Biology 200, Summer 2013
Exam 2 Version C
Name: _________________________________
Section: _______ TA: _________________
Biology 200
Summer Quarter 2013
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.
 Please use a pen. Pen is much easier to read, even with extensive crossing-out. Pencil-written
exams are acceptable, but may not receive full credit to penciled answers on regrades.
 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
information, if incorrect, will lose points.
 Limit your answers to the space provided. If you need extra space, you can use the bottom of this
first page. Indicate “on first page” where necessary.
STOP
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Biology 200, Summer 2013
Name: _________________________________
Exam 2 Version C
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).
Example) A type of enzyme that can create a
post-translational modification
i.
kinase
ii. Ubiquitin ligase
a) A component of the cell cycle that is altered i. __________________ ii. __________________
by phosphorylation.
b) A component of cellular respiration that
i. __________________ ii. __________________
is a by-product in creation of an energy carrier.
c) A reason that a cell might want to stop
before going through a cell cycle checkpoint.
i. __________________ ii. __________________
d) Any part of respiration in which there is a
transfer of a phosphate between molecules.
i. __________________ ii. __________________
[describe as best you can]
e) A positive regulator of passage through
the cell cycle.
i. __________________ ii. __________________
f) An alternative pathway to aerobic
i. __________________ ii. __________________
respiration that might be used at thermal vents
at the bottom of the ocean.
Data for use with Question 2)
mRNA levels
Protein levels
140
Fed3
fed3
Number of proteins
(in tens of molecules)
Number of mature mRNAs
(in tens of molecules)
55
45
35
25
eps41
immC4
luk8.1
15
120
100
ImmC4
80
Luk8.1
Silver
60
Silver
5 min
10 min
15 min
Time
20 min
Page 2 of 6 of Version C
Eps41
5 min
10 min
15 min
Time
20 min
Biology 200, Summer 2013
Name: _________________________________
Exam 2 Version C
Section: _______ TA: _________________
2) [22 points] Eukaryotic Gene Regulation: Interpreting data curves
For 2a-f, answer the multiple-choice or written-answer question by referring to the data on page 2.
The two charts assess different levels of central dogma products from genes named ‘Eps41’, ‘Fed3’, ‘ImmC4’ and ‘Luk8.1’. The charts
refer to the same interval of time within a single cell. The first chart shows RNA levels, while the second chart shows the protein levels
of the same 4 genes as in the first chart.
a) [4 points] i. A histone-regulating enzyme is actively catalyzing reactions at the fed3 gene location
on a chromosome.
This protein is ___________ the histones at the fed3 gene region. Circle one: deacetylating acetylating
This causes DNA near fed3 to be _______. Circle one: Loosely packed
Tightly packed
b) [4 points] If all of the proteasomes are removed from a cell, then we would see Fed3 protein levels
steadily increasing. The other three protein levels are unaffected. Hypothesize why, including any
changes to the Fed3 protein. Be as thorough as possible in 1-2 sentences.
c) [3 points] Two enzymes are activated during this interval. These enzymes make changes to the
eps41 mRNA structure, which affects the life span of the mRNA. Circle the best two choices:
At 5 min: An enzyme adds 5’ caps to many eps41 mRNAs
At 5 min: An enzyme removes 5’ caps from many eps41 mRNAs
At 15 min: An enzyme removes a string of nucleotides from the 3’ end of many eps41 mRNAs
At 15 min: An enzyme adds a 3’ caps to many eps41 mRNAs
At 15 min: An enzyme adds string of nucleotides to the 3’ end of many eps41 mRNAs
d) [4 points] Your lab partner develops the following hypothesis:
“The ImmC4 protein could turn on transcription of a microRNA specific to the luk8.1 gene.”
Does this make sense? Explain what is happening to the luk8.1 mRNA in 1-2 sentences.
e) [4 points] Luk8.1 proteins bind to the DNA on the same chromosome as the fed3 gene. How does
Luk8.1 affect Fed3 protein levels? Explain what the molecules are doing in 1 sentence.
f) [3 points] Choose the most likely explanation for the data on ImmC4:
Proteins are being translated slowly and are never damaged nor degraded
Transcription is increasing and proteins are never degraded
Both transcription and translation are decreasing
Translation is increasing but degradation of the protein is increasing even more
Protein degradation is constant but slower than translation
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Biology 200, Summer 2013
Name: _________________________________
Exam 2 Version C
Section: _______ TA: _________________
3) [21 points] Prokaryotic Gene Regulation: The grc operon
This partial diagram of a chromosome is found only in rare bacteria. The operon produces 3 proteins.
LF2
LF3
Or1
Promoter
Or2
ATG grcZ TAG ATG grcY
In the double-stranded DNA shown, Or1 and
AUG
Or2 are operator sequences that can be bound by
the repressor proteins Q4 and GrcP, respectively.
GrcP functions extremely similarly to the LacI protein.
UAG AUG
TGA ATG
grcP
TAA
UGA AUG
GrcZ
GrcY
UAA
GrcP
LF2 and LF3 are DNA sequences that can be bound by the constitutively-expressed protein H3 and the regulated protein
GrcY, respectively. GrcZ and GrcY are enzymes that catalyze the two reactions needed to synthesize lactose from lipid
precursor molecules previously stored in the cell. In the rare bacteria with the grc operon, lactose is only synthesized
when neither glucose nor lactose is available from the environment.
a) [3 points] The protein GrcP will be bound to the DNA at the Or2 site at which conditions in the cell?
Circle the single best answer for the most GrcP binding at Or2.
Low glucose and low lactose
High lactose and low glucose
High glucose and high lactose
Low lactose and high glucose
b) [6 points] The protein H3 has three binding surfaces. Increased H3 binding to LF2 leads to higher levels of
transcription. Explain what each of these binding surfaces does, in one sentence or less each.
1.
2.
3.
c) [3 points] When GrcP and Q4
are bound to the DNA, transcription levels are the same as if only GrcP
is bound to the DNA. Explain why, in 1 sentence or less.
d) [3 points] A
mutant cell develops a much stronger promoter. Researchers are excited to investigate,
but are shocked to find that the mutant strain cells die before it can be studied fully. Why?
Circle the single best answer: The mutant cannot make lactose and cannot run metabolism reactions
The mutant makes too much lactose and does too much respiration
The mutant cannot make a protein and misses an important step
The mutant makes too many proteins and is less efficient
The mutant makes mutated proteins and has problems with inhibition
e) [3 points] Put
a star on the diagram on 4 different locations where a mutation could lead to faster
synthesis of lactose when conditions in the cell change.
f) [3 points] Why
is it a good idea for GrcP to act as a repressor? Explain in 1 sentence or less.
Page 4 of 6 of Version C
Biology 200, Summer 2013
Exam 2 Version C
Name: _________________________________
Section: _______ TA: _________________
4) [22 points] Respiration chart for putative Martian life
The first number is the number for the new bacteria-like organism on Mars.
The second number (in parentheses) is be the normal number for prokaryotic life on Earth for reference.
Pathway
Glycolysis
Linking Step
Krebs Cycle
TOTALS
CO2
0 (0)
4 (2)
2 (4)
6 (6)
NADH
2 (2)
2 (2)
4 (6)
8 (10)
Net ATP made by substrate
level phosphorylation
FADH2
0 (0)
2 (0)
2 (2)
4 (2)
4 (2)
0 (0)
2 (2)
6 (4)
ATP eventually made by oxidative phosphorylation
From NADH
From FADH2
2.8 (4.8)
4.8 (4.8)
9.6 (14.4)
17.2 (24)
0 (0)
3 (0)
3 (3)
6 (3)
a) [6 points] Name two places in Martian metabolism that have extra steps as compared to Earthling
metabolism. Name these steps in less than one sentence each.
i.
ii.
b) [3 points] Circle the single best answer: In terms of ATP per glucose molecule:
Martian cells have a more efficient metabolism
Earthling cells have a more efficient metabolism
Martian and Earthling cells have equally efficient metabolisms
There is no way to tell a difference in metabolism efficiency
c) [3 points] Somewhat surprisingly, you find that Martian cells can use fermentation. Is Martian fermentation or Earthling
fermentation more efficient? Explain why in 1 sentence.
d) [3 points] Circle the best answer: Compared to Earthling linking steps, the Martian linking step is:
Superior, because it produces more CO2
Superior, because it produces less CO2
Superior, because it produces more FADH2
Superior, because it produces less FADH2
e) [3 points] Circle all correct answers. On Earth, which of these molecules are used by the cell as energy carriers?
Glucose
Fructose
NADH
FADH2
ATP Synthase
CO2
Acetyl-CoA
Complex IV
H2O
f) [4 points] You believe that Martian organisms have organelles. Give evidence for this from the chart above.
Be as specific as possible in 1 sentence, maximum.
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Biology 200, Summer 2013
Exam 2 Version C
Name: _________________________________
Section: _______ TA: _________________
This take home portion should be completed before the exam and turned in at the start of the exam. You can work with
other students, but your words must be your own. Neatness and clarity are important. Course staff (TAs, Ben, or Dan)
will politely refuse to answer questions that directly relate to this take-home portion. You can remove the instructions on
this sheet if you want more room on your version to turn in. Please limit answer to a single page, total.
5) [17 points] A Diagram of Respiration Alleles
To complete this take-home question, you will create 3 mutation alleles. Each will be a mutation of
some part of the respiration machinery in a cell. To display and explain your mutations, you will build
diagrams with pictures, labels, and anything else you need to clearly demonstrate the mechanism of your
mutations and how this affects their phenotypes and heritabilities.
Each diagram should be primarily pictorial. Any labels or written words should be less than complete
sentences. Each diagram should clearly show the phenotypes that are inherited and should be labeled as
Recessive/Dominant/CoDominant. Use these diagrams to display your understanding of the respiration
machinery in general: the best diagrams will include mutations from different parts of cellular respiration to
display the breadth of your understanding.
Artistic talent is not required. Use of color or any other medium that fits on a single page is acceptable
but not necessary. Prioritize clarity over realism. All diagrams should be obviously different than any
published diagrams in any textbook or website or the example below. You can work with other students, but
make sure that your final work is obviously your own.
Example:
Dominant Mutation:
ATP
synthase
Cell
mRNA
DNA
Missense
mutation
Phenotype:
Whether or not it makes enough ATP to
turn flagella and move towards food
ADP + Pi
ATP
Synthase
Gene
Can’t spin
as easily
30% less ATP
produced
Flagella needs 95% of WT
ATP load to move
Evaluation:
4 points: Creating and clearly explaining a correct and reasonable dominant mutation with a clear phenotype.
4 points: Creating and clearly explaining a correct and reasonable recessive mutation with a clear phenotype.
4 points: Creating and clearly explaining a correct and reasonable codominant mutation with a clear phenotype.
5 points: Building a set of diagrams that displays the breadth of your knowledge of cellular respiration.
NOTE: You can use this page, or you can adjust this page to give yourself more space. Typed
answers in fonts bigger than 10-point are helpful to the grader.
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