Learning Objectives, Test 2

Chapter 5, Protein Function

5.1  Myoglobin and Hemoglobin:  Oxygen-Binding Proteins

Know what a prosthetic group is.

Understand an oxygen-binding curve.  9

Describe homologous proteins in terms of invariant residues, conservatively substituted residues, and variable residues.  7

Recognize cooperative binding from the shape of a binding curve.  19

How does hemoglobin act as an allosteric protein?

Describe the cause and benefit of sickle cell anemia.

Describe the Bohr effect.  11

Describe how BPG binding benefits the fetus.  17

5.2  Structural Proteins SKIP

(Just the sub-sections, “Collagen is a triple helix” and “Collagen molecules are covalently cross-linked”.)

Relate the following:  the structure of collagen, proline, vitamin C, and scurvy.  41, 43, 49

5.3  Motor Proteins

(Skipped this section)

Chapter 6, How Enzymes Work

6.1  What is an Enzyme?

Recognize the enzyme commission style of categorizing enzymes.

6.2  The Chemistry of Catalysis

Describe the change in free energy during an enzyme-catalyzed reaction.  13, 14, 15

Recognize acid-base catalysis and covalent catalysis.

Be able to use the terms cofactor, coenzyme, cosubstrate, and prosthetic group.

Know what chemical labeling is.

Sketch the mechanism by which serine proteases cleave the peptide bond.  19, 21, 23, 27, 29

6.3  The Unique Properties of Enzyme Catalysts

Give an example of how the transition state is stabilized by an enzyme.

Explain enzyme catalysis using

a)      Proximity and orientation

b)      Induced fit

c)      Electrostatic catalysis

6.4  Some Additional Features of Enzymes

Given the residues that proteases are specific for, explain how this specificity is achieved by specificity pockets.  45, 47

Explain how the structures of enzymes illustrate convergent and divergent evolution.

Identify zymogens and autoactivation in the activation of enzymes.  49, 51

Explain the purpose of protease inhibitors.

Chapter 7, Enzyme Kinetics and Inhibition  SKIP

7.1  Introduction to Enzyme Kinetics

Given an elementary step for a reaction, write the step’s rate equation.  3, 5, 7

Relate reaction velocity to enzyme concentration.

Describe when an enzyme will become saturated in terms of substrate concentration.

7.2  Derivation and Meaning of the Michaelis-Menten Equation

Understand the derivation of the Michaelis-Menten equation.  21

Relate Vmax to KM.  13, 15, 17, 27

Know what kcat is.

Justify the use of kcat and KM in the best measure of enzyme efficiency.

Know what a Lineweaver-Burk plot is.  23

State three cases where the Michaelis-Menten rate equation is not applicable.

7.3  Enzyme Inhibition

Explain why all irreversible inhibitors are not suicide substrates.

Describe how a competitive inhibitor affects KM and Vmax.

Be able to calculate KI, given the equation

  39

Recognize transition state analogs, and relate them to competitive inhibition.  35, 41

Relate the effect of mixed inhibitors and competitive inhibitors on KM and Vmax, and to enzyme binding sites.  43

Know that allosteric regulation includes positive and negative effectors. 49

Describe how feedback inhibition works.