3511 Announcements, Refresh this page
Cumulative list of problem sets, exams, etc [from 2005]
[
Exam 1 /
Exam 2 /
Exam 3 /
Exam 4 /
Exams 1-3 Histograms /
Exam 4 Histogram /
molecular interactions /
helix/sheet /
amino acids /
SC 7 /
SC 8 /
SC 9 /
SC 10 pt1 /
SC 10 pt2 /
SC 11 /
SC 12-17 /
SC Chap 18 /
SC Chap 19 /
SC Chap 23 /
doyle_presentation
]
May 1, 2009: 9:00 am: Bring your Georgia Tech ID to the exam. Calculators will not be permitted. There are some computational questions. You will be required to set them up, but should not do the calculations.
May 1, 2009: 8:00 am: Some questions from students:
Dear Professor, I have some questions...
Ch. 17 Electron Transport and Oxidative Phosphorylation: For number 16, in choice A, does it mean freely permeable? I know the inner membrane is freely permeable to CO2, H2O, and O2 only, so if it were freely permeable, then choice A would be incorrect, because it is not freely permeable to small ions.
The correct answer is A, meaning that the statement given in A is incorrect because small ions cannot cross. The inner membrane is impermeable to nearly all ions and polar molecules. This is a confusing style of question that will not be on the exam.
Ch. 17 Electron Transport and Oxidative Phosphorylation: For number 19, in choice A, it says that F1 is found in the matrix. I feel like it could go either way-- while F1 actually located on the membrane, the book indicates that it does protrude into the matrix. Therefore, it could be considered as found in the matrix, although it is really found on the membrane. Can you clarify this? Also, can I confirm this with you (this is what I think from what the book said, but I just want to make sure)- that only the F1 structure has a "lollipop" shape and not the entire structure of ATP synthase?
The correct answer is E. I think you are over-interpreting these schematic diagram. The question is not supposed to be tricky.
Ch. 17 Electron Transport and Oxidative Phosphorylation: For number 22, I could not find this in the book, but I have that the products would be FAD and QH2, with FADH being oxidized and Q being reduced.
FADH2 is oxidized to FAD, Q is reduced to QH2.
General questions- are the questions in red not meant for our class, or were those omitted for a previous class (do we need to know those)? And will there be a lot of drawing reactions on the final? Is the format mainly going to be multiple choice/ fill in the blank, or more drawing and short answer?
The red questions are omitted for this class. So ignore them. Yes drawing of reactions will be required - as in the last midterm. But you will not need to do that for any of the metabolic reactions. Use the last midterm and the posted study guides. Watch the movies. There are questions on the movies.
Chapter 16: Citric Acid Cycle: I've been working with a few other students on this, and none of us can agree on a clear answer to number 16, which asks for the two main purposes of the Citric Acid Cycle. We are stuck between two options, B and C. B is "degradation of acetyl-CoA to produce energy and to supply precursors for anabolism." C is "degradation of pyruvate to produce energy and to supply precursors for anabolism."
The correct answer is B.
April 30, 2009:
I have consulted with Dr. Doyle. The policy is that one quiz and one exam will be dropped. If you don't take the final, the final will count as your dropped exam. This policy is final and immutable. I strongly recommend that you take the final no matter what your apparent grade is.
April 29, 2009:
The study guide for glucose catabolism has been added to the list of study guides below (See april 26).
Dear Professor, I calculate my grade be 88%. Is that enough to exempt the final with an A?
Dear Student,
Not with full certainty. You should take the final. If you get cumulative 90% or over you definitely get an A. Once the grades are in, I will look at the distribution, and if there is a reasonable minimum in the frequency distribution, I will lower that cutoff. But if the frequency reaches a minimum at 90%, then I will be forced to leave the cutoff there. I will take other factors into consideration. For example if you did the homework I assigned in class (i.e., if you emailed me your best estimate of the oxidation states of the atoms of pyruvate) or if you came to my office hours and asked questions about course material (as opposed to grades) and you are the highest B, I will definitely push you up to an A. If you did not do the homework, etc, then I am naturally less inclined to do something like that.
April 27, 2009:
Notes on the Final exam: The exam will be about 60% over material after the last midterm. The exam will cover all material listed on the course schedule as posted here (starting April 1).
April 26, 2009:
Study Guides: (these chapters refer to Edition 2, if you have Edition 3, please use the chapter titles to find the correct chapter number.
Chapter 14 (Glucose Catabolism)
Chapter 16 (Citric Acid Cycle)
Chapter 17 (Electron Transport and Oxidative Phosphorylation)
Chapter 24 (Replication)
Chapter 25 (Transcription)
Chapter 26 (Translation)
Previous Exam
April 24, 2009: ANIMATIONS
ATP Synthase
1
/
2
DNA Replication
1
RNA transcription:
1
Translation
1 (clamation)
/
2
/
3
/
4
April 22, 2009 #1
If you have questions about your exam and quiz scores, please contact Anna (annaduraj@gatech.edu), our TA.
April 18, 2009 #2
The final might have a question about this.
April 18, 2009
Office hours for next week are MWF at 3:00 PM in 1309 IBB.
April 15, 2009
A study Guide for Friday's quiz is posted here.
April 12, 2009 #2
Office hours for the next week are - Monday 3:30-4:30; Wednesday 4:15-5:15; Friday, 3:15-4:15. Office hours are conducted in 1309 IBB.
April 12, 2009
A key to friday's exam is posted here.
April 9, 2009
I have carefully compared the test with the study guides below. If you focus on the study guides you will do well. There are no surprises. The test contains fill in-the-blank questions, and will require you to draw structures, including several mechanisms. Check out the red text below, which I just added.
April 8, 2009
Note there is an exam on Friday, April 10.
Enzyme Inhibitors Study Guide (Powers)
1) Reversible Inhibitors
Chapter 12 Part 2a
Competitive Inhibitors (most important), Non-competitive Inhibitors, and Other Types
Example: succinate dehydrogenase
Determination of the type of inhibition with Lineweaver Burke Plots
Problem 19
KI values (Determination with Lineweaver Burke Plots, KI as an equilibrium constant)
Calculations with KI
Problem 20
2) Design of Competitive Inhibitors (Design Compounds with substrate-like features or Compounds that resemble the ts (transition-state Inhibitors)
Examples: Alcohol Dehydrogenase, Serine Proteases (Figure 11-26), Coagulation and natural inhibitors
April 6, 2009, post #2
Note there is an exam on Friday, April 10.
Study Guide and Problems for Enzyme Kinetics Lecture of April 6, 2009 (May)
* Work the following problems:
Chapter 12: Problems 5, 6, 7, 10, 15, 16, 17
(These problems are the same in both the second and third editions of the textbook).
* Learn the following Concepts:
1. Understand the basic idea of formation and decomposition of the ES complex during enzymatic catalysis.
2. Learn the Michaelis-Menten equation, and know the derivation of the MM equation using the steady-state assumption.
3. Understand the meanings of Vmax, Ks, Km and kcat/Km, and understand the differences between Km and Ks. When does Km most closely approximate Ks?
4. Understand Lineweaver-Burk plots and how they are used to determine Vmax and Km.
April 6, 2009
Note there is an exam on Friday, April 10.
A Study Guide for Chapter 11 (Hud)
Read all of chapter 11.
Memorize and understand the five catalytic mechanisms used by enzymes.
Be able to draw NAD+ and NADH (Figure 11-4)
Be able to draw (with proper chemical structures) and explain the mechanism of RNase A (Figure 11-10).
Understand the key points of the lysozyme mechanism.
Be able to draw (with proper chemical structures) the mechanism of a serine protease (Figure 11-29).
Problems to work out (the beginning of each problem is given to help you locate the correct problems in case you have a different version of the text). These will not be collected, but they will be excellent preparation for the exam.
Problems:
1. Choose the best description of an enzyme...
2. Which type of enzyme (Table 11-2) catalyzes the following reactions...
3. What is the relationship between the rate...
5. Draw a transition state diagram of (a) a nonenzymatic...
6. Approximately how much does staphylococcal nuclease...
8. The covalent catalytic mechanism of an enzyme depends...
11. Wolfenden has stated that it is meaningless to distinguish between...
13. Lysozyme residues Asp 101 and Arg 114 are required for...
16. Diagram the hydrogen-bonding interactions of the catalytic triad...
21. Tofu (bean curd), a high-protein soybean product, is prepared...
April 1, 2009
Today in class Dr. Hud started Chapter 11. He talked about the high specificity of enzymatic reactions. But in an exception to this general rule chymotrypsin can hydrolyze both peptides and esters, too. So in comparison to other enzymes chymotrypsin is a sort of molecular garbage disposal. Cofactors: Why do enzymes need cofactors? Why can't protein do it all? Metal ions? All that redox chemistry can be useful. Transition state theory: It is very useful to be able to sketch a reaction coordinate, and understand reaction free energy, forward actviation free energy, reverse activation free energy. What is the definition of a transition state? What is the relationship between reaction free energy and equilibrium constant.
Very few students are taking notes. Some students in the front row are sleeping. This merits a discussion.
May 5, 2005
Questions from student:
Is it CoQ or complex III that pumps 4 protons
to the intermembrane space in the electron transport chain? The figure
shows CoQ, but the reading says it is complex III (p. 506). Yes, you are right.
Figure 17-8 shows that Q pumps the protons but the text on page
506 says that Complex III pumps the protons. Don't worry, its not important.
Is the Electron transport chain and/or oxidative phosphorylation considered
an aerobic process? I think you have identified a sort of sematic issue.
Electron transport is an oxidative process, NADH is oxidized, O2 is reduced, protons
are pumped. ATP synthesis, which is called oxidative phosphorylation, is actually not an oxidative process, in
my interpretation. I am going to check this with some of my colleages (Drs. Powers
and May), who are smarter than I am.
There is a typo on page 217 in the student companion. #21 b should read
117,000, but it reads 11,700. Thank you. I will send that to Judy Voet.
I am still confused about the dissipation of energy stuff. Not only do I not
fully understand the explanations in the book, but how do I find more
information about phosphorescence? You don't believe in the second
law of thermodynamics? Shame on you. (maybe I need clarification of this question.)
Do we need to memorize constant values for calculation of delta G? (faraday's
constant, h, c)? No.
Chapter 17 problem 3 and chapter 18 problem 4 solve the same thing
differently. chapter 17 keeps the order of the more positive reaction and
reverses the more negative, while in chapter 18 the more positive reaction is
reversed. which way is correct?
For Chapter 18, problem 4a, there is an error in the solution. The O2 half reaction should have
a stoichiometric correction of 1/2. You can write these reactions in either direction, but you have to
change the signs of the potentials (or the standard free energies) when you switch direction.
Do you mean to know the start and end products of figure 19-9 or 19-11
(figure 19-10 is not a mechanism) I mean 19-9. I fixed that, thank you.
Will there be any study questions for chapter 21?
No.
May 4, 2005
I will conduct a review session tomorrow night at 6 PM in our classroom.
May 4, 2005
Student question: I had a question regarding Chp 23. The tRNA picture that you showed us
during class, I remember you saying that we need to know where the codons are located on it and its structure.
I cannot find that picture on your website. Are we still supposed to know it? It might not be a bad idea to be familiar with
that figure. It is here:
web.chemistry.gatech.edu/~williams/bCourse_Information/6521/nucleic_acid/trna/trna.html
You need to understand the relationship between the cloverleave (2D) structure and the 3D structure. If I point to a position on
one of them can you find it on the other? BTW the anticodon is on the tRNA. The codon is on the message.
May 1, 2005
There will be a review session, tomorrow (monday) at 6:00 PM in our class room.
April 30, 2005
I am in the process of posting the SC chapters. Justin is helping me scan them.
April 30, 2005
The syllabus has been revised once again. This time four scenarios for point allocation
have been given. The scenario that will apply to you will depend on which portions of the final that you take,
and on the balance of the scores of your midterms and the corresponding chapters of the final.
April 29, 2005
The syllabus has been revised (problems have been added) The revision date on the current syllabus is
April 29a, 2005.
April 29, 2005
Check here at least once a day between now and the final for new info. A new syllabus has been posted.
April 29, 2005
After regrades, the average on the last exam increased to 69.
April 29, 2005
For the final exam, all of you will be responsible for:
Chapter 17
pages 492-499 (stop at section in inhibitors)
pages 500-517 (start at Section C, but you don't need to know all of the fine mechanistic detail, for example pages 507,510)
Chapter 18
pages 529-537 (stop at section B)
pages 540-543. The figure on page 541 shows you the big picture.
Chapter 19
pages 568-582 (skip over the fine mechasnistic detail. For example, for figure 19-9 (not 19-10), know the inputs and outputs, but that's enough)
Chapter 21
pages 685-687 (stop at section B)
Chapter 23
pages 725-747
pages 760-766 (stop at "Loops of DNA...")
April 28, 2005
The powerpoint images from Dr. Doyle's presentation yesterday have been posted (see list above).
April 24, 2005
A histogram for exam 4 has been posted (see list above).
April 24, 2005
The AYSA U11 Boys ended a 2-game losing streak, by defeating Peachtree City, 2 to 1. The last five minutes
were nerve-wracking.
April 24, 2005
Course Survey Reward. If at least 70% of the students registered in this course
complete the online course survey, then there will be a reward of donuts for all on the last day of class.
April 24, 2005
Final Exam. The final exam will be offered in two sessions. Session 1 will be Tuesday, May 3rd at
6:00 PM. Session 2 will be Friday, May 6 at 2:50 PM. Session 2 is the official final exam period for this course. You can take the exam
during either session. If you plan to take the exam during the first session, please inform me by email, by wednesday (4/27) afternoon.
If you attend session 1, you are not permitted to attend session 2.
[The following is a reiterization and minor
clarification of information posted on Feb 16 (below)]
The final exam will be divided into 'chapters'. Each final exam chapter will correspond directly with
one of the midterms, and will cover the same material as the corresponding midterm, and will be in similar format.
The numerical score for each final exam chapter will be compared with that of the corresponding midterm, and the
lower score of the pair will be replaced by the higher score. So if
you have missed a midterm, your score for that midterm will be determined by that chapter of the final exam.
If you got 100% on one of the midterms, you might as well skip that chapter of the final.
April 19, 2005
Frequency histograms for exams 1-3 have been posted.
April 17, 2005
The key for Exam 4 has been posted (above). If you have any issues, please contact me by tomorrow at midnight.
April 14, 2005
Question from Student. I was wondering what do we need to understand or get out of section 3. Catalytic
Mechanisms in Chapter 11. That is a very confusing section of the book. Those are not catalytic mechanisms, those are
features of catalytic mechanisms. The main thing is to understand the mechanism of the serine proteases. Put your energy there. Make sure
you know how that enzyme accelerates the reaction.
Another question from a Student. You said that the we should relate the serine proteases to
bi-bi ping pong mechanism explained on page 334 in chp 12. But how do we go about that since the serine protease mechanism
only shows one substrate? Look at the mechanism very carefully. The second substrate is water. So
A = peptide, B = water, P = fragment with the new N-terminus, Q = fragment with the new C-terminus.
April 14, 2005
The review session is at 2:30 in B6A Boggs (that is not B6, it is next door).
April 14, 2005
The student companion for Chapter 11 has been posted.
April 13, 2005
Question from student. I just wanted to ask you what I should focus on in Chapter 14. I am a
little overwhelmed by the high detail of all the specific reactions, enzymes and compounds. Focus your attention on the schemes
on pages 384, 393 and 414 (these have redundant info). For each reaction/enzyme find the most descriptive paragraph about it
in the bulk of the chapter, but skip over the specific mechanism. For example for enzyme PFK, read everything about it in
section 2C on page 388. There is some additional important information on PFK in section 4 (start page 406, but stop
at the 3rd paragraph of page 408). For Aldolase read section 2D, but stop at "There are two Mechanisms...". For Tim, read the
first 3/4 of page 391,
but stop at "Glu 163 and His 93...". For GAPDH and GPK, read only the first paragraphs of those sections, respectively. But make sure you
read the section on "Coupling between..."on page 396. For the mutase PGM, read only the first paragraph. So basically I am saying that
you need to know the general properties but not the specific mechanisms. If I give a reaction, you should know what it is, what enzyme
catalyzes it, if it is regulated, and how.
April 13, 2005
I will give a review session tomorrow at 2:30. If you are going to attend please send me email so I know how
many to expect. Check back here tomorrow at noon for the location.
April 12, 2005
For the test on Friday: you do not need to memorize reaction mechanisms of the metabolic pathways. But you do need to know them
very well. For example if you are presented with a reaction, you should be able to say where it fits in,
what kind of enzyme catalyzes it, whether of not it is regulated, how it is regulated, etc. I think it is a pretty good idea on memorize
the serine protease mechanism.
April 10, 2005
The course syllabus has been revised. Problem sets have been added.
April 9, 2005
The exam on friday will cover
Chapter 11, pages 281-299, 307-319
Chapter 12, pages 322-342
Chapter 13, pages 353-358, 361-364, 368-370 (CoA, NAD, FAD)
Chapter 14, pages 382-416
Chapter 15, pages 426-428, 452-453
Chapter 16, pages 466-470 (Section 1), 482-487 (Section 4)
April 3, 2005
A new syllabus has been posted, with today's revision date. Please note that the next exam has been rescheduled for Friday,
April 15.
The AYSA U11 Boys Blue team lost their last two games. Very discouraging. But yesterday some of them played up with the U12s and
soundly defeated some other team (never did find out who they were).
Mar 18, 2005
Chapter 11 of VVP is very important. We went over the General Properties of Enzymes in detail (3-1). We have previously talked
about most of what is discussed in 3-2 (Activation Energy, RXN coords, transition states, etc), but reviewed it again here. The
section on General Catalytic Mechanisms (3-3) is sort of indecipherable in the book, because it is written as if those
catagories are separate and independent when in reality they are overlapping and redundant. But we went over it in class
and I clarified it. Omit section 3-4 (lysozyme). Serine proteases (section 3-5), yes, we are doing that, and in detail.
You must know the mechanism (page 313) cold. That is a good project for your spring break.
Mar 14, 2005
The key for exam 3 has been posted. If you have any issues with it you must alert me by wednesday after class.
Mar 13, 2005 8:15 PM
Questions from another smart student:
I have a couple of questions regarding the 2 "is it glucose?" coordinate files.
First, on whatisit1, I don't think it is glucose. It looks more like Galactose
or Talose in a deoxy form.
You are correct, it is galactose, and it is 1-deoxygalactose. The deoxy was not
intentional my part. For some reason many of the sugars that I downloaded from the "Ligand Depot"
are missing their 1-OH groups. I notified them. You will not have to deal with things like that on the
test.
If it is one of these, how can you tell the difference in the
stereochemistry HCOH of galactose in position 2
(highlighted red on page 197) versus the HOCH of talose.
For talose and galactose in the pyranose (6-membered ring) form, there are
4 endocyclic (on the
ring) OH groups (at positions 1,2,3,4). [whatisit1 is missing the OH at the 1
position]. The 5 OH becomes an ether upon cyclization. The
6 OH is exocyclic (ie it is not on the ring). For talose the stereochemistries
at positions 2,3,4 are the same. For whatisit1, you should be able to see that
3 and 4 are up, and 2 is down (when oriented as in my chemdraw figures of glucose). So
it cannot be talose. Orient the ring in the same way as my chemdraw figures. You can then compare the stereochemistries at positions
2, 3 and 4 to those glucose. At position 4 the stereochemistry is wrong for glucose. It is 1'-deoxygalactose.
Whatisit2? I can't find anything to explain the extra OH group at C3. Is it
supposed to be there? It definitely isn't glucose.
Did you consider the ketose sugars? Check on page 198. This one is not missing any atoms.
My son's soccer: the Coweta Cannons did not shoot straight. AYSA U1 Blue are now at 3 wins and 0 losses.
Mar 13, 2005 (later on)
One very smart student noticed that the coordinate file of beta-D-glucose was missing a hydroxyl
group. I fixed it.
Mar 13, 2005
For Chapter 10 and Exam 3, see list below under March 8.
Mar 11, 2005 (later)
The Glucose page has been updated. Review it very carefully and make sure that you understand it. Some questions are posed at the bottom
of the page. Those are coordinate files. You have to figure out if those are glucose or not.
Mar 11, 2005
The Syllabus has been revised. Additional problems have been assigned for Chapters 7-9.
Mar 10, 2005
Later on. A page with some info on carbohydrates is posted here.
Mar 10, 2005
The Student Companion looks like it could be really useful. On the course syllabus, I will be assigning some problems
from it. If you look on the course syllabus under Chapter 8, it says "1,3; SC(1,2,5,7)". That indicates questions 1 and 3
are from the text and questions 1,2,5,7 from the Student Companion. For question SC(1) omit the parts about unonic acid, alditols
and reducing sugars. The idea is not to have all those structures memorized (note Mar 8, 2005 announcement), but to be
very familiar with them.
[My son's U11 soccer team is 2 W and O L so far. Big game against the Coweta Cannons this weekend.]
Mar 8, 2005
For the Exam next week:
Chapter 7. Page 161 up through the middle of page 180.
Chapter 8. All. Please learn the (a) structures of ribose, glucose, galactose, fructose, and sucrose,
(b) cyclization reactions,
(c) cellulose, chiton, glycogen. You will not have to know any specific structures post page 207. But please read
over the WHOLE chapter.
Chapter 9. All. You will not be required to draw any structure in this chapter. However you will be required
to recognize them. You will need to know a fatty acid, or glycerophospholip when you see it. You will be required to
identify various components of lipid molecules. For example if you are shown a structure of a glycerophospholipid,
you should be able to
outline the glycerol, the fatty acid, the phosphoryl group, and the enthanolamine (or whatever X is).
Chapter 10. (updated 3/13)) Pages 239-252, Pages 264-276. We did not cover the thermodynamics of transport (page 265),
so skip that. You do
not need to memorize any structures from this chapter. As I noted in class, there is something wrong with figure 10-35.
Mar 7, 2005
The syllabus has been revised.
Feb 22, 2005 (later)
Protein Electrophoresis. Page 104. The first paragraph of the section in polyacrylamide electrophoresis
is sort of incoherent. It is not correct to say that, "Molecular separations are based on sieving effects as
well as electrophoretic mobiility", because sieving effects are an intrinsic part of electrophoretic mobility.
Size, shape, charge, and matrix (agarose, acrylamide, etc)
effect electrophoretic mobility. Also, the direction of protein migration depends on pH and on the pI.
Finally, electrophoresis cannot be converted to a verb, so don't say "I am electrophoresing this protein".
Feb 22, 2005
Student questions:
Histidine in the book is neutral with two N's and no NH, you drew it with a 1+
charge? At which ph does it have a 1+, 2+ charge or is neutral?
Under physiologal pH (from say from 5-8) histidine is either neutral, with one NH or +1, with two NH's. It is never +2. If you look at the table on
page 80, or the amino acid web page, it is shown as a monocation (+1) with two NH's. That is the predominant state above the pKa,
which is 6.04.
Do we need to memorize the pK's for pI calculations or are you going to
provide those?
Don't memorize those. You need to know what the pI is, but you will not be required to calculate it.
Do we need to know the 3 letter code?
Maybe.
Amino Acid Problem Set:
1f/g) h-donors/acceptors are every NH/=O in the backbone?
If you are asking whether all NH's and Os of the back bone are engaged in hydrogen bonding, the
answer is yes, but remember that assumes it is not near the end of a helix.
At the ends of the helix, you can see the 3 NH's on the N terminus
do not form hydrogen bonds. Check out the C-terminus, you can see that
there are three oxygens there that do not form hydrogen bonds.
1h) h-donors/acceptors in helix are o1, o5...N0, N4...? (i=i+4)
I'm not quite sure what this is asking. Look at the a-helix web page, and you can
that the hydrogen bonds are from Oi to N4i+4
2) how do we draw the 120 degree angle?
You don't need to draw a 120 degree angle, you need to rotate the molecule through 120 degrees.
Draw a tetrahdedran, with two bonds
in the plane of the paper. Rotate around one of those bonds. Three atoms should move.
5) I understand the reasoning about the disulfide bonds fron the answers on
the announcement page but I still do not know how to figure out the fraction
of activity regained!
There is a section of the book related to this question starting on page 151 of VV&P.
The percentiles are not really important. The real answer is yes or no.
Do you get proper folding or no?
Helix Problem Set:
3) do we just add up the turns of each helix? How do we consider the wider
turn of the superhelix?.
You need to figure out what the rise and pitch of a helix formed by residues i and i+7.
4) does this beta sheet have short connections? Is it parallel or
antiparallel? do we alternate amino acids with charges?
The simplest answer is that the sheet is anti-parallel, two strands with one beta-turn.
That turn would work best with pro-gly.
In the sheet, if you want a hyrophobic side and a hydrophilic side, you need to alternate hyrophobic and hydrophilic residues along
the backbone.
Feb 22, 2005
Error in the book, on page 153, section 4C. An n-residue protein does not have
2^n (2 raised to the n) torsion angles. An n-residue protein has 2xn (2 times n) torsion angles.
Feb 19, 2005
Questions/Comments from a student. My responses are red.:
Question: I have a few questions regarding the problem sets.
Which of following aqueous conditions might you expect to denature Techase A?
0.2 M Sodium Chloride
8.0 MUrea
0.1 M 2-Mercaptoethanol
saturated O2
100degreesC
I would say the Urea and the 100 degrees C conditions will cause denaturation. The 2-mercaptoethanol is a
reducing agent used for disulfide bonds, and since there are no disulfide bonds, it is not necessary.
The saturated O2 is used for reduction so would not help in this case. Is my reasoning above correct?
Also, I have no idea what the sodium chloride would do in the solution.
That's right, heat and urea will denature a protein. You can oxidize and reduce disulfides without denaturing. 200 mM NaCl
is very close to physiological and will not denature a protein. It is not generally possible to
denature a protein with salt.
Problem 5:
From my understanding of the readings from pages 152-153, in both cases (a,and b),
the fraction of activity regained will b about 1%.
And that the energy can only be regained at a much higher percentage
if a little bit of 2-mercaptoethanol is added... Is this reasoning correct?
Not quite. The sequence of events is important.
If a protein is denatured then reduced, it assumes the random coil state,
with all disulfide bonds (S-S bonds) broken. If
you then oxidize, you will form incorrect disulfide bonds. These incorrect crosslinks prevent protein
from renaturing properly. However if
you renature first, then oxidize, you will generally reform the correct disulfide bonds, in the native state.
From a-helix/b-sheet problem set.
Problem 4
From my understanding, there are two main issues to this problem. One is to make sure the
antiparallel strands match up in residues so that they nestle efficently between the neighboring sheets,
and two, to make sure that one side is hydrophobic and the other is
hydrophilic (alternating residues in the strand)...Based on this, I came up with this strand which is meant to become a 6*6 beta sheet:
GDAEGD
AEGDAE
GDAEGD
AEGDAE
GDAEGD
No, that is not quite right. Maybe you are thinking about Figure 6-16. When two sheets
stack on each, then you have to consider packing. But for the question here, which refers to an isolated sheet,
that is not relevant. The only real restriction within a sheet is that prolines are not allowed.
You are correct about the alternating sequence, that will give hydrophobic and hydrophillic faces.
The main thing lacking in your answer
is in designing the turns. We will talk about that in class tomorrow.
Feb 19, 2005
The syllabus has been revised. The exam on Wednesday will cover (a) Chapter 4 (all except the section on the
RS system, page 88), (b) Chapter 5, section 2D only (this is the section on electrophoresis), (c) Chapter 6 (all).
Feb 18, 2005
The broken link to the last problem set has been fixed.
Feb 16, 2005
(1) The syllabus has been revised (problem sets updated). The current version has today's date at the top.
(2) An alpha-helix and beta-sheet problem set has been
posted here. (3) New Grading Scheme. As discussed in class today,
the final exam will be divided into 'chapters'. Each final exam chapter will correspond directly with one of the
midterms, and will cover the same material as the
corresponding midterm. The numerical scores for each final exam chapter will be compared with that of the corresponding midterm,
and the lower score of the pair will be replaced by the higher score. So if you miss a midterm, your score for that midterm will be determined
by that chapter of the final exam. If you get 100% on one of the midterms, you might as well skip that chapter of the final. As I mentioned
in class today, if you have issues with this grading policy, please alert me by email within the next 24 hours so we can set
up a meeting to talk about it. Privacy assured.
Feb 10, 2005
(1) I have received questions on the cross-linking question. Look at Figure 4-6 on page 83 to see what I am
asking you there. It is true that under some circumstances other amino acids besides cysteine are involved in cross-links, but not so readily
or so commonly as cysteine. So for now we will assume all cross-links are between two cysteines. Although it is not indicated on Figure 4-6, the
reaction is readily reversible. Add oxygen to oxidize ((x-link). Add BME (yes it smells bad, but it is beta mercapoethanol - a
common reducing agent) to reduce, and break the x-link. (2) I will not be in class on Friday. Someone else will
be proctoring the quiz, after which you can leave. (3) If you have not handed your exam back in, do so on Monday. Do no give
your exam to anyone except me. (4) A revised syllabus has been posted, with revision date Feb 10. Since the original syllabus is obviously
unrealistic, this will be an ongoing process.
Feb 9, 2005
(1) A revised syllabus has been posted, with revision date Feb 9. (2) Please hand your exam back in today.
I am going to look over a few of the questions. (3) A list of issues with the textbook will be maintained (here).
Feb 7, 2005
(1) A Problem set for Chapters 4 and 5 has been posted
(here). (2) There will be a QUIZ ON FRIDAY. For the quiz,
please learn (a) the chemical structures
of all the amino acids, (b) the peptide bond, (c) the amino acid sidechain pKa's, especially histidine. The quiz will contain questions very similar
to 1a-e, 2, and 3 on today's problem set.
Jan 31, 2005
The Key to Exam 1 is posted (here). If you have any issues with
the key, such as alternative interpretations, please contact me
by Wednesday.
Jan 30, 2005
If Georgia Tech is closed on Monday (possible, not likely) the exam will be postponed. If Georgia Tech is open,
then the exam will be conducted on schedule. I have no choice on this. If I give special breaks to so some students,
I am being unfair to the rest.
Jan 28, 2005 (late in the day)
The course syllabus has been updated, this time for real. Also, the error in the answer key for the Molecular Interactions
problem set, noted in class today, has been corrected. In the Key for question 4 (molecule B) the deltaG for the last step is
positive 10 kcal/mole not negative 10 kcal/mol. A positive deltaG signifies an unfavorable process. The transfer
of molecule B from neat solution to water is unfavorable.
Jan 28, 2005 (way way after class)
On the course homepage, some links to free molecular visualization programs have been posted.
Pymol is probably more powerful than Rasmol, but a little more difficult to use.
Jan 28, 2005 (way after class)
There is an exam on Monday. It will cover Chapter 1 (all), Chapter 2 (all), Chapter 3
(sections 1 and 2 only). All material covered in lecture is fair game for the exam. The exam questions will be
very similar to the assigned questions.
Jan 28, 2005 (after class)
A revised course syllabus has been posted. The revision date
on the current syllabus is Jan 28. Note that some additional problems have been added.
Jan 26, 2005 (after class)
The nucleic acid problem set has been revised. A fifth question has been added.
Jan 26, 2005
A problem set for nucleic acids has been posted here.
Jan 24, 2005
I think the sample pH calculation on page 34 is wrong. Anyone else have an opinion? On a related
note, for problem 7, only do 7a, not the rest.
Jan 24, 2005
A pdf file the history of nucleic acid structure has been posted (here)
Jan 24, 2005
The key for the last problem in the Jan 19 problem set have been posted (see link in
problem set.)
Jan 19, 2005
Molecular Interactions problem set has been posted
here.