CPSC 536A: Bioinformatics - Class 2 (2001/01/09)

1. Genome Structure and Organisation


1.1.Organization of Genomes (s. overhead #1)


1.2. Centromer

The centromer is a region roughly in the middle of a chromosome that is needed for the attachment of microtubuli necessary for the separation of replicated sister chromosomes


2. DNA Functions

3. Molecular organization of the cell (s. overhead #2)


4. Prokaryotes vs. Eukaryotes


Prokaryotes: e.g. Bacteria like E.coli (overhead #3a)

Eukaryotes: e.g. Yeast, Mammals (overhead #3b), Plants (overhead #3c)


5. Gene Regulation in Prokaryotes (s. overhead#4)

1. Promoter recognition: appropriate sigma factor necessary

2. Operator: blocking of transcription by binding of a repressor

3. Activator: Enhancement by binding of an activator

4. Control of translation initiation: ribosome initiated translation e.g. structure of mRNA

5. Attenuation of translation: termination of mRNA synthesis

6. Control of transcription stability:

7. Methylation of DNA

8. Degree of supercoiling of the DNA


6. Signal Transduction


6.1. Example: Ion Channels (s. overhead#5)

Ligand binding -> conformation change -> channel opens


6.2. Signal Integration (overhead#6)


6.3.Signal Amplification(overhead#7)

e.g. Amplification of the signal triggered by a photon in the retina of nocturnal animals.


6.4.Signal Network (overhead #8)


note: The inner workings of the cell are EXTREMELY complex (overhead #8beta)


7. Replication and Reproduction (overhead#9)


8. Mutations (s. overhead #10)

DNA level:

Protein level:


Note: The probability of mutations is not uniformly distributed over the genome and the distribution i variable. Some regions (hot spots) are more effected then others. e.g. immune system (overhead#11)