Exam Bio-organic Chemistry (8S140)

Thursday November 23, 2008 14.00–17.00 h

This exam consists of 7 questions.

Explain your answers clearly. Answers may be given in English or
Dutch

1 Organic Chemistry 9 pts

a) Draw the following molecules on your answer sheet, circle each functional
group and write down its name. 3 pts

O O
O
O O
S -
S O O P O
O
N
O O
- -
O P O
O O S
O

b) Draw the structure of ADP. You may use the abbreviation "-A" for the
adenine part of these molecules. Use a Haworth projection for the
carbohydrate part of the molecule. 2 pts

c) Draw the structure of the oxidized and reduced forms of lipoic acid. 2 pts

d) In which metabolic reaction is this cofactor involved (as lipoic amide), and
what is its role? 2 pts

2 Lipids, Terpenes, Steroids 9 pts

a) Draw the chemical structure of a fat containing stearic acid as the only fatty
acid. 2 pts

b) Give a detailed mechanism using curly arrows for the acid catalyzed
hydrolysis of this compound. 3 pts

c) Indicate the isoprene units in the molecule below: 2 pts

1
d) Discuss how the chemical differences between fats and phospholipids lead
to strong differences in water solubility. How are phospholipid molecules
ordered in water? 2 pts

3 Carbohydrates 6 pts

a) Draw a Haworth projection of a short segment (at least a dimer) of

amylose, a polymer of glucose with α-1,4'-glycosidic bonds. 3 pts

b) Draw a Haworth projection of the α-pyranose form of mannose. 3 pts

CHO

HO H

HO H

H OH

H OH

CH2OH

Mannose

2
 4 Glycolysis 11 pts

a) Give the structures of the intermediates in the glycolytic pathway which

lead from glucose to glyceraldehyde 3-phosphate. Indicate at which step
ATP is consumed. 3 pts

b) Triose phosphate isomerase is one of the most efficient enzymes known.

Draw the reaction mechanism of the isomerization this enzyme catalyses.
Include the functional groups of histidine and glutamate at the active site
in your mechanism. 3 pts

c) What limits the turnover rate of this highly efficient enzyme? 2 pts

d) What is understood by "induced fit" in the enzyme hexokinase. Indicate why

this phenomenon is important for the optimal functioning of the enzyme 2
pts

5 Citric Acid Cycle 7 pts

a) Draw the structures of the missing intermediates 1 - 3 in the citric acid cycle
4 pts
b) In which step(s) is an energy rich phosphate ester formed? What is the
name of this energy carrier? 3 pts

3 2

3
 6 Oxidative Phosphorylation 11 pts

a) Describe in general terms where and how the proton gradient is created
that drives ATP synthesis by ATP synthase. 4 pts

b) What are the chemical substrates and the products of cytochrome c

oxidase ?
Which cofactors and metals are involved in the transformation? 4 pts

c) What is the substrate and what are the products of superoxide dismutase?
Describe the stepwise process that leads to the products. Why is it important
that this reaction is catalyzed by the enzyme? 3 pts

7 Orbital controlled reactions

Reminder : Woodward-Hoffmann rules.

1. A thermal electrocyclic reaction involving 4n π -electrons (n=1,2,3..) proceeds with

conrotatory motion. The photochemical process proceeds with disrotatory motion.

2. A thermal electrocyclic reaction involving (4n+2) π -electrons (n=1,2,3..) proceeds

with disrotatory motion. The photochemical process proceeds with conrotatory
motion.

3. A thermal [1,j] sigmatropic H shift occurs in a suprafacial way if j=4n+1. The

corresponding photochemical process is allowed when j=4n-1

4. A thermal [1,j] sigmatropic H shift occurs in an antarafacial way if j=4n-1. The

corresponding photochemical process is allowed when j=4n+1

(See next page for questions)

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In 1972, Heinz Heimgartner investigated the thermal reactions of 1-mesityl-3-
methyl allene (1) and described the results in his Ph.D. thesis (University of
Zürich).

CH3

CH3

H3C CH3 H
1

A
C
CH3 H CH3 H
CH3 H
H CH3
H3C CH2 H3C CH2
2 4
4
B D

CH3 CH3 H
H
H CH2
H3C CH3 H3C CH3
3 5
5

He found that via reaction A, 1 can convert into 2, which then converts into 3
via reaction B. In addition, 1 can also convert into 4, which then rearranges
into 5. This involves the reactions C and D.

a) For each of the reactions A,B,C and D, identify the type of reaction.

b) Use the Woodward Hoffman rules to predict the way each reaction
proceeds (supra- / antara-facial or conrotatory / disrotatory).

c) Explain why 2 does not convert into 5.

SUCCES!