Study guide for cytric cycle cycle was posted.

Revise concept of redox reaccions from general chemistry courses. Reduction, oxidation, oxidant, reductant, Nerst equation.

I would try to post study guides and practice problems more frequently, so you can practice for the quiz and for the exam.

Study guide was posted.

EXAM 3 will be tomorrow Tuesday 17 in Goessmann 64, 7-9 PM. Please remember to communicate in advance if you have a valid conflict. Evening exam policy.

Monday Review session in class. AH office hours 2-4 PM, Lederle 814. TA office ours 5-7 PM Lederle 814.

Study guide was published.

Exam3 Practice problems.

Final Quiz 3 average score 19.2/25, standard deviation 4.3.

NO class on Wednesday Nov 18.

EXAM 3 will be next Tuesday in Goessmann 64, 7-9 PM. Please remember to communicate in advance if you have a valid conflict. Evening exam policy.

Monday Review session in class. AH office hours 2-4 PM, Lederle 814. TA office ours 5-7 PM.

Study guide for chapter 9 and 10 was published. Some exam like problems will be published tomorrow after class.

Quiz average score 19.4/25, standard deviation 4.3. Quiz 3a key. Quiz 3b key.

Q1) 25 points, Q2) 25 points, Q3) 20 points (not considered), Q4) a) 10 points; b) 15 points; c) 5 points. Your total was divided by 80 and multiplied by 25. Your final score is in black and it is over a total of 25 points.

Refresh how to work with carbohydrate structures and their representations. Now is when you need your Organic Chemistries! You may check Chapter 11 in Biochemistry, Voet and Voet, 3rd Edition.

TA review session will be on Monday from 5 to 7 PM

Quiz make up will be in class on Friday. Try to be there early so you can start as soon as the previous class finish.

Refresh how to work with carbohydrate structures and their representations. Now is when you need your Organic Chemistries!

Next Monday Quiz 3. Study Chapter 8 of P&C.

Study guide.

Exersices at the end of Chapter 8 you should be able to do: 30, 32, 33, 35

Try exercise 14 of the Book CD.

Revise the concept of deltaG and spontaneous processes. We will apply it to membrane transport.

Exersices at the end of Chapter 8 you should be able to do: 3, 9, 15, 25

Try exercise 13 of the Book CD.

Think about how can we transport molecules and ions accros membranes.

How do we design membrane transporters? Membrane channels?

To watch the movie about FRAP and protein mobility click here.

To watch the movie about laser tweezers and membrane fluidity click here.

Exam 2 results

Exam 2 was not easy, but people did very well overall! The mean was an 84 with a standard deviation of 11.

Grades have been uploaded onto the SPARK site, and the exam will be returned in class Monday.

Power point slides with Prof. Heuck notes have been posted

Think about how water soluble proteins fold, and how do they differ from membrane proteins?

How do we design membrane proteins? Membrane channels?

To see a visualizer that gives you a sense of scale in biochemistry click here.

Final Exam

The final exam has been scheduled by the registrar's office. The final exam will be Monday, December 14 at 4:00pm in Goessman 64. Time to buy your plane tickets!

Other Michaelis-Menten enzyme kinetics resources

There is a nice simulator allowing you to see the effect of changing [E], [S], etc. from the chemical engineering department at RPI here, and one from the Goodman group in Cambridge here.

Further chymotrypsin exploration

Stryer has a few nice sections on chymotrypsin structure and mechanism here.

Office hours rescheduled

Kursheed is out sick today, so he will reschedule his office hours for later this week.

Exam 2 preparations

Exam 2 will be Wednesday, October 28th 7-9pm in Goessmann 20. I put a study guide for the exam, last year's exam, and the key to last year's exam on the front page of the website. Is there anything else you want for the exam?

Lecture 16 problems

Those of you in lecture saw how powerpoint hung itself in the middle of class. I was able to rescue 21 minutes of the first part of lecture today (the part before powerpoint exploded). I reannotated the powerpoint slides and put both the pdf and the flash on the main page of the web site. Is that enough?

Quiz 2 results

Further reading on topics we talked about in class

•	Fred Hughson wrote a nice review of flu hemagglutinin here.
•	Berg's Biochemistry has a nice treatment of protein purification here and x-ray diffraction here.
•	Cooper's The Cell has a section on protein folding and chaperones here.
•	Albert's Molecular Biology of the Cell has an extensive treatment of protein folding in vivo here.

Interested in working in a research lab?

There will be an undergraduate science research opportunities fair on October 15th at 4-6pm in the atrium of the ISB. More information here.

Reading scientific literature

On Tuesday, we will read a paper from the scientific literature. We are going to read and discuss a paper describing the alpha-galactosidase molecule that we heard about in class today. Scientific papers are written for researchers in the field, not for students in Biochem 523, so there are a lot of extraneous details that go beyond the scope of the course. If you read the papers, you might notice how the excitement of the science sometimes gets hidden in the way papers are written. To help you work through the paper, I posted a reading guide to the Lee 2003 paper.

More info on the work done in the Garman lab

Summary of student feedback

For the most part people were happy with the course so far. In particular, people liked the web content, including the flash and pdfs of the lectures. Some of the adjustments I will make include:

•	Our PRS questions will become more like the questions you will see on the quizzes and exams
•	I will post review material earlier so that people can get a chance to look at it sooner after class.
•	I will try to put links to additional materials for those of you interested in going beyond what we talk about in class.
•	I will mark the correct solution for PRS when we are finished discussing the question.

Some people requested changes that we are not going to make:

•	Most people thought the level and pace was appropriate, with a couple of people saying it was too slow or too fast. We won't change much there.
•	Some people wanted the exam questions to cover exactly what we talk about in class, stating that, for example, they were surprised about the question about calculating the overall charge on the peptide. However, we learned about the charges on the amino acids, how to make a peptide bond, and the single letter code, so I think we learned in class everything you needed to get the question correct. Some questions on the exam will be straightforward knowledge questions, but others will be more challenging, asking you to take what we learned in class and apply it to new problems.
•	Most of the class thought there were enough material to review in preparing for quizzes and exams.

 

SPARK page updated

I put the scores for Quiz 1, Exam 1, and PRS to date up on the course SPARK page (accessible here).

We have had 32 points of PRS points since starting counting PRS scores on the add/drop deadline. If you got at least 90% of those points, you got full credit for PRS. Since we are about 25% of the way through the course, I scaled the PRS to 25 points, since it will be 100 points at the end of the semester. Got it?

Please let me know if the scores I posted are not correct.

Exam 1 results

Overall, people did a nice job on Exam 1. The mean was 82 with a standard deviation of 13.

The exam will be returned in class today.

More on influenza

Gina Kolata's book Flu: the story of the great influenza pandemic of 1918 and the search for the virus that caused it is an interesting read. She describes how that flu affected the world, including showing a picture of a baseball game in 1918 where all the people (including the fans, the umpire, the batter, and the catcher!) are wearing masks. More information here.

Exam preparation

•	I posted a study guide for Exam 1 on the course home page. This includes some interesting problems from the questions at the end of Chapter 4.
•	I posted last year's Exam 1 on the home page.
•	I posted keys for Quiz 1 on the home page.
•	My office hours are 2-4pm on Monday in my office.
•	I will have a review session Tuesday night at 6:45pm in ISB 221 (the regular lecture room location).

Is there anything else you need to prep for the exam?

Hemoglobin

I put the movies that did not play during lecture on the front page of the web site. Quick time player is required.

Here are some other Hemoglobin resources:

• Eric Martz (UMass Microbiology emeritus faculty) has a very nice hemoglobin tutorial.

• The student companion the Pratt & Cornely textbook has nice interactive hemoglobin tutorials also.

See if you can track the changes in the structure that result from the binding of oxygen to the Hb molecule.

Quiz 1 results

Overall, people did well on quiz 1. The mean was 21 with a standard deviation of 5. Congratulations on a nice job on the quiz. Please make sure you have mastered the material from quiz 1, because we will see the material again on exam 1.

The quiz will be returned in class on Friday.

Exam 1

Exam 1 will take place next Wednesday (Sep 30) in Goessmann 20. Today is the last day to schedule a makeup exam.

I posted a study guide for exam 1, last year's exam, and the key to the exam on the main page of the web site. Try the exam first before comparing your answers with the key.

A technical snafu today

Somehow the audio didn't work on today's lecture recording; I think I must have turned off the microphone when I put it on my collar. This afternoon, I recorded a second version of the lecture and posted it on the web site. The version recorded in my office is not the best, because there was no interaction and no questions, but I think it covered pretty much what we talked about in class.

PRS

Now that the Add-Drop period is over and the roster has stabilized a bit, we will start counting PRS questions.

Exams

The room has been assigned for exams 1 and 2. The current exam schedule is:

• Exam 1: W Sep 30 7-9pm in Goessmann 20

• Exam 2: W Oct 28 7-9pm in Goessman 20

• Exam 3: T Nov 17 7-9pm. Room TBA. Note: this has been moved a day earlier than originally scheduled due to a conflict with the Biochem 471 exam.

• Exam 4: During Finals week. Time and date TBA.

 

Quiz 1

Quiz 1 is on Monday. In response to people's requests, I have posted last year's quiz and the answer key to last year's quiz on the main page. Last year, we were about 1/2 a lecture ahead of where we are this year, so we covered some material on peptides last year. There are some practice quiz questions on peptides that are not relevant to this year's quiz. However, it woud not hurt you to learn the material on peptides because we will cover peptides in class next week.

Books on reserve

I put some books on reserve at Du Bois Library, including:

• Pratt & Cornely's Essential Biochemistry

• Voet, Voet, & Pratt's Fundamentals of Biochemistry

• Garrett & Grisholm's Biochemistry

They should be available soon for check out.

Additional reading resources

NCBI has free searchable textbooks!

•	Berg, Tymoczko, and Stryer's Biochemistry, 5th edition is available here.
•	Alberts, Johnson, Lewis, Raff, Roberts, and Walter's Molecular Biology of the Cell is available here.
•	Lodish's Molecular Cell Biology is available here.
•	Griffith's Introduction to Genetic Analysis is available here.

For example, you can read about protein purification by putting that text in the search box in the lower left. Although we don't have any assigned reading for protein purification from our texts, you can find some excellent reading on that topic in one of those texts.

Further information on the books and movies we talked about in class

•	The Double Helix: A Personal Account of the Discovery of the Structure of DNA by James D. Watson. This is an easily read book that describes Jim Watson's idiosyncratic perspective on the events during the race to the structure in the early 1950s. It does nicely capture the excitement of competitive science in a way that few books do. This book starts with the provocative sentence "I have never seen Francis Crick in a modest mood" and continues onwards in that vein. More info.
•	Rosalind Franklin: the Dark Lady of DNA by Brenda Maddox. This book is a much more objective treatment of Franklin's contributions to the structure of DNA. More info.
•	The Eighth Day of Creation: Makers of the Revolution in Biology by Horace Freeland Judson. This book describes the beginnings of the field of molecular biology and has an extensive treatment of the DNA structure story. More info.
•	The movie where Jeff Goldblum plays James Watson was made by the BBC in 1987 and was orignially called Life Story. More info. This same movie seems have been retitled both The Double Helix and The Race for the Double Helix (in the US). There must be huge demand for this movie, because currently only one copy can be found in VHS format only for an astonishing $999.99 from Amazon. More info. Get it if you can find it!

The 1953 papers on DNA structure we looked at in class include:

• Watson and Crick's (pdf)

• Wilkins, Stokes, and Wilson's (pdf), and

• Franklin and Gosling's (pdf).

The last two are somewhat more technical than the first. The Watson-Crick paper contains the great sentence, "It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material." This is one of the great understatements of the scientific literature.

We will test our PRS transmitters today in class.

HHMI Academic Year Internship program

The Howard Hughes Medical Institute (HHMI) sponsors an academic year internship program. Participants receive a stipend to work in a research lab during the academic year. Many of our Biochem 523 students have won these prestigious awards and have used them to do outstanding independent study research in labs all across campus.

More information on the program and the application process is here.

Nobel Lauriate Oliver Smithies comes to campus!

Oliver Smithies invented gel electrophoresis, a technique used in biochemical laboratories every day, and then went on to discover how homologous recombination of DNA works (for which he shared the Nobel Prize in 2007). He will give a talk about his 60+ years in science on Monday, Sep 14th at 4pm in the Campus Center auditorium.

More information here.

Welcome to Biochem 523!

The textbooks for the course will be Essential Biochemistry by Charlotte W. Pratt and Kathleen Cornely (ISBN 0-471-39387-8) and Protein Structure and Function by Gregory A Petsko and Dagmar Ringe (ISBN 0-878-93663-7). These books are available from the UMass textbook annex and other places.

UMass had an online subscription to the Petsko and Ringe book for the past few years, but the book has recently changed publishers, and unfortunately the new publisher does not allow electronic access to the text. The student companion site for the Pratt and Cornely book is here.

In addition to the above texts, you are required to have a PRS-RF transmitter, available from the UMass textbook annex. Please bring your PRS transmitter to class on Friday Sep 11th, as we will be testing them. It would be a good idea to put new batteries in the PRS transmitter at the beginning of the semester; then you won't have to worry about the batteries running out in the middle of the term.