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MBMB 451A Nucleic and Gene Expression: Section1
Fall 2001
9-20-01
---------------------------------------------------------------------------------------For each of the followingmultiple choice questions,
choose the most appropriateanswer.
----------------------------------------------------------------------------------------1. 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
2. Which of the following single-stranded DNA molecules are likely to pair witheach other to
form double-stranded molecules? You need to select two of the following. All are written in
the5’-3’ direction.
(a) GCTTAGCC
(b) TAGTGAAT
(c) ATGACCGGC
(d) ATTCACTA
(e) GCACGTAGG
3. Tm is the temperature at which all of a certain DNA issingle-stranded.
a. true
b.false
4. Type II restriction endonuclease is useful for molecularcloning.
a. true
b.false
5. Which statements about the yeast and mammalian genomes aretrue?
a. Most yeast genes have several introns while most mammalian genes have manyintrons
b. Most yeast proteins are about the samesize as the corresponding mammalian proteins
even though the yeast genes are smaller
c. Most yeast proteins are smallerthan the corresponding mammalian proteins
d. Most genes in the yeast genome are the samesize as genes in mammalian genomes
6. When comparing genes that are conserved between species, theexons are more likely to be
related to one another than the introns.
a. True
b. False
7.
Whichof the following classifications is associated with most eucaryotic DNAsequences
giving rise to mRNA?
A.
nonrepetitive
B.
moderatelyrepetitive
C.
highlyrepetitive
D.
noneof the above
8.
Whichone of the following histones is a component of the core particle?
A.
H1
B.
H2A
C.
H2B
D.
H5
E.
H4
9.
Globin genes:
a. are organized differently in all highereukaryotes
b. are organized into two clusters
c. derive from a common ancestral gene
d. are all expressed simultaneously
10. Which of the following statements about pseudogenes aretrue?
11.
12.
13.
14.
15.
16.
17.
18.
19.
a. They contain stop codons.
b. They are not transcribed
c. They are not translated
d. They could eventually be lost from the genome bydeletion or other mechanism.
e. They could evolve into new geneswith different functions
Regardingnucleosome structure, which of the following statements is correct?
A.
Nucleosomesare spherical structures comprised of RNA, nonhistone proteins and
histoneproteins.
B.
Themajor histones comprising nucleosomes are H1 and H4.
C.
Nucleosomespermit efficient packing of DNA to about one seventh its normal
length.
D.
Thehistone associated with the DNA in the linker region holding nucleosomes
iscalled H2A.
E.
Allof the above.
Whichof the following is a part of the promoter of a tRNA gene in eucaryotes?
A.
INR
B.
boxA
C.
TATAbox
D.
upstreamcontrol element
E.
responseelements
MammalianRNA polymerase I:
A.
synthesizesrRNA
B.
synthesizesmRNA
C.
synthesizestRNA
D.
Noneof the other answers is correct
TheIIA form of RNA polymerase II is
A. the form of the enzyme that is involvedin promoter recognition
B. the form of the enzyme that is involvedin productive elongation
C. caused by phosphorylation of theN-terminus of the largest subunit
D. is also found as a feature of RNApolymerase III
The transcription factor called TFIID
a. is a gene-specific transcription factor
b. binds to the enhancer region
c. helps recruit all the other generaltranscription factors to the DNA template
d. binds to the response element near thestart site of transcription
Zinc finger proteins bind zinc
a. covalently
b. in the presence of DNA
c. by coordination between conservedcysteine and histidine residues
d. in an alpha helical region of theprotein.
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 prokaryotichelix-turn-helix protein
d. are not present in the cell nucleus
Steroid receptor transcription factors
a. all bind the same hormone
b. do not bind DNA in a sequence specificmanner
c. use a consensus sequence to bind zincdifferent from the on e used by the zinc finger
d. have separate domains for transcriptionactivation, DNA binding, and hormone
binding
e. dimerize through amino acids in theC-terminal part of the second finger
Which of the general transcription factors have a DNAhelicase activity
a. TFIIA
b. TFIIB
c. TFIID
d. TFIIE
e. TFIIH
20. bHLH proteins
a. have conserved basic amino acids in theloop
b. cannot homodimerize
c. are always expressed
d. interact with HLH through their basicregions
e. bind DNA through their basic regions
21. All histones undergo post-translational modification ofspecific amino acids. These
modifications:
a. alter the amphipathicity of the histoneprotein
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
22. Which of the following transcription factors are requiredfor RNA polymerase I transcription?
a. TFIIB
b. TFIIIA
c. UBF
d. TFIID
e. TFIIIB
23. Which of the following protein complexes helps remodelchromatin in a covalent fashion:
a. HDAC
b. SP1
c. TFIIE
d. SWI/SNF
e. HAT
The following are a seriesof essay questions
24. What are four different protein modifications that occur onthe histone proteins and help
regulate their function?
25. Describe the five forces that help stabilize the doublehelical structure of DNA.
26. One strand of double helical DNA has the sequence:
5'-GCGCAATATTCTCAAAATATTGCGC-3'
What special type of sequenceis contained in this DNA segment? Write the base sequence of the
complementary strand. Does the double stranded DNA have thepotential to form any alternative
structures - please diagram.
27. List the contents of anucleosome, the 10 nm fiber, and 30 nm fiber?
28. Diagram what are the promoter elementsfound in a typical eukaryotic (1) rRNA, (2) mRNA,
and (3) tRNA genes and theirrelative position in DNA with regard to the transcription start site.
29. A new RNA polymerase activity is discovered in crudeextracts of cells derived from an
exotic fungus. The RNA polymerase initiates transcription only from a single,highly specialized
promoter. Asthe polymerase is purified its activity declines, and the purified enzyme
iscompletely inactive unless crude extract is added to the reaction mixture. Suggest an
explanation for theseobservations.
30. A biochemist replaces the DNA binding domain of the yeastGal4 protein with the DNA
binding domain from the LexA repressor protein andfinds that the engineered protein no longer
regulates transcription of the GAL genes in yeast. Draw a diagram of the different functional
domains you would expect tofind in the Gal4 protein and in the engineered protein. Why does
the engineered protein nolonger regulate transcription of the GAL genes? What might be doneto
make this chimeric protein functional in the activation of transcription ofthe GAL genes.
31. The DNA molecule below is believed tocontain a binding site for protein X. It is labeled at
the 5' end of the top strand (*), then subjected to a footprintingexperiment. In the idealized
gelbelow, there is a band for every base of the labeled strand. On the DNA sequence, point out
thebinding site for protein X.
*(5')GGATTCTAATAAAGTAACGCGTTACGACTTGG
CCTAAGATTATTTCATTGCGCAATGCTGAACC
Also show to the left side of the gel what the dideoxysequencing lane for G (sample containing
dideoxy GTP) if you were sequencingthe top strand with the bottom strand as the template.
32. It is possible to “reconstitute”nucleosomes by mixing DNA and histone octamers in 2M NaCl and then
dialyzing tolow salt. When such experiments were carried out using a specific 225-bpfragment of DNA, the
following results were obtained: Digestion of the productwith micrococcal nuclease gave quantitative
production of 146 bp DNA. Upon cleavageof this DNA with the restriction endonuclease EcoRI at a single
site 100 bpsfrom one end of the DNA, several sharp bands were obtained, with sizes asfollows: 38, 53, 64,
161, 172, and 187 bp. How would you interpret these data in terms of nucleosomepositioning on this DNA?
Pleaseshow a diagram in which the distance of the ends of the nucleosome from theEcoRI cut site is
indicated in base pairs.