Syllabus

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treated in detail in recent editions of Genes by Benjamin Lewin. Genes X ... represented in Genes X. Genes X should be available in the university bookstore.
MCB 406, Spring 2011 M, W, F: 9:00 - 9:50 a.m. – 217 Noyes Laboratory Instructors: Dr. Raven H. Huang, Dr. Craig A. Mizzen Date Day

Topic*

Chapters

Lecturer

1/19

W

Genomes, genes, gene mutations & genetic codes

1, 2

R.H. 1

1/21

F

Methods in molecular biology and genetic engineering

3

R.H. 2

1/24

M

Chromosomes & chromatin

9, 10

R.H. 3

1/26

W

DNA replication

11-14

R.H. 4

1/28

F

DNA recombination

15

R.H. 5

1/31

M

Somatic recombination in the immune system

18

R.H. 6

2/02

W

DNA repair

16

R.H. 7

2/04

F

Prokaryotic transcription: Overview

19

R.H. 8

2/07

M

Prokaryotic transcription: Regulation

26,27

R.H. 9

2/09

W

Eukaryotic transcription: Overview

20

R.H. 10

2/11

F

Eukaryotic transcription: Regulation

28

R.H. 11

2/14

M

Catalytic RNA

23

R.H. 12

2/16

W

RNA splicing

21

R.H. 13

2/18

F

Exam 1, Covers 1/19 - 2/11 (Dr. Huang's lectures 1-11)

2/21

M

mRNA 3’-polyadenylation, 5’-capping, and degradation

22

R.H. 15

2/23

W

RNA editing and modifications

23#

R.H. 16

2/25

F

RNAi: generation of small RNAs

30#

R.H. 17

2/28

M

RNAi: biological functions

30#

R.H. 18

3/02

W

RNAi-like system in bacteria and archaea

30#

R.H. 19

3/04

F

Riboswitches

30#

R.H. 20

3/07

M

Other non-coding RNAs

N/A

R.H. 21

3/09

W

Exam 2, Covers 2/14 - 3/07 (Dr. Huang's lectures 12-21)

R.H. 14

R.H. 22

3/11

F

Protein Synthesis I: Overview, tRNA structure and charging

C.M. 1

3/14

M

Protein Synthesis II: Ribosome structure, Initiation, Elongation

C.M. 2

3/16

W

Protein Synthesis III: Termination, Regulation, Wobble

C.M. 3

3/18

F

Protein Targeting I: Overview, protein secretion

C.M. 4

SPRING BREAK 3/28

M

Protein Targeting II: membrane-associated proteins

C.M. 5

3/30

W

Protein Targeting III: organelles

C.M. 6

4/01

F

Protein Modification I: Overview, analytical methods

C.M. 7

4/04

M

Protein Modification II: glycosylation

C.M. 8

4/06

W

Protein Modification III: lipidation

C.M. 9

4/08

F

Protein Modification IV: proteolytic processing and turnover

C.M. 10

4/11

M

Signal Transduction I: Overview, protein interaction modules

C.M. 11

4/13

W

Exam 3, Covers 3/11 - 4/08 (Dr. Mizzen’s lectures 1-10)

C.M. 12

4/15

F

Signal Transduction II: G-protein coupled receptors

C.M. 13

4/18

M

Signal Transduction III: Tyr kinases

C.M. 14

4/20

W

Signal Transduction IV: Ser/Thr kinases, other signals

C.M. 15

4/22

F

Nuclear Signaling I: Overview, transcription factor regulation

C.M. 16

4/25

M

Nuclear Signaling II: histone modifying activities

C.M. 17

4/27

W

Nuclear Signaling III: chromatin remodeling activities

C.M. 18

4/29

F

Cell Cycle I: Overview, regulation

C.M. 19

5/02

M

Cell Cycle II: cancer

C.M. 20

5/04

W

TBA (review or make up for canceled lectures)

C.M. 21

5/11

W

Exam 4, 9-10 am in Noyes 217. Most questions (~ 70 %) cover Dr. Mizzen’s lectures 11-21, the remainder cover Dr. Mizzen's lectures 1-10.

*Lecture titles and dates are subject to change. #Only cover partial materials presented in the Lectures. Reading for Dr. Mizzens lectures are listed in his lecture notes on the course web page.

COURSE ORGANIZATION Lecture Notes: Copies of the lecture presentations and additional relevant material will be posted on course website http://www.life.illinois.edu/mcb/406/ for downloading and printing. The user name and password required to access this material will be announced in class. Students are responsible for all materials presented or assigned during lectures. Text: No new textbook is absolutely required. However, much of the material in the course is treated in detail in recent editions of Genes by Benjamin Lewin. Genes X (2011, Jones & Bartlett) (covers research through early 2009) is strongly recommended for the much of the course. However, some of the materials covered in the class are not represented in Genes X. Genes X should be available in the university bookstore. We will occasionally list chapters or pages of "relevant" reading from additional sources. Other useful texts: Berg, J.M., Tymoczko, J.L. and Stryer, L. Biochemistry (6th Ed. 2006, W.H. Freeman) Lewin, B., Cassimeris, L., Lingappa, V., and Plopper, G. Cells (2007, Jones & Bartlett) Nelson, D.L. and Cox, M.M. Lehninger Principles of Biochemistry (5th Ed. 2008, W.H. Freeman) Review articles: Copies of relevant review articles and recent original articles will be listed during the lectures. They can be accessed via the links to on-line journals on the UIUC library website or other sources and may be posted on the course web site. Office Hours: Students should consult the tutor during office hours or review sessions before contacting the lecturers. Tutor: Mr. Younguk (Calvin) Sun (Tel: 244-1606; [email protected]) Office hours: Mondays, 1-3 p.m., RM 2410 IGB Lecturers: Dr. Raven H. Huang (411 Roger Adams Lab, Tel: 333-3967; [email protected]) Dr. Craig A. Mizzen (565 Morrill Hall, Tel: 244-4896; [email protected]) Old Exams: Some of previous exams (with and without answers) are available on the course web site. The same user name and password used to access the lecture presentations is required to access this material. Review Session: The times and locations of review sessions will be announced in the lectures. Attendance at review sessions (usually held about two nights before an exam) is optional; students may enter and leave as they wish. Because the size of the class does not permit significant discussion during lectures, these review sessions provide a good opportunity to ask questions in a less formal setting.

Grading Procedures: 1. There are four one-hour exams with equal weight. Three of them will be administered during the lecture periods. The fourth will be administered during the final exam week of the semester. The final numerical score of each student will be the average of these four exams. Therefore, you have to attend all the classes and take all the exams. 2. Final letter grades are assigned based on performance and gaps in the distribution of the final numerical scores. Based on past experience, if your scores usually fall at or near the class average for most of the exams, your final grade is likely to be a B. Our experience over the last several years has shown that there is little difference in the grade distribution of graduate and undergraduate students. Therefore, final grades will be given out for all students based on a single grading scheme. There will NOT be separate grading curves for undergraduate and graduate students. 3. We will not excuse absences from any of the hourly exams and make-ups will not be given for missed hourly exams. Obligations such as job interviews, medical school interviews and planned trips are not valid excuses. 4. All examination papers (including the final) will be returned as soon as possible after the day of the exam. Because of the size of the class, it may take more than a week to grade the exams and record the grades. Answer keys will be posted on the course website after exams are returned. 5. Students who have compared their answers with the key and who then believe that their papers have been incorrectly graded may return their exam to the tutor with a note that describes in detail the grading error. Exams that are submitted for re-grade may be subjected to re-grade of ALL ANSWERS. Re-graded papers may be picked up from the tutor. Grade corrections will be made only during the two weeks immediately following the date when the exams are returned. 6. Students who give or receive aid on exams will receive an E in the course and may be dismissed from the University.