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CELL BIOLOGY

State Competition
Science Olympiad
2016
This will be a 150-point, 50 minute test with a 30 question multiple choice section and a 4
question open response section. In addition, there is a 7 question tie-breaker section. An answer
sheet is provided with this test; please use it to fill in your multiple choice answers for the regular
part of the test.

Multiple Choice (30 questions, 60 points)


1) What is the approximate number of base pairs contained in the shortest human
chromosome?
a. 2.5 x 108 bp
b. 3.6 x 105 bp
c. 3.8 x 106 bp
d. 4.6 x 107 bp
e. 5.9 x 106 bp
2) At what level of packing does DNA typically achieve a packing ratio of 7?
a. Beads on a string
b. 30-nm chromatin
c. Looped domains
d. Condensed coils
e. Metaphase chromosome
3) At the highest level of DNA packing, what is the packing ratio?
a. 7
b. 40
c. 7000
d. 14000
e. 21000
4) Core DNA is the DNA associated with the histone octamer. How many loops does core
DNA form around the octamer?
a. 1 loop
b. 2 loops
c. 3 loops
d. 4 loops
e. 5 loops
5) There are two distinct DNA components involved with the nucleosome. Besides the core
DNA, what is the other DNA component?
a. Package DNA
b. Centromeric DNA
c. Proximal DNA
d. Linker DNA
e. Bundle DNA

6) What is the effect of lamin phosphorylation by the M-phase CDK kinase?


a. The nuclear lamina dissasembles and the nuclear envelope breaks down
b. The nuclear lamina and nuclear envelope are reassembled
c. The phosphorylated filaments recruit the chromosomes to the center of the cell
d. The phosphorylated filaments recruit the chromosomes to the ends of the cell
e. Cytokinesis is initiated
7) A researcher testing plant products as potential new therapeutics notes that molecule X
induces cultured human cells to arrest within the S phase of the cell cycle. Which of the
following is the most likely target of molecule X?
a. The G1 cyclin-CDK enzyme
b. The anaphase-promoting complex (APC)
c. A microtubule-based motor protein
d. A topoisomerase
e. An RNA ligase
8) What is the necessary condition(s) for full activity of the M-phase CDK?
1. Association with the appropriate cyclin
2. Presence of an activation phosphorylation
3. Removal of an inhibitory phosphorylation
4. Ubiquitylation
5. Proteolysis of an inhibitor protein
a. 1 only
b. 1 and 2 only
c. 1 and 3 only
d. 1, 2, and 5 only
e. 1, 2, and 3 only
9) Mitochondria and peroxisomes have which of the following properties in common?
a. They are both implicated in certain diseases resulting from mutations in the
organelles own DNA
b. They both release cytochrome c during programmed cell death (apoptosis)
c. They both function to eliminate excess hydrogen peroxide
d. They both contain phospholipids synthesized in the endoplasmic reticulum
e. They both use electron transport to produce ATP
10) Assume a mammalian cultured cell line has a 20 hour cell cycle: G1 is 10 hours, S is 5
hours, G2 is 4 hours, and M is 1 hour. Assume that the population of cells is uniformly
distributed around the cell cycle. You pulse label the population for 5 minutes with 3Hthymidine. 6 hours later, what percentage of the cells undergoing mitosis are labeled with
3-H thymidine?
a. Almost none of them
b. Roughly 25%
c. Roughly 50%
d. Almost all of them
e. Insufficient information

11) During mitosis, H1 is phosphorylated at multiple CDK1 consensus sites. What effect
does this cause?
a. Recruit additional factors for O-glycosylation
b. Promote nuclear envelope breakdown
c. Promote mitotic chromosome condensation and repress transcription during
interphase
d. Decrease affinity of H1 for mitotic chromosomes
e. Increase affinity of H1 for mitotic chromosomes
12) Scientists want to determine whether a high fat diet resulting in obesity also causes
endoplasmic reticulum (ER) stress. Which of the following is NOT consistent with the
presence of ER stress:
a. Increased activation (phosphorylation) of the ER stress sensors
b. Decreased expression of ER chaperones such as BiP
c. Increased activation of the ER-associated degradation pathway (ERAD)
d. Increased autophagy of ER
e. Decreased synthesis of secretory proteins
13) An acidic pH is required for which of the following cellular functions?
a. Exocytosis of regulated secretory granules
b. Folding of proteins in the endoplasmic reticulum
c. Phagocytosis of bacteria
d. Synthesis of lysosomal enzymes
e. Uncoupling of low density lipoprotein from its receptor
14) The p-arm of which type of chromosome can be translocated without significant harm?
a. Metacentric chromosomes
b. Acrocentric chromosomes
c. Telocentric chromosomes
d. Holocentric chromosomes
e. None of the above
15) CDK activity will increase due to all of the following except
a. High cyclin concentrations
b. Dephosphorylation by cdc25
c. High p53 concentrations
d. Degradation of p21
e. Phosphorylation of cyclin B1
16) The following amino acids have an R group that includes a hydroxyl (-OH) group:
a. Glycine and proline
b. Serine and tyrosine
c. Leucine and tryptophan
d. Aspartate and glutamine
e. Histidine and lysine

17) The following equation may or may not be relevant to this question:
G = G' + 2.303RTlog10([B]/[A]). In order for the reaction ADP + Pi ->ATP to
proceed spontaneously,
a.
b.
c.
d.
e.

Blood glucose levels should be low


An allosteric activator of atp synthase should be provided
[ADP], [Pi], and [ATP] should all be low
[ADP] and [Pi] should be high and [ATP] should be low
[ADP] and [Pi] should be low and [ATP] should be high

18) Which of the following are "adapter proteins" that help bring other proteins together but
have no enzymatic activity of their own?
a. BRCA1 and BRCA2
b. Protein Kinase A and Protein Kinase B
c. FADD and TRADD
d. Initiator caspases
e. Executioner caspases
19) A biochemistry graduate student isolates all the enzymes of the TCA cycle and adds OAA
and acetyl CoA, including the appropriate energy precursors, cofactors, and water. Which
of the following will not be a direct product of his experiment?
a. ATP
b. GTP
c. NADH
d. CO2
e. FADH2
20) Membrane proteins generally
a. Are about five amino acids long
b. Are hydrophilic
c. Include lots of hydrogen bonding among the amino acids
d. Form hydrophobic protein channels through which lipids can pass
e. Have alpha pleated sheets as their secondary structure
21) To ensure that chromosome duplication occurs only once per cell cycle, the initiation
phase of DNA replication is divided into two distinct steps that occur at different times in
the cell cycle. What enzyme plays a main role in these steps?
a. Helicase
b. Topoisomerase
c. M-Cdk
d. Primase
e. ATPase

22) Upon undergoing apoptosis, animal cells are able to express a normally intercellular
phosphatidylserine on the extracellular cell surface which signals to neighboring cells to
phagocytose the dead cell. What is an accepted mechanism for the translocation of
phosphatidylserine occur?
a. Phosphatidylserine is normally transported from the outer monolayer to the inner
monolayer, but upon cell death the phospholipid translocator that mediates this
change is inactivated
b. A scramblase that transports phospholipids in both directions is activated
c. An intercellular signal binds to phosphatidylserine causes a conformational
change that causes a flip-flop of phosphatidylserine across the cell membrane
d. a and b
e. All of the above
23) WhichofthebelowarenecessaryforDNAreplicationtoproceedinthenextcellcycle?
a.
APC/CactivationleadstotheinactivationofCdksandthedestructionofgeminin
b.
ORCandCdc6aredephosphorylatedandCdt1isactivated
c.
GemininaccumulatesandinhibitstheCdt1thatisnotassociatedwithDNA
d.
aandb
e.
bandc

24) What is true about the licensing of replication origins?


a. A large complex called the preRC is formed at the replication origin
b. The origin recognition complex binds to replication origins throughout the cell
cycle
c. Licensing occurs during late mitosis and early in the G phase
d. DDK is activated, driving origin activation by recruiting transcription factors to
the site
e. Cdt1 associates with proteins at replication origins and activates it to an open state
25) WhyisAPC/Cinactivationimmediatelyaftermitosisespeciallyusefulinrapid
embryoniccellcycles?
a. Itpreventsrapidcyclinaccumulationfromoccurring
b. ItpreventsthecellfromreachingthethresholdCdc20APC/Cactivityneededfor
entryintotheG1phase
c. ItallowsthecelltoquicklybeginaccumulatingnewMcyclinforthenextcycle
d. ItallowsfortheincreasedproductionofCKIsforthenextcycle
e. ItallowsthecelltoquicklybeginaccumulatingnewScyclinforthenextcycle
26) What is a result of MAP-kinase cascade activation?
a. Inactivation of gene regulatory factors called E2F proteins
b. An increase in the production of transcription regulatory proteins such as Myc
c. A decrease in G1/S-CdK and S-CdK activities
d. An active Cdh1 is able to activate the APC/C complex
e. Inhibition of Cdc25 activity occurs, blocking entry into mitosis

27) Progression through the cell cycle is highly influenced by DNA damage. What are the
two phases in which the cell cycle control system can readily detect DNA damage?
a. Start and the G1/S transition
b. Start and the beginning of the G1 phase
c. Start and the G2/M transition
d. Start and the beginning of the G2 phase
e. None of the above
28) DNAdamageinitiatesasignalingpathwaybyactivatingoneofapairofrelatedprotein
kinasescalledATMandATR,whichassociatewiththesiteofdamageandphosphorylate
varioustargetproteins.Whatisanendresultofthispathway?
a. p53activatestheG1/SCdkandSCdkcomplexes
b. p21bindstoG1/SCdkandSCdkcomplexes,inhibitingtheiractivities
c. Aubiquitinligase,Mdm2,targetsp53fordestructionbyproteasomes
d. Chk1andChk2arephosphorylated
e. MCdKismarkedfordegradation

29) WhichRNAisnotsynthesizedwithinthenucleus?
a. mRNA
b. tRNA
c. miRNA
d. siRNA
e. snRNA
30) Whatistrueaboutp53concentrationwithinundamagedcells?
a. Itishighlyunstableandpresentinlowconcentrations
b. Itisnotnormallytranscribedinundamagedcells
c. Itexistsinhighamountsbutinaninactiveform
d. p53activityinanundamagedcellmaintainsnormalregulationofthecellcycle
e. Itsconcentrationfluctuatesasitisdegradedoverthecourseofthecellcycle

Free Response (4 questions, 90 pts)


Question 1 (25 pts): Biological Monomers and Polymers Nucleic Acids
While on an exploratory mission to a new solar system, your amazing feline sidekick brings you
a microscopic alien organism consisting of nucleic acids and proteins. Conveniently, this
organism is able to infect E. coli cells, making it easy to study in the laboratory.
a) After returning to Earth, you grow this organism with either radioactive phosphorus (32P) or
radioactive sulfur (35S), in an attempt to discover which macromolecule is acting as the genetic
material. Which macromolecule(s) will be labeled with each radioisotope? Explain how you
know.
Nucleic acids contain phosphorus in their sugar-phosphate backbone (and so will be
labeled with radioactive phosphorus), while sulfur is found in the amino acids cysteine
and methionine (and so proteins will be labeled with radioactive sulfur).
2 pt Nucleic acid labeled with phosphorus + explanation
2 pt Protein labeled with sulfur + explanation
4 pts total
b) You are unsure if the nucleic acid in your organism is DNA or RNA. Describe three structural
differences that can be used to distinguish between DNA and RNA. Suggest a simple experiment
that could be used to distinguish between the two.
Differences between DNA and RNA include:
1) DNA is usually doublestranded, while RNA is mainly singlestranded.
2) DNA contains thymine and RNA contains uracil.
3) The ribose component of DNA lacks a 3OH group.
Other answers may also be accepted; these are the three simplest.
Any reasonable experiment that demonstrates knowledge of the differences between
DNA and RNA will be accepted. (e.g, radioactive/fluorescent labeling of uracil/thymine,
DNase/RNase digestion, etc.)
3 pt 3 differences between DNA and RNA (1 pt each correct)
1 pt Reasonable experiment
4 pts total
c) Suppose that the inherited material of the organism is determined to be nucleic acid, more
specifically, DNA. You find that the DNA of the organism contains 15.2% adenine, 15.1%
thymine, 35.1% guanine, and 34.6% cytosine. Based on this information, is the organism more
likely to be carrying doublestranded or singlestranded DNA? Explain your reasoning.
This organism contains doublestranded DNA. Within the bounds of experimental error, the
percentage of adenine in the DNA equals the percentage of thymine, and the percentage of
guanine equals the percentage of cytosine. In doublestranded DNA, adenine forms base pairs
with thymine, while guanine forms base pairs with cytosine; hence, the ratios of G:C and A:T
should be 1:1. In singlestranded DNA, this ratio would not necessarily be observed.
1 pt DNA is doublestranded
2 pt Explanation involving %A=%T and %G=%C
3 pts total

d) Prior to sending your alien genome in for sequencing, it is necessary to amplify the genome
via PCR.
i) Name the molecular interaction between base pairs that the first step of PCR is designed to
disrupt.
1 pt Hydrogen bonding
ii) You set the PCR machine to run using standard concentrations, temperature, and time settings
known to be successful for a majority of amplification reactions. However, after you purify the
reaction, you find only miniscule amounts of DNA in the test tube containing viral DNA.
Another reaction, containing a human DNA fragment, run in parallel on the same PCR machine
under the same conditions (excluding appropriately different primer sequences), amplifies well.
Hypothesize why the viral PCR reaction may have failed, and propose a solution that may solve
the problem.
The viral DNA sequence contains an unusually large percentage of G/C base pairs. G/C
pairs are held together by three hydrogen bonds, while A/T base pairs are held together by only
two. As such, it requires more energy to separate a G/C base pair than it does to separate an A/T
base pair. A DNA sequence that contains many G/C base pairs would require more energy to
denature. Raising the temperature at which melting occurs during your PCR cycle may solve the
problem.
1 pt Recognize that this viral DNA has large percentage G/C
2 pt Explanation of hydrogen bonding in base pairs
1 pt Suggest raising melting temperature
iii) Your lab is poor, so instead of using a high fidelity polymerase with a very low error rate, you
must use a more error prone but much cheaper polymerase. Because of this, during your PCR
reaction two abnormal base pairs are formed: in one instance, an adenine pairs with a guanine,
and in another instance, 153 base pairs away, a cytosine pairs with a thymine. How will the DNA
double helix be affected by each of these mismatches?
Adenine and guanine are purines, and have two aromatic rings. Thymine and cytosine are
pyrimidines, and have one aromatic ring. The distance between sugar phosphate backbones in a
non-mismatched helix of DNA is enough to accommodate a purine hydrogen bonded to a
pyrimidine. A pairing of two purines will be too large for this space, and may cause the double
helix to buckle outwards. A pairing of two pyrimidines will not completely fill the space, and
may cause the double helix to buckle inwards.
1 pt Correctly identify A and G as purines and T and C as pyrimidines
1 pt Purines have two aromatic rings, pyrimidines have 1
1 pt 2 purines take more space than purine/pyrimidine
1 pt 2 pyrimidines take less space than purine/pyrimidine
9 pts total

e) After sequencing, you find to your disappointment that your alien organism was simply a
stowaway bacteriophage. However, you notice something oddthe phage genome is 400
nucleotides in length and encodes two proteins, one containing 120 amino acids and one
containing 80 amino acids. At first glance, why does this seem abnormal to you? Propose a
reasonable explanation for how this might occur.
Every amino acid is encoded in mRNA by a 3 nucleotide codon. In order to have a 120
amino acid protein and an 80 amino acid protein (200 total amino acids), you would need 600
nucleotides of coding DNA. This organism has 400 nucleotides total. While most prokaryotes
have very streamlined genomes containing almost entirely protein coding DNA, with genes
organized sequentially, most organisms and eukaryotes need to package more genes into a
proportionally smaller amount of nucleic acid. To accomplish this, organisms sometimes contain
multiple open reading frames and multiple start sites, allowing one sequence of DNA to encode
for multiple proteins.
1 pt Recognize that 200*3 = 600 > 400 and explain
1 pt Multiple ORFs/start sites
2 pts total
f) Some E. coli seem to have developed resistance to your bacteriophage. In an attempt to isolate
the resistance gene, you create genomic and cDNA libraries of resistant E. coli. Does a given
gene in the cDNA library differ from the same gene in the genomic library, and if so, how? How
might your answer change if instead libraries were made using HEK (human embryonic kidney)
293T cells?
Because prokaryotic RNA does not contain intervening introns, differences between the
cDNA and genomic DNA gene in E. coli will be minor. However, because the cDNA library is
created by reverse transcribing mRNA, upstream and downstream promoter and enhancer
regions will not be present in the cDNA clone. In the case of the eukaryotic HEK 293T cell, the
cDNA clone will lack introns along with the 5 and 3 flanking regions, while the genomic DNA
clone will definitely contain introns, as these are only spliced out during eukaryotic mRNA
processing.
1 pt Very minor difference between the two in prokaryotes
1 pt Recognize that cDNA is reverse transcribed mRNA
1 pt Recognize that in eukaryotes, cDNA lacks introns
3 pts total

Question 2 (25 pts): Biological Monomers and Polymers - Proteins


While proteins can vary greatly in structure and function from each other, they still have
fundamental commonalities. Some major commonalities that come to mind are that amino acids
are building blocks and that there are characteristic secondary structures that form in a relatively
predictable pattern.

a) You are given a sequence of a human protein. It is as follows:


VILNIFRAAMWVLLSILMEGVPDKMMECRNQT
What can you infer about the secondary structure and possible function of this protein? Why? At
what point in the sequence might the protein experience a structural/functional change, and why?
Be specific in your explanation.

1 pt Alpha Helix structure


1 pts 3rd or 4th amino acid indicating a helical turn
1 pt Position 22 Proline notation
1 pt Proline is a helical breaker b/c of rigidity/angle changes in protein
1 pt Polar/charged amino acids following position 20
5 pts total

b) Lets assume that someone comes to you with a new, human disease that concerns
malfunctions of this protein. You get the sequence back, and it reads:
VILNIFRAVMFVLLSILMEGVPDKMMEHRNQT
How conserved is this sequence, percentage-wise, and how drastic are the changes to the
sequence?
1 pt Conservation percent calculation
1 pt Realizing that the first two mutations havent changed in polarity
2 pt Pointing out that cysteine mutation is a major change
4 pts

c) What problems might you predict are occurring with this protein with each of these new
mutations?
2 pts Disulfide bond disruptions as what will result (can give credit if mentioned in part
b)
2 pts Structural changes resulting from likely loss of inter/intradomain linkages, tertiary
and quaternary structure changes
4 pts
total
d) How might a heat assay with a reducing agent comparing the wild-type and the mutant protein
function at various temperatures help with narrowing down potential causes of the problem?
Why might it not be useful to assay at a temperature above 100F?
1 pt Explanation of sensitivity to heat
2 pts Comparing wt to mutant on the basis that as heat increases - will likely get close to
mutant if cysteine is the problem
1 pt Result expected if isnt disulfide problem (anything reasonable)
1 pt Realization that proteins will denature at high heat
5 pts total

e) The genome is, on a whole, flexible to change. One of the aspects which makes it so flexible
to mutation is that there are multiple ways to code for the same amino acid. Explain what kind of
mutation(s) the codon redundancy protects the genome from.
Then, consider the following scenario: You have a bacterial enzyme with an active site exactly
20 amino acids long and uses every amino acid just once. each of the amino acids is necessary,
and none are sufficient nor can substitute for the other. if you were to design a drug against this
enzyme, which amino acid(s) would you want to target such that the bacteria cannot generate an
escape mutation in the genome for just this protein and why?
Looking at the codon table, it is clear that only two amino acids have only one codon that
correspond for that residue: Trp and Met. We would want to target one of these two, as changes
in the genome are least flexible concerning these amino acids. Because Trp or Met are present in
the enzyme and are NECESSARY and cannot have a substitution, the bacteria cannot escape
from this drug, since there are no other DNA sequences that can compensate. (Ideal answer is
Trp, since AUG codes for a start codon and were only looking to modify this protein in
particular, but if students provide good argument for Met, see EC description).
1 pt
1 pt
1 pt
2 pt
2 pt

Point mutations
Same amino acid can be coded for multiple ways
Listing Trp and Met
ONE codon codes for each, respectively
Necessary vs sufficient discussion on selection of these

Question 3 (25 pts): Cellular Homeostasis


One day, you come home from lab to discover that your pet cat has managed to form a liposome
in buffer containing 5mM KCl and ATP at pH7 (Buffer #1). Joining in the fun with your cat, you
decide to place the formed liposome into a buffer containing 50mM KCl and ATP also at pH7
(Buffer #2).
For each subpart below: Answer the questions (remember to justify your answers!), taking care
to describe what would happen very shortly after liposome formation, and then after a long
period of time, when relevant.
a) For this first case, consider a liposome without any incorporated proteins.
(i) Will K+ move across the membrane, and if so, in which direction does it move?
1 pt No
1 pt Ions cannot pass through the membrane unless there is a channel, pump, or
transporter that allows movement of the ion.

(ii) What happens to the concentration gradient across the liposome bilayer over time?
1 pt Nothing.
1 pt Ions cannot pass through the membrane unless there is a channel, pump, or
transporter that allows movement of the ion. If no ions can flow, then the concentration gradient
cannot change.

(iii) How does the magnitude of the membrane potential across the lipid bilayer change over
time?
1 pt It doesnt.
1 pt It remains at zero the whole time. Ions cannot pass through the membrane unless
there is a channel, pump, or transporter that allows movement of the ion. Ions traveling through
channels is what creates a membrane potential in the first place.
6 pts total

b) You now repeat the experiment from the introduction, but using liposomes into which the
H+ /K+ ATPase (isolated from stomach epithelial cells) is incorporated in the same orientation as
it is in the cell, with the ATP-binding site inside the liposome.
(i) Will K+ move across the membrane, and if so, in which direction does it move?
1 pt Yes
1 pt inward
1 pt The H+/K+ ATPase brings K+ into the cell and pumps H+ out of the cell.

(ii) What happens to the K+ and H+ concentration gradients across the liposome bilayer over
time?

1 pt The H+/K+ ATPase brings K+ into the cell and pumps H+ out of the cell.
1pt An H+ gradient will be created so that H+ is higher outside the liposome.
1 pt The K+ gradient will initially dissipate (as it starts off higher outside than inside), but
once the concentration gradient of K+ reaches zero, the pump keeps pumping, thus creating a
new gradient where K+ becomes higher inside.

(iii) How does the magnitude of the membrane potential across the lipid bilayer change over
time?
1 pt It does not change.
1 pt No net charge is flowing across the membrane. The outside and inside of the
liposome remain neutral.
8 pts total

c) You now repeat the experiment from the introduction, but using liposomes into which only a
K+ channel is incorporated.
(i) Will K+ move across the membrane, and if so, in which direction does it move?
1 pt Yes
1 pt inward
1 pt K+ begins higher inside than outside. When the channels are first open, K+ will want
to flow down its concentration gradient (from the outside to the inside). This results in the inside
of the liposome becoming positive. Thus, eventually, K+ will want to stop flowing inside
because it is positive and thus repelled by the + charge inside the liposome. Thus eventually there
will be no net flow of K+ because an equilibrium has been reached (where the membrane
potential across the liposome membrane is equal to the Nernst potential for potassium).
(ii) What happens to the concentration gradient across the liposome bilayer over time?
1 pt Very little.
1 pt It may decrease slightly because K+ is flowing inward, but then it reaches an
equilibrium, and the number of ions that must flow to create the membrane potential at that
equilibrium is miniscule compared to the number of ions that create the concentration gradient.

(iii) How does the magnitude of the membrane potential across the lipid bilayer change over
time?
At first, the inside of the liposome will be becoming more and more positive, but
eventually the membrane potential will stabilize at the Nernst potential for K+. K+ begins higher
inside than outside. When the channels are first open, K+ will want to flow down its
concentration gradient (from the outside to the inside). This results in the inside of the liposome
becoming positive. Thus, eventually, K+ will want to stop flowing inside because it is positive
and thus repelled by the + charge inside the lipsome. Thus eventually there will be no net flow of
K+ because an equilibrium has been reached (where the membrane potential across the liposome
membrane is equal to the Nernst potential for potassium)
6 pts, reward/take off points using your own discretion
11 pts total

Question 4 (15 pts): Bioenergetics and Enzymes


2) In which two organelles is ATP synthase located? Specifically, which two regions make
up ATP synthase and where are they located in each organelle?
Located within the mitochondria (1 pt) and chloroplast (1 pt), ATP synthase consists of
two regions:
the FO portion (1 pt) embedded (1 pt for embedded or something similar) within the inner
mitochondrial membrane and thylakoid membrane (2 points for stating both).
the F1 portion (1 pt) of the ATP synthase is outside the inner mitochondrial
membrane/thylakoid membrane, but inside the matrix of the mitochondria/chloroplast (1
pt)
8 pts
3) Describe in detail the binding-change model postulated by Paul Boyer for ATP synthesis.
ATP synthesis is dependent on a conformational change in ATP synthase generated by rotation of
the gamma subunit. In particular, the binding change mechanism involves the active site of a
subunit's cycling between three states. In the "open" state, ADP and phosphate enter the active
site; in the diagram to the right, this is shown in red. The protein then closes up around the
molecules and binds them loosely the "loose" state (shown in orange). The enzyme then

undergoes another change in shape and forces these molecules together, with the active site in the
resulting "tight" state (shown in pink) binding the newly produced ATP molecule with very
high affinity. Finally, the active site cycles back to the open state, releasing ATP and binding
more ADP and phosphate, ready for the next cycle of ATP production.
7 pts

Tie-Breaker Questions (10 pts)


1) One new cancer therapy that does not appear to lead to drug resistance, even after several
cycles of treatment with and withdrawal of the drug, is
a. endostatin
b. Taxol
c. gene therapy
d. antibodies to the HER2 receptor
e. marijuana
2) If you mix a person's blood with anti-A serum and find that the blood agglutinates, you
can conclude that the person's blood type is
a. A
b. B
c. A or AB
d. A or O
e. B or O
3) If a proto-oncogene mutated into an oncogene in an otherwise normal cell, the immediate
result would most likely be
a. apoptosis
b. arrest of the cell cycle
c. that the cell would become malignant
d. rapid mutations of other genes

e. not much; perhaps a slight quickening of the cell cycle


4) Inside a human host, bacterial cells coated with antibodies may become targets of
a. apoptosis
b. cell-cycle arrest
c. phagocytosis
d. autoimmune reactions
e. cytokines
5) Which of the following "zones" in the sarcomere does not change length during muscle
contraction?
a. the zone where there is overlap between actin and myosin filaments
b. the zone where there is only actin (no myosin)
c. the zone where there is only myosin (no actin)
d. the zone consisting of the full length of the myosin filaments
e. the sarcomere as a whole

6) Why can a mutation in the regulatory region (e.g., promoter) of a proto-oncogene result
in a cancer-causing oncogene? How could this problem be corrected using antisense
oligonucleotides?
A mutation in the regulatory region can cause a cell to express a normal protein at inappropriate
times (e.g., all the time) and at inappropriate levels (e.g., higher-than-normal concentrations). If
the protein promotes cell growth or division, changes in its expression might lead to unregulated
growth and divison. Antisense oligonucleotides can sometimes be used to decrease the
expression of these sorts of proteins. An antisense oligonucleotide is a string of 10-30
nucleotides complementary to the mRNA coding for a particular protein. Once introduced into a
cell, these "oligos" bind to the section of mRNA to which they are complementary, thus
preventing the mRNA from being translated intro protein (since ribosomes can't translate doublestranded nucleic acids).
2 pts
7) How can p21, p53, cdc25, and ATM lead to arrest of the cell cycle? Please explain what
these molecules do and how they are affected by each other.
ATM is a protein that senses breaks in DNA and then triggers the activation of either of two
pathways (depending on whether the cell is in G1 or G2.). In one pathway, cdc25 becomes
phosphorylated and thus gets inactivated, meaning that it cannot dephosphorylate cdk's. Since
the cdk's remain in their phosphorylated and inactive state, they do not move the cell through the
next checkpoint. In the other pathway, ATM causes the stabilization of p53, which then acts as a

transcription factor inducing the synthesis of p21, a cdk inhibitor. Inhibition of cdk's then causes
the cell cycle to stall.
3 pts