Syllabus

Chemistry 431C

Biochemistry

Spring 2007

 

Instructor:                              Dr. Jamil Momand, Ph.D.

 

Class location and time:        Salazar Hall, Room C367B

                                                MWF 9:30-10:20

 

Office Hours:                         Physical Sciences Building, Room 803

                                                M 4-5 PM; T 10-11 AM, W 2-4 PM

                                                Office Phone: (323) 343-2361

                                                Email: jmomand@calstatela.edu

                                                Department Phone: (323) 343-2300

                                                Website: http://www.calstatela.edu/faculty/jmomand/

 

Course Prerequisite:              Grade of C or better in CHEM 431B

 

Required Text:                       Nelson and Cox, Lehninger Principles of Biochemistry 4th edition, W. H. Freeman and Co., NY 2005 (ISBN: 0-7167-4339-6)

 

Supplemental Matl:               Library reserve website: http://www.calstatela.edu/library/opac/reserves.html

 

Midterm Exams:                    20 Apr., Chapters 21, 23,

                                                16 May., Chapters 24-26

 

Final Exam:                            Wed, 6 Jun, 8:00-10:30 AM

 

Grading:                                 Two Quizzes                  50 points

Exam 1             200 points

                                                Exam 2             200 points

                                                Final Exam                   300 points

                                                Writing assignment        100points

                                                Total                            850 points

 

Writing Assignment: The student will write a minimum 3-page critique on an assigned research article on the topic of transcription.  The critique will include a restatement of the hypothesis being tested, a summary of the results, and a conclusion of the work in your own words. A handout detailing the requirements of the critique will be made available to students.

 

The writing projects are due at the beginning of class 25 May.

 

Make-up Exams: A signed note should accompany all requests for make-up exams, no later than two days after the scheduled exam from either an employer or a physician.  The note must include a phone number for verification.

 

Make-up Quizzes: There will be no make-up quizzes.

 

General Biochemistry Subjects to be covered:

 

  • Lipid Metabolism: Fatty acids, triacylglycerols and lipoproteins.  Utilization and transport of fat and cholesterol, fatty acid biosynthesis, biochemical insights into obesity.

 

  • Lipid Metabolism: Membrane lipids, steroids, isoprenoids and eicosanoids.  Metabolism of glcerophospholipids, steroids, and lipid soluble vitamins; synthesis and biological actions of prostaglandins, thromboxanes and leukotrienes

 

  • Metabolic Coordination, Metabolic Control and Signal Transduction.  Interdependence of the major organs in fuel metabolism and hormonal regulation of fuel metabolism; mechanisms of hormone action; signal transduction, oncogenes and cancer.

 

  • Replication.  Classic experiments demonstrating fundamental principles in replication; DNA polymerase, accessory proteins, fidelity of DNA replication, retrovirus replication.

 

  • DNA modifications.  DNA methylation, restriction enzymes, DNA damage and repair, recombination, transposable elements, gene amplification.

 

  • Transcription. Experiments demonstrating the existence of mRNA, RNA polymerase, initiation, elongation, and termination; review of transcriptional regulation literature.

 

  • Translation. Genetic code, tRNA charging, ribosome structure, mechanism of translation, inhibition by antibiotics, folding and post-translational modifications.

 

  • Writing. Peer-reviewed paper analysis, critique writing.

 

Grading Scale:

 

A=791-850 pts

A-=748-790 pts

B+=723-747 pts

B=689-722 pts

B-=663-688 pts

C+=630-662 pts

C=596-629 pts

C-=553-595 pts

D+=518-552 pts

D=467-517 pts

LECTURE SCHEDULE

Biochemistry III (Chem 431c)

Spring 2007

 

Lecture

Date

Topic

Reading

Homework

1

26 Mar

Course logistics-objectives, assignments, grading policy, exams, lectures, writing, how to study, prerequisites. Overview of fatty acid synthesis, malonyl-CoA, fatty acid synthase

Ch. 21, pp. 787-789

 

2

28 Mar

Fatty acid synthase (continued), sequence of events, subcellular location of fatty acid synthesis, acetyl CoA transport from mitochondria to cytoplasm, regulation of F.A. synthesis, eicosanoids

Ch. 21, pp. 789-801

21.1-21.3

 

30 Mar

No Lecture-Chavez Holiday

 

 

3

2 Apr

Prostaglandins, thromboxanes, COX, aspirin, Celebrex, Vioxx, synthesis of phosphatidic acid, triacylglycerol, triacylglycerol cycle

Ch. 21, pp. 801-806

21.4-21.7

4

4 Apr

Glyceroneogenesis, membrane phospholipids, phosphatidyl inositol, phosphatydyl choline, cholesterol synthesis

Ch. 21, pp. 806-813, pp. 816-820

21.10, 21.13, 21.15-21.16

 

6 Apr

No Lecture

 

 

5

9 Apr

Human plasma lipoproteins, cholesterol uptake, atherosclerosis, inhibitors of HMG-CoA reductase, steroids

Ch. 21, pp. 821-829

 

6

11 Apr

Quiz 1. Overview of hormones, neuroendocrine system, discoveries of hormones, receptors, review of Scatchard analysis, radioimmunoassay, ELISA

Ch. 23, pp. 881-886

 

7

13 Apr

Peptide hormones, catecholamines, eicosanoids, steroids, vitamin D, vitamin A, thyroid hormones, nitric oxide, insulin, glucagon, diabetes, ketosis

Ch. 23, pp. 886-892, pp. 902-910

23.3-23.13

 

16 Apr

 No lecture

 

 

8

18 Apr

Obesity, regulation of body fat, leptin, neuropeptide Y, α-MSH, metabolic disease

Ch. 23, pp. 910-917

http://cbs2chicago.com/video/?id=25675@wbbm.dayport.com&cid=7; http://video.google.com/videoplay?docid=-6583788741119043625

23.14

 

20 Apr

Midterm 1 Chapters 21, 23

 

 

9

23 Apr

Chromosomes, prokaryotes, eukaryotes, analysis of the human genome, centromere, telomere

Ch. 24 pp. 923-930

24.1-24.11

10

25 Apr

DNA supercoiling, linking number,

Ch. 24 pp. 930-937; pp. 938-943

 

11

27 Apr

DNA replication, origin of replication, semiconservative replication, 5’→3’ direction

Ch. 25, pp. 948-952

25.1-25.5, 25.7

12

30 Apr

Instructor help for writing papers

 

 

13

2 May

Polymerases, accuracy of DNA replication, initiation, elongation, termination

Ch. 25, pp. 953-963; http://nobelprize.org/educational_games/medicine/dna/a/replication/replication_ani.html

25.8

14

4 May

DNA damage, repair and mutation, different repair mechanisms

Ch. 25 pp 963-978

25.9-29.12

15

7 May

DNA recombination, meiosis, transposable elements, immunoglobulin genes

Ch. 25 pp 978-991

25.13

16

9 May

Quiz 2. RNA polymerase, promoters, initiation, elongation, termination

Ch. 26 pp. 995-1007; http://student.ccbcmd.edu/biotutorials/protsyn/tsc.html

26.1, 26.2, 26.4,

17

11 May

RNA processing, capping, introns, exons, 3’ end processing, mRNA degradation, retroviruses, AIDS, cancer, telomerase

Ch. 26 pp. 1007-1014, pp. 1020-1027

26.3, 26.6-26.10

18

14 May

RNA and evolution

Ch. 26 pp. 1027-1031

 

 

16 May

Midterm 2 Chapters 24-26

 

 

19

18 May

Regulation of gene expression, lac operon

Ch. 28 pp. 1081-1094

28.1-28.6

20

21 May

Trp operon, SOS response

Ch. 28 pp. 1094-1098, 

28.7, 28.9-28.10, 28.12

21

23 May

Eukaryotic transcription regulation yeast galactose metabolism regulation

Ch. 28 pp. 1102-1110

 

22

25 May

Eukaryotic transcription-RNA interference

Ch. 28 pp. 1110-1111,

 

 

28 May

Holiday-Memorial Day

 

 

23

30 May

Protein metabolism, genetic code, aminoacyl-tRNA synthetase

Ch. 27 pp. 1034-1044

27.1a, 27.4, 27.5, 27.10, 27.12,

24

1 Jun

Protein synthesis, ribosomes, stages of protein synthesis. Student Opinion Surveys

Ch. 27 pp. 1044-1056

27.13, 27.14, 27.15

 

6 Dec

Final exam (8-10:30 am)

 

 

 

 

Choice of articles on transcription and/or RNA regulation to be reviewed by students:

 

Barberis et al (1995) Cell 81, 359-368

Brent and Ptashne (1985) Cell 43, 729-736

Bryant and Ptashne (2003) Mol Cell 11, 1301-1309

Chien et al (1991) PNAS 88, 9578-9582

Chong et al (2005) MCB 25: 2632-2643

Cosma et al (1999) Cell 97, 299-311

Dodd et at (2001) Genes Dev 15, 3013-3022

Dove and Hochschild (1998) Genes Dev 12, 745-754

Dunn et al (1984) PNAS 81, 5017-5020

El-Deiry et al (1992) Nat. Genet 1, 45-49

Gunawardane et al (2007) Science 315, 1587-1590

Hochschild and Ptashne (1986) Cell 44, 681-687

Krol et al (2007) Mol Cell. 25, 575-86

Lau et al. (2006) Science 313, 363-367

Luo et al (2004) PNAS 101, 2259-2264

Park and Roeder (2006) MCB 26, 4006-4016

Revet et al (1999) Curr. Biol. 9, 151-154

Yao et al (2001) MCB 21, 5979-5991

 

Review articles to help you understand the articles above:

 

Tolia and Joshua-Tor (2007) Nat CB 3, 36-43

Ptashne (2005) TIBS 30, 275-279

Instructions for Writing Assignment

Chemistry 431C

 

A paper will be assigned to you from the instructor.  To get feedback on your writing please submit a rough draft first to the Writing Center located at the library (x35350, Lib PW 2097).  Once you have received feedback from the Writing Center you may hand in the corrected draft, proof of Writing Center review, and original research article to the instructor by May 14 for more feedback.  The final draft is due May 25, at the beginning of class.  START EARLY!!

 

Instructions for Writing Assignment

 

Write a minimum three page summary of the paper assigned to you.

 

In the summary include: 1) a description of the hypothesis being tested; 2) a description of the results (it is useful to describe each figure or table); 3) the major conclusion of the work; 4) a new question that builds on the article’s findings.  The paper must be written in your own words.  Do not attempt to plagiarize; if you do you will get a zero on the paper and you will fail the course.  The paper and a photocopy of the original research article must be handed in together.  Only word-processed papers will be accepted.

 

Specific Instructions:

 

1.      Title page

 

            Top center of page: Title of Article Reviewing and Complete Names of all Authors.

 

            Example:          An analysis of “_________________” by ______________

 

            Middle of page:            Name of student

                                                Date

 

            Bottom of Page:            CHEM 431C

                                                California State University at Los Angeles

                                                Dr. Jamil Momand

 

2.      Text should be typed double-spaced, using 12-point font size, with 1” margins (top, bottom, sides).

3.      The text should be at least 3 pages in length (not including the title page).

4.      All pages, except the title page must be numbered at the bottom, center.

5.      The summary should include:

a.       Introduction

                        Background information

                        Hypothesis being tested

b.      Data analysis

Describe the method used to generate each figure or table.

Reiterate, in your own words, the conclusion drawn from each figure or table.

                        Describe, in your opinion, the most compelling data presented.

c.       Conclusions

                        Determine whether the authors answered the hypothesis they presented.

                        Describe strengths and weaknesses of the paper.

                        Describe what should be the next question the work raises.

                        Describe the importance of the work to society’s scientific knowledge.

 

6.      References

 

Author, year, title, source, volume and page numbers.

Websites