Dec. 14, 2007
Grades were posted around 6 pm in D2L and also submitted to the university electronically. All the faculty participated -- we agonize over the final cut-offs. Several people actually did move up a letter grade from the 3 pts of extra credit for the evaluation online. If you want to look at your final exam with the handwritten key for reference, come by Dr. Z's office in January.
Drs. Baldwin & Ziegler will be out of town for a couple of weeks starting 12/15, but should have email access starting 12/16.
Have a great holiday!
Dec. 6, 2007
Help session today 1:30-3:00 in the classroom -- bring questions (and clickers if not already turned in). Also, remember that Trahern Jones is available 9:30-1:30 today, and Megan Paul during her usual hours this evening.
Remember that next Mon. 12/10 at 5 pm, the course evaluation (3 pts extra credit opportunity) will automatically go offline on D2L -- it's set for that deadline, so don't wait.
Dec. 5, 2007
Be sure you turn in your clicker today if you haven't already done so. Your TA will have your problem sets #11 and your quiz #4 if you'd like to pick those up today at class.
Additional reading for lecture 39 (in Nelson & Cox, Lehninger Principles of Biochemistry, 4th ed.):
- protein-DNA recognition p. 1087-1095
- p53 function p. 472
- nucleases p. 307-309
- nucleosomes p. 938-940
Remember the help session tomorrow (Thurs.), 1:30-3:00 pm, in regular classroom. Bring your questions about the material, including problem sets, old exams, etc.
The final exam will certainly include the following:
- a Henderson-Hasselbalch calculation
- a free energy calculation for a metabolic reaction
- a free energy calculation for ion transport across a membrane
- a linked functions question
Final exam grades and final letter grades for the course should be posted by Friday evening Dec. 14. Please do NOT email questions about how you did or when things will be graded while we're doing the grading, because the time pressure to get it done in 2 days is pretty intense and we'll be quite busy. When grades are posted, that will be in the course announcements. No electronic answer key will be constructed so none will be posted for Exam 4 and Exam 4 will not be returned, but you may come to Dr. Ziegler's office in January if you'd like to look over your graded exam and a hard copy of the key.
Dec. 3, 2007
The lipid structure on the quiz was supposed to be phosphatidylcholine (that was one of the answer choices), but in fact it was phosphatidylserine. Rather than make distinctions among wrong answers, all students will receive the 2 pts for that question, so some students picked up an additional 2 pts.
Dec. 2, 2007
The last of the lecture notes for the semester are posted, Nucleic Acids 2, in 2 parts to keep the size manageable:
Nucleic Acids 2, part 1 (PDF)
Nucleic Acids 2, part 2 (PDF)
Please bring clickers to turn in before or after class Monday to your T.A. Be sure they get your name crossed off the section's sign-out sheet from beginning of semester. If you forget to bring yours on Mon., bring it Wed.
Quiz keys are posted: Form A PDF; Form B PDF
P.S. 11 is due Monday 12/3.
Nov. 30, 2007
Course evaluations: We very much value your feedback in our efforts to keep improving this course. The course evaluation is now "live" on D2L (click on "Content"), and participants will earn 3 pts of extra credit. It will remain available for 10 days, from today (Friday 11/30) through 5:00 pm Monday Dec. 10. The survey records which of you participated in order for us to award the extra credit, but not whose responses are whose, so your ratings and comments will be anonymous. After we decide on the minimum points required for each letter grade at the end of the course, we will go back and look at extra credit for anyone within 3 pts below a cut-off -- in such cases, the 3 pts would lift you to the higher letter grade. Thank you very much for taking the time to provide your input.
A few practice problems on nucleic acids have been posted, since there's no problem set on nucleic acids: [PDF]
Regraded exams may be picked up after class today or Monday. Changes have been entered in D2L.
Nov. 29, 2007
A clarified slide on Ion-Selective Channels has been posted for Transport part 3 notes, top slide on p. 6. You can either just reprint one page, p. 6 of those re-posted/corrected notes Transport part 3 (PDF), or print out the clarified slide as a stand-alone: Ion Channel Clarified Slide (PDF).
First set of Nucleic Acids notes are posted in 3 parts:
Nucleic Acids 1- part 1 (PDF)
Nucleic Acids 1- part 2 (PDF)
Nucleic Acids 1- part 3 (PDF)
Nov. 28, 2007
P.S. 11 due date has been extended to MONDAY, 12/3. However, note that problems on the problem set may be useful in studying for the quiz this Friday. You're welcome to turn in the problem set to your T.A. this Friday if you wish. Problem sets should be ready to return to you on Wed. 12/5 OR on Thurs. 12/6 at the help session, OR you can pick it up from your T.A. after that.
Next week assistance hours: normal office hours/preceptor hours will be held Mon.-Wed., except that Trahern Jones will NOT hold his usual 4-hour Wed. night hours on 12/5, but instead will be available for 4 hours Thurs. a.m. 12/6 (Dead Day), from 9:30 a.m. to 1:30 p.m. The faculty-lead help session will be from 1:30 to 3:00 pm on Thurs. 12/6. Megan Paul will hold her normal hours on Thurs. 12/6 p.m.
Nov. 25, 2007
Notes for upcoming Mon. and Wed. lectures (Transport) are posted in 3 parts:
Transport part 1 (PDF)
Transport part 2 (PDF)
Transport part 3 (PDF)
Exam regrading requests due by 4 pm Wed. 11/28
Nov. 19, 2007
Exam grades are posted on d2l. Tentative/approximate grade distribution is also posted. Regrading requests will be due by 4 pm on WED. 11/28.
If you want to pick up your exam Tues., see Irene Barriga in the BMB office, 362 BioWest, and be prepared to show an ID.
P.S. 11 (last one!) is posted, not due 'til Fri. Nov. 30.
Final exam help session on Dead Day had to be rescheduled due to conflict with a CoS awards reception. The help session (with faculty) will be 1:30-3:00 pm on Dec. 6, Dead Day, in CESL 103, the regular classroom. Note different time from what was on original lecture schedule.
Nov. 18, 2007
You're only responsible for lipids material through p. 7 in 2nd half of lipids notes. Prostaglandin H2 synthase (cyclooxygenase, "COX") will come up again in Dr. McEvoy's lecture, and you've already seen it in one of Dr. Baldwin's lectures. As a reminder, here's the jmol routine about its inhibition by NSAIDs:
http://www.biochem.arizona.edu/classes/bioc462/462a/jmol/cox12/cox121.htm
Drs. Baldwin and Ziegler will be out of town Tues. through Sat., probably without email access.
Exam keys are posted: Form A (yellow) PDF; Form B (white) PDF.
Nov. 16, 2007
Notes on membrane proteins (for Mon.) are also posted in 2 parts -- still very large, sorry!
Membrane Proteins part 1 [PDF]
Membrane Proteins part 2 [PDF]
Nov. 15, 2007
Notes on Lipids for Fri. (tomorrow) are posted in 2 parts because for some reason the file size was huge (too many high resolution graphics?) We'll probably only get through 2/3 of the material, through membrane lipids and (hopefully) lipids as intracellular signals, and you wouldn't be responsible for the rest.
Lipids part 1 [PDF]
Lipids part 2 [PDF]
We hope to be able to give back exams on Mon. after class.
Nov. 14, 2007
Exam today: If you tend to ask a lot of questions during the exam, it would be nice if you could sit in front rows (either section of room) or back rows of front section, or in end seats, so we don't have to climb repeatedly over other people to answer questions. We don't want to discourage questions, but we don't want to disturb other students if possible. Backpacks, etc. UNDER SEATS to facilitate our climbing through rows.
Nov. 13, 2007
Chad Park has also rescheduled his office hour for tomorrow (Wed.), 11:00 a.m.-12 noon, in 251A BioWest. Dr. McEvoy's office hour this week is tomorrow (Wed.), 9:00-10:00 a.m.
Remember the preceptors' review session tonight, 7:00-9:00 pm, 301 Chavez.
No ruler is needed on the exam after all.
Nov. 9, 2007
Last 3 slides (discussion questions and conclusions) about penicillin from end of class Fri. are posted [PDF]. Exam won't have a lot of carbohydrate material on it, and certainly nothing about glycosaminoglycans, proteoglycans, or glycoproteins since we didn't get to those in class.
Despite an enormous investment of his time, the podcast Dr. Baldwin made for enzyme mechanisms isn't work (sound won't synchronize with slides, a software problem of some sort). However, the general consensus is that the enzyme bisubstrate kinetics and reversible inhibition overviews on those podcasts are very useful.
Nov. 8, 2007
2nd part of lecture notes on Carbohydrates, including learning objectives, is posted [PDF].
P.S. 10 (due Fri. 11/16) is posted -- mainly carbohydrates and a little enzyme regulation, so it would be worthwhile working on it this weekend to get some practice working with carbohydrates before the exam.
Office hours: Monday is a holiday. Dr. McEvoy is rescheduling her office hour for next week from Mon. to WED. 9:00-10:00 a.m.
Erika's Tues. 9:00-10:00 office hour -- she'll be there; you don't need an advance appointment.
2 of the preceptors (Steve and Erin) have volunteered to hold a special review session for the exam Tues. evening, 7:00-9:00 p.m., room 301 Chavez.
Drs. Baldwin and Ziegler will be out of town with no email access from Fri. night to Tuesday morning. If you have questions over the weekend, Dr. McEvoy will be checking email, and you can certainly try emailing other course personnel also.
A student after class asked about how Vitamin K analogs (drugs like dicoumarol, and poisons like warfarin) would inhibit clotting, mimicking vitamin K deficiency and causing hemorrhaging. That wasn't clear in Wed. lecture, so here's a PDF explaining it if you're interested. It's NOT required material for the exam.
Nov. 7, 2007
Reminder: Exam 3 (Wed. 11/14, after the Veterans' Day holiday) will cover enzyme kinetics/inhibition, enzyme mechanisms, enzyme regulation, and carbohydrates, as well as material on recent problem sets/discussion sections.
To view Dr. Baldwin's podcasts, your browser must have Adobe Flash Player installed. A free Flash Player is available from Adobe by going to their download center at http://www.adobe.com/downloads/. Most on-campus computers should have Flash installed as it is a pretty standard browser plug-in. If the campus computer has a Flash Player and you still cannot view the podcast, it is likely that the file is being blocked (by a firewall, etc.?) and you should talk to the IT support for the computer lab that you are using.
Nov. 6, 2007
Most of the carbohydrates notes are posted [PDF] -- 2nd set of notes will be just a few additional slides on glycoproteins, and some learning objectives for carbohydrates. (Additional figure showing boat conformation was added late Tues. night to original slide at bottom of p. 12 in notes.)
Dr. Baldwin has done 2 podcast reviews of enzyme inhibition, part 1 and part 2. Please email Erika from D2L website (her D2L email is linked there) to let her know if you find the podcasts useful. They took Dr. Baldwin a LOT of time and effort to make, and he needs your feedback! These and the earlier podcast on bisubstrate kinetics are also linked on the lecture notes directory.
Nov. 5, 2007
Just to be sure you all knew by the time we got out of class today -- the answer to the clicker about PKA that was inadvertently posted in the Enz. Regulation lecture notes was correct as posted (#3 was correct)!
Oops -- don't worry about the second "reading assignment" shown in Enz. Reg. 2-3 notes -- "chapter 14" pages were material on Ca2+-CaM from another textbook. What you need of that material will be covered in class.
Nov. 4, 2007
A clicker was put on the front desk of the classroom a couple of weeks ago, in a "container". If you lost your clicker, just describe the container to Dr. Z. and you can re-claim it.
Quiz grades are posted on D2L. The quiz mean was 11.6, and median was 12. That's still significantly higher than the average for Quiz #1.
Nov. 2, 2007
P.S. 9 key and Quiz keys (Form A PDF, Form B PDF) are posted.
Biochem seminar today (4:05 pm, BioWest 208) is being given by Prof. Neel Ghosh, UA Chem Dept., on "New methodologies for targeting and detecting protein-protein and protein-nucleic acid interactions".
Exam 3 (Wed. 11/14, after the Veterans' Day holiday) will cover enzyme kinetics/inhibition, enzyme mechanisms, enzyme regulation, and carbohydrates, as well as material on recent problem sets/discussion sections.
Nov. 1, 2007
Notes for Enzyme Regulation 2-3 (about 1.5 lectures, for part of Fri. & next Mon.) are posted [PDF].
Remember Quiz #3 tomorrow.
Oct. 31, 2007
Happy Hallowe'en!
Besides previously assigned reading on enzyme regulation in Lehninger Principles, chapter 6, there's some information being covered in class in Chapter 14, pp. 389-391.
Regraded exams will be available in class today (Wed.)
Oct. 28, 2007
Exam regrading requests are due by 4 pm Monday (tomorrow). Envelope will be on table at front of room during class.
Notes for Enzyme Mechanisms 4 (for tomorrow, Mon.) are posted [PDF].
Notes for Enzyme Regulation 1-2 (about 1.5 lectures, for Wed. & about half of Fri.) are posted [PDF].
Oct. 26, 2007
P.S. 9 is posted.
P.S. 8 is due today.
Quiz #3 is next Friday.
Oct. 25, 2007
Notes for Enzyme Mechanisms 3 (for tomorrow, Fri.) are posted [PDF].
Oct. 24, 2007
We're trying an experiment: Dr. Baldwin has recorded a short (< 10 min) podcast review of bisubstrate kinetics. Please try it!
Some people's quiz #2's were attached to other peoples' exams during the reassembly process. The only ones Dr. Z. still has are in the E's and H's, which may mean that the attached quizzes were "out of phase" throughout that part of the alphabet. PLEASE CHECK THE QUIZ AT THE BACK OF YOUR EXAM 2, and if it's not yours, please return it to Dr. Z. so the rightful owner can pick it up.
Oct. 23, 2007
Notes for Enzyme Mechanisms 2 (Lecture 25, for Wed.) are posted (PDF). Sorry, the PDF file is huge -- must be some high resolution graphics in it.
Oct. 22, 2007
Exams will be returned at the end of class today. Grade curve (approx. letter grades) is posted -- grades were definitely lower than Exam 1, and lower than last year's Exam 2. Range was 13 pts to 96 pts. We didn't set out to write a much harder exam, but it turned out that way. Keep working hard on problem sets (150 possible pts) and remember that there are still 290 pts of exam grades to be determined.
Regrading requests will be due Mon. 10/29 by 4 pm.
Oct. 19, 2007
Notes for Enzyme Mechanisms 1, continued (Lecture 24, for Mon.) are posted (PDF)
P.S. 8 (due next Friday) is posted. Remember that since there's no class today (Fri.), P.S. 7 is due Monday at 3 pm.
Exams will be returned to you on Monday (no news yet on grades or curve).
Oct. 16, 2007
Notes for Enzyme Mechanisms 1 (including irreversible inhibition) are posted [PDF].
Oct. 15, 2007
Exam today -- bring calculator (memories cleared) and a ruler, or use the neon-green strips of notecards we'll provide at the exam as "straight-edges". You can't use your own notecards or credit cards, etc.
Oct. 13, 2007
Enzyme Kinetics 3-Inhibition notes have been RE-posted with some typos corrected (noted in class yesterday) but some features have also been added to graphs, such as the relationship of the "inhibited" Vmax to the "uninhibited" Vmax for noncompetitive and uncompetitive inhibition; units have been added to axes of graphs. Except for the units on p. 6 graphs, the only changes since Friday afternoon were on page 10 and after. If you printed the original notes between Friday and Sat. 5:15 pm, you'll get all the corrections/additions if you re-print pp. 10-16 and add just add units to graphs on p. 6.
Oct. 12, 2007
Enzyme Kinetics 3-Inhibition notes are posted [PDF]
P.S. 7 is posted [PDF].
Be sure to bring a small ruler as well as a calculator (with memories cleared) to exam on Monday.
Oct. 11, 2007
Dr. Baldwin has pulled together a collection of about 40 multiple choice & short answer questions on enzyme kinetics for you to study, not as sample exam questions, but just as a study guide [PDF] to help you review enzyme kinetics (no enzyme inhibition questions included). No, the answers aren't posted.
Dr. Baldwin's enzyme kinetics review clickers and additional slides from beginning of class 10/10 [PDF]
Some Study Objectives for Bisubstrate Reactions:
- Know how to write Cleland kinetic mechanisms for ordered and random sequential, and for ping pong reactions.
- Know distinguishing features mechanistically (presence/absence of ternary complex; presence/absence of modified enzyme form connecting two half reactions) for sequential vs. ping pong reactions.
- Realize that for ORDERED sequential reactions, you can't measure simple equilibrium binding affinity of second substrate by itself, only of first substrate, whereas for random sequential reactions, you can measure equilibrium binding individually of both substrates.
- For reaction S1 + S2 --> P1 + P2, be able to recognize (or sketch) double reciprocal plots of 1/vo vs. 1/[S1] for several different concentrations of [S2], and know how those let you distinguish sequential from ping pong, but not random from ordered sequential. Realize that you can't obtain a REAL "Vmax" unless BOTH substrates are saturating, which you can't get from a primary plot like this -- you need to get Vmax values for one substrate at several different concentrations of the other substrate, and plot those to extrapolate to infinite concentration of second substrate to get Vmax with both substrates saturating.
Oct. 10, 2007
Quiz grades are now re-posted after correcting grading of #2. Mean and median were 13.9 and 14. Good job!
Oct. 8, 2007
Oops -- the answer keys for the quiz had the question about conformational stability worded differently from how it was worded on the quizzes you took. I must've modified the key and forgot to change the question version or vice versa. Anyway, the posted key now matches the quiz you actually took, and quizzes will be regraded to fit the question as you received it, so all the posted quiz grades will presumably change by either +3 or –3 points in the next day or so. I'm really sorry -- the buck stops (and starts) with me! And thanks very much to the only student who asked me about it today. M.Z.
Lecture 21 (Enzyme Kinetics 2, Bisubstrate Reactions) notes for Wed. are posted [PDF].
Oct. 7, 2007
The Lecture 20 (Enzyme Kinetics 1) notes for Monday, originally posted last Thursday, have been modified (new slides added) in the first 8 pages of notes as well as having new slides added at the end, so consider this version (PDF) as all new. The original was still useful for studying if you were studying enzyme kinetics over the weekend.
Oct. 6, 2007
The error mentioned at the end of class Friday, on top slide on p. 4 of Enzymes Introduction notes, has been corrected. You can either correct it in your notes by hand or print the corrected p. 4 from the posted notes.
Dr. McEvoy is out of town from Thurs. until next Wed.; Dr. Ziegler will cover Dr. McEvoy's Monday office hour (10/8, 9:00-10:00 a.m.)
Quiz 2 keys (form A, form B) are posted, as is P.S. 6 key.
Oct. 4, 2007
1st 8 pages of notes for 2nd enzymes lecture (for Mon., but might start Fri.) (Enzymes: Kinetics 1, PDF). A few more pages will be added before Mon., and announcements will give page numbers for the additional slides.
Notes for Friday are posted (Enzymes: Introduction, PDF).
Oct. 3, 2007
One slide added to 3rd set of Hb notes (HbS, sickle hemoglobin), and preceding slide altered a bit -- both are on p. 14 in PDF notes, if you want to just print p. 14.
Oct. 2, 2007
Notes for Contractile Proteins are posted [PDF].
Oct. 1, 2007
Error on p. 16 (top slide) of 3rd set of Hb lecture notes: Hb Milwaukee is NOT a mutation in distal His. It's a mutation in the Val (βV67E) near the distal His that normally helps keep heme Fe in Fe2+ state. With Glu instead of Val, the anionic Glu forms a coordination bond to the Fe, and stabilizes the oxidized Fe3+ form of the heme (metHb). PDF file has now been fixed -- you could just reprint p. 16 and substitute it.
Regrading is finished -- pick up your regraded exams in class.
Sept. 29, 2007
Clickers from the 4 Hb lectures are posted (no answers!) for you to use in studying for quiz and exam.
Sept. 28, 2007
Typo in 3rd set of Hb lecture notes, bottom of p. 7 of PDF file: 2,3-bisphosphoglycerate has about 5 negative charges at pH 7, not 3. It was corrected in PDF notes Friday 5:30 pm.
P.S. 6 is posted.
Sept. 27, 2007
3rd set of hemoglobin lecture notes [PDF] (for Fri-Mon) is posted.
Sept. 26, 2007
"Thinker" material will start promptly 15-20 min after beginning of discussion sections this week.
Remember that regrading requests for Exam 1 are due by 4 pm Friday.
Sept. 24, 2007
Correction on top slide on p. 8 of 1st set of hemoglobin notes: typo (mental slip?) -- correct proximal His to F8, and distal His to E7. (PDF is now corrected.)
Second set of Hb notes are posted, for Wed.-Fri. [PDF], including material at the end on linked functions (pp. 8-9), with questions/"assignment" to do/think about prior to a clicker for Friday.
Sept. 22, 2007
Notes are posted for first couple of lectures on myoglobin/hemoglobin [PDF] (new last slide, bottom of p. 17, added early afternoon 9/23).
Sept. 21, 2007
Exams will be given back AFTER class today. Check that points were correctly transcribed from individual pages onto the cover sheet. REMEMBER not to write ANYTHING on the exam itself if you might want something to be regraded.
Regrading requests: turn in graded exam just as you received it to Dr. Ziegler in envelope at front of classroom, with an attached note explaining what page and problem number you think was not graded appropriately. Note that for subjective partial credit decisions, one person graded a single page on every exam and was as consistent as they could be (with notes for reference). We can't go back and change partial credit for just one student. Deadline for turning in regrading requests is 4 pm next Friday, September 28.
The Exam 1 keys are posted: [Form A] [Form B]
Exam 1 grades are now up on D2L (as of right after class).
Exam 1 approximate letter grade distribution is posted through "Gradebook" link at left.
A "handout"/reading assignment on linked functions with Cys ionization as an example is posted. You should find it useful for P.S. 5.
Sept. 20, 2007
Lecture notes for
Dr. Cordes' guest lecture tomorrow on protein evolution are posted [PDF].
We hope to be able to post exam grades tomorrow afternoon and give them back after class tomorrow.
P.S. 4 is due tomorrow, hard copies to be handed in as usual.
P.S. 5 is posted. Problem #3: be sure you do the measurements on the graph, and work on calculating fraction unfolded, fraction folded, Keq for unfolding, and ΔGo' for unfolding BEFORE you come to discussion section next week!
Sept. 19 , 2007
Today's lecture on protein folding will be very important in your ability to do P.S. 5 (to be posted this Fri., due Sept. 28), so pay particular attention to experimental determination of protein conformational stability (ΔGo'unfolding).
Remember that tomorrow (Thurs.) discussion sections are NOT meeting in normal time/place. It's computer lab "open house" 8 am-4 pm in 243 BioWest for P.S. 4. That lab is not an open-use UA lab and is not available at other times for you to use.
Sept. 14 , 2007
Be sure when you get graded problem sets back to look at the posted answer keys -- those are more complete or extensive than you might need to get full credit, but you're likely to learn something from reading the explanations. While the questions are different on the exams each year, taking the 2005 and 2006 exams for practice, with a 50-min time limit, and then carefully reading the posted keys, would be a helpful way to get ready for a timed exam of the style of the one this Monday.
Megan Paul's preceptor hours tonight will be in the in the lowest level of the ILC (furthest from the library, where there are a lot of tables) from 5-9 pm , not in the Sci & Eng Library, which closes at 6 pm on Fridays.
Note that Dr. McEvoy has an office hour from 9-10 on Monday, and Dr. Park from 11-12 on Monday a.m. if you have last-minute questions.
Sept. 13 , 2007
Grades for Quiz #1 were posted on D2L on Tuesday. The mean was 10.9 and median was 10 for quizzes actually taken. (The average calculated in D2L includes zeros for students who didn't take the quiz at all.) Quizzes will be given back when exams are given back, stapled to the back of your exam, and the quiz key is posted if you want to study the material, but if you're so anxious to get yours back that you can't wait 'til about Mon. 9/24, come to Dr. Z's office and she'll give you your quiz.
IMPORTANT: Be sure your name is on EVERY page of the exam -- the pages are separated for grading, and a blank p. 5 in the stack consisting of all the page 5s being graded by one staff member could present a real puzzle. Who should get the points for the unidentified p. 5, or p. 4 or p. 3, when we're reassembling exams to record and give back?
Be sure your calculator memories are cleared before coming into the exam. Remember that documentation for a university-excused absence is required for you to take a make-up, and that if you have an official excuse, you must contact Dr. Z. by phone or email before the exam and set up a make-up time for the first day you're cleared to return to work and school. If you're not at the exam and haven't contacted Dr. Z, we'll assume you've dropped the course.
Sept. 12 , 2007
1-page supplementary material for today's (Wed.) lecture: helical wheel [PDF]
p. 10 (2 more slides) added to Protein Tertiary Structure notes -- just print p. 10, no changes in earlier slides.
Note: The posted previous exams (2005, 2006) did not appear to require students to know the 1-letter codes for the amino acids. This fall, as mentioned in class, the 1-letter codes are absolutely essential for you to know, and will be used extensively on the exams.
Megan Paul (preceptor) will hold her availability hours on FRIDAY evening, 5-9 pm, instead of Thurs. evening this week, since a) you don't have a problem set due this Fri., and b) that will permit you to ask questions about Friday's material (quaternary structure of proteins) before the Mon. exam. Email Megan if you want to meet with her Friday evening.
Questions for this week's discussion sections (nothing for students to hand in): problems/questions
Sept. 10 , 2007
Correction in LEC 9-10 Tertiary Structure notes, bottom slide on p. 3: G of product < G of reactant (not ΔGs); corrected PDF is now posted.
This week in discussion sections we'll review some material, including peptide charge properties, pI calculation for peptides, and how the environment of an ionizable group affects its pKa; problems/questions for review).
Sept. 8 , 2007
Notes are now posted for Protein Tertiary Structure (Mon.-Wed.) and Protein Quaternary Structure (Fri.), completing the notes for material covered on Exam 1 (Mon. Sept. 17).
Sept. 7 , 2007
Keys are posted for P.S. 3 and for Quiz #1 [Form A] [Form B]
Sept. 6 , 2007
Secondary Structure notes are posted (for tomorrow).
Problems/questions to be discussed next week in discussion section in review/help sessions for exam (nothing to hand in, no problem set due next week).
Sept. 5 , 2007
Trahern will have an extra hour of availability tomorrow (Thurs.) from 1:00-2:00 to make up for having to terminate his hours this evening at 8 p.m. Email him if you want help.
Remember that Quiz #1 is on Friday, covering all material up through amino acids and peptide structure in today's lecture, but on the quiz there won't be any peptide charge questions or pI calculation. Regarding calculations in general, on quizzes we don't permit use of a calculator at all, so there won't be any actual calculations with natural logs, though you'll need to understand the concepts/relationships involved in free energy changes. On the quiz, any questions involving pH, pKa, and base/acid ratios would have integral numbers for logs to the base 10, so no calculator would be needed; in fact, if you understand the concepts involved in acid dissociation reactions, you could answer the question(s) without having to use the Henderson-Hasselbalch equation itself at all. A table of pKas of amino acid functional groups will be shown on screen during the quiz (without names of amino acids). No equations will be provided on the quiz or exam.
Next week in discussion sections we'll review some material, including peptide charge properties, pI calculation for peptides, and how the environment of an ionizable group affects its pKa.
Aug. 31, 2007
Problem Set 2 is due today. Please be sure that your name and your TA name AND section number are on your problem set, and that it is clear and legible.
Be sure you check your recorded grades (at this point just P.S. 1) in D2L to be sure they were entered correctly. Bring in any graded papers for which you find an error -- we try hard to enter grades accurately, but with human beings doing it, and so many graded assignments in this course, occasionally there's a mistake and we want to correct those!
Problem Set 3 is posted. Please note in the context of P.S. 3 that there are practice problems/answers on charge properties of peptides posted, linked under the Peptides lecture notes (next Wed. lecture) on the lecture notes directory, and that the table of "generic" pKa values for the 9 types of ionizable groups in proteins is also posted under the Peptides lecture notes (also on cover sheets of exams).
When you use your clicker, check to be sure you're getting a green light briefly showing when you answer -- that confirms that your radio signal was received by the receiver and is being counted. If it's a yellow light, your clicker channel needs to be re-set, as follows: Press and release "go" button. Light should be flashing alternating red and green. Immediately, while light is flashing, press 4-1, and then press "go" button again. You should see a solid green light, confirming successful channel setting.
Aug. 29, 2007
The Amino Acids lecture notes (PDF) were re-posted about 11:30 a.m. with 4 new slides (2 new pages, current pages 19 and 20), so if you printed the notes before, just print pp. 19-20 for the new slides and insert after p. 18. (Footer on revised PDF notes is "LEC 5-6 Amino Acids-revised 8/29/07".)
Next Monday, Sept. 3, is the Labor Day holiday, but Erin Palmer (preceptor) has kindly agreed to have availability hours Mon. evening, from 7:00-9:00 pm. If you want to meet with her then, please email before the weekend.
Drs. Baldwin and Ziegler will be out of town with no email access from Fri. night until Mon. evening.
Aug. 28, 2007
Tomorrow (Wed.) you need to know all 20 amino acid structures -- Dr. Baldwin will have a pre-quiz ready in clicker format, 10 sec per amino acid. (Real quiz is a week from Friday.)
Error correction on Bioenergetics sample calculations linked in notes: [ADP] in question 1 is 0.14 M, not 0.22 M. (Answer used 0.14 M in calculation, but I forgot to change concentration in the question to 0.14 M.)
Aug. 27, 2007
PDF notes for Bioenergetics have been reposted with 3 new ppt slides that weren't in original PDF. No need to reprint whole file -- new slides (which shifted later pagination) are now at top of p. 5, top of p. 8, and bottom of p. 14.
P.S. 1 answers are posted. (That won't usually be here in announcements -- the live link will just appear on P.S. page.) Sometimes there's more detail in posted answers than would be required for a student answer.
Discussion section room changes for sections 3 and 5 (Dr. McEvoy's sections):
Section 3, Thurs. 2:00-2:50 pm is now in PAS 418.
Section 5, Thurs. 3:00-3:50 pm is now in S SCI 312.
Here's the corrected URL for the BioMATH tutorial website that Dr. Baldwin mentioned in class last Wed.:
http://www.biology.arizona.edu/biomath/BioMath.html
Be sure TA name and section # are both on your problem set (as well as your name). No "PIN" is needed -- that's a holdover from an old problem set template.
Aug. 24, 2007
Error in Wed. 8/22 PDF lecture notes on noncovalent bonds and H2O, p. 4, top slide, has been corrected: dielectric constant of a vacuum is 1, not 0!
Addition to Bioenergetics learning objectives (middle of top slide on p. 3):
Explain the concept of free energy coupling, including additivity of free energy changes for coupled reactions.
Lecture notes access username and password are posted on the course D2L site.
Aug. 23, 2007
Please bring clickers to class starting Friday. Remember NOT to carry them loose in backpacks and pockets, because every time keypads are bumped they turn on, running the battery down. Store in a box -- cardboard, or metal (Altoids-type boxes are ideal!) Lithium button battery is #2032 "medical", 3V DL2032/CR2032.
ERROR in P.S. 1, question #5 (posted version is correct as of 7:45 a.m. Thurs., with the change indicated in red.) Correct version:
5. (1 pt) (Original numbers were wrong – correct ones are here in red.) For the α-carboxyl group of an amino acid with a pKa of 2.0, calculate the ratio of carboxylate ion [R–COO–]/carboxylic acid [R–COOH] at pH 2.2, and then the fraction of the total carboxyl group in solution that is neutral at pH 2.2. (Show your work.)
Problem set 2 is posted.
Here's the URL for the BioMATH tutorial website that Dr. Baldwin mentioned in class Wed.:
http://www.biology.arizona.edu/biomath/BioMath.html
Aug. 20, 2007
Welcome to Bioc 462a for fall 2007! Check the homepage frequently, as this is our means of communicating with you. Previous announcements from this site are posted in reverse chronological order here in the Announcements Archive.
Syllabus and and lecture schedule for 2007 are linked under "course information" on menu bar at left. You're responsible for the contents of the syllabus -- course policies, etc. For lecture notes access (so you can print and bring to class) you'll need the username and password (all lower case) posted here and printed on the hard copy syllabus handed out the first day of class; username and password will be removed from this announcement after the first week of classes.
username: bioc462a
password: protein
Lecture notes will be posted in PDF format the day before the relevant class, if not before (see "Lecture Notes" link (menu at left).
Note that the textbook is required: Nelson & Cox, Principles of Biochemistry, 4th edition (2004). The posted lecture notes in fall 2007 will generally be PDF versions of powerpoint, a simple outline format with copies of the figures to be discussed. For detailed notes, students will be expected to TAKE NOTES IN CLASS, and to prepare by reading the textbook before coming to class. The most convenient way to take notes will presumably be by writing on the posted PDF notes.
On Tues. 8/21 and Wed. 8/22, there will be a 60-90-minute introductory chemistry REVIEW session on chemical equilibrium and concepts of pH and pKa, for which detailed PDF notes are posted. The same review will be given twice, on Tuesday 8/21 5:00 - 6:15 pm (BioW 301) , and again on Wed. 8/22, 4:00-5:15 pm (CESL 103, right after class). It will be expected starting on Wed.-Thurs. 8/22-8/23 in discussion sections that students will be thoroughly familiar with this review material, since it is fundamental in biochemistry. It is also expected that students will be able to work with logarithms -- here's a quick refresher review of logs [PDF].
First day handouts (ask for these if you miss the first class): 1) syllabus, 2) lecture schedule. Problem sets will be posted online on Fridays, but will not be handed out in class. Always bring a print-out to discussion section with you. Problem Set 1 (for Wed.-Thurs. 8/22-8/23, due Mon. 8/27) is posted. Normally problem sets will be due the next day after discussion section (Friday), but for the first week only, problem set 1 won't be due until Monday Aug. 27.
Discussion sections WILL meet on Wed. 8/22 (honors) and Thurs. 8/23 (other sections), to work on the first problem set. UA is lending students in this class personal responder units ("clickers") for use this semester, and those will be distributed in discussion sections the first week. You MUST attend the discussion section for which you are registered (except in unusual cases, e.g., if you have a 1-time conflict, in which case you should clear attendance at a different section that week with both instructors).
•It is expected that you will have almost finished the problems before you come to discussion section, so that the last 20-25 min of discussion section can be spent on a new problem not posted in advance.
•BE SURE TO BRING A CALCULATOR TO DISCUSSION SECTION MEETINGS when that week's problem set involves calculations, as will frequently be the case.
•You will also often find the course textbook useful for reference during discussion section meetings.
Biochemistry 462a
http://www.biochem.arizona.edu/classes/bioc462/462a/462a.html
Department of Biochemistry and Molecular Biophysics
The University of Arizona
zieglerm@u.arizona.edu
All contents copyright © 1998-2007. All rights reserved.
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