BICH/GENE 631 - Biochemical Genetics - Spring 2007

 

The goal of this course is to examine how molecular biologists go about framing and attacking questions about biological phenomena, using a combination of the tools of genetics and biochemistry. We will try to understand the larger ideas behind different classes of experiments, and how these experiments address common questions that arise in molecular biology. Our goal is to illustrate these ideas using examples from the literature.

Instructors

John Mullet

306A Biochemistry jmullet@tamu.edu

Gary Kunkel

406A Biochemistry g-kunkel@tamu.edu http://www.tamu.edu/classes/bich/kunkel/hp.html

Jorge Cruz-Reyes

321A Biochemistry cruzrey@tamu.edu

 

Course Policies

Prerequisites

You should have already had survey courses in molecular biology, genetics and/or biochemistry. You should be able to understand both the terminology used and, more importantly, what is not covered here. We expect you to be familiar with the material taught in BICH431 and will proceed accordingly. Equivalent coursework at other institutions or your ability to demonstrate that you have acquired the requisite knowledge by other means (e.g., research experience) will substitute for BICH431.

 

Class lectures

The material covered during lectures will emphasize genetic and biochemical approaches to answering questions. Since most funding agencies favor hypothesis-driven research, wherever possible, experimental approaches will be framed in terms of the question to be answered and the background work that led the investigators to pose that question. However, technology is essential for answering these questions, and we will encounter many different experimental techniques throughout the semester. This is not a methods course, though, so our goal will be familiarize you with why the method was used, its basic principles and any limitations in interpretation of the data rather than a detailed listing of technical steps.

We strongly encourage you to ask questions during lecture when something being covered is not clear.

 

Reading assignments

There is no textbook. In the schedule of lectures that follows, required readings are listed. In addition, the required reading list is attached and is available online with hyperlinks underlined from which you can download the papers in pdf format. Additional reading that you may find of interest or useful will be supplied by each instructor. Experimental results will be shown in lecture from some other papers that are not required reading. The references for these papers will be provided during lecture.

 

It is strongly suggested that you read the required papers BEFORE each lecture, at least a cursory read. Then you will understand lectures better and be able to ask questions. After each lecture, you should reread the papers with more care.

Problem sets

Each instructor may assign one problem set during their section of the course based on the reading and lectures and on extending your thinking from the course materials. For example, problems may ask you to critique or extend an experiment in a particular paper, or propose an experiment to figure out a hypothetical system that looks something like what you have seen in the papers. Each problem set will be worth 20 points.

 

Exams

Three exams will be given on the dates listed in the schedule. Exams will occur in the evening. Each exam will be worth 100 points.

 

The American with Disabilities Act (ADA)

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. See the Honor Council Rules and Procedures at http://www.tamu.edu/aggiehonor.


Schedule of lectures and exams.

 Class

Date

 Topics

 Required Reading

1

1/16 T

Kunkel

Class organization, requirements and goals.

Model organisms.

 

 Part I – Mutants/Knockouts/Genomics

 

 

Identifying genes - inventory of components.

biochemical vs. genetic approaches

Hunting for mutants in yeast

mutagenesis, kinds of mutations

 

 

 

2

1/18 R

Kunkel

 

Hunting for mutants in yeast (cont.)

segregation - how many genes affected in mutant?

complementation - how many new genes?

linkage

1. Carlson, Osmond, and Botstein

3

1/23 T

Kunkel

Hunting for mutants in a vertebrate model system

Inbreeding; Mosaics

2. Mullins et al.

4

1/25 R

Mullet

Isolation of mutations - selections vs. screens

3. Szybalski

5

1/30 T

Mullet

From mutation to cloned gene - approaches

Cloning by complementation

4. Kranz & Holm

6

2/1 R

Mullet

Reverse genetics - from protein or RNA to gene

 

7

2/6 T

Mullet

Making knockouts – targeted homologous recombination.

5. Melton

6. Jiang & Gridley

8

2/8 R

Mullet

Making knockouts – transposon mutagenesis and

other random insertion methods.

7. Salyers et al.

 

9

2/13 T

Mullet

Suppression and synthetics

 

8. Carlson, Osmond, Neigeborn & Botstein

 

10

2/15 R

Mullet

Genetic analysis of signal transduction pathways: Epistasis relationships

9. Lau et al.

11

2/20 T

Mullet

Pathway analysis from biosynthetic to developmental

10. Jarvik & Botstein

EXAM 1 – February 22, 6-8PM, Room 107 Biochem.

Part II – Gene Regulation - Transcription

12

2/22 R

Kunkel

Cataloguing transcriptional components

Transcription factor modularity

11. Felsenfeld

12. Ptashne & Gann

13

2/27 T

Kunkel

Transcriptional synergy

13. Tanaka

 

14

3/1 R Kunkel

Mechanisms of transcriptional synergy

14. Sauer et al.

15

3/6 T

Kunkel

ATP-dependent chromatin remodeling/histone modification

15. Kadonaga

16. Jenuwein & Allis

16

3/8 R

Mullet

Recruitment to promoters: eukaryotes and prokaryotes

17. Lomvardas & Thanos

(also see Ptashne & Gann)

3/12 – 3/16 Spring Break

17

3/20 T

Kunkel

Epigenetic transcriptional regulation: DNA methylation and deacetylation

18. Nan et al.

18

3/22 R

Kunkel

Action at a distance – looping mechanisms for enhancer function

19. Wang & Giaever

19

3/27 T

Kunkel

Action at a distance (cont. ) - sliding mechanisms for enhancer function

20. Herendeen et al.

EXAM 2 – March 29, 6-8PM, Room 107 Biochem.

Part III – Posttranscriptional Gene Regulation

20

3/29 R

Cruz-Reyes

A network of protein-protein interactions regulate RNA splicing

21. Denker et al.

21

4/3 T

Cruz-Reyes

Control of mRNA stability by recruitment of the “exosome”

22. Chen et al.

22

4/5 R

Cruz-Reyes

Expansion of the genetic code via RNA editing

23. Schnaufer et al.

23

4/10 T

Cruz-Reyes

Cell-fate determination by localized gene regulation in early Drosophila embryos

24. Niessing et al.

24

4/12 R

Cruz-Reyes

Regulation of translation by “tiny” RNAs

25. Hutvagner & Zamore

25

4/17 T

Cruz-Reyes

Regulation of telomere length

26. Lin & Blackburn

26

4/19 R

Cruz-Reyes

Co-transcriptional maturation of mRNA

27. Lacadie & Rosbash

27

4/24 T

Cruz-Reyes

TBA

28.

28

4/26 R

Cruz-Reyes

TBA

29.

EXAM 3