L15 - genomics and gene projects Flashcards
Why do we use comparative genomics with model organisms?
Predict the functions of the proteins they code for
What are the computational analyses of sequences?
Predicting:
- function
- protein localisation
- protein domains/modification
Identifying regulatory sequences
Characterising protein families
What is the human gene MSH2 involved in
DNA repair
What is the yeast equivalent of MSH2 human gene?
MSH2
What disease is caused by problems with the MSH2 gene?
Hereditary non-polyposis colon cancer
What is the human gene CFTR involved in
Metal and multidrug resistance protein
What is the yeast equivalent of CFTR human gene?
YCF1
What disease is caused by problems with the CFTR gene?
Cystic fibrosis
What is the human gene DM involved in
Ser/Thr kinase
What is the yeast equivalent of DM human gene?
CBK1
What disease is caused by problems with the DM gene?
Myotonic dystrophy
What are the benefits of studies in model organisms
Functional characterisation of mutant proteins.
What were the functional characterisation of mutant proteins that were revealed through analysis of MSH2 proteins?
Defects in critical protein-protein interactions
Reduced steady state levels of MSH2
Mutations affected the activity of the mismatch repair complex
How many differences can two unrelated humans have (minimum?)
3,000,000
Give an example of a programme that can predict protein localisation
PSORTII
Give an example of a programme that can predict protein domains/modifications
BLAST
Give an example of a programme that can predict phosphorylation sitess
NetPhos
What are the approaches that can be taken re: phosphorylation site analyses?
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
What does identifying regulatory sequences mean?
Identify all promoters containing a transcription factor binding site.
How do we characterise protein families?
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)
