Answers Name ____________________

Student Number ____________

BMB7010 Biochemistry December 13, 2007
Fifth Exam (Evans) Page 1 of 5
Answer only in the space provided. (100 total points)

1. Identify the following in one or two words. Be specific.

a. An enzyme that does not use ATP but alters

topoisomerase I
DNA supercoiling by cutting the DNA duplex once.

b. A regulatory protein that can increase the transcription of

CAP
many catabolic operons in bacteria when glucose is low.

c. An antibiotic that resembles the aminoacyl adenylate

part of aminoacyl-tRNA and causes premature release puromycin
of the nascent polypeptide chain during translation.

d. The eukaryotic transcription factor that binds to the TFIID (or TBP okay)
TATA box.

e. A common DNA binding motif found in bacterial

helix coil helix
DNA binding proteins

f. A large dynamic complex consisting of five different

snRNAs, many proteins and a precursor mRNA molecule. splicesome

e. The base in the first position of the anticodon that allows

Inosine (wobble -1)
tRNA to recognize the maximum number of codons.

f. a repair mechanism that can correct the mutation

base excision repair
caused by the deamination of cytosine to uracil,

(16 points)

2. A circular DNA molecule is shown in the diagram.

a. Give the expression used to calculating

the linking number

Lk = Tw + Wr

b. Calculate the twist (Tw) 25 Linking Number = 23

negative (right handed) supercoils
-2 (4 points)
c. Calculate the writhe (Wr)
 Name ____________________
BMB7010 Biochemistry December 13, 2007
Fourth Exam (Evans) Page 2 of 5

3. Indicate which of the following apply to prokaryotic and eukaryotic protein synthesis.
Check one or both or no boxes.
Prokaryotic Eukaryotic

a. The mRNA has multiple start and stop codons. X

b. The large ribosomal subunit has 3 RNA molecules. X
c. The small ribosomal subunit has 1 RNA molecule. X
X
d. The small ribosomal subunit binds to the Shine X
Delgarno sequence.

e. The translated mRNA is circular. X

f. The charged initiator tRNA binds to the P site. X X

g. The initiator tRNA has formyl methionine attached. X

h. The is a single release factor that recognizes a X

stop codon.
(8 points)

4. Indicate which of the following statement regarding enhancers is true.

True False

a. enhancers are transcription factors. X

b. enhancers can be located upstream, downstream or in X

the middle of the transcribed gene.

c. enhancers can increase or decrease the rate of transcription. X

d. enhancers only work in certain cell types X

e. enhancers are trans-acting elements. X

(5 points)

5. One form of thalasemia results from a single point mutation in which an G is

replaced with an A (boxed residues).

normal 5 C C T A T T G G T C T A T T T T C C A C C C T T A G G C T G C T G
exon
mutant 5 C C T A T T A G T C T A T T T T C C A C C C T T A G G C T G C T G
 Name ____________________
BMB7010 Biochemistry December 13, 2007
Fourth Exam (Evans) Page 3 of 5

a. What is the consequence of this mutation?

sequence spliced differently because new 3 splice site is generated.

b. How would you expect it to affect the structure of the protein?

depends the frame which is not given in the problem. It could either
be longer because of the extra codons or shorter because it is (4 points)
out of frame and a stop is encountered (this is what happens).
6. There are three major structural forms of DNA. Identify which DNA form(s) have
following properties. Check one or more or no boxes.
DNA A DNA B DNA Z

a. The major form found in chromosomal DNA. X

b. Forms when the relative humidity is less than 75%. X

c. A double stranded, antiparallel, left handed helix. X

d. The bases tilt 11o relative to the helix axis. X

e. Stabilized by high salt concentration. X

(5 points)

7. The E. coli DNA polymerase holoenzyme is shown below. Identify the function,
given in the list below, of each of the following components and write the corresponding
letter in the space.
DnaB
I
2 J

2 F

DnaB G

List (12 points)

A. 3-5 proof reading exonuclease. F. The clamp loader
B. 5-3 exonuclease that removes RNA primer G. A helicase
C. Interacts single strandedDNA binding proteins. H. Topoisomerase II
D. Ligase for joining Okasaki fragments. I. catalyzes polymerization
E. Recognizes the origin of replication. J. The sliding clamp.
BMB7010 Biochemistry December 13, 2007
Fourth Exam (Evans) Page 4 of 5

8. Identify the following,

a. The activated intermediate in the reaction that attaches the aminoacyl adenylate
amino acid to the tRNA or AA-AMP
editing or
b. The site on the aminoacyl tRNA synthetase that removes an
proofreading site
amino acid that has been incorrectly attached to tRNA.
CCA 3 (acceptor
c. The attachment site of the amino acid on tRNA. stem okay)

d. The GTP binding protein that protects the aminoacyl-tRNA EF-Tu

from hydrolysis.

e. The tRNA loop that base pairs with the codon on mRNA. anticodon loop
(5 points)

9. Many proteins, protein domains and sequences interact in regulation of eukaryotic

transcription. Match the following functions with the items in the list and write the letter
in the space provided.

a. binds to the estrogen response element. G

b. catalyzes the acetylation of histone tails. F

c. bridges the activation domain of transcription factor and RNA polymerase. J

A or H
d. binds to acetylated histones.

e. may block transcription by partially occupying the major groove. C

A. Bromodomain F. histone acetyl transferase

B. ERE G. nuclear receptor.
C. CREB H. co-activator
B. CBP I. co-repressor
C. 5-methylcytosine J. mediator
(10 points)

10. Compare the regulation of the lac and pur operons in E. coli. Check the appropriate
box or boxes (6 points) .
lac operon pur operon

a. a regulatory protein binds to the operator X X

b. requires a inducer for transcription X

c. requires a co-repressor for transcription

 Name ____________________
BMB7010 Biochemistry December 13, 2007
Fourth Exam (Evans) Page 5 of 5

lac operon pur operon

d. there are multiple operons of this type in the X
bacterial genome. (8 points)

11. Identify the following involved in the synthesis of a integral membrane protein.

a. The ribonucleoprotein that recognizes the nascent Signal Recognition

polypeptide as a membrane protein. Particle or SRP

b. A protein conducting channel in the ER membrane. Translocon

c. A enzyme that often cleaves off the signal sequence

inside the endoplasmic reticulum. Signal Peptidase

Signal Recognition Particle

d. The ER protein that binds GTP and serves as a
Receptor or SR Receptor
docking site.
(8 points)

12. Identify the following components in the transcription bubble shown in the diagram
and write the corresponding letter in the space.

a. nascent RNA C B
A
b. DNA coding strand B

A D
c. DNA template strand E
E
d. RNA DNA hydrid
C
D F
e. elongation site
F
f. direction polymerase moves G
(12 points)

13. Answer the following true or false. True False

a. Transcription is blocked by histones in bacteria. X

b. The nucleosome core contains 2 copies of 4 histones and

about two turns right handed DNA superhelix. X

c. Chromatin remodeling engines move histones exposing

genes for expression. X
(3 points)