Biol/Chem 472  Winter 2008 Study guide for the final exam.

 

The exam will be held Tuesday morning 3/18 in SL 140, from 10:30-12:30am.  If the room is available by 10:15am we can start then and go until 12:45pm.  I will have drop-in office hours all day Monday 3/17 from 9am-5pm.  The final exam will be comprehensive.  You will be given copies of some pathways (e.g. for glycolysis, TCA and representative schemes for amino acid and fatty acid metabolism etc.).  The exam handouts will not have specific enzyme names (except for those involved in fatty acid and amino acid metabolism).  The major focus of the exam (at least 50 points) will be gluconeogenesis, pentose phosphate pathway, fatty acid metabolism, amino acid metabolism and regulation/integration of metabolic processes. 

Bring a calculator.  It is a very good idea to review the following topics in preparation for the exam.

 

Bioenergetics

DG = DG°’ + RTlnQ + nzℱDY                       DG°’ = -nℱDE°’       DG°’ = -RTlnKeq

 

Cofactors

What chemistry do they perform?  Includes:  NAD(P)H, FAD, CoASH (and AcSCoA), TPP, PLP, biotin, lipoic acid, cobalamin. 

Know “business end” structures for biotin, NADH, TPP, CoASH.

 

Pathways

 

            At this link is the list of enzyme mechanisms I expect you to know.  Focus most of your energy on the enzymes we have covered since the last exam.      

 

Focus on enzymatic mechanisms and regulation in: (1) gluconeogenesis; (2) PPP (especially transketolase and tranaldolase); (3) fatty acid synthesis and b-oxidation; (4) ketone body metabolism; (5) amino acid metabolism: deamination, urea cycle, where the carbon skeletons of amino acids enter the TCA cycle (i.e., glucogenic/ketogenic amino acids; see Fig 26-11 p 995).  I will provide you with the names of the enzymes we have discussed in Chapters 25 (fatty acid metabolism) and 26 (amino acid metabolism).

 

Strong review (i.e. know mechanistic details) of: glycolysis (anaerobic and aerobic); TCA cycle.  Know what intermediates are common to the pathways we have discussed (i.e. a-KG, OAA, AcSCoA, GAP...etc. etc.).  I expect you to know the names of the glycolytic/gluconeogenic and TCA cycle enzymes.

 

Review (i.e. know regulatory steps, substrates and products): membrane function; glycogen storage and breakdown. I will provide names for these enzymes when needed.

 

I expect you should be able to: follow fates of C and N atoms in these pathways; identify regulatory points; and calculate free energy changes for individual steps.

 

Regulation

regulation of enzyme activity: feedback inhibition, allostery, substrate availability, covalent modification (phosphorylation/dephosphorylation)

regulation by hormones: effects of insulin, glucagon, epinephrine on liver, muscle and adipose cells (phosphorylation/dephosphorylation cascades), the role of cAMP in these processes.

Regulatory enzymes (and their effectors) in: glycolysis, gluconeogenesis, glycogen metabolism, TCA cycle, FA metabolism, amino acid metabolism.

 

            Some important figures to look at re: regulation can be downloaded here

 

Central role of the Citric Acid Cycle  (see some relevant figures here)

How do carbohydrates, fats and amino acids enter the cycle? (catabolic processes)

How are cycle intermediates converted to carbohydrates, fats and amino acids?  (anabolic processes)

 

Coupling of electron transport and ATP synthesis via the H+ gradient across the IMM

Chemiosmotic hypothesis

How does e- transport generate a H+ gradient?

            What is the stoichiometry of H+ transported/NADH or FADH2?

            Function of ATP synthase: H+ translocation; “binding/change” model of ATP synthase activity

How does the structure of the ATP synthase “c” ring determine the net yield of ATP/(NADH or FADH2)?

 

Calculations of metabolic cost/yield interms of ATP equivalents

Net yield of ATP from catabolism of glucose/glycogen, fatty acids, amino acids

ATP cost for synthesis of glucose/glycogen, fatty acid

 

Impact of enzyme loss-of-function on fuel metabolism

Predict/rationalize the metabolic consequences of losing the function of protein “X”? (e.g., “what would be the consequences to an animal of losing glucose-6-phosophatase activity in the liver?”)

How does loss of protein “X” function affect regulation of other processes in the same cell (or in different tissues via hormonal control)?  (e.g., “What would be the consequences of loss of the phosphorylation site on protein phosphatase-1 inhibitor?”)

 

Fatty Acid Metabolism

Transport of fats; activation for catabolism; transport across mitochondrial membranes

            b-oxidation of saturated, unsaturated and odd-chain fatty acids

            calculation of ATP equivalents for FAs

FA biosynthesis: transport of citrate; synthesis of malonyl-CoA

Regulation of FA metabolism (e.g., transport to mitochondrion/ACC activity/effects of hormones on FA metabolism)

 

Amino acid catabolism

De-amination (role of PLP-dependent transaminases; glutamate DH)

            Ornithine cycle

            Fates of carbon skeletons following de-amination (glucogenic vs. ketogenic amino acids)

Regulation of amino acid catabolism (CPS I activity affected by N-acetyl glutamate)

 

 

Review all your quizzes and the midterm exams.  In addition, the following problems are recommended for review: 

Chapter 17       6, 7, 8e, 9, 10

Chapter 18       4, 7, 8

Chapter 20       5, 7

Chapter 21       1, 4, 10, 11, 12

Chapter 22       2, 3, 5, 7, 10

Chapter 23       2, 6, 8

Chapter 25       2 (see p918), 3, 5, 6, 7

Chapter 26       2, 3

 

You can get some practice problems from a previous 472 final exam here.

 

I will post brief answers to the practice exam at this link.

 

Recall that past exams are also available for additional practice problems by following links given in prior study guides.