L15 - genomics and gene projects

Question 1

Why do we use comparative genomics with model organisms?

Answer 1

Predict the functions of the proteins they code for

Question 2

What are the computational analyses of sequences?

Answer 2

Predicting:
- function
- protein localisation
- protein domains/modification

Identifying regulatory sequences

Characterising protein families

Question 3

What is the human gene MSH2 involved in

Answer 3

DNA repair

Question 4

What is the yeast equivalent of MSH2 human gene?

Answer 4

MSH2

Question 5

What disease is caused by problems with the MSH2 gene?

Answer 5

Hereditary non-polyposis colon cancer

Question 6

What is the human gene CFTR involved in

Answer 6

Metal and multidrug resistance protein

Question 7

What is the yeast equivalent of CFTR human gene?

Answer 7

YCF1

Question 8

What disease is caused by problems with the CFTR gene?

Answer 8

Cystic fibrosis

Question 9

What is the human gene DM involved in

Answer 9

Ser/Thr kinase

Question 10

What is the yeast equivalent of DM human gene?

Answer 10

CBK1

Question 11

What disease is caused by problems with the DM gene?

Answer 11

Myotonic dystrophy

Question 12

What are the benefits of studies in model organisms

Answer 12

Functional characterisation of mutant proteins.

Question 13

What were the functional characterisation of mutant proteins that were revealed through analysis of MSH2 proteins?

Answer 13

Defects in critical protein-protein interactions
Reduced steady state levels of MSH2
Mutations affected the activity of the mismatch repair complex

Question 14

How many differences can two unrelated humans have (minimum?)

Answer 14

3,000,000

Question 15

Give an example of a programme that can predict protein localisation

Answer 15

PSORTII

Question 16

Give an example of a programme that can predict protein domains/modifications

Answer 16

BLAST

Question 17

Give an example of a programme that can predict phosphorylation sitess

Answer 17

NetPhos

Question 18

What are the approaches that can be taken re: phosphorylation site analyses?

Answer 18

1) Investigate protein phosphorylation in vivo and if so whether the identified threonine residue is
important.
2) Test genetically and biochemically the potential role of the programme predicted kinase.
3) Does the phosphorylation change in a cell cycle dependent manner?
4) Mutate the threonine residue to a glutamic acid, an aspartic acid or an alanine residue to
investigate role of phosphorylation

Question 19

What does identifying regulatory sequences mean?

Answer 19

Identify all promoters containing a transcription factor binding site.

Question 20

How do we characterise protein families?

Answer 20

protein families (eg kinase) have well characterised homology within catalytic doman. genome analysis allows inference of the function of uncharacterised proteins (eg kinase) by family studies and allows identification of conserved and organism-specific families of said protein (eg kinase)