mikkelson@breakr.enet.dec.com (snopes) (04/24/91)
On a recent midterm for an introductory-level biology class, there were a few questions that I felt had better answers than the ones the instructor considered "correct". No amount of persuading or reasoning would make him change his grading, but for my own satisfaction I'd like to see how others would answer these simple multiple-choice questions: A "high-energy bond" a) absorbs a large amount of free energy when the phosphate group is attached during hydrolysis. b) is formed when ATP is hydrolyzed to ADP and one phosphate group c) is usually found in each glucose molecule; that is why glucose is chosen as the starting point for glycolysis. d) none of the above When NAD combines with hydrogen, the NAD is a) reduced b) oxidized c) phosphorylated d) denatured e) none of these The oxygen released in photosynthesis comes from a) carbon dioxide b) glucose c) ribulose biphosphate d) water e) atmospheric oxygen Which of the following has the most energy? a) AMP b) ADP c) ATP d) glucose e) NADPH +--------------------------------+--------------------------------------------+ | NOTE: No part of this signature may be reproduced, stored in, or introduced | into a retrieval system, or transmitted in any form or by any means | (electronic, mechanical, photocopying, recording, or otherwise) without prior | written permission, except in the case of brief quotations embodied in | critical articles and reviews. <mikkelson@breakr.enet.dec.com> | * David Mikkelson Digital Equipment Corporation, Culver City, CA USA * +--------------------------------+--------------------------------------------+
lamoran@gpu.utcs.utoronto.ca (L.A. Moran) (04/24/91)
David Mikkelson posted some questions from a recent introductory biology quiz at some school in California. I could not resist answering although I will probably regret it. I teach an introductory biochemistry course but my area of expertise is closer to molecular biology. 1. A "high-energy bond" a) absorbs a large amount of free energy when the phosphate group is attached during hydrolysis. b) is formed when ATP is hydrolyzed to ADP and one phosphate group c) is usually found in each glucose molecule; that is why glucose is chosen as the starting point for glycolysis. d) none of the above The term "high-energy bond" is very imprecise but it is useful when describing biochemical reactions. A high energy bond is one whose hydrolysis proceeds with a large negative change in free energy. The phosphoanhydride bonds in ATP are typical examples of "high-energy bonds" (note that this is not the same as bond energy). Answer (a) is wrong because it refers to absorption of energy during hydrolysis and this is ambiguous. Answer (b) is incorrect because ATP has one more high energy bond than ADP and not the other way around. Answer (c) is incorrect because glucose does not contain bonds that are readily hydrolysed. Thus answer (d) is correct. I suspect that this question was poorly written and that answer (a) was the one that the examiner wanted to be correct. 2. When NAD combines with hydrogen, the NAD is a) reduced b) oxidized c) phosphorylated d) denatured e) none of these Strictly speaking the NAD should be followed by a plus (+) sign to show that it is the oxidized form. When it combines with a hydride ion (H-) it is reduced. Answer (a) is probably the answer that was expected but if a a student of mine demonstrated that she knew the difference between "hydrogen" and hydride ion then I would give her a mark for (e). The question is poorly designed. I doubt very much that this little bit of trivia is important in an introductory biology course. 3. The oxygen released in photosynthesis comes from a) carbon dioxide b) glucose c) ribulose biphosphate d) water e) atmospheric oxygen The released oxygen is derived from the photolysis of water. Thus answer (d) is correct. I can't see any serious problem with this question. 4. Which of the following has the most energy? a) AMP b) ADP c) ATP d) glucose e) NADPH This is an impossible question for an introductory biology course. The molecule with the most "energy" is the one with the most covalent bonds. It is easy to understand this if you think about the amount of energy which would be needed to make the molecule. The answer is (e) but I'm sure that the examiner expected (c) because he/she really meant to ask which molecule contained the most USABLE energy. The question should be dropped from the exam. David, can you tell who teaches this course (ie. who made up the exam) and where it was taught? I would also like to know what textbook was used. -Larry Moran Dept. of Biochemistry
msw1633@summa.tamu.edu (WHITSITT, MARK STEVEN) (04/25/91)
In article <1991Apr24.134105.25827@pa.dec.com>, mikkelson@breakr.enet.dec.com (snopes) writes... >..... for my own satisfaction I'd like to see how others > would answer these simple multiple-choice questions: > > A "high-energy bond" > > a) absorbs a large amount of free energy when the phosphate group is > attached during hydrolysis. > b) is formed when ATP is hydrolyzed to ADP and one phosphate group > c) is usually found in each glucose molecule; that is why glucose is > chosen as the starting point for glycolysis. > d) none of the above > a) is wrong because a phosphate group is not attached in *hydrolysis* b) is wrong because hydrolysis breaks bonds; it doesn't *form* them. c) is wrong because the high energy bonds must be added by phosphorylation during glycolysis (ie F-6-P) in order to gain energy in the form of ATP. These high energy bonds are not present in glucose per se. --This leaves d) as the correct answer. >When NAD combines with hydrogen, the NAD is > > a) reduced b) oxidized c) phosphorylated d) denatured e) none of these > Very simple. NAD is the oxidized form which is subsequently *REDUCED* when combined with H to form NADH. >The oxygen released in photosynthesis comes from > > a) carbon dioxide b) glucose c) ribulose biphosphate > d) water e) atmospheric oxygen > the answer is d) water (I'm pretty sure, but it's been a while :) ) >Which of the following has the most energy? > > a) AMP b) ADP c) ATP d) glucose e) NADPH > glucose has the "most energy" potential as more high energy bonds can be formed and subsequently utilized in ATP. But looking at each individual molecule, The gamma Phosphate high energy bond probably makes it the one with the most usable physiological energy. NADPH, however, has more bonds overall (high energy or otherwise) and may be considered to be the most energetic. This question is a very poorly worded question and would require that the person answering had heard the lecture in which the teacher explained his rationale and what exactly he meant by "the most energy" Don't you agree? Mark S. Whitsitt, N5RJF Texas A&M University, Dept of Biochemistry Bitnet: MSW1633@TAMSIGMA College Station, Tx. 77843-2128 Internet: MSW1633@SIGMA.TAMU.EDU (409) 845-0832 "You can't throw darts when you're empty, man" -- another Schadelism
sarima@tdatirv.UUCP (Stanley Friesen) (04/26/91)
In article <1991Apr24.134105.25827@pa.dec.com> mikkelson@breakr.enet.dec.com (snopes) writes: > A "high-energy bond" > a) absorbs a large amount of free energy when the phosphate group is > attached during hydrolysis. > b) is formed when ATP is hydrolyzed to ADP and one phosphate group > c) is usually found in each glucose molecule; that is why glucose is > chosen as the starting point for glycolysis. > d) none of the above I choose (a). (b) is simply backwards, and (c) is essentially irrelevant, though I suppose a (weak) case might be made for (d) on the grounds that (a) is worded rather poorly. >When NAD combines with hydrogen, the NAD is > a) reduced b) oxidized c) phosphorylated d) denatured e) none of these It is (a) reduced. Taking on hydrogen is the opposite of taking on oxygen. [I.e. it is energetically equivalent to *losing* oxygen]. And since, in chemistry, the word for loss of oxygen is 'reduction', thus NADH is the reduced form of NAD. The NAD form of the molecule is the oxidized form, and there is no phosphate involved, so phosphorylation is not involved. >The oxygen released in photosynthesis comes from > a) carbon dioxide b) glucose c) ribulose biphosphate > d) water e) atmospheric oxygen The answer here is (d) water. The hydrogen in the water ends up on the NAD (or a related molecule), leaving raw oxygen. The oxygen in the carbon dioxide is retained in the resulting glucose. (Sugars do, after all, contain oxygen as well as carbon and hydrogen). Ribulose biphosphate is not involved in photosynthesis (it sounds like a early precurser to RNA). >Which of the following has the most energy? > a) AMP b) ADP c) ATP d) glucose e) NADPH The answer is (d) glucose, because it can be oxydized into carbon dioxide to produce a great many ATP molecules (I think about 30 in aerobic respiration). -- --------------- uunet!tdatirv!sarima (Stanley Friesen)
frist@ccu.umanitoba.ca (04/26/91)
In article <212@tdatirv.UUCP> sarima@tdatirv.UUCP (Stanley Friesen) writes: >In article <1991Apr24.134105.25827@pa.dec.com> mikkelson@breakr.enet.dec.com (snopes) writes: ... other answers to Quiz deleted > >Ribulose biphosphate is not involved in photosynthesis (it sounds like >a early precurser to RNA). > >--------------- >uunet!tdatirv!sarima (Stanley Friesen) Ribulose bisphosphate is the acceptor for CO2 in the reductive pentose cycle aka Calvin cycle for carbon fixation. This reaction is catalyzed by ribulose bisphosphate carboxylase/oxygenase (RUBISCO). Ribulose bisphosphate is, therefore, about as intimately involved in photosynthesis as you can get! For those interested, the reaction in plants with C3 metabolism is 3 Ribulose-bis-P + 3 CO2 --> 6 glyceraldehyde-3-phosphate In plants with C4 and CAM metabolism, phosphoenol pyruvate is the initial CO2 acceptor, and carbon is transferred by way of intermediates to the Calvin cycle. =============================================================================== Brian Fristensky | Department of Plant Science | "There's a big ... machine in the sky... University of Manitoba | some kind of electric snake... coming Winnipeg, MB R3T 2N2 CANADA | straight at us." frist@ccu.umanitoba.ca | "Shoot it," said my attorney. Office phone: 204-474-6085 |"Not yet," I said,"I want to study its habits" FAX: 204-275-5128 |H.S. Thompson, FEAR & LOATHING IN LAS VEGAS ===============================================================================
mroussel@alchemy.chem.utoronto.ca (Marc Roussel) (04/27/91)
I realize that other people have posted correct solutions, but I'm hoping to start a meta-discussion, so please bear with me. Also, I hope Stanley doesn't view this as a personal attack. It isn't meant to be. In article <212@tdatirv.UUCP> sarima@tdatirv.UUCP (Stanley Friesen) writes: >In article <1991Apr24.134105.25827@pa.dec.com> mikkelson@breakr.enet.dec.com >(snopes) writes: >> A "high-energy bond" >> a) absorbs a large amount of free energy when the phosphate group is >> attached during hydrolysis. >> b) is formed when ATP is hydrolyzed to ADP and one phosphate group >> c) is usually found in each glucose molecule; that is why glucose is >> chosen as the starting point for glycolysis. >> d) none of the above > >I choose (a). >(b) is simply backwards, and (c) is essentially irrelevant, though >I suppose a (weak) case might be made for (d) on the grounds that (a) >is worded rather poorly. It's a little worse than that. Hydrolysis is the process in which a chemical group is removed by the action of water. (a) is therefore nonsense. > >> a) reduced b) oxidized c) phosphorylated d) denatured e) none of these > >It is (a) reduced. >Taking on hydrogen is the opposite of taking on oxygen. >[I.e. it is energetically equivalent to *losing* oxygen]. >And since, in chemistry, the word for loss of oxygen is 'reduction', >thus NADH is the reduced form of NAD. This definition of reduction is bizarre to say the least. Oxidation and reduction have to do with electrons, not with oxygen. >>Which of the following has the most energy? >> a) AMP b) ADP c) ATP d) glucose e) NADPH As someone else pointed out, this question is bizarre. What kind of energy are we talking here? Free energy? (Probably...) As I promised, I now wish to start a meta-discussion around this exam. I have always thought of service courses as a mistake of monumental proportions: the content is usually watered down and the emphasis is all wrong. I think that this exam is an ideal example of what happens to students whose exposure to a subject comes via a service course: they get a muddled view of the field. Note that I'm not just talking about Stanley (who probably gave more or less the answers the original instructor expected), but about the instructor who set this exam. I think it's clear that he never got a proper grounding in chemistry from the questions he asked. Should this worry us? I think so. There's enough material to learn in an undergraduate degree without forcing students to waste their time on the drivel which usually winds us passing for a curriculum in service courses. I speak partly from experience as an instructor in one particular service course. The problems as I see them are many and varied. The root problem however is class sizes. Administrators like service courses because they see it as appropriate for these to have very high student to teacher ratios. This makes it difficult to set a high standard (because one is then forced to prepare fairly standard exams to avoid spending all of one's time marking) and even more difficult to get the kind of feedback one needs to decide how appropriate one's approach to a subject is for the particular group being taught. As a result of the generally low standards in service courses, the large publishing houses seem to have decreed that all textbooks intended for them shall be thoroughly pablumized. The whole experience seems to be designed to turn students off, no matter how hard an individual instructor tries to find ways to reach them. As if that weren't bad enough, try asking the target department what they think should be in your course! You'll get a list twenty miles long. Mind you they don't expect you to cover anything in any depth... Just give the students "a general overview". Needless to say, this is no help at all. The question I must ask myself is "Should we bother?" I can teach my class about redox chemistry until I'm blue in the face, but if the biology teacher expects them to "know" that oxidation has something to do with oxygen, what am I to do? (I don't mean this as an attack on biologists. The same is true of many chemists w.r.t physics, physicists w.r.t. math, and so on.) I think about these questions a lot these days. I have no solutions, but I'd love to hear from you if you have any ideas. Should we do away with service courses altogether or just think up new and more creative ways to deliver them? Should we replace them with frequent extradepartmental guest lectures in mainstream courses? I await your opinions. Sincerely, Marc R. Roussel mroussel@alchemy.chem.utoronto.ca
shahn@hstbme.mit.edu (Sam Hahn) (04/27/91)
The majority of these questions are very poorly worded and could be interpreted in a number of ways. Let me play the "devil's advocate" and answer some of these questions nonconventionally. > A "high-energy bond" > a) absorbs a large amount of free energy when the phosphate group is > attached during hydrolysis. > b) is formed when ATP is hydrolyzed to ADP and one phosphate group > c) is usually found in each glucose molecule; that is why glucose is > chosen as the starting point for glycolysis. > d) none of the above (D) is the correct answer. (A) is wrong because phosphate groups are not attached during HYDROLYSIS. (B) is wrong for the same reason as (A). (C) is wrong because more than a single high energy bond is present in glucose...furthermore I'm not sure if glucose even contains "high energy" bonds. Oxidative phosphorylation derives energy from glucose not because it absorbs the energy of bond hydrolysis but because it uses redox reactions to alter chemical composition. I'll have to look in my old organic chemistry book to see what the bond energy is for C-C and C-O and O-H bonds. > When NAD combines with hydrogen, the NAD is > > a) reduced b) oxidized c) phosphorylated d) denatured e) none of these (A) is the answer. The reaction is really NAD+ plus H- yields NADH if I recall correctly. What you are really doing is adding one proton and two electrons. The net effect is the addition of one electron or the REDUCTION of oxidation state. IF THE REACTION IS TAKEN TO BE LITERALLY: NAD plus H yields NADH the answer would be (E) since no reduction or oxidation has taken place. Clearly no phosphorylation or denaturation has occurred. > The oxygen released in photosynthesis comes from > a) carbon dioxide b) glucose c) ribulose biphosphate > d) water e) atmospheric oxygen Oh boy, now you are really stretching my recall: Ok, I recall that in oxidative respiration, the H20 that is generated comes from atmospheric oxygen. Therefore, working in reverse, the oxygen released from photosynthesis must come from water or (D). > Which of the following has the most energy? > a) AMP b) ADP c) ATP d) glucose e) NADPH BAD BAD BAD BAD question. What does that mean? Does it mean which has the most readily accesible energy? Most chemical energy? My interpretation would be to use the old E=MC2 routine and say that the largest molecule has the most energy. I don't remember the structure of NADPH but I think ATP is still larger so I will say (C). What where the "correct" answers? Sam
sarima@tdatirv.UUCP (Stanley Friesen) (04/28/91)
In article <1991Apr26.142343.9514@ccu.umanitoba.ca> frist@ccu.umanitoba.ca writes: >Ribulose bisphosphate is the acceptor for CO2 in the reductive pentose >cycle aka Calvin cycle for carbon fixation. This reaction is catalyzed >by ribulose bisphosphate carboxylase/oxygenase (RUBISCO). Ribulose >bisphosphate is, therefore, about as intimately involved in photosynthesis >as you can get! >For those interested, the reaction in plants with C3 metabolism is > >3 Ribulose-bis-P + 3 CO2 --> 6 glyceraldehyde-3-phosphate Quite. As I remeber the details of this is there not also a + 12 H (in the form of NADH or some such, from the light reaction of photosynthesis) Also, as I add up the numbers, doesn't this reaction also produce something else (like 3 H2O ??). [I seem to remember that the generic formula for sugars (i.e. carbohydrates) is (CH2O)n]. leading to a reaction formula (for the dark reaction) of: 3 Ribulose-bis-P + 3 CO2 + 6 NADH2 -> 6 Glyceraldehyde-3P + 3 H2O + 3 NAD [Of course the light reaction involved removing the hydrogen from *6* H2O]. Or am I getting mixed up somewhere? -- --------------- uunet!tdatirv!sarima (Stanley Friesen)
sarima@tdatirv.UUCP (Stanley Friesen) (04/28/91)
In article <1991Apr26.185708.19178@alchemy.chem.utoronto.ca> mroussel@alchemy.chem.utoronto.ca (Marc Roussel) writes: <In article <212@tdatirv.UUCP> sarima@tdatirv.UUCP (Stanley Friesen) writes: <>In article <1991Apr24.134105.25827@pa.dec.com> mikkelson@breakr.enet.dec.com <>(snopes) writes: <>> A "high-energy bond" <>> a) absorbs a large amount of free energy when the phosphate group is <>> attached during hydrolysis. <>> ... <>I choose (a). <>... <>I suppose a (weak) case might be made for (d) on the grounds that (a) <>is worded rather poorly. <It's a little worse than that. Hydrolysis is the process in which a <chemical group is removed by the action of water. (a) is therefore <nonsense. Oops, I guess I didn't read that very carefully!! This is one of those cases where the intended meaning was so obvious to me that I didn't analyze it in detail. What is the term used in biochemistry for the process of dissociating water into H and O? <>> a) reduced b) oxidized c) phosphorylated d) denatured e) none of these <> <>It is (a) reduced. <>Taking on hydrogen is the opposite of taking on oxygen. <>[I.e. it is energetically equivalent to *losing* oxygen]. <> .. <This definition of reduction is bizarre to say the least. Oxidation and <reduction have to do with electrons, not with oxygen. Well, I currently you are indeed correct, that is how it is defined *now*. But historically the term 'oxidation' refered to a reaction in which oxygen was added to another compound. And I think that at a beginning level it is important to base the descriptions on this intuitive definition of oxidation rather than jumping right into talking about electrons. [I mean the beginner is likely to say 'but what do electrons have to do with oxygen?']. In a sense my comment was not a 'definition' so much as a description. It is after all true, that oxygen and hydrogen are opposite in thier affinities for electron, and thus impose opposite oxidation/reduction states. [For you beginners - the most natural ion of oxygen is (2-), the most natural ion of hydrogen is (+) - the bare proton, thus two hydrogens have exactly the opposite effect as one oxygen] Then of course one may go on from here and notice that pH is the log of the hydrogen ion concentration and relaize that acid/base reactions are closely related to oxydation/reduction reactions (in fact in some senses they are the same thing). As I said, this can get quite confusing to the beginner, going from oxygen to alkali. <>>Which of the following has the most energy? <>> a) AMP b) ADP c) ATP d) glucose e) NADPH < <As someone else pointed out, this question is bizarre. What kind of <energy are we talking here? Free energy? (Probably...) < As I promised, I now wish to start a meta-discussion around this exam. <I have always thought of service courses as a mistake of monumental <proportions: the content is usually watered down and the emphasis is all <wrong. I think that this exam is an ideal example of what happens to <students whose exposure to a subject comes via a service course: they <get a muddled view of the field. Note that I'm not just talking about Stanley <(who probably gave more or less the answers the original instructor <expected), but about the instructor who set this exam. Yeah, I suppose I did, I am real good at that. I also like to try to present things in a simple way for the beginner. Sometimes I suppose I get carried away and make things *too* brief. < I speak partly from experience as an instructor in one particular <service course. The problems as I see them are many and varied. The <root problem however is class sizes. Administrators like service <courses because they see it as appropriate for these to have very high <student to teacher ratios. Oh, just *lovely*, the *worst* possible criterion! A high student/teacher ration is just asking for poor education. The best courses are always the ones with relatively *few* students, so the teacher can give everyone some time and attention. (And so everyone can ask all the questions they want). < This makes it difficult to set a high <standard (because one is then forced to prepare fairly standard exams to avoid <spending all of one's time marking) and even more difficult to get the kind <of feedback one needs to decide how appropriate one's approach to a subject <is for the particular group being taught. As a result of the generally <low standards in service courses, the large publishing houses seem to <have decreed that all textbooks intended for them shall be thoroughly <pablumized. The whole experience seems to be designed to turn students off, no <matter how hard an individual instructor tries to find ways to reach <them. Yeah, its true I can scarcely stand most bginning texts. < I think about these questions a lot these days. I have no solutions, but <I'd love to hear from you if you have any ideas. Should we do away <with service courses altogether or just think up new and more creative <ways to deliver them? Should we replace them with frequent <extradepartmental guest lectures in mainstream courses? I await your <opinions. I do not know the answer here. It is difficult to figure out. Of course the most boring class I ever took was when I (stupidly) decided to take the non-calculus physics rather than the calculus physics. (Dumb - I bet even the calculus intro to physics course would have been - in your words - pablum). -- --------------- uunet!tdatirv!sarima (Stanley Friesen)
frist@ccu.umanitoba.ca (04/29/91)
In article <221@tdatirv.UUCP> sarima@tdatirv.UUCP (Stanley Friesen) writes: >In article <1991Apr26.142343.9514@ccu.umanitoba.ca> frist@ccu.umanitoba.ca writes: >>Ribulose bisphosphate is the acceptor for CO2 in the reductive pentose >>cycle aka Calvin cycle for carbon fixation. This reaction is catalyzed >>by ribulose bisphosphate carboxylase/oxygenase (RUBISCO). Ribulose >>bisphosphate is, therefore, about as intimately involved in photosynthesis >>as you can get! > >>For those interested, the reaction in plants with C3 metabolism is >> >>3 Ribulose-bis-P + 3 CO2 --> 6 glyceraldehyde-3-phosphate > >Quite. As I remeber the details of this is there not also a >+ 12 H (in the form of NADH or some such, from the light reaction of > photosynthesis) > >Also, as I add up the numbers, doesn't this reaction also produce something >else (like 3 H2O ??). [I seem to remember that the generic formula for >sugars (i.e. carbohydrates) is (CH2O)n]. > >leading to a reaction formula (for the dark reaction) of: >3 Ribulose-bis-P + 3 CO2 + 6 NADH2 -> 6 Glyceraldehyde-3P + 3 H2O + 3 NAD >[Of course the light reaction involved removing the hydrogen from *6* H2O]. > >uunet!tdatirv!sarima (Stanley Friesen) Okay, here it is, straight out of PLANT BIOCHEMISTRY (Goodwin & Mercer): (6) D-ribulose 1,5-diphosphate (RuDP aka RuBP) | v (6) [enediiol of RuDP] | + 6CO2 v (6) 2-carboxy-3keto-D-ribitol 1,5-diphosphate | + 6H20 v (12) D-3-phosphoglyceric acid |<- 12 ATP |-> 12 ADP v (12) 1,3 Diphosphoglyceric acid |<- 12 NADPH + 12H+ |-> 12 NADP+ + 12Pi v (12) 3-Phosphoglyceraldehyde | v and so forth through the Calvin cycle, and all of this effort just to make ONE hexose sugar (Fructose 6-phosphate). =============================================================================== Brian Fristensky | Department of Plant Science | "There's a big ... machine in the sky... University of Manitoba | some kind of electric snake... coming Winnipeg, MB R3T 2N2 CANADA | straight at us." frist@ccu.umanitoba.ca | "Shoot it," said my attorney. Office phone: 204-474-6085 |"Not yet," I said,"I want to study its habits" FAX: 204-275-5128 |H.S. Thompson, FEAR & LOATHING IN LAS VEGAS ===============================================================================