Click here for last
year's exam (i.e., supplemental practice problems)
A key with brief answers (without
work) is available at this
link. Note, on the exam you are expected to explain your answers
and/or show your work..
The exam will be held Thursday morning
5/12, in SL130,
from
This list is not guaranteed to be comprehensive, but it is a very good idea to review the in-class assignments and the following topics in preparation for the exam.
General: I still expect you to be familiar with amino acid structures because the sidechain structures determine active site features. Also know 1 letter code & general properties (e.g., polarity, sidechain charges at pH = 7).
Enzyme Chemistry:
How do enzymes accelerate reactions (GABC, electrostatic stabilization, covalent, proximity effects)? Use RNase A and chymotrypsin as examples that illustrate these different strategies for rate acceleration (i.e., how does the catalytic triad function? How does the oxyanion hole function?)
thermodynamic vs. kinetic stability
what is rate acceleration (ratio of kcat and kuncat); how is it calculated from DDGŦ ?
what is the difference between DG and DGŦ ? How are each calculated?
Interpretation of energy diagrams (G vs. reaction coordinate; see p 173 and 181)
Enzyme Kinetics:
What are Vmax, KM, kcat and how are they derived from kinetic data?
How can the slope and y-intercept in a Lineweaver-Burk plot be used to calculate Vmax, KM, and kcat?
What is the Michaelis-Menten model? Why is the plot of v0 vs. [S] hyperbolic?
Predicting whether a mutation in an enzyme active site will affect KM (i.e. S binding) or kcat (effects on catalytic step) or both.
Thermodynamics:
DG = DG°’ + RTlnQ (how is DG°’ calculated? What values are used in the Q term?)
biochemical vs. chemical standard state (i.e. the different treatment of water and protons)
how is ATP utilized in biochemical reactions
DG°’ = -RTlnKeq
solving for DG°’ using coupled reactions
“energy charge” of a cell, effect on regulation
calculation the “cost” in terms of ATP for a pathway (e.g., “how many ATP are required to synthesize two moles of GAP from F-6-P?”)
Regulation:
feedback inhibition, allostery, covalent modification (zymogens; phosphorylation)
predicting control points in a pathway (e.g., based on DG, etc.); how is pathway regulation affected by the cellular energy charge?
Glycolysis/Fermentation:
General features of pathways (what are intermediates and products; which
steps are subject to regulation, where is ATP consumed/generated; where do redox reactions occur)
carbon/electron/phosphate flow in pathway (i.e., following the fates of the C atoms in glucose in the pathway)
familiarity with mechanisms of enzymes (glucose -> lactate or EtOH), such that products for reactions could be predicted (i.e. “predict products formed if aldolase acted upon subtrate XYZ”)
cofactors: NAD+/NADH and TPP (what chemistry does each cofactor perform?)
Expect to
see some intermediates and real or hypothetical pathways that we have not
discussed (but which bear similarities to the pathways we have discussed). You may be asked to predict how one compound
is converted to another in one or more enzymatic steps. You will not be expected to have mastery of
reactions we have not discussed in lecture; however, you will be expected to
predict how a reaction on an unfamiliar substrate would proceed if a familiar
enzyme were to act on it (i.e. know the general mechanism of an “aldolase”
[C-C bond cleavage of a beta-hydroxy keto compound] or “isomerase”
[migration of a carbonyl group as in TIM or PGI], TPP-dependent decarboxylation, etc.).
I strongly encourage you to study the mechanisms we have discussed in
lecture so that you develop a strong sense of the methods that nature employs
to bring about chemical conversions (i.e., H+ transfer to generate carbon nucleophiles,
use of dehydration in enol formation, redox of ketone/alcohol using
NADH/NAD+, use of
carbon nucleophiles in C-C bond cleavage/formation,
etc.).