I590: Introduction to genomics for non-biologists (3CR)
Spring
Semester 2005: Tuesday/Thursday,
9:30am-10:45pm, Eigenmann 921
Instructor: Haixu Tang
Description: We aim to introduce the
broad frontiers of contemporary biology to the students who intend to
work on biology-related problems but so far have no biology
background. This class will cover important themes in molecular
genetics and cell biology, including
- biochemistry of proteins and nucleic acids;
-
metabolic pathways;
-
3D structure of biological molecules;
- genetic mechanisms;
- internal organization of
the cell: membrane, intracellular compartments and traffic, and the
cell cycle;
- cell
communiation;
- immune system;
- development
of multicellular organisms;
-
diseases;
-
biotechnologies in genomics and proteomics.
This course is designed for non-biology-major
graduate
students working in the biology-related areas, particularly
bioinformatics and computational biology. Therefore, we assume the
students are mature students who want to learn biology contents as
quickly as possible so they can return to their biology-related
projects and collabrate with biologists smoothly. We expect after
taking
this class, the students will be able to (1) understand the main idea
in biological literatures; (2) communicate with biologists with no
difficulty; (3) write the summary of the biological essence in their
biology-related projects without much help from biology collabrators.
Textbook: Alberts, Johnson, Lewis, Raff, Roberts, Walter: Molecular biology of the cell, 4th edition. This is an expensive book and we mainly use it as a reference. However, if you intend to continue working on biology-related problems, I recommend you buy this excellent textbook. Certainly you can also refer this book from its online version at NCBI website with a text searching fashion: Some of the topics from the course can not be found in this book. We will distribute complementary lecture notes and reading materials along the course for these topics. We also recommend the students to read the book Campbell, Reece and Simon, Essencial Biology, for a general idea of biology.
Preliminary
syllabus [This may change!]:
| Week |
Date |
Contents |
Lecture notes |
| 1 |
1/11 Tue. |
Introduction
to the class and to molecular biology |
MBC chap 1, slides |
| 1/13 Thr. |
Genetic variations |
note, slides |
|
| 2 |
1/18 Tue. |
Biochemistry of biomolecules: proteins, nucleic acids, glycans, lipids, etc. | MBC chap 2, slides |
| 1/20 Thr. |
Catalysis and the Use of Energy by Cells I
|
MBC chap 2, slides |
|
| 3 |
1/25 Tue. |
Catalysis and the Use of Energy by Cells II (Homework 1) |
MBC chap 2, slides |
| 1/27 Thr. |
Mendelian genetics I. |
Notes: 1,
slides |
|
| 4 |
2/1 Tue. |
Mendelian genetics I. |
slides |
| 2/3 Thr. |
Mendelian genetics II. |
Notes:
2.
slides |
|
| 5 |
2/8 Tue. |
The Shape and structure
of proteins |
MBC chap 3, slides |
| 2/10 Thr. |
DNA,
chromosomes and genomes (Homework 1 due) |
MBC chap 4, slides |
|
| 6 |
2/15 Tue. |
DNA
replication, repair and recombination (Homework 2) |
MBC chap 5, slides |
| 2/17 Thr. |
DNA
replication, repair and recombination |
MBC chap 5, slides |
|
| 7 |
2/22 Tue. |
Central
dogma: from genome to proteins (Prokaryotes) |
MBC chap 6, slides |
| 2/24 Thr. |
Central
dogma: from genome to proteins (Prokaryotes) |
MBC chap 6, slides |
|
| 8 |
3/1 Tue. |
Central
dogma: from genome to proteins (Eukaryotes) (Homework 2 due) |
MBC chap 6, slides |
| 3/3 Thr. |
Regulation
of Gene expression: transcriptional regulation |
MBC chap 7, slides |
|
| 9 |
3/8 Tue. |
Regulation
of Gene expression: transcriptional regulation |
MBC chap 7, slides |
| 3/10 Thr. |
Mid-term exam | ||
| Spring
access (3/12-3/20) |
|||
| 11 |
3/22 Tue |
Regulation
of Gene expression: post-transcriptional regulation |
MBC chap 7, slides |
| 3/24 Thr. |
Topics in
biotechnology: 1. Genome sequencing and annotation |
Genomes, chap 6, slides |
|
| 12 |
3/29 Tue. |
Topics in biotechnology: 2. Manipulating proteins, DNA and RNA (Homework 3) |
MCB chap 8, slides |
| 3/31 Thr. |
Topics in biotechnology: 2. Manipulating proteins, DNA and RNA | MCB chap 8, slides |
|
| 13 |
4/5 Tue. |
Topics in biotechnology: 3. Gene expression analysis | note,
slides |
| 4/7 Thr. |
Topics in biotechnology: 4. Proteomics: Mass spectrumetry and protein-protein interaction (Homework 3 due) |
note 1,
2, slides |
|
| 14 |
4/12 Tue. |
Cell membrane (Homework 4) |
MBC chap 10,11 slides |
| 4/14 Thr. |
Intracellular compartments and protein localization | MBC chap 12, slides |
|
| 15 |
4/19 Tue. |
The cell
cycle and the programmed cell death | MBC chap 17, slides |
| 4/21 Thr. |
Immunity (Homework 4 due) |
MBC chap 24, slides |
|
| 16 |
4/26 Tue. |
Development
of multicellular organisms |
MBC chap 21, slides |
| 4/28 Thr. |
Cancer and infectious disease |
MBC chap 23,35, slides |
|
| 17 |
5/2 Tue. |
Final report due |
|