BIOCHEMISTRY II
BIOL-354000
SPRING 2009

Lecture: 10-10:50 MWF, CNS 333
Discussion: 4-4:50 p.m. M, CNS 115

Instructor:  Asma HatoumBiology Department


Office Hours:

  • T, Th 1:00-2:00 PM 
  • or by appointment
Office:  167 CNS
Office Hours: 1pm Mon and Wed
Telephone: 274-1274
E-mail:  ahatoum@ithaca.edu


Tentative Schedule

Textbook:
    “Molecular Biology of the Gene”  (sixth edition) by J. D. Watson et al.


Course Description:

This is the second half of a year-long course in biochemistry.  The primary focus of this course is on 1) the processes by which macromolecules such as DNA, RNA, and protein are synthesized and maintained within the cell, 2) the mechanisms by which these processes are regulated, and 3) the impact an impairment of these processes has on the organism as a whole.

Course Goals:

By the end of the course, you should be able to:

  1. Describe in detail the mechanisms of and macromolecules involved in genome maintenance, gene expression, and the regulation of gene expression.
  2. Describe several modern biochemistry and molecular biology techniques used in scientific research.
  3. Solve textbook biochemistry and molecular biology problems as well as problems based on data from primary research articles.
  4. Recognize several ways in which biochemistry and molecular biology influence daily life at the level of the organism.
  5. Demonstrate self-directed learning in biochemistry by reading and understanding peer-reviewed articles from the primary literature.
  6. Effectively communicate current issues in biochemistry and molecular biology in both written and oral forms.

Assessment:

The following are designed to test and ensure consistent progress on all six of the stated learning goals:

  1. Midterms (50% total, 25% for each in-class exam).  The questions on the exams will be a combination of multiple-choice, short-answer, and/or short essay.
  2. Homework assignments (25%).   Throughout the semester, written homework will be assigned and graded. 
  3. Final paper and oral presentation (25%).  Instead of an in-class final, you will be assigned a final paper and oral presentation on a current topic in biochemistry.  Further details will be provided toward the second half of the semester.

Grading scale:            

                                    B+       87-89               C+       77-79               D+       67-69

A         93-100             B         83-86               C         73-76               D         63-66               F < 60

A-        90-92               B-        80-82               C-        70-72               D-        60-62              

Attendance:

 

The undergraduate handbook states the general policy that students are expected to attend classes and that they are responsible for all material even when absent. 

 

Lectures:  It is very important to be present at every lecture and discussion section, or you will miss information and fall behind.  Although I will make Powerpoint presentations available on Blackboard, some material covered in class will not be included on the Powerpoint.  

Exams:  If for a valid reason you cannot attend a scheduled exam, you must contact me a week in advance.  If you are sick or it is an emergency, contact me or leave a message on my voicemail before the exam begins and provide written documentation with your excuse as soon as possible.  Failure to provide a valid reason for the absence can result in as little as a full letter grade off, or as much as a zero grade.  Please note that traveling early for a vacation is NOT a valid excuse for missing an exam.   

Academic Honesty:

All work that you submit must be your own.  Please familiarize yourself with the definition of plagiarism.  Academic dishonesty can lead to a zero grade on that assignment, a failing grade in the course, academic code probation, or suspension or expulsion from the College depending on the gravity of the violation and the decision of the judicial board.

Students with Disabilities:

In compliance with Section 504 of the Rehabilitation Act of 1973 and the Americans with Disabilities Act, reasonable accommodation will be provided to students with documented disabilities on a case-by-case basis.  Students must register with the Office of Academic Support Services (607-274-1005, TDD 607-274-7319, acssd@ithaca.edu) and schedule an appointment with their instructors as soon as possible to discuss their needs.


Tentative Schedule (subject to change): 

 

 

Week of

 

 

TOPIC

 

Readings (chapters in Watson et al)

Homework assignments (due Friday at the beginning of class)

Jan. 19

Introduction / Review

(No class on Martin Luther King Jr. Day, Jan 19)

1-5

 

Jan. 26

DNA & RNA molecular structure

6

 

Feb. 2

Chromatin and Nucleosomes

7

HW 1

Feb. 9

DNA Replication

8

 

Feb. 16

DNA Mutation & Repair

9

HW 2

Feb. 23

DNA Recombination & Transposition

10-11

 

Mar. 2

DNA Recombination & Transposition (cont’d)

Review (Mar. 4)

Midterm 1 (Mar. 6) covers Ch 1 – Ch 11

10-11

 

Mar. 9

No class on Spring Break, Mar. 9-13

N/A

N/A

Mar. 16

Transcription

12

 

Mar. 23

RNA Splicing

13

 

Mar. 30

Translation & the genetic code

14-15

HW 3

Apr. 6

Transcription regulation in prokaryotes

16

 

Apr. 13

Transcription regulation in eukaryotes

17

HW 4

Apr. 20

Regulatory RNAs

18

 

Apr. 27

Regulatory RNAs (cont’d)

Review (May 1)

18

HW 5

May 4

Midterm 2 covers Ch 12 – Ch 18

 

 

 
*Final draft of the paper is to be submitted on Wednesday May. 6 by 4:30 PM (the day of the final exam.) 


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Last updated 1/2009