EXAM 3 PREPARATION
November 24, 2003
Knowing is not enough, we must apply. Willing is not enough, we must do.
Goethe
Exam 3 will cover the enzymes (properties, classification, kinetics, inhibition, efficiency,
bisubstrate reactions). The second major topic will be DNA structure, replication and repair. The
material is found in your textbook and in Biochemical Strategies.
Enzymes (Chapter 11)
Know the meaning of terms such as catalyst, cofactor, stereospecificity, substrate, product,
transition state, rate-determining step. Know the meaning of enzyme activity, unit of enzyme
activity. Be able to solve problems that deal with specific activity, turnover number. Know the
various systems for naming enzymes. Be able to give examples of reactions catalyzed by the 6
categories of enzymes. Be able to determine, if given a reaction, the name or EC category of the
enzyme catalyzing the reaction. Know the effects of temperature, pH, substrate concentration on
enzyme activity. Don’t just know what happens, be able to tell why it happens. Know the
similarities and differences between a coenzyme and a cofactor. Know how NAD+ functions with
oxidoreductases such as alcohol dehydrogenase. Know the mechanisms of all reactions discussed
in lecture. The function of zinc in carbonic anhydrase, the catalytic triad in proteases. Know the
meaning of zymogen, the activation of chymotrypsin,
Enzyme Kinetics (Chapter 12)
Know the important kinetic constants, vo, Km, Ki,, Vmax, kcat. Know the difference
between a first order, second order and zero order reaction as they apply to enzymes. Know how
rate constants the form and breaking the [ES] complex. Know how the rate of the reaction is
affected by [S], [E], inhibitors. Know the value of Km as a predictor of substrate affinity and the
meaning of steady state. Know the Lineweaver-Burk double reciprocal plot, the parameters such as
slope, X and Y intercepts. Know how to distinguish competitive from non-competitive inhibition
using a Lineweaver-Burk plot. Know the difference between a reversible inhibitor and an
inactivator. Know how to determine enzyme efficiency. Know the different types of bisubstrate
reactions. Know how allosteric factors apply to enzymes. Know the meaning and mechanism of
feedback inhibition. Be able to do problems 3, 4, 6, 7, 8, and 11 at the end of Chapter 12.
DNA Structure (Chapter 23)
Know the similarities and differences between A, B, and Z DNA. Focus on parameters such
as the bases per turn, the diameter of the helix, major and minor grooves, base tilt, right or left
handed helices. Know how syn- and anti-, C2’-endo and C3’-endo3, hydration, affect the type of
DNA. Know the meaning of supercoiling, linking number, turns and twists, writhing number,
topoisomers. Know the function and mechanism of topoisomerase I and II. Know melting curves
relative to base composition (G+C, A+T). Know the meaning base stacking. Know the basis of
protein-DNA interactions. Structural motifs such as helix-turn-helix, zinc finger, leucine zipper.
DNA Replication and Repair (Chapter 24)
Know the meaning of the terms associated with replication. Know the significance of
Meselson and Stahl’s experiment, Cairn’s replication fork, Okazaki’s fragments, Kornberg’s
polymerase I. Know how reactions on the leading and lagging strand differ. Know the importance
of a template and primer, single strand binding proteins, DNA gyrase, the composition and function
of the primosomes. Know the difference between pol I and pol III in terms of mechanism, bound
exonuclease activity, function, processivity, Know the reaction catalyzed by a reverse transcriptase,
telomerase, DNA ligase. Know how environmental factors can damage DNA. Know the basis of
the Ames test to measure carcinogens. Know the various repair mechanisms, how they differ and
perhaps how they overlap. Know the meaning of SOS repair, error prone repair, recombination
repair. Know what is special about each of these repair mechanisms.