Biol/Chem 472  Winter 2007 Study guide for midterm Exam #1

 

The exam will be held Wednesday evening 2/6, in SL110, from 6:00-8:00pm.  Bring a calculator.  The focus will be chapters 16, 20 and 17.  You will be given handouts that show the names and structures of intermediates for the pathways we have discussed.  You are expected to know the names and mechanisms of several enzymes.  You will be expected to draw reaction mechanisms.  In addition, the ability to predict the fates of isotopic labels will be expected.  I recommend that you practice drawing mechanisms for the enzymatic steps.  Your understanding of the principles of bioenergetics and metabolism will also be tested with more conceptual problems.

 

The exam may include questions on the following topics:

 

Bioenergetics

Calculations based on: DG = DG°’ + RTlnQ  and for ion transport: DG = DG°’ + RTlnQ  +  nzFDY

DG°’ = -nFDE°’  where DE°’ = E°’acceptor - E°’donor

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?”)

 

Glycolysis (including homolactic and ethanolic fermentation)

            carbon/electron/phosphate flow in pathway

            mechanisms of enzymes (from glucose to lactate or EtOH)

            cofactors:  NAD+/NADH (know structure/function of nicotinamide portion)

                        TPP (know structure/function of the thiazole ring)

 

Regulation

            feedback inhibition, allostery (especially for PFK), covalent modification

            predicting control points in a pathway (e.g., based on DG, etc.)

effects of mutations/knockouts on flux (e.g. which intermediate[s] would accumulate if a certain enzyme were knocked out?)

how is pathway regulation affected by the cellular energy charge?

 

 

Expect to see some intermediates and short pathways that we have not discussed (but which will 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 (such as on homework #3).  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.).  This is one of the stated goals of the course:  you should be able to rationalize steps in unfamiliar pathways based on your knowledge of the reactions we discuss in lecture.  You WILL be tested on this; thus, 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 (e.g., H+ abstraction to generate carbon nucleophiles, use of dehydration in enol formation, redox of ketones/alcohols using NADH/NAD+, use of carbon nucleophiles in C-C bond cleavage/formation, etc.).  When drawing mechanisms certain “shortcuts” are allowed:

1) H+ transfer is generally allowed since the solvent is water and/or the active site will have sidechains that act as general acids or bases.  You don’t have to draw the source of the H+ explicitly; however, you must show clearly how electrons move when a H+ is removed or added to another atom (e.g., in the conversion of an enolate to a carbonyl compound).

2) It is not necessary to draw out Schiff base formation on exams (although you are encouraged to do this at some point to fully appreciate the process).  Simply indicate “Schiff base formation/cleavage” and show water leaving or attacking the appropriate site (e.g., see the aldolase reaction).

3) The tetrahedral (or trigonal bipyramidal) intermediates that result from nucleophilic attack on a carbonyl (or phosphate) are “understood”.  You can omit them (i.e., as in the figure from the text for the GAPDH mechanism: see step #2 where the intermediate is drawn out and step #5 where it is not).  I prefer to see the intermediate, but I won’t dock you for not showing it.

 

Preparing for the exam:

            - Work as many recommended problems from the text as possible and see me for help if needed.

            - Rework graded homework problems “from scratch” and use the keys afterward (not vice versa)

- Work the exam questions from W07 here.   I will post brief answers to the problems here.