Download Exam 2 Full v4A Bio200 Sum12

Biology 200, Summer 2012
Exam 2
VERSION A
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Name: _________________________________
Section: _______ TA: _________________
Biology 200
Summer Quarter 2012
Exam #2
DO NOT OPEN EXAM UNTIL DIRECTED TO DO SO
Make sure you have 6 pages, including this one. Print your name and information on ALL pages.
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exams are acceptable, but it is often difficult to give full credit to penciled answers on regrades.
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When asked, provide concise and clearly written answers. We may deduct points if you do not
fully answer the question or if your answer is too vague or too confusing for us to follow. Extra
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this first page. Indicate “on first page” where necessary.
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Biology 200, Summer 2012
Exam 2
Name: _________________________________
Section: _______ TA: _________________
1. (18 points) Fill in the blank
For each, write TWO different answers that fit the description given. Be as specific as possible. It is
acceptable to use the same answer for different questions. The full 3 points will be awarded for a correct pair
of answers (+1 for a single correct answer).
Ex)
A type of gene implicated in cancer
i. tumor suppressor
ii. oncogene
progression or mutation
a)
A metabolic energy carrier that is utilized before i. __________________ ii. __________________
the linking step and after glucose phosphorylation.
b)
An alternative to aerobic respiration
that occurs in the absence of oxygen.
i. __________________ ii. __________________
c)
A transcription factor.
i. __________________ ii. __________________
d)
A molecule with lower redox potential than
the electron-carrier Q (ubiquinone).
i. __________________ ii. __________________
e)
Growth media conditions that result in very
i. __________________ ii. __________________
little ß-galactosidase production.
2. [15 points] Organelles
For each organelle, describe the function of an enzyme that you would expect to find at that organelle and not
in most other parts of the cell. The name of the enzyme is not necessary. You should mention a possible
substrate and a reaction that is catalyzed. Answer each in one sentence or less. Be as specific as possible.
Also, fill in the blanks with the number of the correct microenvironment that is created by the organelle. Each
can be used only one time. +2 for each answer enzyme, +1 for each microenvironment.
__7_Example) Chloroplast: Enzymes change small carbohydrates into
Microenvironments
larger carbohydrates using the energy from sunlight.
2) dilute & aqueous
3) acidic
6) basic
7) allows sunlight in
9) rich in lipid building
blocks
11) low in mutating agents
14) rich in traffic-directing
signal proteins
16) rich in motor proteins
17) non-cytoplasmic
protein folding conditions
____a) Rough ER:
____b) Golgi apparatus:
____c) Lysosome:
____d) Nucleus:
____e) Cytoskeleton:
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Biology 200, Summer 2012
Exam 2
Name: _________________________________
Section: _______ TA: _________________
3. [21 points] Gene Regulation
a) (6 pts) You are developing an understanding of the similarities and differences between prokaryotes and
eukaryotes. In 3-4 bullet points, describe 3 of the advantages that a single-celled prokaryote has over similar
eukaryotes. Be as specific, clear, concise and thorough as possible. Complete sentences are not necessary.
1.
2.
3.
100
b) (3 pts) The Silver gene promoter: (Check ALL true answers):
____ Binds basal transcription factors tightly
____ Binds basal trancription factors poorly
____ Binds to regulatory transcription factors all of the time
____ Is NOT a double-stranded region of DNA
AMOUNT of mRNA
The data graph shows the total cellular levels of mRNA from 4
Black
eukaryotic genes. Below the graph is a schematic of the transcription 80
and translation of the “Purple” gene. Each circle in the Purple
protein represents an amino acid.
Purple
60
Gold
40
Silver
20
5 min
10 min
15 min
Time
20 min
c) (3 pts) The Black gene is undergoing histone modification at Time 0. What type of change do you predict is
taking place and why? Enter the correct word choice into the following.
This causes [More or Less] acetylation of the histones? __________
This change in negative charges on the histone causes DNA to be [More or Less] tightly packed? ______
d) (3 pts) Imagine that over time, the Gold protein becomes more often targeted for modification by a
ubiquitin ligase. How would the level of the gold protein change over time and why? Check in front of ALL
correct answers.
___
___
___
___
Gold
Gold
Gold
Gold
protein levels stay steady because the mRNA level is steady
protein levels increase because Ubiquitin stabilizes proteins
protein levels decrease because ubiquitin marks proteins for degradation
protein levels are unpredictable because of the CAP protein
e) (3 pts) The Purple protein can have either 10 or 13 amino acids. There is
no change to the Purple gene DNA. Explain, including the location of the
mechanism in the cell, in one sentence or less.
DNA of Purple gene
Immature mRNA of Purple
gene
Purple protein
forms
f) (3 pts) Which statements could explain the Purple data over time? (Check in front of ALL correct
answers.)
____ At time 1 and 18, the conditions favor the activation of an enhancer protein for this gene
____ At time 12, the conditions favor the degradation of an enhancer protein for this gene
____ At time 1 and 18, the conditions favor the binding of a repressor
____ At time 12, the conditions favor the degradation of a silencer protein for this gene
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Biology 200, Summer 2012
Exam 2
Name: _________________________________
Section: _______ TA: _________________
4. (16 points) The Kev Operon
5'
3'
LBS2
LBS3
P
Or1
Or2
ATG KevX TAG ATG KevW TGA ATG
AUG
UAG AUG
KevP
TAA
UGA AUG
3'
5'
UAA
In the prokaryotic dsDNA shown above, Or1
and Or2 are operator sequences that can be bound by the repressor proteins R1 and R2, respectively. R1 and R2
are similar to the E. coli LacI protein. The coding regions for genes KevX, KevW and KevP are shown as well as
the DNA sequences that encode the start and stop codons for each gene.
LBS2 and LBS3 are DNA sequences that can be bound by the proteins T2 and T3, respectively. P is the
promoter for the Kev operon. The proteins KevX and KevW are used to synthesize temporary protective
proteins in the event of an attack by amoeba predators.
a) (4 pts) This organism can recognize when there are no amoebae present. The prokaryote will react efficiently.
When amoeba are gone: (Check in front of ALL correct answers.)
____ KEV X will be bound to LBS 2
____ T2 will be bound to LBS 2
____ R1 will be bound to OR 1
____ KEV Y will be bound to OR2
____ R2 will be bound to LBS 3
____ T2 will be bound to OR 2
b) (4 pts) A mutation is analyzed that alters the UGA codon to a CGA codon. What would be the consequence
of that mutation to the protein and to the cell? (Check in front of ALL likely consequences.)
____ The Kev mRNAs are produced normally
____ The Kev proteins are produced normally
____ The cell can fight amoeba normally
____ The Kev mRNAs have major errors
____ The Kev proteins have major errors
____ The cell is more vulnerable to amoeba
c) (4 pts) T3 is a protein that activates transcription of the Kev operon. T2 lowers expression of Kev mRNA.
Both proteins have DNA binding sites that are fairly similar (LBS2 and LBS3 have similar sequences). Besides
the DNA binding region, what is true about the T2 and T3 proteins? (Check in front of ALL correct answers.)
___
___
___
___
A surface of
A surface of
A surface of
A surface of
T2
T3
T2
T3
protein prohibits RNA polymerase binding
protein prohibits RNA polymerase binding
protein recruits RNA polymerase binding
protein recruits RNA polymerase binding
___
___
___
___
T2 allosterically inhibits T3
T3 allosterically inhibits T2
T2 is acting like the lac operon CAP protein
T3 is acting like the lac operon CAP protein
d) (4 pts) The KevP gene encodes a protein that can be released from the prokaryotes and digested by amoeba.
If not digested, this protein will diffuse back into the prokaryote and bind tightly between P and Or1. Why is
this logical for the regulation of Kev gene expression? (Answer in one sentence or less).
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Biology 200, Summer 2012
Exam 2
Name: _________________________________
Section: _______ TA: _________________
5. [21 points] Cellular Respiration
Shown below are several sets of 3
components from aerobic respiration. Put
each set in correct order by labeling the first
of the set with a “1”, second = “2”, 3 = last.
You must have the entire order correct for
credit, but there may be multiple correct
orders for a single set. (3 points each)
Example)_1_Glucose __3_ Krebs Cycle _2_Pyruvate
a)___ ATP synthase
___ Linking step
___ Q electron transporter
b) ___ Acetyl-CoA
___ proton motive force
___ commitment step
c) ___ production of water
___ FADH2
___ pyruvate
d) ___ cytoplasmic NADH
___ production of CO2
___ Complex IV
e) ___ cutting a carbohydrate into two pieces
___ a series of oxidation reactions
___ transport into the mitochondria
e) (3 pts) Eukaryotic mitochondria require a huge amount of ADP in order to create ATP. Where does
all of that cellular ADP come from? Answer in 2 sentences or less.
f) (3 pts) Choose one of the two statements below. Disagree with the statement, and support your
argument. Make your case in 2 sentences or less. You only need to complete one argument.
Statement #1: The purpose of the Kreb’s cycle is to oxidize carbon-containing molecules.
Statement #2: A eukaryotic organism would rather consume pyruvate than glucose.
I disagree with statement # ____ because:
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Biology 200, Summer 2012
Exam 2
Name: _________________________________
Section: _______ TA: _________________
Take Home: Cancer History
Cancer is a complex and extremely diverse system of related diseases. We know that these diseases are the
result of multiple mutations in cells causing an array of intracellular changes. No single mutation is cancer.
Somehow, the combinations of multiple changes lead to malignant unregulated cell growth.
6. (8 points) Your task is to define a few possible mutations that could contribute to cancer. For each
mutation, you should indicate as specifically as possible how the mutation occurred, where in the cell and in
the body the mutated cell is located, and the mechanism that allows this mutation to lead to cancer. Be
creative where necessary. You should do this in less than one sentence for each mutation (If necessary, you
can use two short sentences). Research outside of Bio200 lectures and labs is not necessary, but is allowed if
you want to find specific examples of parts of this question. Show the diversity of what you know: mutation
descriptions should be as different from each other as is possible while still being specific and correct.
Example) This mutation is in a gene that encodes a signaling molecule to start apoptosis.
A random DNA polymerase III error in a white blood cell’s signal receptor gene causes the loss of
social control so that the cell won’t kill itself when it picks up further DNA damage.
a) This mutation is in a gene that either encodes a cytoskeletal molecule or an enzyme that works on a
cytoskeletal molecule.
b) This mutation is in a gene whose product works in or travels through the Golgi apparatus.
c) This mutation affects the passage of the cell through the cell cycle.
9. (4 points) Given the mutations you’ve described, imagine a cell with all three mutations. Write a description
of an additional mutation that would be needed for this cell to progress further towards outright malignant
cancer. Again, a single sentence should be enough room to be specific, creative, and correct.
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