Unless noted otherwise, please draw them in the correct protonation state for pH 4



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C483 Exam 2 2014
______________________________

Name
Instructions: Please read all questions carefully. Use structures if they are called for. Unless noted otherwise, please draw them in the correct protonation state for pH 7.4. Do not use acronyms unless specifically directed. If you need more space, use the back of your paper. No calculators or electronic devices. Answers should be short and to the point. If you have extra material that is incorrect, points will be deducted. This is a one hour exam, but you have two hours to complete it. Good luck.



1) 6 pts Draw the structure and show the mechanism for conversion of ubiquinone to ubiquinol.


2) 6pts total Here are some common biological half reactions. Going in the forward direction, please note if they are reductions, oxidations, or neither- and state the number of electrons involved in the transformation.
2 pts a)_________________________________ number electrons__________________________

4 pts(1,3) b)_________________________________ number electrons__________________________






3) 4 pts What four basic roles do lipids play?
4) 8 pts Dialkyl fluorophosphates are excellent irreversible inhibitors of serine proteases. Draw a mechanism for this inhibition. Why are such molecules better inhibitors than acylfluorides? (give two reasons).


5) 5 pts What is the role of the carboxylate (Asp or Glu, depending on the enzyme) in the catalytic triad of serine proteases? (Use structures and appropriate diagrams to explain this.
6) 7 pts The kcat for hydrolysis of a series of ester substrates catalyzed by serine proteases, is usually about the same, regardless of the nature of the leaving group being cleaved. However, kcat usually varies for amide substrates and is substantially slower, changing even more as a function of leaving group. Explain this phenomenon and draw a free energy profile that accounts for this.


7) 6 pts The three forms of metabolic pathways are: Give an example of each.
______________________________ example_______________________
______________________________ example_______________________
_______________________________ example_______________________

8) (2 pts each, 10 pts total) Answer the following short answer questions
a) A nonphotosynthetic organism that requires an organic carbon source such as glucose, is called a/an ______________________

b) __________________reactions are those by which the cell synthesizes needed materials, such as proteins and nucleic acids, while ______________reactions are those by which the cell degrades material for energy and building blocks.


c) A moiety common in the head group of all phosphotidates is _____________________


d) Three common amino alcohols found in phosphotidates are _____________________, ____________________ and __________________________
e) Enzymes responsible for the phosphorylation of alcohols are called ________________

9. (2 pts each, 10 pts total) True or false
a) ______Relatively strong binding of reactants in the enzyme active site is necessary for efficient catalysis
b) ________Vitamin K is a lipid vitamin with antioxidant activity
c) ________ Dihydroxyacetone could be described as a ketotetrose
d) ________ Amylopectin is an entirely linear polymer of D-glucose units found in natural starch
e) _________Epimers are two carbohydrates that differ only in in the configuration of groups at a single chiral center

10. (2pts each, 20 pts total) Fill in the blank
a) Monosaccharides that form six-membered rings are called __________________________
b) Glycolysis is the principle mode of energy generation in the muscle under ______________________ conditions.
c) ____________________________ are inactive enzyme precursors activated by removal of one or more portions of the precursor molecule
d,e) Activation of an enzyme by a substrate-initiated conformation change is called__________________________. _____________________ is an enzyme that utilizes this strategy.
f) For a substrate with a positive charge, ______________________ or _________________ might be present near the binding site on an enzyme to aid in substrate binding.
g) Rate enhancement by the binding of reactants close to each other in the enzyme active site is called the ________________________
h) The most frequently found residue in the active site of enzymes is _________________________
i) The cofactor(s) that links one electron and two electron redox processes is(are) called _____________________
j) Draw the structure of sphingosine_____________________________________


11. 8 pts Draw the transformations of glycolysis starting with glucose and ending with pruvate. You must use structures. You get two free mistakes and then one point off for each additional error. Omission of a structure, step, or product, will count as two errors. Do NOT use acronyms.

12. 10 pts. Suggest a process by which a fatty acid is converted to a thioester. Why do we need such a process?

Extra credit 15 pts. Each error costs 3 pts.
Give the overall equation and draw the mechanism for the pyruvate dehydrogenase reaction. You must draw enough of the structure of ALL cofactors involved in the reaction so that the chemistry they undergo is obvious. Omission of a required cofactor will count as two mistakes.
Points

Possible earned


1)6 ________
2)6 ________
3)4 ________
4)8 ________
5)5 ________
6)7 ________
7)6 ________
8)10 ________
9)10 ________
10)20 ________
11)8 ________
12)10 ________
EC15 ________
Total 115 ------------------




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