Foundations of Biology I, Fall 2014

Dr. Lesley Ashmore

Midterm Exam 3
Directions: Before beginning, first mark your NAME and PEOPLESOFT ID on the scantron sheet.
Reach each question carefully. Some answers may be partially correct- you must select the BEST ANSWER and mark
that response on your scantron sheet. Ensure that you leave enough time to enter all answers on your scantron sheet.
MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.
___C__1) How does the cell access the energy stored in a molecule of ATP in order to catalyze endergonic chemical
reactions?
A) One of the three phosphate groups is removed and heat is released; the heat is used to do work
B) One of the three phosphate groups comes off and collides with another molecule, transferring kinetic energy to
that molecule
C) One of the three phosphate groups is attached to something else by an enzyme
D) One molecule of ATP is attached to an enzyme and that alters the shape of the enzyme, allowing the enzyme to
catalyze multiple endergonic reactions
E) ATP binds to an allosteric regulatory site on an enzyme, allowing it to catalyze reactions
__C___2) Why do leaves appear green?
A) green is the color of the excited electrons
B) chlorophyll absorbs green wavelengths best
C) the combination of pigments in leaves including chlorophyll absorbs most wavelengths except green
D) green is the color emitted by electrons that absorb a photon then fluoresce (release energy in the form of a
photon as they fall back to their ground state of excitement)
E) thylakoid membrane phospholipids are green in color
__B___3) What can be said about any cell at equilibrium?
A) it is an unstable system-- ions tend to flow to one side
B) it is stable and there is no net movement of ions across the membrane
C) it can immediately use its membrane to do cellular work
D) there is no movement of any solutes or ions across the membrane (at all)
E) it is a state of low entropy and has a high free energy
__E___4) Imagine you have discovered a chemical that reduces NAD+/NADH and FADH+/FADH2 whenever it

encounters the oxidized version in the cell. What do you predict will be a consequence of this chemical on the cell?
This would be a magical chemical indeed! It performs all the functions that the first three steps of glycolysis
are forreducing NADH and FADH2 (filling them with high-energy electrons). If we had a chemical to do this for us,
we wouldnt need to burn glucose at all.
A) the cell will increase the rates of the first three steps of respiration to compensate
B) the electron transport chain will cease to function once electrons run out
C) ATP production in the mitochondria can occur without the need for oxygen
D) the rate of fermentation must increase so the cell can survive
E) ATP production in the mitochondria can occur without the need for glucose
__C___5) Considering where the first three steps of respiration take place, which enzymes that catalyze these metabolic
pathways will pass through the endomembrane protein sorting pathway to reach their destinations?
The endomembrane sorting pathway is only for proteins that will end up (1) in the lysosome, (2) stuck into a
membrane, and (3) released (secreted) from the cell. The enzymes of glycolysis are cytoplasmic; the second two steps
take place in the mitochondrial matrix (the equivalent of the stroma). None of them will be made through the

endmembrane system.
A) only those involved in glycolysis
B) only those involved in the citric acid cycle
C) none of them will
D) only those involved in pyruvate processing and the citric acid cycle
E) all of them will

__E___6) The source of electrons for the electron transport chains in photosynthesis is ___________
and in respiration it is_____________.
A) water, oxygen
B) glucose, water
C) carbon dioxide, oxygen
D) oxygen, carbon dioxide
E) water, glucose
___A__7) Shewanella putrefaciens is a hardy little bacterium that uses iron, manganese, or even uranium(!) as its final
electron accepter in the mitochondria instead of oxygen during respiration. However, it still oxidizes glucose in the first
three steps of respiration. Which aspect of respiration will change?
Oxygen is the final electron acceptor at the end of the electron transport chain, accepting electrons and protons
to form water. (CO2 is released during the earlier steps and will still be released by those steps even in this
bacterium.) If oxygen is not the final acceptor, then we wont make waterwell make something that has the metal
and hydrogen atoms.
A) H2O is no longer produced at the end of the electron transport chain-- it's a compound with hydrogen and
the metal
B) An organic compound containing the metal and carbon is produced instead of CO2

C) The electron transport chain results in the pumping of the metal ions across the inner mitochondrial (christae)
membranes instead of protons
D) NADH and FADH2 carry fewer electrons from every molecule of glucose that is oxidized
E) These organisms must rely on fermentation and substrate level phosphorylation to make ATP without oxygen
___B__8) Which step of making ATP is the active step (the step that requires energy input?)
The first and third step of glycolysis require ATP, but the other eight reactions do not and ultimately release
more energy than was invested in the first and third step. Making and maintaining the proton gradient requires the
energy in this process.
A) moving protons across a membrane through the ATP synthase molecule
B) moving protons across a membrane to create an electrochemical gradient
C) the citric acid cycle (as a whole, not individual steps)
D) glycolysis (as a whole, not individual steps)
E) reducing NAD+/NADH and FADH+/FADH2

Use the following information to answer the next SIX questions below.
You have found a wonderful new chemical that you believe will work well as an herbicide (a chemical
that specifically kills plants but should be harmless to animals). This chemical diffuses into plant
chloroplasts, into the thylakoid membranes, and creates passive proton channels, which prevents the
plant from maintaining a working proton gradient.
You saturate an adult plant with this chemical (enough to ensure all chloroplasts are completely
affected). Explain what effect this chemical will have on each of the following processes.
There was some confusion over whether this chemical also affected mitochondria or other portions of the cellI
tried to make it clear that it only affects thylakoid membranes. So the creation of proton channels here is similar
to the 2012 exams brown fat problems. Almost everything in this system will still work: electrons from water
are still excitable, theyll still flow through both photosystems, protons will still be pumped into the thylakoid
lumens, and NADPH will still be reduced. HOWEVER the pumped protons will promptly leak back out again,
wasting all that energy the chloroplasts would normally use to make ATP, so ATP production in the chloroplast

halts as soon as the proton gradient reaches equilibrium.

So ATP becomes the limiting factor for the Calvin cyclewe have unlimited electrons from water and all the CO2
we need, and NADPH production is unaffected. The Calvin cycle can continue until ATP stores run out. Students
who pick this answer (#13 below) and that this will make an effective herbicide (#14B) get full credit.
Now, clever students would recall that plant cells also contain mitochondria, which can burn glucose in order to
make more ATP. So we can still run the Calvin cyclewe just need to get ATP from another organelle, and
everything will be fine, right? So the Calvin cycle can continue indefinitely (#13) and thus this chemical makes a
lousy herbicide because it doesnt kill the plant (#14). Students who picked these answers also get full credit.
REALLY savvy students will take another step back and wonderis this ultimately sustainable? Can we make
enough ATP from respirationfrom burning glucoseto make glucose? If you took the time to think about how
much ATP goes into making a molecule of glucose (18 ATP) versus how many come out of the process (20-38),
you might see that this puts the plant at a HUGE disadvantage, energy wise. Remember that many other cellular
processes require ATP as well. Probably, in the long run, this is not sustainable. But we dont know for certain,
and as far as I could determine after a halfhearted Pubmed search, nobody else has performed this thought
experiment and calculated it all out. So with this line of reasoning, again, the Calvin cycle can continue until ATP
stores run out, and the plant slowly starves to death.
Therefore, Im allowing both lines of thought because they both show an excellent understanding of the
mechanisms of photosynthesis. But Im giving an extra half point to students who chose The plant starves to
death because it shows a deeper understanding of the big picture. These were the toughest questions on the
exam.
__E___9) Can photons still excite electrons in photosystems I and II?
A) yes, until the plant's store of ATP and/or NADPH runs out
B) no, this process will halt the instant this chemical takes effect in the thylakoids
C) yes, until the proton gradient reaches equilibrium
D) yes, until the source of electrons runs out
E) yes, this part of the system is unaffected
___A__10) Will electrons still flow through the electron transport chains of photosystem II and I?
A) yes, this part of the system is unaffected
B) yes, until the plant's store of ATP and/or NADPH runs out
C) no, this process will halt the instant this chemical takes effect in the thylakoids
D) yes, until the source of electrons runs out
E) yes, until the proton gradient reaches equilibrium
__D___11) Is ATP produced in the chloroplasts?
A) no, this process will halt the instant this chemical takes effect in the thylakoids
B) yes, until the plant's store of ATP and/or NADPH runs out
C) yes, until the source of electrons runs out
D) yes, until the proton gradient reaches equilibrium
E) yes, this part of the system is unaffected
__A___12) Will NADP+ be reduced to NADPH in the chloroplast?
A) yes, this part of the system is unaffected
B) yes, until the plant's store of ATP runs out
C) no, this process will halt the instant this chemical takes effect in the thylakoids
D) yes, until the proton gradient reaches equilibrium
E) yes, until the source of electrons runs out
_A or C (see above)____13) Can Rubisco still catalyze the fixation of CO2 molecules to RuBP
A) yes, until the cell runs out of ATP
B) yes, until the cell runs out of NADPH

C) yes, this process is unaffected by the chemical

D) no, this process will halt the instant this chemical takes effect in the thylakoids
E) yes, until the source of electrons runs out
A or B (see above)___14) Would this make an effective herbicide (one that will only affect and eventually kill plants, not
animals)? Why or why not?
A) No. The plant can make sufficient ATP for the Calvin cycle using respiration, so the chemical will not alter
the lifespan or function of the plant.
B) Yes. It will halt a vital part of energy capture in plants and cause the plants to slowly starve to death as
their glucose/starch stores are depleted, but will not affect animals
C) No. It targets a process or protein that is found in both plants and animals and is therefore not selective
enough.
D) Yes. It will cause photosynthesis to stop in seconds, killing the plant within minutes, but will not affect
animals.
E) Yes. It will cause both photosynthesis and respiration to stop within seconds, but only in plants.
Use this picture to answer the following THREE questions.

___A___15) How many genes are required (minimum) to encode malate dehydrogenase?
You only need one set of instructions to make two identical subunits.
A) one
B) two
C) three
D) four
E) cannot determine from this information
___A___16) We have found a lot of variations (polymorphisms) in the coding region of the gene between people that do
not affect function. But we have never seen a single adult person with a loss-of-function allele of this gene. Speculate:
what is a good explanation for this observation?
Clearly this gene DOES get mutated, otherwise there wouldnt be any variations. And we know that this
enzyme is vital for the citric acid cycle to continue because we absolutely require the substrate oxaloacetate for the
first step of the cycle. Mutations ONLY alter primary structureanything that alters secondary and tertiary without
altering primary could damage the protein, but it doesnt count as a mutation. Therefore the most logical
explanation is that if you cant perform this reaction, you cannot perform the third step of respiration, and you suffer
from a huge energy deficitso youre dead before you reach adulthood. Which is sadly true.
A) This enzyme is absolutely vital for the citric acid cycle. Mutations that decrease the function of this
enzyme are fatal and thus we will never see a living person with a phenotype.

B) People with mutations in this enzyme have no phenotype because the reactions in the mitochondria can
continue indefinitely without this enzyme.
C) Because we never see a phenotype, there muse be a protective mechanism in place that keeps this particular
gene from ever being changed.
D) Mutations may not always alter the primary structure of the enzyme, even if they affect other levels of protein
structure
E) People with mutations in this enzyme have no phenotype because there are other enzymes in the cycle that
produce NADH, so this enzyme is redundant. They only produce slightly less ATP per molecule of glucose than
wild type people.
__A___17) We create a new allele of the malate dehydrogenase gene that encodes a nonfunctional protein. We inject it
into normal, healthy cells. The new gene is transcribed and translated along with the cell's original working malate
dehydrogenase genes. Enzyme homodimers that form between working and nonworking subunits can no longer catalyze
reactions. What kind of mutation have we created? (Choose the best answer)
When a protein from a mutant allele interferes with a wild type proteins function, that is the definition of
dominant negative.
A) dominant negative
B) recessive
C) loss of function
D) null
E) incomplete penetrance
__C___18) If we inhibited malate dehydrogenase with a drug, how would it affect respiration?
A) we would see a buildup of oxaloacetate in the cell
B) there would be less NADH produced for every glucose, so there would be slightly less ATP produced for every
glucose
C) the citric acid cycle would eventually stop when it ran out of oxaloacetate
D) ATP could no longer be made by any means, even fermentation
E) it would not affect the citric acid cycle or respiration
__E___19) Oxygen must pass through two membranes to exit the chloroplast. What mechanism will be employed by the
cell to move it?
A) the chloroplast will have a channel protein in these membranes through which oxygen can passively diffuse
B) the oxygen must be temporarily fixed to an organic molecule in order to pump it out of the chloroplast
C) the chloroplast will have a protein pump in these membranes which does not require energy because oxygen's
concentration gradient means oxygen flows out
D) the chloroplast will have a protein pump in these membranes which requires energy to move oxygen against
its concentration gradient
E) none-- oxygen can pass freely through membranes and will passively diffuse out
__E___20) Imagine we radioactively labeled the oxygens of water used by a plant during photosynthesis. After
photosynthesis we would find the label in which molecule?
People who get this one wrong probably either didnt think about it (even on final exams, most say it ends
up in glucose), or overthought it! I just meant, when water is split in photosynthesis, what happens to the
oxygen?
A) carbon dioxide
B) water
C) rubisco
D) glucose
E) gaseous O2 (waste)
___E___21) Homologous chromosomes _____.

A) do not separate until the second meiotic division during the production of gametes
B) are identical copies of each other
C) are connected by a centrosome during meiosis and are called sister chromatids
D) are the same size, but carry very different genes
E) carry the same genes in the same order, though exact DNA sequences in those genes may differ

Use the following graphs to answer the next three questions below. Each question is asking how
"X" (underlined in each question) affects phosphofructokinase activity.

___D___22) In this question, the X-axis begins at 0 M. The graph that best describes the relationship between increasing
concentrations of ATP and the activity of the enzyme phosphofructokinase is:
This was a clicker question in class. ATP is both a substrate AND a regulatory inhibitor of phosphofructokinase.
A) graph A
B) graph B
C) graph C
D) graph D
E) graph E
__E___23) In this question, the X-axis begins at 0 M. The graph that best describes the relationship between increasing
concentrations of fructose-6-phosphate and the activity of the enzyme phosphofructokinase is:
F-6-P on the other hand is simply a substrate. The enzyme rate continues to increase with more substrate until all
active sites are full, then the rate levels out.
A) graph A
B) graph B
C) graph C
D) graph D
E) graph E
___B___24) In this question, the X-axis begins at 10-7 M (pH 7). The graph that best describes the relationship between
increasing concentrations of H+ ions and the activity of the enzyme phosphofructokinase is:
Changing the pH of the cytoplasm will begin to denature any enzyme that is optimized for pH 7 pretty quickly. We
also mentioned in class (as an aside) that this particular enzyme is negatively regulated by acid conditions. You didnt need to
know that in particularyou should be able to predict that altering pH will have a detrimental effect on enzymes, and you
should remember that the cytoplasm is kept around a neutral pH 7.
A) graph A
B) graph B
C) graph C
D) graph D
E) graph E
__A___ 25) Dominant alleles:
E had a typo and should have read A and D. Doesnt matter, D is false, so E is false.

A) always mask the presence of recessive alleles

B) are always more common in the population than recessive alleles
C) are always stronger than recessive alleles
D) always encode working proteins (vs. recessive alleles which encode nonfunctional proteins)
E) And D are both correct
__D____26) Many plants can reproduce asexually and through self-fertilization. Is there a difference?
A) yes, asexual reproduction confers a fitness advantage since it is faster and more efficient
B) no; both processes require the production of flowers and expend the same amount of energy on the part of the
plant
C) no, both processes produce offspring that are genetically identical to the original parent
D) yes, the products of self-fertilization are not genetically identical to the original parent; asexual
reproduction produces genetically identical offspring
___A___27) Which of the following statements best explains the paradox of sex?
A) All other things being equal, asexual organisms should produce more offspring than sexual organisms, but
sexual organisms often end up out competing asexual organisms.
B) Asexual organisms produce identical offspring via mitosis, whereas sexual organisms first produce gametes via
meiosis
C) Asexual reproduction results in more genetic variation in populations than sexual reproduction, but sexual
reproduction predominates among animals on Earth
D) Most organisms on Earth replicate via sexual reproduction, even though genetic homogeneity is more
evolutionarily advantageous
E) From an evolutionary perspective, sexual reproduction only makes sense in unchanging environments
___D___28) You have pure-breeding mice that are white with short tails and smooth ears. You cross them to your friend's
mice, which are pure-breeding black with long tails and smooth ears. The F1 offspring are all white with long tails and
smooth ears. Which of the following traits are definitely dominant?
A) black coats
B) smooth ears
C) cannot determine from this single cross
D) long tails
E) short tails

____C__29) You cross two of the F1 offspring to a pure-breeding black, long-tailed mouse with
smooth ears. What do you expect to see in the progeny?
A) 1/2 white with long tails, 1/2 black with short tails
B) 3/4 black with long tails, 1/4 white with long tails
C) 1/2 white with long tails, 1/2 black with long tails
D) 1/2 white with long tails, 1/2 white with short tails
E) 3/4 white with long tails, 1/4 black with long tails
__A___30) You find a mouse with crumpled ears. You cross it to a smooth-eared pure-breeding mouse and find that half
of the offspring have crumpled ears, and half have smooth ears. What can you conclude about your crumple-eared parent
mouse from these data?
If smooth was dominant, and you crossed the crumpled mouse to the homozygous smooth-eared mouse, all the
offspring would be smooth-eared. So crumpled is dominant. If the crumpled parent was homozygous, then all of the offspring
would have crumpled ears. So the mystery parent is heterozygous and crumpled ears are dominant.
A) It was heterozygous and crumpled ears are the dominant trait
B) it was heterozygous and crumpled ears are the recessive trait
C) it was homozygous and crumpled ears are the dominant trait
D) It was homozygous and crumpled ears are the recessive trait
___B___31) The mechanisms of sexual reproduction (meiosis) specifically increase genetic variation in all the following
ways except:
Is part of the process of meiosis to cause random mutations? No. Random mutations occur in the DNA
before or during replication, and is not a part of the normal meiosis process. Random mutations do contribute to
genetic diversity but they are not part of the meiosis process.
A) crossover resulting in homologous recombination
B) random mutations
C) donation of only one set of chromosomes by each parent (law of segregation)
D) random assortment of the parents' paternal and maternal chromosomes in each gamete (law of independent
assortment)
E) all of the above are correct
___D___32) What is photorespiration?
A) respiration that occurs in the presence of photons
B) substrate level phosphorylation of ATP using energy from photons
C) mitochondrial respiration in plant cells
D) when Rubisco uses O2 as a substrate instead of CO2
E) the production of ATP in the chloroplasts

____B__33) Chloroplasts and Mitochondria both have two layers of membranes, the inner of which is highly folded.
Why?
I clarified this question (why the folding) then realized that I **meant** it to be read both ways. A highly
folded membrane indicates that membrane is doing something important and therefore needs an increased
surface area. But a cell doesnt need a separate compartment to utilize a gradientall it needs is a membrane.
So B is correct.
A) They have two layers of membrane because they contain their own DNA, which they must protect from mixing
with that of the host cell.
B) The inner membranes are highly folded to increase surface area, because they contain the electron
transport chains and the ATPases that generate ATP.
C) The inner membranes are highly folded because they contain phospholipids that are unsaturated, which
means their tails have a lot of kinks in them that distort the membrane
D) They have two layers of membranes because they utilize an electrochemical gradient to generate ATP, and all
such gradients require a separate compartment in the cell to function.

__A___34) Which processes do anaerobic respiration (respiration in absence of oxygen) and

fermentation have in common?
A) glycolysis
B) electron transport in mitochondria
C) ATP made via ATP synthase
D) all of the above, though they are different processes
E) they are the same process
__C___35) After telophase I of meiosis, the chromosomal makeup of each daughter cell is _____.
A) tetraploid, and the chromosomes are each composed of two sister chromatids
B) diploid, and the chromosomes are each composed of two sister chromatids
C) haploid, and the chromosomes are each composed of two sister chromatids
D) haploid, and the chromosomes are each composed of a single chromatid
E) diploid, and the chromosomes are each composed of a single chromatid
__C___36) In an animal that switches between sexual and asexual reproduction, when is sexual reproduction more likely
to occur?
A) when males and females find each other
B) When females outnumber males
C) when conditions for survival are unfavorable
D) when conditions for survival are favorable
E) What conditions favor sexual over asexual remains a complete mystery.
__B___ 37) An diploid organism has 16 total chromosomes in its somatic cells. During meiosis I, how many tetrads does
it have lining up along the metaphase plate?
16 chromosomes and diploid means that there are 8 pairs of homologous chromosomes. Thus there are 8
tetrads. Homologous chromosomes separate during anaphase I and each daughter cell gets 8 (and is thus haploid).
Confusion for students at this point comes from the fact that we refer to two sister chromatids attached at the
centromere as one chromosome.
A) 4
B) 8
C) 16
D) 32
E) varies by organism
___D__38) Does secondary active transport require energy to transport a solute across a membrane? Choose the best
answer:
Think of the glucose transporter that uses the sodium gradient to transport glucose. Glucose is the solute.
The relative concentrations of glucose dont matter, its the relative concentrations of the sodium that drive the
transport of glucose. The transport itself (of the solute and the ion) is passivebut energy is required for maintaining
the sodium gradient.
A) yes, because the solute is phosphorylated as part of the transport process, and that makes it an endergonic
reaction
B) no, because the transport through the transporter is passive-- the solute flows through it to equilibrium
C) no, because the energy in the solute's concentration gradient is sufficient to power the transporter
D) yes, it takes energy to establish and maintain the electrochemical gradient that powers the transport of the
solute
E) yes, because ATP is required for the conformational change in the transporter that forces the solute across the

membrane against its concentration gradient

Use this picture to answer the following TWO questions.

The image above is Coenzyme Q10, also called Quinone, abbreviated "Q." It is a component of the mitochondrial electron
transport chain and serves a function in mitochondria that is nearly identical to that of "PQ" in plants, shuttling electrons
between cytochrome complexes.
___D___39) Coenzyme Q10 ("Q") falls into the category of:
Look at that long hydrocarbon tail! Theres nothing else it could be.
A) a polypeptide
B) a nucleic acid polymer
C) an enzyme
D) a lipid
E) a carbohydrate
__D____40) If we had a drug that inhibited Q, which of the following statements would be true:
The electron transport chain would stall, and elements AFTER Q would stay oxidized instead of cycling
between oxidized and reduced. Elements BEFORE Q in the chain would stay full of electronsthey would remain
reduced.
A) elements of the electron transport chain between Q and O2 would remain reduced
B) NAD+ and FADH+ would remain oxidized
C) protons could still be pumped by the other proton pumps in the cytochrome complexes
D) NADH and FADH2 would remain reduced
E) electron transport could continue by simply skipping the Q step