Download E. None of the above

Name_____________________________________
MBMB 451A Nucleic and Gene Expression: Section1
Fall 2000
9-21-00
The structures shown below will be used for the next 5 questions
E. None of the above
1.
2.
3.
4.
5.
Which of the chemical structure(s) shown on above is that of a nucleoside?
Which of the structure(s) contains a deoxyadenosine?
Which of the structure(s) contains a uridine?
Which is or contains a nucleotide moiety?
Which contains a phosphomonoester?
---------------------------------------------------------------------------------------For each of the following multiple choice questions,
choose the most appropriate answer.
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6. Formation of Z-DNA is favored by
a. high salt concentration
b. alternating adenine and guanine residues
c. methylation of guanosine
d. increase in pH
e. change in temperature
7.
Which of the following is a process of formation of a double helix between
complementary deoxypolyribonucleotide strands?
A.
translation
B.
denaturation
C.
renaturation
D.
transcription
E.
transformation
8. Which of the following single-stranded DNA molecules are likely to pair with each other to
form double-stranded molecules? You need to select two of the following. All are written in the
5’-3’ direction.
(a) GCTTAGCC
(b) TAGTGAAT
(c) ATGACCGGC
(d) ATTCACTA
(e) GCACGTAGG
(f) CGTGCATCC
9. Tm is the temperature at which all of a certain DNA is single-stranded.
a. true
b. false
10. Type I restriction endonuclease is useful for molecular cloning.
a. true
b. false
11. Which statements about the yeast and mammalian genomes are true?
a. Most yeast genes have some introns while most mammalian genes have many introns
b. Most yeast proteins are about the same size as the corresponding mammalian proteins
even though the yeast genes are smaller
c. Most yeast proteins are smaller than the corresponding mammalian proteins
d. Most genes in the yeast genome are the same size as genes in mammalian genomes
12. When comparing genes that are conserved between species, the introns are more likely to be
related to one another than the exons.
a. True
b. False
13.
Which of the following classifications is associated with most eucaryotic DNA sequences
giving rise to rRNA?
A.
nonrepetitive
B.
moderately repetitive
C.
highly repetitive
D.
none of the above
14.
Which one of the following classes of histones is not a component of the core particle?
A.
H1
B.
H2A
C.
H2B
D.
H3
E.
H4
15.
Regarding nucleosome structure, which of the following statements is correct?
A.
Nucleosomes are spherical structures comprised of RNA, nonhistone proteins
and histone proteins.
B.
The major histones comprising nucleosomes are H1 and H4.
C.
Nucleosomes permit efficient packing of DNA to about one seventh its normal
length.
D.
The histone associated with the DNA in the linker region holding nucleosomes is
called H2A.
E.
All of the above.
16.
If the DNA strand which is complementary to the strand of DNA which is transcribed
into RNA has the following base sequence:
AGCTCACTG
(nontranscribed strand)
The RNA transcribed would have which of the following sequences?
A.
CAGUGAGCU
B.
AGCUCACUG
C.
AGCTCACTG
D.
CAGTGAGCU
E.
None of the other answers is correct.
17.
Which of the following is not a part of the promoter of a mRNA gene in eucaryotes?
A.
INR
B.
box A
C.
TATA box
D.
enhancers
E.
response elements
18.
Mammalian RNA polymerase II:
A.
synthesizes rRNA
B.
synthesizes mRNA
C.
synthesizes tRNA
D.
None of the other answers is correct
19.
The highly phosphorylated form of RNA polymerase II is
A. the form of the enzyme that is involved in promoter recognition
B. the form of the enzyme that is involved in productive elongation
C. caused by phosphorylation of the N-terminus of the largest subunit
D. is also found as a feature of RNA polymerase III
20. The transcription factor called TFIID
a. is a gene-specific transcription factor
b. binds to the enhancer region
c. helps recruit all the other general transcription factors to the DNA template
d. binds to a response element near the start site of transcription
21.
Which of the following conditions can explain why genes are not always active when
their transcription factors are present?
a. the presence of coactivator proteins
b. the absence of a displacing protein
c. the lack of chromatin structure over the transcription factor binding site
d. the context of the transcription factor binding site
22. Homeodomain proteins:
a. form a structure with three  sheets
b. contact DNA primarily through  helix 3 and an N-terminal arm
c. are similar in structure to prokaryotic helix-turn-helix protein
d. are not present in the cell nucleus
23. bHLH proteins
a. have conserved basic amino acids in the loop
b. cannot homodimerize
c. are always expressed
d. interact with HLH through their basic regions
e. bind DNA through their basic regions
24. All histones undergo post-translational modification of specific amino acids. These
modifications:
a. alter the amphipathicity of the histone protein
b. are permanent
c. occur in the core region of the histones
d. occur at specific times during the cell cycle
e. none of the above
25.
Which of the following is the correct structure of an RNA:RNA duplex:
A. A-form
B. B-form
C. Z-form
D. hairpin
E. none of the above
26. Which transcription factors contain TBP
a. TFIIB
b. TFIIIA
c. SL1
d. TFIID
e. TFIIIB
f. UBF1
27. Which of the following protein complexes helps remodel chromatin in a noncovalent fashion:
a. HDAC
b. coactivator
c. TFIID
d. SWI/SNF
e. HAT
f. none of the above
28. The linking number (L) of a closed-circular, double-stranded DNA molecular is changed by:
A. supercoiling without the breaking of any phosphodiester bonds
B. underwinding without the breaking of any phosphodiester bonds.
C. breaking one of the strands, unwinding or rewinding the DNA, then rejoining the
strands.
D. breaking all hydrogen bonds in the DNA
29. For a closed-circular DNA molecule of 10,000 base pairs in the fully relaxed form, the
linking number (L) is about:
A. 10,000
B. 950
C. 100
D. 9.5
E. 2
30. List the contents of a nucleosome, the 10 nm fiber, and 30 nm fiber?
31.
Describe in one or two sentences the role of each of the following types of proteins in the
regulation of gene expression in eukaryotes: (a) basal transcription factors; (b) transactivators; (c)
coactivators
32. Diagram what are the promoter elements found in a typical eukaryotic (1) rRNA, (2) mRNA,
and (3) tRNA genes and their relative position in DNA with regard to the transcription start site.
33. TFIIIA is a transcription factor required for the expression of 5S rRNA genes. This protein
contains nine zinc finger domains, and binds to an internal region of 5S rRNA genes and to 5S
rRNA itself.
(a) Describe how you would map the DNA binding sites of the TFIIIA protein
(b) What specific mutations would demonstrate that the zinc fingers are required for
DNA binding?
(c) You find that a deletion of 19 amino acids from the C-terminus of TFIIIA binds DNA
as well as wild type, but fails to activate 5S rRNA transcription. Propose an explanation
(d) Xenopus oocytes synthesize and store large amounts of 5S rRNA. As 5S rRNA
accumulates, TFIIIA binds to it. What effect will this have on transcription of 5S genes? What
kind of regulatory mechanism is working here?
34. You are studying a nuclear receptor gene and want to find out if nucleosomes are positioned
or phased over the promoter region. You know the DNA sequence of the gene and the 5' flanking
region and decide to use the method of indirect labeling to map the position of the nucleosomal
binding sites in vivo. There are two EcoRI restriction cut sites located 0.8 kb upstream and 1.2 kb
downstream of the start site of transcription. Chromatin from isolated nuclei is digested with
varying amounts of DNase I. Next protein is removed by phenol extraction and the DNA
recovered by ethanol precipitation. The DNA is cut with EcoRI and analyzed by Southern
blotting. The DNA probe used hybridizes near the EcoRI cut site upstream of the start site and
autoradiography of the blot produces the pattern shown on the next page. Using this data indicate
where the nucleosome core particles are positioned on this DNA with regard to the start site of
transcription. Indicate what would the result have looked like if the nucleosomes were randomly
positioned on this DNA sequence.
indicated are 100 bp increments