Biochemistry I

 Bio 421/Chm421

Department of Biology

Iona College

Fall 2008

 

Instructor:      Yourha Kang, Ph.D.                           Meeting time: M, W, F 11:00-11:52

                        Cornelia 105                                        Meeting place: Cornelia Hall C011                            

633-2260                                                                       

                         ykang@iona.edu

 

Office hours: M W F 12p.m. – 1 p.m.

 

Course website: www.iona.edu/faculty/ykang/index/bio421.htm

The website has a copy of the syllabus, as well as links to interesting and helpful sites. 

 

Course Description:  This course is an introduction into the field of biochemistry, a science that has traditionally focused on amino acids and proteins.  Therefore, the major part of the course will focus on the amino acids that make up protein, protein structure, and protein function.  We will put particular emphasis on the enzymes, a group of proteins with catalytic function; enzyme kinetics, types of enzymatic reactions, and regulation of enzymes will be covered.  The next part of the course will examine carbohydrates and lipids, the other major metabolites (along with nucleic acids) found in all living organisms.  During the last part of the course, we will study the metabolism of sugars. 

 

Course Objectives: By the end of the semester, the student should be able to understand and know about:

  1. the chemical properties and structures of proteins, carbohydrates and lipids
  2. the biological functions of proteins, carbohydrates, and lipids
  3. how enzymes work and are regulated
  4. sugar metabolism
  5. some of the recent biochemical research that is going on today

 

Required textbook:
Lehninger Principles of Biochemistry, 5th edition by Nelson, D. and Cox, M.  2008. WH Freeman and Co. New York, NY.

(I also recommend the student companion that goes with the book).

Lecture and Attendance:  Students will be responsible for all material covered during lecture.  Attendance in class is expected.  Attendance in the exams and the final are mandatory and can only be made up with prior approval from the instructor.   All assignments must be handed in on time (non-excused lateness results in a 10% deduction for every day that it is late).  If you are absent, you may e-mail me the assignment no later than the beginning of class on the due date.  Plagiarism and/or cheating will not be tolerated and will result in an automatic “F” for the course.
Grading:
                Exams 1-3                            20% each, 60%total
                Final (Cumulative)               20%
                Assignments 1-4                   5% each, 20% total

               

 

Tentative Schedule

DATE

TOPIC

READINGS

8/27-8/29

Introduction: life, water, macromolecules

Chapter 1 & 2

9/3-9/15

Amino acids and protein structure

Chapter 3 & 4

 

1st Assignment due 9/15

 

9/17-9/24

Protein function

Chapter 5

 

Review Questions for Exam 1

 

9/26

Exam I

 

9/29-10/8

Enzymes; enzyme kinetics

Chapter 6

10/10-10/17

Carbohydrates

Chapter 7

 

2nd Assignment due 10/20

 

10/20-10/24

Lipids

Chapter 10

 

Review Questions for Exam II

 

10/27

Exam II

 

10/29-11/5

Membranes and Signaling

Chapters 11 & 12

11/7-11/10

Introduction to Metabolism

Chapter 13

11/12-11/21

Sugar metabolism

Chapter 14 & 15

 

3rd Assignment due 11/14

 

11/24-12/3

Citric Acid Cycle

Chapter 16

 

Review Questions for Exam III

 

12/1

Exam 3

 

12/3-12/8

Oxidative phosphorylation

Chapter 19

 

4th Assignment due 12/10

 

 

Final Exam during finals week

 

 

Links:
Textbook Website: http://bcs.whfreeman.com/lehninger5e/

Another textbook website:  http://bcs.whfreeman.com/biochem6/
Origins of life website and the role of RNA: http://www.geocities.com/CapeCanaveral/Lab/2948/orgel.html
NCBI (Pubmed):  http://www.ncbi.nlm.nih.gov/
SCOP database: http://scop.mrc-lmb.cam.ac.uk/scop/

CATH database: http://www.cathdb.info/

Inner Life of the Cell: http://multimedia.mcb.harvard.edu/media.html

Structural Programs:

            VAST and others from NCBI: http://www.ncbi.nlm.nih.gov/Structure/index.shtml

            CE: http://cl.sdsc.edu/ce.html

            FSSP (Dali database): http://ekhidna.biocenter.helsinki.fi/dali/start

Human genome project:  http://www.genome.gov
Diploid genome sequence of an individual human: http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0050254
Website on fMRI: http://www.fmri.org/index.html
Website on thalassemia and sickle-cell anemia:  http://sickle.bwh.harvard.edu/index.html
Aspartate transcarbamoylase website (R and T states):
                    http://tutor.lscf.ucsb.edu/instdev/sears/biochemistry/tw-enz/atcase/atcase.htm
Protein Data Bank:  http://www.rcsb.org/pdb/
Harvard Biology links:  http://mcb.harvard.edu/BioLinks/biochem.html
Bio Explorer:  http://biolinks.net.ru/Methods_and_Protocols/ 

U.S. Department of Commerce:  http://molecularbiology.forums.biotechniques.com/forums/index.php

Biochem Links: http://www.biochemlinks.com/bclinks/bclinks.cfm
Vitamins: http://web.indstate.edu/thcme/mwking/vitamins.html
Kinesin animation: http://www.scripps.edu/cb/milligan/projects.html
Movement of flagella: http://www.cco.caltech.edu/~brokawc/Demo1/BeadExpt.html
Blood clotting animation: http://www.mhhe.com/biosci/esp/2002_general/Esp/folder_structure/tr/m1/s7/trm1s7_3.htm
Action potential animation: http://www.lifesci.ucsb.edu/~mcdougal/neurobehavior/modules_homework/lect3.dcr