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Biology 200, Summer 2014
Exam 2
Name: ________________________________________
Section: (circle one) A or B
TA: _______________
Biology 200
Summer Quarter 2014
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.
Page
Points Awarded
2
out of 20 points
3
out of 22 points
4
out of 21 points
5
out of 20 points
6: Take
home
out of 17 points
Total:
out of 100 points
Exam 2
Name:_____________________________
1. [20 points] Co-regulation of Deinococcus radiodurans genes
The two promoters in this region of dsDNA produce proteins that regulate each other’s transcription.
Promoter->
ecA6
EcA6
GAT fdd2
GTA AAT
GAU fdd2
GUA AAU
Fdd2
fdd1
fdd1
GTA
<-Promoter
GUA
Fdd1
The EcA6 protein binds tightly at the site indicated by a triangle ( ).
The Fdd2 protein binds at the site indicated by a diamond ( ). There are two primary physical surfaces on
the Fdd2 protein: one that binds to DNA and one that binds very well to RNA polymerase.
The Fdd1 protein is an enzyme needed for metabolism of glucose.
/6 a) Explain the regulation of these two promoters shown in terms of the molecular mechanisms
that increase or decrease gene expression. Specifically discuss the effects this will have on expression.
Answer in 3-4 sentences, max.
/4
b) Briefly describe a simple experiment to determine which promoter is the strongest.
Answer in 1-2 sentences, max.
/3
c) Mark the single correct statement:
_____ The eca gene is an operon which is constitutively expressed.
_____ The fdd gene is an operon which is not constitutively expressed.
_____ The eca gene is a promoter which is not constitutively expressed.
_____ The fdd gene is a promoter which is constitutively expressed.
/3 e) Deinococcus cells occasionally acquire DNA mutations in which a single base pair is inserted.
At which of the locations above with a “ “ will an insertion mutation have little or no effect?
Clearly circle two stars.
/4 d) In the lac operon: Two kinds of DNA mutations can disrupt negative regulation of lactose
metabolism. What are they?
Draw/diagram your answer clearly here.
Page 2 of 6
Total: _____
Exam 2
Name:_____________________________
2. [17 points] Glycolysis and the Krebs Cycle
/4 a) Identify the parts of the diagram
where an oxidation/reduction reaction is happening.
Put a small star at each redox reaction.
/4 b) If a normal e. coli cell could find a plentiful
source of one molecule to metabolize, which would
be the most beneficial? Circle one molecule in the
diagram, and explain why in 1-2 sentences or less.
/4 c) Indicate an example of useful feedback
inhibition. Add this to the diagram with clear labels.
/5 d) Imagine a mutation that makes this enzyme
non-functional. What will happen to the cell?
Describe the first molecular effect and longer term effects in 1-2 sentences, total.
3. [5 points] Molecular derivation of dominance/recessiveness
A species of basilisk (a diploid lizard) has at least two phenotypes for water-running ability. The relevant gene has three
different alleles: P, Q, and R. The R allele produces a normal enzyme that codes for a functional protein that is part of the
webbing between hind toes. The P allele codes for a 36% stronger and more elastic webbing protein capable of producing
more running force on water. The Q allele produces an enzyme that rapidly cleaves products of the P, Q and R alleles.
/5 a) Which allele is dominant to the other two alleles based on the phenotype? Explain or diagram
clearly how you know this.
Page 3 of 6
Total: _____
Exam 2
Name:_____________________________
4. [8 points] Cell cycle
/4 a) Which would be worse for a unicellular eukaryote: A mutation in which Rb was 72% stronger
in binding to E2F, or a mutation in which Rb never binds to E2F?
Answer in 1-2 sentences, max.
/4 b) Cyclin-dependent kinase is most active only after being bound to cyclin. Why is this useful
for the cell? Mark all correct answers:
____ CDK is controlled by a regulatory phosphate that is altered by cyclin binding.
____ CDK levels are too consistent to regulate the cell cycle correctly without cyclin.
____ CDK does post-translational modifications that are fast enough to regulate the cell cycle.
____ CDK has a tertiary structure that is unchanged by cyclin.
/5
5. [13 points] Respiration
a) Describe the chemical reaction shown. What part of the overall respiration scheme is it? Why
is this part of the respiration scheme especially useful? Answer in 1-2 sentences, max.
Carbohydrate intermediate + NADH  Alcohol + NAD+
/4 b) A new drug is advertised as a cure for obesity. This drug is a 2% inhibitor for a single enzyme
in respiration. You decide not to invest in the company. Why? Answer in 1-2 sentences, max.
/4 c) Which mutation would be most beneficial for most eukaryotes? Mark the single best answer.
_____ Fermentation starts whenever glucose is available.
_____ ATP synthase is translated in large quantities in the cytoplasm.
_____ The linking step proceeds without its normal redox reaction.
_____ All hydrophobic tails in mitochondrial membranes are lengthened.
_____ Excess ATP is not stored as fat.
_____ FADH2 is instantly and freely converted to NADH.
Page 4 of 6
Total: _____
Exam 2
6. [20 points] Tuning levels of Clvnd protein
The concentration of the protein Clvnd in
eukaryotic cells is dynamic and controlled by a
group of 6 genes. Details of these genes are to the
right. Use this data to answer the questions
below.
/4 a) Either Mntr or AkrN codes for a histone
acetyl transferase. Which is it? Explain why you
know in 1-2 sentences, max.
Name:_____________________________
Gene Name
Knockout mutant
Mechanism
Mntr
Increases [Clvnd]
?
AkrN
Decreases [Clvnd]
?
Clbs5.1
Increases many [x]s
?
LakeE
?
Splicing modulator
349.4
?
microRNA gene
michless
?
?
/4 b) Clbs5.1 is a gene that codes for part of the proteasome. Cells without Clbs5.1 have higher
levels of some but not all proteins in the cell. Explain why in 1-2 sentences, max.
/4 c) LakeE proteins are enzymes. What specific chemical reaction is catalyzed at their active sites?
Be specific in 1 sentence, max.
/4 d) The Michless proteins usually increases Clvnd expression. However, the increase is lost if the
chromosome is mechanically pulled straight. Explain why in 1-2 sentences, max.
/4
e) : Mark all that are true:
_____ The 349.4 gene is involved in one of the most efficient ways to regulate Clvnd expression.
_____ Regulation by 349.4 is not possible without the RISC complex.
_____ 349.4 can’t change the concentrations of any protein that has been injected into the cytoplasm.
_____ The gene for 349.4 is unlikely to encode a start codon.
Page 5 of 6
Total: _____
Exam 2
Name:_____________________________
Page 6 of 6
Total: _____
Exam 2
Name:_____________________________
[17 points] 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 obviously your own. Neatness and clarity are important. Course staff
(TAs, Ben, or Kyle) 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. Creativity will help.
/17 7) Build a visual diagram as a teaching tool for future students to study the Electron Transport Chain and
Oxidative Phosphorylation. This diagram should be readable and interpretable by an unguided Bio200 student
who has not yet studied cellular respiration but understands central dogma, gene regulation and biomolecules.
Diagrams will be graded on the following rubric:
5 pts: The diagram contains all elements of the Electron Transport Chain correctly and clearly labeled
5 pts: The static diagram accurately and depicts the flow and motion of electrons and protons
3 pts: The intended audience would find this diagram clear, concise and a good stand-alone learning tool
2 pts: The diagram accurately demonstrates some aspect of eukaryote-specific gene regulation on the ETC
1 pt: The diagram contains reference to some difference between prokaryotic and eukaryotic gene regulation
1 pt: The diagram differs from the standard side-cut of membranes that we see in most textbooks and lab materials
Special note: Mitochondria have their own DNA, which is probably due to their evolutionary origin as independent cells.
More information is available on Page 560 of Freeman, and Wikipedia is a good resource for this particular topic. It is not
strictly necessary to present this information in your diagram, but it may be useful.
Page 7 of 6
Total: _____
Exam 2
Name:_____________________________
NOTE: You can use this page, you can adjust this page to give yourself more space. Typed answers
in fonts bigger than 10-point are helpful graders. Neat hand-drawn responses are perfectly OK.
Page 8 of 6
Total: _____