Download Practice Exam 2

Biology 200, Autumn 2014
Practice Exam 2
How to Use this Practice Exam:
I post practice exams to allow you to get a real sense of the experience of taking a Biology 200
exam. The best way to use each exam is as follows.
1. Do NOT answer the questions as a problem set.
2. Study material using your lecture and lab notes and do problem sets FIRST.
3. When you feel you are fairly prepared, put away all of your notes and sit down in a
quiet place where you will not be interrupted for an hour or more. (Note – this exam is
WAY longer than a typical exam!)
4. "Take" the exam without stopping to check notes or the book.
5. At the end of the exam, "grade" your responses. THEN go back and try and figure out
the ones you answered incorrectly. Use your notes/book if you need to at this point.
6. If you are still confused, contact an instructor or TA during their office hours or by email
so that you can get your questions answered.
NOTE: This exam may or may not reflect the content of the exam as presented this quarter,
nor will it necessarily be the same length (in fact, this one is way longer – I've added several
questions for your use). Use these questions as a guideline as to the types of questions that
may appear on your exams. THEREFORE YOU MAY FIND QUESTIONS ON
MATERIAL WE HAVE NOT COVERED, OR THERE MAY BE MATERIAL NOT
EXAMINED IN THESE TESTS THAT YOU WILL BE RESPONSIBLE FOR.
Biology 200, Autumn 2014
Practice Exam 2
PRACTICE EXAM 2
***************************************************************************************************
1. Shown below is a portion of a parent strand for DNA replication.
a. Create an Okazaki fragment complementary to this strand, by writing its sequence and
drawing an arrow to represent the phosphodiester backbone. Assume that the box
represents the template for the enzyme primase. Label this fragment “Okazaki 1”.
5’
A G C G T A A T T G G A C T A C G T T A G G G
3’
b. Draw the end of a second Okazaki fragment using any unpaired parent strand as template.
Label this fragment “Okazaki 2”.
c. The closest replication fork is to the… (Circle one)
right
left
…of this diagram.
d. The two Okazaki fragments you drew need to be joined.
i. If DNA polymerase I completely did not work, between which two nucleotides
on the NEW strand would there be a gap in the phosphodiester backbone? ________
ii. If DNA pol I were normal, but instead ligase did not work, between which two
nucleotides on the NEW strand would there be a gap in the backbone? ________
e. If the left end of the DNA shown above is the end of the chromosome, would telomerase
add DNA to the 3’ end after replication was completed? Why or why not? (1-2 sentences)
Questions 2-4: Circle ALL that apply!
2. Eukaryotic transcription requires ____________ to occur.
a. basal transcription factors binding a promoter in DNA
b. histone modification (such as acetylation of histone lysines) to decondense chromatin
c. activator proteins to bind to enhancers
d. chromosome condensation
3. Eukaryotic mRNA molecules….
a. have exons spliced out before translation.
b. get "capped" by an enzyme before export to the cytoplasm.
c. usually contain multiple open reading frames.
d. can be spliced differently in different cells.
4. Active telomerase enzyme…
a. helps repair damaged genes at the end of chromosomes.
b. requires an RNA template that is used for DNA synthesis.
c. can be found in all cells of a human body.
d. adds nucleotides onto the 5’ end of the chromosome.
Biology 200, Autumn 2014
Practice Exam 2
5. The cell cycle is regulated so that cells only divide at the right time and in the right
conditions. The following DNA sequence represents the beginning of the open reading frame
for an imaginary proto-oncogene protein. The bottom strand is the template.
5’ ATGCCCTTGAAAAGATGC 3’
3’ TACGGGAACTTTTCTACG 5’
a. What is the sequence of the portion of the protein coded for by this DNA? (Genetic code
is on the last page)
b. A new version of this gene is discovered. The resulting protein is much shorter. On the
diagram above, circle a SINGLE base pair, then in the space below describe a specific
change to that base pair and how it will result in a shorter protein. (There is more than
one possible correct answer. You only need to give us one.)
c. Assume that your mutation in “b” makes this proto-oncogene non-functional. Describe
how this will affect cell cycling and whether this mutation is more likely or less likely to
lead to cancer.
6. The diagram below shows a single replication fork of a very short linear chromosome at a
single point in time. This chromosome has the unique feature of having a single origin at one
end of the molecule. The thin lines represent DNA and the thicker lines RNA.
a. Label the polarity of the ends of the PARENT strands by filling in the blanks (i-iv) on the
diagram.
i.
b.
ii.
iv.
iii.
b. At the site labeled “b”, what enzyme is currently working? ______________________
c. Is topoisomerase needed for replication of this chromosome? ____________
d. Which of the following subunits are needed for DNA replication as shown? (d = deoxy)
(Circle)
ATP
cAMP
UTP
dGTP
ADP
dATP
e. Will telomerase be needed in an organism with only this chromosome? __________
f. Explain your answer for “e” in 1-2 sentences:
Biology 200, Autumn 2014
Practice Exam 2
7. The following diagram depicts the sucrose operon found in many species of prokaryotic
cells. SucA, SucB, and SucC code for enzymes involved in sucrose metabolism. SucR codes
for a repressor protein which binds to the operator of the sucrose operon and functions in a
similar fashion to the lac repressor. CBS stands for “CAP binding site”.
CBS
promoter
operator
SucA
SucB
SucR
SucC
a. What does the presence of the CAP binding site tell you about the promoter of this operon?
(Answer in 1-2 sentences).
b. The presence of which of the following molecules regulates this operon? (circle all that
apply)
glucose
lactose
sucrose
tryptophan
c. On the graph below, draw a line approximating the levels of SucA enzyme present in the cell
over time in the absence of sucrose and glucose. You ONLY NEED TO SHOW THE
GENERAL TREND OF EXPRESSION!
more
SucA
enzyme
little
Time
d. Imagine that the gene for the CAP protein were mutated so that CAP bound to the CAP
binding site and recruits RNA polymerase/sigma in the absence of cAMP. Under which
conditions would you see a constant high level of SucA enzyme expression? (Circle all that
apply and assume that there is an infinite supply of the sugars)
glucose alone
glucose + sucrose
sucrose alone
e. Briefly explain your answer to “d” in 1-2 sentences below.
lactose
Biology 200, Autumn 2014
8. In the diagram to the right, a cell is in the process of dividing.
Assume this cell is part of a DIPLOID organism.
Practice Exam 2
a) The diploid organism has a chromosome number
2N= _________.
b) This is a cell in: (Circle one)
Meiosis I
Meiosis II
Mitosis
c) The products of this division are: (Circle one)
diploid
haploid
d) Circle all of the following proteins that are being used in the cell above:
kinetochore proteins
histones
synaptonemal complex
microtubules (spindle fibers)
DNA polymerase
e) Name a cell in the testes in which you would find chromosomes arranged in the way
shown above.
f) Name a stimulus in a female that will trigger the completion of a cell division such as the
one shown above.
9. Imagine a newly discovered eukaryote on Earth that has long linear chromosomes that are
made purely of double-stranded RNA. These chromosomes have several origins of replication
each. In this new organism, replication is catalyzed by an enzyme very similar to the RNA
polymerase that carries out transcription. This enzyme can use RNA as a template.
a. Which of the following proteins would you need in this new organism for complete
chromosome replication? (Circle ALL that apply)
Initiator proteins
RNA topoisomerase
RNA telomerase
Primase
b. Would this organism still have a leading strand and a lagging strand at each replication
fork? Explain in a few words.
c. RNA polymerases cannot proofread. Will this new species have a higher, lower or same
mutation rate compared to other Earth eukaryotes? Explain in a few words
d. Compared to a normal eukaryote with the same length chromosomes, would this new
organism need more or less energy to replicate its chromosomes? Explain in a few words.
Biology 200, Autumn 2014
Practice Exam 2
10. Each description below describes a lab experiment performed with sea urchin gametes.
Place an X in the box for every event that you expect will occur in that experiment. If NONE
of the events occur, then put an X in the column labeled "none".
Experiment
Acrosome
Reaction
Cortical
Granule
fusion
Sperm
Nucleus
transfer
Frequent
Polyspermy
None
a. Normal gametes are mixed in normal
seawater
b. Normal gametes are placed in Ca++ free
seawater
c. Sperm without bindin proteins are mixed
with normal oocytes
d. Oocytes that have nothing in their cortical
granules are mixed with normal sperm
e.Oocytes that have no fertilizin molecules
are mixed with normal sperm.
f. Oocytes are injected with Ca++, no sperm
are added.
11. Check the appropriate boxes based on the cell cycle diagram. Check
as many boxes as apply. All descriptions will have at least one answer,
some more than one.
Description
a. Phase when histone acetyltrans-ferases
(HATs) have very low activity.
b. Phase when DNA polymerase I is
active
c. Phase when the cell checks that
organelles have been duplicated
d. Phase when tumor suppressors are
most active
e. Phase that is skipped during meiosis II
f. Follicle cells will go through this phase
during follicle development
g. Phase in which sister chromatids
separate.
M
G1
S
G2
Biology 200, Autumn 2014
Practice Exam 2
12. a. Consider the first two columns of this table and predict the mutant protein's activity
(compared to wild-type) in the third column.
Protein that is mutant
Type of mutation
I. Transcription factor
(TF)
Early stop (nonsense)
mutation in 2nd codon
II. Histone
acetyltransferase (HAT)
III. Histone deacetylase
(HDAC)
Is protein activity higher
or lower than normal?
Single base-pair
insertion in 4th codon
The HAT acetylates
histones of a tumor
suppressor
The HDAC
deacetylates histones
of a proto-oncogene
3 base-pair insertion that
ultimately prevents the
protein's degradation
b. Now consider each protein's function in the last column. In which
case will the mutation be most likely to lead to cancer? (Circle ONE)
Wild-type (normal)
protein function
The TF activates a
proto-oncogene
I
II
III
c. Explain your answer to 'b' in 1-2 sentences:
13. The trapezoid below represents a small portion of the wall of a seminiferous tubule shown
over time. The cells in each of the panels are all originally derived from cell A in the first panel.
All daughter cells are shown.
Outside of tubule
A
B
D
C
E
Lumen of tubule
For each question, answer with the letters A-E. Some answers will only have one
letter, some more than one, and not all letters will necessarily be used.
a.Which cell(s) are diploid? ________________
b. Which cell(s) are going through mitosis? ________________
c. Which cell(s) are at the same stage as the large cell labeled G in the drawing? __________
d. Which cell(s) will have active DNA polymerase III? _______
e. In which cell(s) are homologous chromosomes paired before cell division?________
G
Biology 200, Autumn 2014
14. Follicle cells in mammalian ovaries have estrogen receptors that bind to
estrogen (shown to the right). Estrogen stimulates follicle cells to divide
as the follicle grows.
Practice Exam 2
a. Considering the highly hydrophobic structure of estrogen, where are
estrogen receptors most likely found in the cell? (Circle one)
- inside cell
- crossing the cell membrane with an extracellular and intracellular side
b. Imagine that a transcription factor is activated by the presence of estrogen and then binds to
genes with an "ERE" – estrogen responsive element. Which of the following proteins most
likely is coded for by a gene that has an ERE? (Check ALL that apply)
____ ribosomal protein
____ transcription factor needed for ovary development
The diagram below shows a "map" of gene X, which has a single enhancer (the ERE shown).
Each number indicates a potential site for a three base-pair deletion. Site "3" is the first three
nucleotides of Intron 1.
Gene X
5'
3'
ERE
P
1
2
Exon1
Intron1
3
Exon2
4
Intron2
Exon3
3'
5'
5
For questions c-e, list all the mutations that apply. (Assume each mutation occurs alone)
c. Which of the mutations could change the sequence of the processed mRNA? _____________
d. Which of the mutations could change the number of processed mRNA molecules? ________
e. Which of the mutations could change the sequence of the protein? _______________
f. Gene X codes for a protein that is critical for the zygote's first cell division. If mutation "4" of
gene X occurs only in follicle cells, but not oocytes, could it have an effect on zygote
development? Explain in a few words.
Biology 200, Autumn 2014
Practice Exam 2
15. The diagrams below show cells with the Lac Operon and Lac I (gene for the repressor) on a
chromosome and a second Lac Operon and Lac I gene introduced on a plasmid. Determine
the level of β-galactosidase protein production in each cell type under the described
conditions. In each blank write either "+" for significant production and "-" for very little or no
protein production.
a.
P LacI
CBS P O LacZ
(chrom.)
P LacI
CBS P O LacZ
In this cell, all DNA sequences are wild-type (there are no
mutations).
glycerol alone: ____ glucose alone: ____ lactose alone: ____
(plasmid)
b.
P LacI
CBS P O LacZ
(chrom.)
P LacI
CBS P O*LacZ
(plasmid)
c.
P LacI
CBS P O LacZ
(chrom.)
P LacI*
CBS P O LacZ
In this cell, all DNA sequences are wild-type, except for the
operator sequence on the plasmid which has changed so it
no longer binds to the repressor protein.
glycerol alone: ____ glucose alone: ____ lactose alone: ____
In this cell, all DNA sequences are wild-type, except for the LacI
gene on the plasmid, which has a mutation that makes the
repressor protein no longer able to bind DNA.
glycerol alone: ____ glucose alone: ____ lactose alone: ____
(plasmid)
16. Imagine a "Pi repressor" that binds to DNA when not bound to Pi (inorganic phosphate),
and releases when bound by Pi. Genes for which of the proteins below would likely have the
DNA binding site for this repressor? (Check the blanks of all that apply)
______ Release factor
_____ Tumor suppressor protein that
functions during G1
_____ Enzyme that converts amino acids
to an intermediate of glycolysis
______ DNA polymerase I
Biology 200, Autumn 2014
Practice Exam 2
17. In the lab, you have three different plasmids, each containing a different version of the LacI
gene (that codes for the Lac Repressor protein).
Types of mutations:
a. Match the repressor structure with the most likely LacI
1. frame shift early in coding
gene mutation. Each type of mutation will be used once.
sequence
______ Repressor protein A: has normal protein sequence
2. silent mutation in 4th codon
______ Repressor protein B: cannot bind lactose, but it
3. Single amino acid change
can bind the operator
(missense)
______ Repressor protein C: binds neither lactose nor DNA
b. You insert the mutant LacI genes from above into normal E. coli bacteria that already have
their own wild-type LacI gene and wild-type Lac Operon on their chromosomes. Predict the
amount of
β-galactosidase enzyme production in each cell by writing a "-" for low or no production, and a
"+" for high production.
Cell type
Lactose
alone
Glucose
alone
a. Normal E. coli with no plasmid added
b. Normal E. coli with Repressor A added
c. Normal E. coli with Repressor B added
d. Normal E. coli with Repressor C added
e. E. coli cell which ONLY has Repressors
B and C
18. Write the letter for the ONE BEST choice that describes what happens in a eukaryotic cell
with each mutation below, using the letters in the box. Not all choices will necessarily be used.
_____ HAT (histone acetyltransferase) enzyme is less active
Choices:
_____ Intron splice site is deleted at the beginning of an intron
A. Increase in gene expression
_____ Enhancer element deleted that is 1000 base pairs upstream
of (before) the promoter
_____ Deletion of 4 base pairs within exon 3 of a gene with
5 exons
B. Decrease in gene expression
C. Protein sequence change
D. No changes
_____ Deletion of 4 base pairs in the middle of intron 3 in a gene with 5 introns
_____ Regulatory transcription factor that activates formation of the transcription complex
now has a stronger binding site for mediator proteins.
Biology 200, Autumn 2014
FOR REFERENCE ONLY:
Practice Exam 2