DO NOT OPEN EXAM UNTIL DIRECTED TO DO SO
 Make sure you have 4 pages of questions and six pages total.
o Turn in only the last page. You can keep the rest of the exam or recycle it.
o Each question on this exam is worth 5 points each.
 Mark all multiple-choice answers on your Scantron sheet using a #2 pencil. Please make sure to include
your Student ID number correctly. Questions with multiple-choice answers are marked with numbers.
 Mark all written answers using a pen on the last page of this exam only. Questions with written answers
are marked with letters.
 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.
 For all numbered questions: Choose only the single best answer.
Codon Table
Second Position
U
UUU
U
UUC
UUA
UUG
Phe
Leu
C
A
G
CUC
CUA
Leu
UCU
UCC
UCA
A
UAU
Ser
UAC
A
UGG - Trp
G
CCU
CAU
CGU
U
CCC
CCA
Pro
CAC
CAA
ACU
AAU
ACC
Thr
AAC
AUA
ACA
AUG - Met
ACG
AAG
GUU
GCU
GAU
GUA
GUG
C
UGA - Stop
AUU
Val
U
UAG - Stop
CAG
GUC
UGC
Cys
UAA - Stop
CCG
Ile
UGU
Tyr
UCG
CUG
AUC
G
GCC
GCA
GCG
Ala
AAA
GAC
GAA
GAG
His
Gln
Asn
Lys
Asp
Glu
CGC
CGA
Arg
CGG
AGU
AGC
AGA
AGG
GGA
GGG
A
G
Ser
Arg
GGU
GGC
C
U
C
A
G
U
Gly
C
A
G
Third Position
First Position
CUU
C
[20 points] Respiration and molecular genetics
/5
1) In a new species of unicellular eukaryote, only one of these mutations is lethal. Choose the
single mutation that is most likely to be quickly and completely lethal.
1a) The ATP made in the Krebs cycle is transported instantly to the cytoplasm.
1b) A third mitochondrial membrane is formed within the matrix but containing no Krebs enzymes.
1c) FADH2 is produced by the Krebs cycle but now carries slightly higher-energy electrons.
1d) ATP synthase transports H+ and produces ATP, but does with the opposite spin direction.
1e) Enzymes in the space between mitochondrial membranes convert protons into larger molecules.
/5
2) Which version of ATP synthase is most likely to improve overall ATP yield?
2a) An F1 region that has four binding sites for ADP and Pi.
2b) An F0 region that can move out of the membrane into the mitochondrial matrix.
2c) A proton-binding pocket that can also bind and transport rare lithium ions instead of protons.
2d) Fused F1 and F0 that cannot rotate independently of each other.
2e) A catalytic region that binds only to the substrates ATP and Pi.
/5
3) Which change is most likely to improve the fitness of a eukaryote that is producing ATP via
fermentation?
3a) A cellular injection of a large concentration of FADH2 into the mitochondrial matrix.
3b) An increase in the concentration of glucose-1-phosphate outside of the cell.
3c) A cellular transplantation of molecular oxygen from the mitochondrial matrix into the cytoplasm.
3d) A cellular injection of glucose into the cytoplasm.
3e) A loss-of-function mutation in the enzyme that produces NAD+.
/5
A) Write your answer to this question on the last page.
While prokaryotes are typically haploid, it is possible to bioengineer an E. coli cell with partial
diploidy. For this example, a wild-type cell has been injected with a single gene. This gene contains a
working promoter and the reading frame encodes a mutant version of the lac repressor protein that
can bind to either lactose, glucose, or the operator sequence. You know from previous breeding
experiments that this mutant allele is recessive to the wild-type allele. Explain this
dominant/recessive relationship at the molecular level. Explain in 2-3 sentences, max.
Page 2 of 6
P
P
CDK
P
Cyclin
+
CDK
Cyclin
[20 points] Respiration and prokaryotic gene regulation
P
Rb
Growth factors
E2F
Rb
E2F
S-phase
Choose the single best answer for each multiple choice question.
/5
4) Which of the following is true about the molecules regulating the G1-to-S checkpoint?
4a) E2F binds directly to cyclin when the concentration of cyclin is low.
4b) E2F binds more tightly to Rb than to the promoters of S-phase-related genes.
4c) Rb is likely to bind to all transcriptional regulator proteins.
4d) Transcription of Rb is activated in the presence of CDK.
4e) CDK-dependent phosphorylation does not change the shape of the Rb protein.
/5 5) In a prokaryote, which of the following mutations would give a fitness advantage over the
wildtype allele?
5a) A factor that blocks translation of ETC complex proteins if the cell is storing ATP energy.
5b) A gene that helps to store pyruvate by increasing activity of the linking step enzyme when
glucose is low.
5c) A protein that blocks production of NADH when the cell has run out of FADH2.
5d) A protein that helps to transcribe the gene encoding the ATP synthase enzyme only when there is
no proton gradient across the inner mitochondrial membrane.
5e) A function-decreasing modification to the protein that holds together the structure of the
mitochondria when the cell is crawling rapidly.
/5
6) Dusk and dawn are relatively long events to microorganisms. The most successful marine
microorganisms are able to live using only weak sunlight to harvest small amounts of energy. Which
kind of gene regulation would you expect to see in light-to-dark regulation transitions?
6a) Changes in transcriptional regulation by altering RNA polymerase recruitment
6b) Changes in translational regulation
6c) Changes in post-transcriptional regulation by physical modifications to proteins
6d) Changes in post-transcriptional regulation by physically destroying proteins
6e) Changes in protein structure by alternative splicing
/5
B) Write your answer to this question on the last page.
Draw and label a rough energy diagram for the complex set of reactions that proceed from glucose
entering a cell until the final production of ATP. In this diagram, show:
 The level of energy of the intermediate molecule, making sure to indicate the overall trends
 Note at least two different kinds of energy being used (chemical, gradient, mechanical, etc)
Page 3 of 6
[20 points] Superhero Gene Regulation
Genetic analysis of Superwoman’s and Superman’s cells have revealed a crucial finding: Their
superpowers are brought on by a relatively simple combination: All cells have extremely high levels
of expression of the genes that aid in either glycolysis or the Krebs cycle. Scientists are attempting to
bioengineer superpowers into human cells, and they have asked for your advice.
/5
7) Which of these mutations is most likely to increase expression of part of glycolysis or part of
the Krebs cycle? Mark the single best answer.
Example: Increased expression of all HDAC-encoding genes in the cell.
7a) Changing the splicing pattern of the gene encoding ATP synthase.
7b) Producing a new micro-RNA that binds to the mRNA for the gene for Complex II
7c) A deletion in a silencer binding site related to the promoter for the linking step enzyme.
7d) A new Ubiquitin tagging site on a Krebs cycle enzyme.
7e) A change causing a single histone protein to be more negatively charged.
/5
8) Which enzyme is important for a metabolic step in which energy is invested in the system?
Mark the single best answer.
8a) The enzyme that carries out the linking step.
8b) The enzyme that helps to trap glucose in the cell using phosphorylation.
8c) The enzyme that cuts a CO2 molecule off of a 5-carbon Krebs intermediate.
8d) The enzyme that oxidizes a 4-carbon Krebs intermediate.
8e) The enzyme that splits the 6-carbon, 2-phosphate molecule in glycolysis.
/5
9) When you examine the contents of a cell, you find that RNA polymerase is binding to many
promoters more often than expected. Which answer is most likely to match this phenotype?
9a) A loss of function mutation in the ubiquitin ligase that binds to a Krebs cycle enzyme.
9b) A synonymous mutation in the reading frame of a gene that helps to build mitochondria.
9c) A non-frameshift deletion in the region encoding the active site of a spliceosome protein.
9d) An insertion mutation allowing a long, flexible, sigma-like protein to bind many DNA sequences.
9e) A missense mutation that causes HDACs to change the histones in the region around the gene for
RNA polymerase.
/5
C) Write your answer to this question on the last page.
The product of a gene is used to down-regulate the function of the Krebs cycle in order to create fatty
storage molecules when energy is plentiful. Draw a diagram of the negative regulation of expression
of this gene using transcriptional regulation. Be sure to make it clear how this mode of regulation is
specific for this gene and not all genes.
Page 4 of 6
[20 points] Use this diagram to answer questions 10, 11, 12 and D. Unless otherwise noted, you can
assume that regulation in this species operates under the same general principles as in the lac operon.
P
Gene B
P
O
QuadF Operon
Q2
B
P
Q3
Q1
Complex B-K
binds to DNA
when also
bound to Ca++
Gene S
S
Complex K
QEnzJ
Complex S-Q3
binds to DNA
/5 10) Which of the following is true about positive or negative regulation in this cell?
10a) Protein B is likely a positive regulator of expression of Gene B.
10b) Q2 is likely a regulator of expression of Gene S.
10c) Complex B-K is likely to influence regulation in response to changing calcium levels in the cell.
10d) Complex S-Q3 is likely to influence regulation in response to changing calcium levels in the cell.
10e) Protein Q1 is likely a negative regulator of calcium concentrations.
/5 11) Which of the following is likely to be true about the binding of S-Q3 to the DNA?
11a) This forms a negative feedback loop that is valuable because it decreases waste.
11b) This forms a positive feedback loop that is valuable because it rapidly increases production.
11c) The regulation of Gene S requires histone modification.
11d) Part of S-Q3 is likely to bind well to the RNA polymerase enzyme.
11e) Prokaryotes do not have feedback loops in the regulation of their genes.
/5
12) Which of these answers about the DNA sequences shown here is most likely to be true?
12a) The sequence marked ‘O’ would lose function if located between Gene B and the gene for
QuadF.
12b) The sequence marked ‘P’ for both Gene S and Gene B is exactly the same.
12c) The sequence marked ‘B’ does not have a start codon.
12d) The sequence marked ‘S’ encodes an enzyme necessary to help build the Complex K structure.
12e) The three sequences marked ‘P’ are have no similarity to each other.
/5
D) Write your answer to this question on the last page.
Why does it make sense for the prokaryote to use this operon structure instead of individually
regulating each of the four Q genes? Explain in 2-3 sentences, max.
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This page is blank.
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TURN IN THIS PAGE & Scantron (you can keep the question pages
Name: _____________________________________
Student ID #: ________________ Lab Section: __________
Written Answers (Include written work here. Tear off this sheet to turn in along with your Scantron form)
A) Explain in 2-3 sentences, max.
B) Draw and label a rough energy diagram here.
C) Diagram the mode of negative regulation here.
D) Explain in 2-3 sentences, max.
Scores
A)
B)
C)
(please don’t write
anything here)
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D)
Written Total:
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