is distinguished from the dissociation constant, KD for enzyme-substrate binding.
4.) Use the Michaelis-Menton equation and Lineweaver-Burk plots to compute: an enzymatic reaction rate
(vo), Vmax, Km, kcat, catalytic efficiency (kcat/Km), fraction of enzyme molecules bound to substrate, and
fractional velocity. Be able to interpret the meaning of kcat and Km data in an experimental context.
5.) Describe what is meant by catalytic perfection.
6.) Describe and identify competitive, uncompetitive, and mixed inhibition. Use Lineweaver-Burk plots to
distinguish between the mechanisms and calculate Ki and/or [I] values. Know how each mechanism
affects the observed values of Vmax and Km.
Catalytic Mechanisms
1. Describe and know examples of: acid/base catalysis, metal ion catalysis, and covalent catalysis.
2. Provide and understand arrow-pushing mechanisms for the reactions catalyzed by carbonic anhydrase,
chymotrypsin, RNase, and lysozyme. Identify the residues and relevant interactions that comprise the
catalytic triad and oxyanion hole of serine proteases. Understand the experiments that led to the
elucidation of the currently accepted mechanism for lysozyme.
3. Apply elements of specific mechanisms to other examples
4. If given the structure of an HIV protease inhibitor, describe key features that make it effective.
Regulatory Mechanisms
1. Understand the following regulatory strategies and provide examples:
a. Allosteric enzymes: ATCase
b. Protease regulation: zymogens
Chap. 7
Simple sugars: chirality, epimers, anomers, furanose and pyranose formation to yield hemi-acetals (or
hemiketal), reducing sugars
Structures of: glyceraldehyde, dihydroxyacetone, glucose, ribose, fructose
Disaccharides: Linkages, recognition of reducing ends
Polysaccharides:
Describe the structures of starch, glycogen, cellulose, including the nature of the glucose linkages, and
describe functional significance
Recognize the structures of and functional significance of:
Peptidoglycans and Glycosaminoglycans: specifically, hyaluronate (synovial fluid) and
chondroitin (connective tissues), explain the importance of the negative charges

Glycobiolgy examples: Significance of glycosylation; action of glycosyltransferases and glycosidases, N vs O

linked glycoproteins
Specific examples: EPO, blood types, News of the Week plant defense mechanisms, virus/carbohydrate
recognition