Biochemistry 440, Sections 201, 501, Fall Semester 2008
Room 107 Biochemistry, meets MWF 9:10-10:00AM

 

Instructor: Gary R. Kunkel, Associate Professor of Biochemistry
office: 406A Biochemistry Building
phone: 845-6257
e-mail: g-kunkel@tamu.edu
webpage URL: http://www.tamu.edu/classes/bich/kunkel/hp.html

Office hours: Please arrange a time either by contacting me by email, telephone, or after lecture.
ATMentors office hour: Mon., 10-11AM

Course coverage: BICH 440 is the first half of a two-semester course in general biochemistry. Broadly, 440 is divided into four sections:
I. Fundamental chemical interactions within and between biological macromolecules; structures and properties of amino acids and peptides; three-dimensional structure of proteins
II. Structures and conformations of carbohydrates; structures of lipids and membranes; membrane transport
III. Composition, structure and experimental manipulation of nucleic acids
IV. Enzyme kinetics and mechanisms; binding of ligands to proteins

Prerequisites: CHEM 228 (both semesters of organic chemistry)

Textbook: Biochemistry, Updated Third Edition, by Garrett and Grisham

Examinations:
Three "hour" exams during regular class time
Exam #1 Wednesday, September 24, 100 pts
Exam #2 Wednesday, October 22, 100 pts
Exam #3 Wednesday, November 19, 100 pts

Final exam: Monday, December 8, 8AM-10AM, 150 pts
The final exam is required of all students

You should bring a calculator to all the exams. The memory bank on all calculators must be emptied before the exam begins.

Make-up exams for any of the hour exams will be offered to students only in the cases of officially recognized absences (see University Rules, section 7), or by special request in advance of the exam. Except under extenuating circumstances, the make-up exam must be completed within one week of the regularly scheduled exam that was missed. Therefore, you must notify me as soon as possible regarding such excused absences.

If you want any exam answers re-graded, requests must be submitted to me in writing along with the entire exam. The deadline for submitting exams for re-grading is one week after the exam is returned in class.

Problem Sets (60 pts, total): Six problem sets will be assigned. Many of the problems will be a selection from those given at the end of the chapter in your book. Problem sets will be due at the beginning of class on Wednesdays specified by * on the Lecture and Exam Schedule. You may work on the problems with other students, but MUST turn in answers written by you. Each problem set will be worth 10 pts, and only scores of 10, 8, 5, or 0 pts will be assigned. In order to receive full credit, you must show your work. Answer keys will be posted online and outside my office. Problem sets turned in one hour to two days late will receive half-credit. Problem sets will not be accepted for grading if more than two days late, unless accompanied by an excuse for a university-recognized absence.

Grading:
Section 501: The course grade will be determined based only on the total points accumulated from the exams and problem sets (total possible points = 510). There will be no opportunity to earn extra credit by doing extra work. The exams are likely to be challenging, so grades will not be determined based on delineation along a 90%/80%/70%/60% cut-off.
Section 201 (Honors): Exams and problem sets will be the same as for students enrolled in Section 501. Honors students will be required to attend seven extra sessions to present, discuss, and answer questions about published research papers. To calculate course points, cumulative points from exams and problem sets will be multiplied by a factor of 0.8 (max. possible = 408). 20% of the course grade (102 pts) will be assigned from work performed during the extra session.


The American with Disabilities Act (ADA) is a federal anti-discrimination statute that provides comprehensive civil rights protection for persons with disabilities. Among other things, this legislation requires all students with disabilities be guaranteed a learning environment that provides for reasonable accommodation of their disabilities. If you believe you have a disability requiring an accommodation, please contact the Department of Student Life for Students with Disabilities in Room 126 of the Koldus Building, or call 845-1637.


Aggie Honor Code: "An Aggie does not lie, cheat, or steal or tolerate those who do." Academic integrity is paramount in all activities during this course. On each exam, you will be required to sign a statement acknowledging that you have observed this honor code. See the Honor Council Rules and Procedures at http://www.tamu.edu/aggiehonor.


Lecture and Exam Schedule

* = problem set due at beginning of class on that day

 M 08/25  introduction  Chap. 1
 W 08/27  noncovalent interactions  Chap. 1
 F 08/29  properties of water; weak acids/bases; pH  Chap. 2
 M 09/01  buffers  Chap. 2
 W 09/03  biochemical thermodynamics  Chap. 3
 F 09/05  amino acids: functional groups and ionization  Chap. 4
 M 09/08  amino acids: properties and separation  Chap. 4
 W 09/10*  peptide bond; peptides  Chap. 5
 F 09/12  protein analysis and sequencing  Chap. 5
 M 09/15 protein purification  Chap. 5 Appendix
 W 09/17*  weak interactions in proteins; protein secondary structure  Chap. 6
 F 09/19  protein secondary structure  Chap. 6
 M 09/22  fibrous proteins; globular proteins; getting ready for Exam 1 Chap. 6
 W 09/24  EXAM 1  
 F 09/26  protein folding; multisubunit proteins  Chap. 6
 M 09/29  mono-, oligo-saccharides  Chap. 7
 W 10/01  polysaccharides / glycoproteins; proteoglycans  Chaps. 7
 F 10/03  lipids  Chap. 8
 M 10/06  lipids / lipid bilayers  Chap. 8
 W 10/08*  membranes / membrane proteins  Chap. 9
 F 10/10  membrane transport  Chap. 9
 M 10/13  nucleotides  Chap. 10
 W 10/15*  polynucleotides; hydrolysis of polynucleotides  Chap. 10
 F 10/17  structures of nucleic acids; denaturation/renaturation  Chap. 11
 M 10/20  DNA supercoiling; RNA structure; getting ready for Exam 2 Chap. 11
 W 10/22  EXAM 2  
 F 10/24

 recombinant DNA

 Chap. 12
 M 10/27  DNA sequencing; PCR  Chaps. 11,12
 W 10/29  chemical reaction rates; enzyme kinetics  Chap. 13
 F 10/31  enzyme kinetics  Chap. 13
 M 11/03  no class  
 W 11/05*  enzyme inhibitors; multisubstrate reactions  Chap. 13
 F 11/07  experimental determination of rate constants  handout
 M 11/10  enzyme mechanisms: general properties  Chap. 14
 W 11/12* mechanism of serine proteases  Chap. 14
 F 11/14  other enzyme mechanisms  Chap. 14
 M 11/17  enzyme specificity Chap. 15
 W 11/19 EXAM 3  
 F 11/21  allosteric enzymes; reversible covalent modification Chap. 15
 M 11/24  binding of ligands to proteins  handout
 W 11/26 no class - Happy Holiday! Beat TU!  
 F 11/28  Thanksgiving Holiday  
 M 12/01 dissociation constants; cooperative binding of ligands handout
 M 12/08  FINAL EXAM (8 - 10 AM)