Challenges for Hardies
Response to Challenges to exam 2:
Summary:
We will grant 17 c,e; 24 d,e; 33 d,e
Question #4
I selected option (D) because it states, "…based on binding to a steroid hormone". My understanding is that steroid hormones themselves act as transcription factors and not that transcription factors acted on steroid hormones to induce their control.
Response: The steroid hormones bind to nuclear receptors, which then act as transcription factors. Hence the activity of the nuclear receptors as transcription factors is altered by binding to the steroid hormone.
question #6:
In lecture it was stated that AUG was required in vivo as an initiator sequence for
fMET. "All organisms use a special "initiator" met-tRNA for the first amino acid. In
prokaryotes the methionine is formylated, giving rise to the terminology
"fmet-tRNA". "Synthesis of the peptide bond is carried out by an active site within the large
subunit rRNA." The question states the order forced translation of poly U to produce poly
phenylalanine was preformed in vitro. I why answer C was correct now, making
reference to the specific example giving in lecture, but I feel that answer choice A
(translation in vitro doesn't work the same as in vivo) should also be true.
Because the experiment is demonstrating a forced manipulation of a purely poly-U
strand, which created poly phenylalanine, is different than the in vivo translation
which would require the sequence AUG as an initiator in order to translate.
Therefore some component of the in vivo translation (manipulation of the ribosomal
binding sequence) would need to work differently than the in vitro translation in
order for the experiment to occur.
Response: While it is true that the experiment depends on translation starting nonspecifically in vitro, that's not the purpose of the experiment. This was a classic experiment involved in breaking the genetic code.
#17
I was confused on this question because I thought C was true – according to chapter 29 page 8
" The passage of hydrolysis products, the bulk of lipids and acid from the stomach into the duodenum stimulate the subsequent release of secretin and cholecystokinin. Both of these stimulate pancreatic secretions while cholecystokinin stimulates the release of bile..Pancreatic lipase hydrolyzes an emulsified triacylglycerol to a monoglycerol and two fatty acids as illustrated"
Would this indicate that the food has now traveled from the stomach to the small intestine? So isn't this taking place in the small intestine? And the questions asks what "does not happen in the digestion of triacylglycerols in the small intestine"?
Which of the following does NOT happen in the digestion of triacylglycerols in the small intestine?
I chose "e. The digestion products of triacylglycerols are absorbed by passive diffusion and then transported to the liver where they are resynthesized into triacylglycerols" because in Chapter 29, page 8 it states, "resynthesis occurs in the mucousal cells of the jejunum".
Response: Credit will be given for 17e (in addition to the intended 'correct' answer c) - what the student says about the statement in the syllabus conflicting what is stated in choice e is correct.
Further clarification by SCH; As we will be studying further in upcoming chapters, dietary fatty acids are resynthesized to TG in the intestinal cells, exported into the blood stream in chylomicrons, and delivered to cells that either need fatty acids for energy production, or function to store them for future use (most prominently, muscle and adipose tissue). Statement e is definitely not true.
Question 22: What changes as glycolysis switches from operating in an aerobic (glucose à pyruvate) to anaerobic (glucose à lactate) manner?
The answer provided is “D” – the NET yield of NADH from glycolysis alone.
I understand the question now and understand why the answer is “D”. However, I think answer C should be considered for credit. By the way I interpreting the question was which one will change in number of amount. Because during glycolysis, one molecule ofNADH is formed and during anaerobic reaction of pyruvate converting to lactate, one NADH is consumed back to NAD+, so the NET yield of NADH is zero (which does not change in amount). On the other hand, glycolysis still uses 2 ATPs and produces 4 ATPs; therefore, the NET yield of ATP is 2 (which increases in amount of ATP). So choosing answer C is just a different way to interpret the question since the question does not specifically ask for what kind of changes.
Even if the challenge for question 22 is not accepted,Ihope that the questions for the last exam will be more specific and clearer so students can understand better what being asked.
Response: Challenge to 22 not accepted since the question clearly specified NET change in NADH and ATP.
Question #24. I put E) Is stimulated by one of it's products.
Question 24:
Phosphofructokinase (PFK) ______.
---
d. is inhibited by one of its substrates
e. is stimulated by one of its products
Answer e. was counted as correct and answer d. was counted wrong, but both d. and e. should be correct according to page 6 of chapter 15: "Regulation of phosphofructokinase is carried out byATP and citratewhich inhibit the enzymeand byADP and AMP which stimulate it"
Reaction: F-6-P + ATP --> F-1,6-BP + ADP + H+
Response: Credit will be given for 24e (in addition to the intended 'correct' answer d) - d and e are both equally correct - this was simply a mistake in constructing the question.
Question #29 "Once pyruvate enters the mitochondria, ______"
E should also be correct.
Justification: When pyruvate enters the mitochondria, it does not yield equivalents of nucleotide triphosphate by substrate level phosphorylation, because the 3 carbon atoms from pyruvate are oxidized BEFORE nucleotide triphosphate equivalents are produced in the Citric Acid Cycle. The first carbon is released after pyruvate is "oxidatively decarboxylated be means of a multienzyme complex called pyruvate dehydrogenase" (Ch. 16, Page 4). The second mole of carbon is released by action of the enzyme isocitrate dehydrogenase and the third mole of carbon is released by action of alpha-ketoglutarate dehydrogenase (Ch. 16, Page 7). Thus, all three carbon molecules are completely oxidized before any substrate level phosphorylation by action of succinyl CoA synthetase are produced making choice E also correct.
Response: Challenge to 29 not accepted since it only asked if pyruvate gave rise to NTP by substrate level phosphorylation (nothing was implied or stated about the timing (i.e. before the carbon atoms were oxidized to CO2 or not) ... it only asked it did
give rise to NTP, and it does, so e is not correct.
Question #33 "Which one of the following would NOT occur upon treatment of preparation of mitochondria with a specific inhibitor such as cyanide?"
E should be correct.
Justification:The answer D "ATP would be produced by substrate level phosphorylation" was the answer given to NOT occur upon treatment of preparation of mitochondria with a specific inhibitor such as cyanide. ATP would still be produced by substrate level phosphorylation because specific inhibitors act to "block electron transport at a specific site…" (Ch. 16, Page 19). Thus, the specific inhibitors would indeed block oxidative phosphorylation which occurs specifically in the inner membrane of the mitochondrion. However, the question does not specify which portion of the mitochondrion that specific inhibitors on, so substrate level phosphorylation would still be occurring in the mitochondrion via the Citric Acid Cycle in the matrix of the mitochondrion.
I selected option (E). The answer was (D) however it does not specifically ask what happens in the mitochondria so I approached it from a cellular level. I believeATP would be produced bysubstrate-level phosphorylation in the cytosol at least until NADH & FADH2 accumulate to the point where substrate-level phosphorylation stops. The cell could also operate in an anaerobic manner to bypass the ETC where specific inhibitors act.
This challenge is regarding question 33.
Key answer: D (ATP would not be produced by substrate level phosphorylation)
I believe that choice E, none of the above (all would occur upon treatment of a preparation with a specific inhibitor), is correct.It is my understanding that when a preparation of mitochondria is treated with a specific inhibitor, the electron transport chain is disrupted but substrate level phosphorylation would still occur via the 1 GTP -->1 ATP produced per TCA cycle (which is within the mitochondria).
#33 – electron transfer would not "cease" when treatment with cyanide. Since it affects the pathway after complex IV, there is still reduction potentials for an electron to transfer down the complexes that come before.
Response: Credit will be given for 33e (in addition to the intended 'correct answer d); it IS possible that the cell could also operate glycolysis in an anaerobic manner to bypass the ETC where specific inhibitors act, thus allowing ATP to be produced by substrate level phosphorylation. The statement that electron transfer would not "cease" is incorrect. If complex IV is blocked with cyanide, electron transfer would cease since complex IV would accumulate in the reduced form and thus the system would backup, first with cytochrome c accumulating in its reduced form, then complex III, then ubiquinone, and so forth.
Note added by SCH: Unless this cell is some sort of anaerobic microbe, it's going to die fairly quickly from inability to maintain its energy charge.
Question 48:
The answer key is “E” – “All of the above correctly identify where the atom is incorporated.”
However, I would like to challenge for another answer to be accepted as a correct answer, which is answer A.
In exam 2, 2009 provided on the class website, question 30 indicated:
30. Which of the following is CORRECT:
a. Pyridoxal phosphate is a cofactor in glutamate dehydrogenase
b. The oxygen in urea comes from bicarbonate
c. The enzymes of the urea cycle are inhibited by N-acetylglutamate.
d. Dihydrofolate reductase is one of two enzymes required to convert folic acid to tetrahydrofolate.
e. None of the above is correct.
The answer original answer was “B”.
And the challenge accepted “E” as another answer with the explanation below:
(2) Question 30: "e" will be scored correct (in addition to the intended correct answer "b"); Answer "e" is being accepted due to discrepant diagrams presented indicating the origins of the different atoms of urea.
According to the challenge response, answer “E” is accepted because some other sources said something different but “B” is still a correct answer. Therefore, “the oxygen in urea comes from bicarbonate.”
The reaction that fixes NH4+ with ATP and bicarbonate is catalyzed by carbamoyl phosphate synthetase and “this enzyme is found in the mitochondrion where the NH4+ is released from glutamate by glutamate dehydrogenase” (Dental biochemistry manual). And the only bicarbonate involves in the urea cycle is in the mitochondria. This leads statement “A” – [The oxygen is incorporated in the cytosol] to become an inaccurate statement. Therefore, “A” should be accepted as an answer for question 48 since the question asks for a “DOES NOT correct” statement.
On question 48, there are two possible answers: A & E.
As I studied for this test, I used the 2009, 2010, and 2011 exams to get some practice questions. In exam 2 from 2009, there was a question that asked the following:
30. Which of the following is CORRECT:
a. Pyridoxal phosphate is a cofactor in glutamate dehydrogenase
b. The oxygen in urea comes from bicarbonate
c. The enzymes of the urea cycle are inhibited by N-acetylglutamate.
d. Dihydrofolate reductase is one of two enzymes required to convert folic acid to tetrahydrofolate.
e. None of the above is correct.
The correct answer was B, confirming that oxygen in urea comes from bicarb.
As I was deciding between A & E on our exam, I thought back to this question and put A, that there wasn't an oxygen added to the urea in the cytosol because it came from the bicarb in the mitochondria where the nitrogen is fixed to form carbamyol phosphate.
I understand that the syllabus tells us that the oxygen comes from water and that occurs in the cytosol which is why I think that E should remain a correct answer as well.
I want to challenge question 48 (the answer given was E, but I believe that A should also be accepted because of the answer to a question on a past exam):
In the synthesis of urea, the four different atoms are incorporated in different steps. In the following, which does not correctly identify the organelle where that atom is incorporated into urea?
A: The oxygen is incorporated in the cytosol.
B: The carbon is incorporated in the mitochondrion
C: One nitrogen is incorporated in the mitochondrion
D: One nitrogen is incorporated in the cytosol
E: All of the above correctly identify where the atom is incorporated
The correct answer was stated to be E. However, in the 2009 exam for question 30, shown below, the answer given was B, which stated that the oxygen in urea comes from bicarbonate--the response to the challenge for this question even states that B was "the intendedcorrect answer". This indicated that the oxygen in urea comes from bicarbonate and is therefore incorporated in the mitochondria, which would mean that the statement in A would be wrong and therefore could be considered a correct answer to this question.