Challenges to exam 1 questions and responses are given here. In summary, we will accept question 49 c in addition to 49 e. The other challenges are not accepted.
Question 7.
I would like to challenge that answer A is also false. In the manual, chapter 11, pg. 9, it says at the top of the page that "Bacteria also often carry small circles of DNA called episomes or plasmids, which contains few other genes. Often these plasmids carry genes that specify resistance to antibiotics, thus they may be called resistance factors, or R-factors Therefore, A is also an incorrect statement because R-factors are not circular DNA, rather they are genes on the plasmid specifying resistance to antibiotics.
The challenge makes the case that the sentence cited in chapter 11 could be read so as to be misleading. But the sentence in the chapter about R factors says: "The genes that specify bacterial drug resistance are frequently found to reside on plasmids called R-factors." [emphasis from the manual], which seems unambiguous to me. I'm sure I also said in class that the DNA is called an R-factor and that the genes are called resistance determinants. So I'm not inclined to regrade this question, but I will keep in mind that not everything we tried to communicate was communicated perfectly when we decide what to do about students very close to a grade threshold at the end of the course. The reason this question puts emphasis on a terminology issue like this is that you will encounter multiple briefings and recommendations about R factors, and when you hear the term, you must understand that the stakes are much higher than just that a bacterium has an antibiotic resistance determinant. The R factor mediates multi antibiotic resistance, plus a sophisticated means to spread it.
Question 8
I believe this was an unfair question based on the wording of answer choice B, which states "glycine, because of its lack of a side chain, allows the strands of the triple helix to have close contacts." However, the notes indicate that glycine does not "lack" a side chain, but rather it's side chain (R group) is H. Stating that glycine "lacks" a side chain indicates that there is simply nothing present at this position.
The manual, chapter 4 (pg. 3), states: "note that, if R is not H (as it is in amino acid glycine), then C(alpha) has four different groups attached." And the lecture powerpoint, slide 6, states "in glycine, the R group is a second H atom, so glycine is not chiral…"
I chose answer choice D because Serine is phosphorylated by kinase- as stated in lecture powerpoint, slide 19. It is for this reason that I believe this was an unfair question, and all answers should be accepted.
The question wasn't about terminology, it was about functions in collagen. The function of glycine in collagen is as indicated. There is no such function as that suggested for serine in collagen. The claim is that by describing the H in the R position of glycine as not being a side chain, that the disclaimer is flawed and makes the question unreadable. One wouldn't normally call a single atom a chain. More importantly, it is not reasonable to believe that the question was written to test knowledge of some nuance of terminology like that.
Question 12:
Answer choice A is also incorrect (therefore should be a correct answer because of question) In chapter 9, page 7, paragraph 3 the T cell independent activation of B cells contradicts A. It states that when surface Ig on B cells bind antigen the Fc region directly activates B cell WITHOUT the need for T cell collaboration. Furthermore, on page 3 of the same chapter (paragraph 3) it states that for T dependent activation the B cell will ingest the antigen, present it on MHC II to present to Th cell without the use of Ab. The difference of these two pathways for B cell activation was my reasoning for choosing answer A. Therefore, answer A should also be accepted.
Statement "a" is not false. It is, in fact, the usual way for a B-lymphocyte to become activated. The alternative mentioned by the student, to become activated without T cell involvment, does happen for large repetitive antigens, like a bacterium. Swtiching of memory cells to IgM never happens. That's the false option.
Question 19-
I believe this was a mis-leading question because INR is the same thing as Prothrombin Time (PT), which is expressed in units of time. The notes (manual, chapter10 (pg. 16)),states INR is"the time required to coagulate…" and "prothrombin timeis subject to variation based on the source of thromboplastin used by the testing laboratory." The ch.10 powerpoint also describes Prothrombin time (PT/INR) as the "time to clot normalized by normal controls and adjusted for the potency of the thromboplastin is called INR…"
I believe answer choice A should also be given credit because this is expressed in units of time (10 minutes). It is misleading to offer this as an answer choice. This question was simply unclear.
"Normalized" in International Normalized Ratio essentially means PT divided by the PT of a normal control. That makes a normal result equal to 1. The history is that PT was reported in number of minutes, but there could be significant variation on what the average PT was from one lab to another or even one day to another based on variations in the reagents used. The INR is reported as PT/PTnormal with a further adjustment by a parameter supplied by the manufacturer of the reagents designed to remove any variation caused by quality of the reagents.
Question 39.
The lecture and material consistently placed emphasis on the peptide bond having a partial double bond character and residing in a plane configuration for the backbone of the polypeptide chain. The –H and –R group were not emphasized as being in the backbone, but rather as extending inside or outside the secondary structure based on hydrophilic or hydrophobic properties. I would like to challenge this question based on the wording of “backbone of a polypeptide chain” and believe ANS A (0) should be acceptable.
Question 39
Although the point was emphasized in class that the bond was partially planar, the number of bonds involved in this was never discussed. It was emphasized only that the peptide bond was not allowed to rotate. It is in the manual, but the instructor stated that his questions would come only from the powerpoints and lectures. It also is not in the conference. Therefore, all answers should be accepted.
The powerpoint has a slide in which the two rotatable bonds are shown (phi and psi). These two rotatable bonds were discussed in class, punctuated by the comment that the field of protein folding is lucky that one bond was not rotatable.
Question 48
Protein phosphorylation is considered a reversible modification because:
Correct answer: E. None of the above is the reason protein phosphorylation is considered a reversible modification.
Challenge answer: B. The free energy change for the phosphorylation reaction in the cell is close to 0KJ/mol.
Slide 16 from the Enzymes and reaction rates lecture states that "delta G values between 5 and –5 KJ/mol: reaction is easily reversible."
The question states that protein phosphorylation is reversible. Specific values for change in free energy for protein phosphorylation are not given in the slides nor in the manual. Based on the information provided, B would be a logical conclusion and is proposed to be accepted as correct.
It was stated multiple times in class that phosphorylation was reversible only because phosphatases can remove the phosphate. The delta G value both protein kinase and protein phosphatase reactions are very negative.
Question 48.
Phosphorylation is the process of putting a phosphate group on an amino acid for regulation outside the cell. Protein kinases phosphorylate tyrosine, threonine, and serine. Protein Phosphatases remove the phosphate and reform ATP. I believe the question was misleading and that Answer D should be acceptable.
Phosphatases do not reform the ATP.
49. Which of the following three statements is/are correct?
I. Any cofactor can be a prosthetic group.
II. Every cofactor is also a coenzyme.
III. Every coenzyme is also a cofactor.
a. only I
b. only II
c. only III
d. I and II
e. I and III
Slide 6 on the ppt says that cofactors can be called coenzymes (if they're "organic") or just cofactors if they're inorganic. Then you can have a prosthetic group which is a "tightly bound" cofactor. So that means if the cofactor is not tightly bound or if its a coenzyme then it can't be a prosthetic group. In that case that would make 1 wrong because any cofactor cannot be a prosthetic group. It could also be a coenzyme or just a loosely bound cofactor. So for 49 I believe C is right, because 3 is the only correct choice.
I answered [c. only III] because the way I understood cofactors as per the presentation/notes is that a cofactor can be either a coenzyme or a metal. There is a subset of cofactors known as prosthetic groups that are tightly bound. Not every cofactor is a prosthetic group.
The correct answer for this question is [e. I and III].
The reason I did not choose e is because when reading statement I, I do not agree that ANY cofactor can be a prosthetic group. There are some that just are not occurring in nature, and it will not happen. I think to me it is more of a wording problem. I understood the actual theory behind the question. Therefore, C should also be accepted.
Question 49: I do not believe statement I is correct. We were only given the definition of a prosthetic group in Ch 7 page 2 where it describes heme as a prosthetic group. Now in Ch 6 page 6 cofactors, coenzymes are described but prosthetic groups are not described at all. There is no way for us to correctly answer this question with the information given to us. Therefore, C should also be accepted.
Question 49. Which of the following three statements is/are correct?
I. Any cofactor can be a prosthetic group.
II. Every cofactor is also a coenzyme.
III. Every coenzyme is also a cofactor.
a. only I
b. only II
c. only III
d. I and II
e. I and III
Answer on key: E
Answer that should be accepted: C
In the enzyme lecture powerpoint (on slide 6), a prosthetic group is defined as a “tightly bound cofactor, such as heme in hemoglobin”. Weakly bound cofactors cannot be prosthetic groups; therefore ANY cofactor cannot be a prosthetic group. Statement I is false.
Answer c is acceptable.
Question 50
The answer stating that some enzymes were slow should also be accepted. Slow is a relative term, and some enzymes are, in fact, slow compared to other enzymes. Although this may not have been the intent of the question, the graph does show this fact.
The graph was discussed in class and the point was made several times that enzymes need to speed up reactions to the point where the energetics determine if the reaction occurs.