Name____________________

BIO 366 FALL 10 EXAM 2

October 21, 2010
MULTIPLE CHOICE QUESTIONS (4 POINTS EACH)
1. Which of the following description of eukaryotic gene intron sequences is incorrect?
a. introns are never found upstream of the first exon
b. most higher eukaryotic genes contain multiple introns
c. most introns are 50-200 bp long
d. some intron sequences are retained in some mature mRNAs
e. some introns encode transcription control elements
2. Which of the following is true for the human -globin gene family cluster but not
rRNA gene clusters?
a. all gene members are identical in sequence
b. none of the genes have introns
c. all members are expressed as active genes
d. all genes are part of a single transcription unit
e. Alu repeat sequence elements are present between some members of the cluster
3. Which of the following types of sequences are encoded by retroviruses but never by
retrotransposons?
a. polymerase that copies RNA into DNA
b. endonuclease that can cut genomic DNA
c. LTR (long terminal repeat sequence)
d. virus capsid protein
e. virus envelope protein
4. Which of the following is true for 30 nm chromatin fibers but not 10 nm fibers?
a. nucleosomes contain two copies each of histones H2A, H2B, H3, and H4
b. more nucleosomes per unit length of DNA
c. presence of H1 histone
d. more turns of DNA surrounding each nucleosome
e. DNA is more accessible to nuclease
5. Which of the following is not a property of eukaryotic centromere sequences?
a. often present as repeat sequences
b. serve as attachment sites for microtubules of the mitotic spindle apparatus
c. sequence is similar for all chromosomes of the same organism
d. serves as origin of replication
e. does not encode proteins

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6. How does the telomerase enzyme differ from other DNA polymerases?
a. does not require a primer
b. does not require a template
c. copies only A-rich sequences
d. requires an associated RNA containing the template sequence
e. c and d
7. Which of the following proteins binds lactose in order to activate E. coli lac operon
transcription?
a. RNA polymerase
b. sigma factor
c. catabolite activator
d. lac repressor
e. -galactosidase
8. Why is DNA looping required for activation of the E. coli glutamine synthetase gene
(gln) by the nitrogen regulatory protein C (NtrC)?
a. the polymerase binds to two sites far apart from each other
b. 54 binds far upstream of the start site
c. NtrC protein binds to an upstream enhancer sequence and to the polymerase
d. gln gene promoter has no control regions
e. both 54 and 70 must bind to the promoter
9. Which of the following is characteristic of eukaryotic genes whose promoters
possess CpG islands instead of TATA boxes?
a. only found in lower eukaryotes
b. multiple transcription start sites in a region of 20-200 bp
c. transcribed by a modified pol II
d. promoter doesnt bind transcription factors
e. transcribed infrequently
10. Which of the following is true for analysis of transcription control elements using
the linker scanning method but not the deletion analysis method?
a. the overall size of the fragment linked to a reporter gene is kept constant
b. plasmid transfection is used to measure the effects of change in sequence
c. a different reporter gene is required
d. the results can only map elements to fragments larger than 1 kbp
e. cells used for transfection must contain transcription factors that bind to the elements

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11. The eukaryotic Pax6 gene contains many transcription control elements. Which of
the following correctly describes their location in the gene?
a. within exons only
b. upstream of the start site only
c. all downstream of the promoters
d. within introns only
e. within introns and upstream of the start site
12. Which of the following incorrectly describes the properties of eukaryotic
transcription factors?
a. always bind to a specific DNA sequence
b. DNA-binding domain is separate from activation or repressor domain
c. DNA-binding domain is always at the N-terminal end of the protein
d. activation domain can be at the N- or C-terminal end of the protein
e. activation domain of one factor can work with DNA-binding domain of another
13. Which of the following is characteristic of the DNA-binding domain in bZIP and
bHLH transcription factors?
a. helix-turn-helix motif
b. coiled-coil amphipathic helices
c. ability to bind zinc ions
d. rich in acidic amino acids
e. unstructured region
14. Which of the following distinguishes general transcription factors from other types
of transcription factors?
a. not tissue-specific
b. required for all genes transcribed by pol II
c. all contain a TATA box-binding subunit
d. contain acidic activation domains
e. a and b
15. Which of the following incorrectly describes the properties of the mediator complex
involved in eukaryotic gene transcription?
a. binds to pol I, pol II, and pol III
b. contains more than 20 subunits
c. some subunits are required for only a subset of pol II genes
d. forms a bridge between transcription factors and the pol II pre-initiation complex
e. required for transcription in both lower and higher eukaryotes
16. Which of the following correctly identifies the location of the promoter region for
RNA polymerase III genes?
a. downstream of start site
b. ~50 bp upstream of start site
c. ~90 bp upstream of start site
d. ~50 bp region overlapping start site and one at ~155 bp upstream
e. none of the above
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17. Which of the following enzymatic reactions occurs first when mRNA precursors are
capped?
a. addition of GTP to 5 end of mRNA
b. removal of gamma phosphate from mRNA 5 end
c. removal of pyrophosphate from mRNA 5 end
d. methylation of GTP at the 7 position
e. methylation of ribose on first nucleotide in the mRNA chain
18. Which of the following correctly describes the location of the A residue branch point
utilized in splicing of eukaryotic introns?
a. at the very 3 end of the intron
b. near the 5 end of the intron
c. in the exon near the 5 splice site
d. 20-50 bases upstream of the 3 end of the intron
e. in the exon downstream of the 3 splice site
19. Which of the following serves as a binding site for SR proteins (rich in ser and arg)
that facilitate recognition of correct splice sites in mRNA precursors?
a. pyrimidine-rich region
b. cap
c. poly(A) tail
d. U4 snRNA
e. exonic splicing enhancer
20. Which of the following protein factors recognizes the AAUAAA polyadenylation
signal sequence on precursor mRNAs??
a. CPSF
b. PABPI
c. maturase
d. CStF
e. TAP
21. Hair cells in the inner ear system of vertebrates respond to particular sound
frequencies depending on their position. Which of the following plays a major role in
this phenomenon?
a. different isoforms of the fibronectin protein
b. multiple K+ ion channel genes
c. multiple Ca+ ion channel genes
d. alternatively spliced mRNAs encoding a Ca+ ion channel
e. alternatively spliced mRNAs encoding a K+ ion channel
22. Which of the following generally determines whether a mRNA will be degraded
rather than display translational inhibition when bound to miRNAs or siRNAs?
a. processing pathway of the miRNA or siRNA precursor
b. perfect base-pairing to mRNA target
c. base-pairing to coding region of mRNA
d. base-pairing to 5 UTR
e. short poly(A) tail
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SHORT ESSAY QUESTION: (12 pts)

ANSWER ONLY ONE AND USE THE SPACE ALLOTTED
1. Describe the general structure of nuclear receptor transcription factors and how their
activity is regulated, and provide the name of one such transcription factor.
Nuclear receptor transcription factors are composed of a variable N-terminal domain, followed
by a conserved DNA-binding domain, and a C-terminal transcription activation or repressor
domain that includes a ligand binding site. Lipid soluble hormones that freely traverse the
plasma membrane act as ligands that change the conformation of the ligand-binding domain
into an active form. Examples of nuclear receptor transcription factors include the estrogen
receptor, progesterone receptor, glucocorticoid receptor, thyroxine receptor, retinoic acid
receptor, and vitamin D3 receptor.

2. Describe how translation of ferritin mRNA is regulated by iron concentration.

The ferritin mRNA contains two iron response elements (IRE) in its 5 UTR. The IRE-binding
protein (IRE-BP) is activated to a form that binds IRE when iron concentrations are low. The
bound IRE-BP proteins prevent scanning of ferritin mRNA by the 40S ribosomes and thus
inhibit its translation. When iron concentrations are high the IRE-BP is converted to a form that
no longer binds IRE elements. This promotes translation of ferritin mRNA and the resulting
ferritin protein binds excess iron.

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