May 7, 2008

The Exam 4 Keys have been linked to the study guides page. The plan is to finish the grading by Monday evening and then work on getting all of the scores entered into the gradebook and calculate final grades. Everything will be completed and posted on the D2L website by Thursday afternoon, May 15, at the latest (probably earlier). You will be able to pick up your graded exams from the biochemistry main office anytime after Wednesday, May 14.

Good luck on finals and have a productive and/or fun summer.


May 4, 2008

We did not cover all of the material included in the study guide problem sets from 2005 and so you can ignore the following questions in these problem sets:

Carbohydrate Metabolism: ignore questions 6, 7, and 10.
Lipid Metabolism: ignore questions 7, 13, 14, and 20.
Amino Acid Metabolism: ignore questions 8, 9, 10, and 11.
Metabolic Integration: ignore question 8.


May 1, 2008

The scores for Quiz 4 have been added to the gradebook. The average was a bit higher than Quiz 3 with the mean being 14/20 (70%) excluding scores of zero.

Review session for Exam 4 is Monday, May 5, in ILC 120 after class. I can stay until 5pm to answer your questions. The exam is Wednesday, May 7, at the regular class time and the format will be the same as exam 3 (short answer and circle the correct response).


April 30, 2008

The "General Concept Review Questions" handout for exam 4 has now been posted to the Study Guides page. The purpose of this handout is to provide you with another way to study major metabolic concepts in preparation for exam 4. Remember that these are not exam questions (there are plenty of those to choose from), but rather "big concept questions" that will guide your studying.

The course evaluations for the second half of the course are now open on D2L. To get your 2 extra points you need to finish the evaluations by midnight on May 5 (Monday). Your comments about what you liked and disliked about the course, and your suggestions for improvement, are much appreciated.

April 26, 2008

I posted a revised version of the Lecture 37 ppt "print" file on the lectures page. It contains the corrected carbon counting slide, and also the slides with "red questions" that I added right before my lecture.

I also made another slight revision to the lecture 36 slide describing the hydrolysis of palmitate from the fatty acid synthase complex at the end of the entire synthesis reaction. It now more clearly shows how the water is used.

April 23, 2008

Oops, I made a mistake and need to correct it. This is for slide 12 in Lecture 36 related to why only 6 H2O are generated when there are 7 dehydration steps in the fatty acid synthase reaction cycle for palmitate. The student that suggested it was the acetyl-CoA addition clued me in "on the fly" that my answer of the ATP hydrolysis step could not be the reason because there are seven of those for the seven malonyl-CoA that are produced. That would have been 7 H2O as some of you may have realized.

I thought about it some more when I got back to my office and realized it is actually the Palmitoyl thioesterase reaction in the final step, this is a hydration that requires H2O. I have now updated the ppt. files to show this, and corrected the red question in slide 13 to say "dehydration."

April 22, 2008

The exam scores have been uploaded to the D2L grade page and the grade distribution has been posted to the study guide page (click here).

Please do not to write anything on exam itself for regrading purposes. Since we are handing back the exams tomorrow (Wednesday, April 23) in class, the deadline for turning in regrading requests will be the end of class one week later, on Wed. 4/30. Envelope to collect regrading requests will be in class on front table through next Wed.

April 21, 2008

Link to Miesfeld's In-Class PowerPoint Slides (click here)

Dr. Ziegler could not make it to office hours today, she can make appointments for later in the week.

I posted a revised ppt. file for Lecture 35. I was having problems with the file size but finally figured it out. No major changes to the text, just better management of file size and placement. I also updated the supplemental reading file with a figure reminding you of the structure of triaclyglycerols as is also included in the ppt. file.

The exams have been graded, there was at least one perfect score, and a fair number of scores in the 90s, however, plenty in the 30s and 40s as well. The scores will be posted today and the exams and Quiz 3 handed back today or on Wednesday.

Quiz 4 is one week from today and Exam 4 is the last day of class on May 7.

April 18, 2008
Correction on slide 18 of the Lecture 34 notes regarding glucose regulation of liver glycogen phosphorylase. I decided that I had the "T state" labeled wrong in this drawing and have now changed it to "Liver glycogen phosphorylase b" to reflect the T state that is still phosphorylated. This is consistent with my definition of "a" being active and "b" being inactive, regardless of the phosphorylation state (forget what the original biochemists did to decide on the "a" and "b" forms which reflected phosphorylation and a very confusing nomenclature).

April 17, 2008
The key to Exam 3 has been posted, the grading will be done over the weekend. It looks like the mean will be less than 60, probably between 55 and 60. Some questions were answered correctly by most students, whereas, other questions were not answered correctly by very many students; these were often the harder "thinking" questions.

I am still working on the lecture notes for tomorrow and will post them tonight.

April 15, 2008
The key to Exam 3 will be posted Thursday after 6pm. Hopefully, the grading will be complete by Friday evening (I am the hold-up), with grades posted sometime over the weekend. If everything goes smoothly with the grading, we should be able to hand back the exams on Monday. Regrades will be due one week after the exams are returned.

April 13, 2008
Just to give you a heads up, this is the text you will find on the cover sheet of the exam:

"Read the questions carefully and think about your answer before writing anything down. While some of the questions will look very familiar, others require that you use what you have learned about basic biochemical principles to answers questions about metabolism. This is not a fact-based exam, the information you need to orient your thinking is given in the question.

Hint: Go through and answer the questions you know first, and then go back and answer the rest. Manage your time wisely."

You can use a calculator on the exam if you would like, however, it should not be necessary if you remember how to add and substract numbers with values of less than 1.

April 10, 2008
The ppt. file I used for lecture yesterday had two "red questions" that were not on your ppt. file (print), so I went ahead and updated the Lecture 31 ppt. file on the lectures page. There was also a better concept explanation on the slide for the oxygen evolving complex (oxidation of water), so I replaced that slide as well.

Exam 3 review is 4-5pm in Chavez 11. I will do my very best to get the Calvin cycle slides (lecture 32) posted as soon as possible. I might have to give up on the real life stuff I like to add (and my illustrations) if I run out of time ;-{

April 9, 2008
Clarification on the extra credit for completing the online course/instructor surveys.

Dr. Ziegler's evaluation runs April 3-11 on the D2L site under "content."
Dr. Miesfeld's evaluation runs April 28-May 5 in the same place.

The TAs can see who did the evaluations, but not what was written. The instructors can see the evaluations but not who posted the comments. So, it is an anonymous evaluation using the security of the D2L site.

You receive 2 pts for each evalution (4pts. total for doing both Ziegler and Miesfeld). These points are not averaged into the curve, but instead used to raise your total points if you fall near the grade cutoffs at the end of the course. We appreciate your feedback and the extra 4 pts. is good insurance if you fall with 4 pts. of the grade cutoff.

April 8, 2008
Although I am pretty sure that all of my best exam questions are already represented in the study guide problems I assembled several years ago, I went ahead and added two more years of my old exams (2002, 2004) covering metabolism to the study guides page. Note that in 2002, the signal transduction lectures were covered on exam 4, and other material was covered in exam 3, so be sure to look at both exams for that year in your review for exam 3 this year.

Of course each year I write a new exam, but I would like to think that I covered the same KEY CONCEPTS every year over the past 5 years or so. Moreover, the degree of difficulty of questions I asked each year is pretty similar because I always give plenty of practice problems with answers and expect students to read them in preparation for the exam (similar questions show up year after year). I shoot for about 20-30% new questions each year based on new material I cover in the lectures, or material that I covered in more detail.

Importantly, I do emphasize different topics each year which is why the PowerPoint slides for Spring 2008 are the primary study source. The second source would be the "Supplemental Reading Materials", the third would be the Study Guide Questions and Old Exams, and the fourth would be the Berg textbook. After that, I suppose you could use a cautious Google topic search if you are still desperate to learn even more biochemistry, although I would be careful because not everything on the web is accurate as you already know.

April 7, 2008
I apologize for having to speed up at the end of the lecture today. I guess I was having too much fun watching ATP motor movies.

An important set of slides in lecture 30 are those showing data from isolated mitochondria in which the amount of oxygen consumption is plotted versus time. Amount of ATP synthesis is also plotted on these graphs. These are important concepts because they link ETS to ATP synthesis using experimental data. You will need to understand these data for the exam, there are several study questions related to this concept.

I probably did not explain well enough that "oxygen consumption" can also be rephrased as "ETS activity" meaning the rate of redox reactions in the electron transport system. Since reduction of oxygen to form H2O is the last step of the ETS, and oxygen consumption can be measured in the lab, then amount of oxygen consumed is a measure of ETS activity over time. See the labeled graph below.

The higher level concept here is to explain why adding oligomycin blocks both ATP synthesis and ETS activity (blue rectangles), and moreover, why subsequent addition of DNP allows ETS activity to increase even though ATP synthesis is still blocked by oligomycin (red rectangles).

The reason oligomycin alone stops BOTH the ETS system and ATP synthesis, is that the protons must have somewhere to go after they are pumped into the inter membrane space, otherwise the concentration and charge gradient is just too steep for *anymore* protons to be pumped. Since oligomycin does not allow protons back into the matrix, they build up in the inter membrane space. By adding DNP, the proton circuit is restored and the ETS activity goes up again.

DNP "punches a hole in the membrane" by allowing H+ to flow down the gradient without going through the ATP synthase complex. The proton circuit is restored by DNP addition as protons can be pumped out of the cell, as a result of ETS activity, and come back into the cell through the DNP "hole." Therefore, DNP leads to increased ETS activity (the proton circuit is restored) without the ATP synthase complex functioning (blocked by oligomycin).


April 5, 2008
Quiz 3 has been graded. The mean was ~58%, not including the 12 people who did not take the quiz. The distribution of scores was good (see below), but the mean is lower than I was shooting for which was ~65%. Perhaps the two signal transduction lectures from before spring break were just too long ago.

Exam 3 will be one week from Monday (April 14) and covers up through lecture 32. There is a review session scheduled for Thursday, April 10, from 4-5pm in Chavez 111.

April 3, 2008
The supplemental readings for lectures 29-34 have now been posted to the lectures page. I am still working on the ppt. slides for the lecture tomorrow but they are taken from the supplemental reading, so you can read that material first if you won't have time to download the ppt file later this evening.

Remember that the 20 pt. quiz tomorrow starts at 3pm and runs for 10 mins. The material for the quiz comes from the ppt lecture notes beginning with Signal Transduction 1 (Dr. Gang).

April 3, 2008