SYLLABUS

CHEMISTRY 156 - BIOCHEMISTRY

Fall 1999

General Information

Prerequisites Chemistry 52

Suggested Prerequ. Biology 152

Instructor Clemens Richert, Room Pearson 310 B, Tel. extension 73475

Office Hours Thursdays 1:30 - 4:30 PM

Text D. Voet, J.G. Voet, C.W. Pratt, Fundamentals of Biochemistry (Wiley)

Room Pearson Hall, room P 106

 

Understanding, or at least rationalizing life on a chemical level - Introductory Thoughts.

Today, many of the components of cells are known on an atomic level. For a number of organisms, the genome, i.e. the entirety of the genetic information, has been sequenced. Anyone with a biochemistry education can now write down this genetic information as a structural formula of double-stranded DNA. Assuming that processing of messenger RNA and posttranslational modifications are predictable, the same person can also write down the structural formulae of all proteins encoded in this genetic information. Membranes encapsulating cells are known in their chemical composition, as well as most metabolites. How do these chemical spring to life? Well, I hope that you will be able to answer this question at the end of this course .....

We will cover biochemistry from a chemical perspective. Chemical structures and reactions will be presented on increasing levels of complexity. First, the most important building blocks of life, sugars, amino acids, nucleic acids and lipids will be discussed. Then we will see how these building blocks are being used to build biomacromolecules, but at the same time are also metabolites that the enzymatically active among these biomacromolecules act on. The three-dimensional structure of biomacromolecules is the result of folding and association, driven by interatomic forces. The same interatomic forces (hydrogen bonding, ion pairs, van der Waals forces and hydrophobic effect) also govern enzymatic catalysis, which we will discuss next. Finally, we will study the interplay between the simple and complex molecules, both on the level of selected metabolic pathways and on the level of the regulation of these pathways. Emphasis will be placed on the organic chemical and physical chemical understanding of these processes. A sound background in organic chemistry is therefore indispensable.

What does organic chemistry have to do with biology and medicine is what one might ask at the end of a the usual two semester introductory course. This course should provide at least partial answers to this question.

 

Course outline

I. The Key Building Blocks of Biological Systems

1. Lipids: components of membranes and energy depots

2. Sugars: metabolites and building blocks for oligo- and polymers

3. Nucleosides and nucleotides: cofactors and the letters of the genetic alphabet

4. Amino acids: the universal building blocks for proteins

5. Cofactors: chemical specialist that enrich the repertoire of enzymatic reactions

II. The Structures of Selected Biomacromolecules: Proteins and Nucleic Acids

1. Protein conformation: general considerations

2. The common secondary and tertiary structure elements

3. Protein Folding and structure prediction

4. Structures of DNA and RNA

Course outline, continued ...

III. The Basics of Enzymatic Catalysis

1. Transition State Theory

2. Types of Catalysis

3. Kinetics

4. Inhibition

5. Case Studies

IV. Metabolism

1. Primary Metabolism and Energy

2. Regulation

 

 

LECTURE DATES (6-3 + BLOCK)

Mondays: 1:05 PM - 2:20 PM Wednesdays: 11:30 AM - 12:45 PM

Mondays Wednesdays

September 8

13 15

20 22

27 29

October 4 6

12* 13

18 20

25 27

November 1 3

8 -

15 17

22 24

29

December 1

6 8

* NOTE: Day follows Monday schedule

 

Exams First exam October 6 11:30 AM

Second exam November 17 1:05 PM

Final exam December 20 12:00, noon

 

 

Grading Scheme

Grading Relative Weight

2 Exams 50 %

Assignments 10 %

Final Exam 40 %

You can earn a maximum of 1,000 points in this course.

The points earned translate into grades according to the following scheme:

Course Grade Final Score % of Maximum Score

A+ 934-1000 93.4-100

A 867-933 86.7-93.3

A- 800-866 80-86.6

B+ 734-799 73.4-79.9

B 667-733 66.7-73.3

B- 600-666 60-66.6

C+ 534-599 53.4-59.9

C 467-533 46.6-53.3

C- 400-466 40-46.6

D+ 334-399 33.4-39.9

D 267-333 26.7-33.3

D- 200-266 20-26.6

F < 200 <20

As detailed above, you can collect 100 points for the assignments, 2x250 points for the 'hour exams', and 400 points for the final. Thus, you can calculate your current grade after every of the tests taken.

Here is an example of how you can calculate your current grade after two exams:

3 Assignments (out of 5 to be graded) 43 points (out of 60)

Exam I 198 points (out of 250)

Exam II 112 points (out of 250)

Maximum number of points possible at this time:

60 (Assignments) + 250 (Exam I) + 250 (Exam II) = 560

Earned by you :

43 (Assignments) + 198 (Exam 1) + 112 (Exam II) = 353

353 / 560 x 100 = 63.0% of maximum score = B- as your current grade.

 

The average grade in this course is usually somewhere between a B and a B+.

The exams will be cumulative and will be in-class, closed-book exams.

Exam Regrades. If you feel an error was made in the grading of your exam, you may submit the exam together with a written description of the error to me for regrading. Only exams written in ink will be considered for regrades. All regrade requests must be submitted within 24 hours (next weekday) after return of the graded exam. Please note that your entire exam will be regraded, possibly leading to a lower overall score. I reserve the right not to write future letters of recommendation for students who submit frivolous regrade requests. All regrades are final. It has been my experience that very few of the submitted regrade requests are justified. In the majority of all cases, the student submitting the regrade request has overlooked an error in her or his answer. Please consider this before you submit a regrade request.

Make-up Exams. If you miss an exam without legitimate excuse, a score of 0 will be entered for that exam. The only acceptable excuse is a note from the Office of the Dean of Students. The note must state the days for which it is valid and must state explicitly that, in the opinion of the Dean, the reason for missing the exam warrants a make-up exam without penalty. The note has to be handed in one school day from the last day for which the excuse is valid. An oral or written (at my discretion) make-up exam will be given immediately upon receipt of a valid excuse.

Unfortunately, late assignments cannot be accepted under any circumstances.

If you are unsure as to what will be on exams, please note that both the material presented in class and in the reading assignments will be covered in the exams. The emphasis is on the material presented in class, and on a chemical understanding, and not just memorization of facts. Old exams will be handed out prior to the exams to give you a feeling for the level on which questions will be asked.

 

 

Miscellaneous

A Student Council will be held at the end of the lecture on the last Wednesday of every month.

The Chem 156 Homepage on the Web

URL: http://microvirus.chem.tufts.edu/biochem/index.html

Or: Go to Chemistry Department Homepage (http://www.tufts.edu/departments/chemistry/), click on Research Groups, select Richert Group (http://microvirus.chem.tufts.edu/), go to Biochemistry Homepage at the lower left corner of the homepage.

It has been my experience that trying to catch up with classes by trying to engage in a lengthy email correspondence with the teacher is inefficient, both for you and for me. Thank you for your understanding.

There is a sign-up sheet on my office door for office hour meetings. Please sign up in advance to avoid waiting times.

Copies of transparencies used in class can be found in a blue binder on a book shelf in my outer office (P 310). The binder is labeled "Chem 156". Please return the sheets immediately after copying, so that other students may access them.

 

 

Enjoy Biochemistry!