Name:___________________________________ Chemistry 27 Spring 2004 Exam 3 Chemistry 27

Professor Gavin MacBeath

Harvard University

Spring 2004 Hour Exam 3 Friday, April 30, 2004 11:07 AM - 12:00 PM

Discussion Section (Day, Time): ____________________________________________ TF: ____________________________________________

SOLUTIONS

Directions:

1. Do not write in red ink. Nothing in red ink will be graded. 2. Write your name on every page of the exam.

3. Provide your answers in the designated space.

4. The last page of the exam has a table of amino acids, cofactors, and DNA bases for you to use. You may use the back of this amino acid page for scratch work, but nothing written on this page will be graded. 5. You should have 9 pages total. We have provided plenty of space for each answer. 6. All intermediates must be drawn as a distinct step. You need not draw out proton transfers as a distinct step. 7. Molecular model kits are permitted. 8. A significant fraction of your exams are photocopied before they are returned.

Question 1 2 3 4 5 Total

Page 1 of 9

Score /12 /16 /28 /24 /20 /100

Name:___________________________________ Chemistry 27 Spring 2004 Exam 3

1. (12 pts) Please draw an arrow-pushing mechanism for the following FADH2-dependent reaction. You may use the abbreviated structure of FADH2 in your mechanism. O O2

O

FADH2

FAD

O

H2O

:B H N N H

3 pts

N

3 pts

N

O N

N H O O + B H H

O O H B+

B:

H

OH H B+

+ O+

O

Note:

3 pts This carbon is partially negative because of the following resonance form:

N N

O

O

Your mechamsim cannot involve the nuclephilic attack of this carbon by oxygen: N N H O B:

O H

H

O

Page 2 of 9

3 pts O O

:B

Name:___________________________________ Chemistry 27 Spring 2004 Exam 3

2. (16 pts) Enzyme A is an NAD+-dependent enzyme that catalyzes the oxidative decarboxylation of 1. OH

O

Enzyme A NAD+

NH3+ CO2H

NH3+

CO2

1

A) (12 pts) Please propose an arrow-pushing mechanism for this reaction. You may use the abbreviated structure of NAD+ in your answer. B:

+

H

B H O

O

HO2C

H

O

CO2H CO2H

4 pts

HO2C

CO2H O

H2N

O

4 pts HO2C

O H

H CO2H

B:

2 pts

+

N R

O

H H

O

H2N

HO2C

CO2H

N R 2 pts for structure of NADH

H HO2C

O

O H O

O H

8 pts

O

B: NH2

N+ R

CO2H

H

2 pts

HO2C

CO2H

CO2 H H

O NH2

N R 2 pts for structure of NADH

Page 3 of 9

O HO2C

CO2H

Name:___________________________________ Chemistry 27 Spring 2004 Exam 3

B) (4 pts) The hydride from 1 adds to the Re face of NAD+. Suppose the following deuterated NAD+ cofactor was used by the enzyme. Please draw the structure of the resulting NADH, clearly indicating stereochemistry. H D

O NH2

N R

Page 4 of 9

Name:___________________________________ Chemistry 27 Spring 2004 Exam 3

3. (28 pts) Aerobic organisms suffer from chronic DNA damage due to the formation of oxygen free radicals. These free radicals are known to react with guanosine to produce 8oxoguanosine (oxoG). Unlike the natural guanosine, oxoG is capable of base pairing with adenosine in normal double stranded DNA. O H N

H N

O N

N

NH2

R

8-oxoguanosine (oxoG) A) (8 pts) Please draw base-pairing between oxoG and adenosine. H H

O

N

H2N oxoG

N R

N N

N N

N

NH

H

N

R A

O

B) (8 pts) Failure to repair the 8-oxoguanosine will cause a mutation to be propagated in the DNA following DNA replication. The following diagram outlines two rounds of DNA replication of a damaged sequence containing an oxoG (Go). Please identify the bases represented by W, X, Y, and Z. 5'-ATGoATA-3' ||| ||| 3'-TAY TAT-5' 5'-ATGoATA-3' ||| ||| 3'-TAW TAT-5' 5' - ATGATA - 3' |||||| 3' - TACTAT - 5'

damage

5'-ATGoATA-3' ||| ||| 3'-TAC TAT-5' 5'-ATXATA-3' |||||| 3'-TACTAT-5'

W

= A

X

= G

Y

= A

Z

= T

Page 5 of 9

5'-ATZATA-3' |||||| 3'-TAWTAT-5'

Name:___________________________________ Chemistry 27 Spring 2004 Exam 3

C) (12 pts) A DNA repair enzyme, hOGG1, is known to catalyze the cleavage of oxoG, which then allows the cell to replace the damaged base. The cleavage reaction, shown below, involves a nucleophilic lysine residue and proceeds through an imine intermediate. Please provide an arrow-pushing mechanism of the following cleavage reaction. You do not need to show the mechanism of imine hydrolysis. O

H N

DNA-O

NH

O N

NH2

OH

1'

1'

H2N

DNA-O

NH

O

DNA-O

N

O

O

H N N H

N

O

H2N

DNA-O

Lys249

NH2

Lys249

O H N

NH

O

DNA-O

N

O

N

DNA-O

NH2

4 pts

1'

H+

O

H 2N

N

DNA-O

DNA-O

H

Lys249

Lys249

2 pts DNA-O OH

2 pts

N

DNA-O H

H

DNA-O

:B

OH N

Lys249

DNA-O

H Lys249

2 pts

DNA-O

O-DNA

OH

Imine hydrolysis

N DNA-O

H 2N

OH O

H Lys249

2 pts

Page 6 of 9

Lys249

Name:___________________________________ Chemistry 27 Spring 2004 Exam 3

Alternative O H N

NH

O N

O H N

N

H+

NH

O

DNA-O

tautomerization does not required for credit NH2 DNA-O

DNA-O N

O

N

NH2

2 pts

DNA-O

H2N

DNA-O

H+

O

O

N

2 pts

DNA-O

H Lys249

Lys249

2 pts

DNA-O

DNA-O

DNA-O OH

OH

2 pts

N H

DNA-O

Lys249

N DNA-O

:B

OH

2 pts

H N

H Lys249

DNA-O

H Lys249

Imine hydrolysis 2 pts O-DNA H 2N

OH O

Lys249

Some partial credit was given if the imine was hydrolyzed prematurely, and the same mechanism was performed through an aldehyde intermediate (2 pts)

Page 7 of 9

Name:___________________________________ Chemistry 27 Spring 2004 Exam 3

4. (24 pts) Caproic acid, a 6-carbon saturated fatty acid, is synthesized by a fatty acid synthase A. O HO

Caproic acid A) (9 pts) Suppose caproic acid is synthesized from radiolabeled malonyl-CoA. For each of the following labeled versions of malonyl-CoA, please indicate which atoms will be labeled in the resulting caproic acid by placing a star over the appropriate atom. If you feel that no label will be incorporated, then circle “no label”. 3 pts each O *

HO O

O

O

*

HO

S-CoA O

HO *

no label

HO

O

HO

no label

O S-CoA

O*

*

O S-CoA

HO

no label

B) (12 pts) You generate mutants of the fatty acid synthase A that produce variants of caproic acid. Please state what domain(s) of what module(s) was deleted to give rise to each of the following variants: 4 pts each O

O

HO O HO

=

KR1

=

DH2

=

ER in both modules

OH

O HO

C) (3 pts) How many modules does fatty acid synthase A have? 2 modules

Page 8 of 9

Name:___________________________________ Chemistry 27 Spring 2004 Exam 3

5. (20 pts) Molecule A is a potential anti-cancer agent. However, molecule A will not be active until it undergoes hydrolysis to form molecule B. O H

Ph HO

N

O

H

H N HO

H

H

Molecule A

O HO

Ph

Molecule B

A) (6 pts) Please identify two structural features that make molecule A a potential anticancer drug and explain how they work. 1. Flat aromatic rings can intercalate DNA (3 pts) 2. Ene-dieye can undergo the Bergman cyclization and damage DNA (3 pts) (Also, 3. Trans epoxide to prevent Bergman cyclization from occurring before activation) B) (2 pts) Please explain why molecule A is not active. (1 sentence only) Trans-epoxide prevents the Bergman cyclization from happening because it would yield a overly strained structure (unstable product).

Page 9 of 9

Name:___________________________________ Chemistry 27 Spring 2004 Exam 3

C) (12 pts) Please provide an arrow-pushing mechanism for conversion of molecule A to molecule B, using the structure provided below. You do not need to redraw the final product (molecule B). You may abbreviate your structures as necessary.

A: O H

H OH -

Ph N

H

HO H

+

O

O

Ph

N

O

H

H

4 pts

A:

H OH

H A

HO

H

N

H 4 pts

4 pts

Molecule B

Page 10 of 9