Genomics/genome Project Flashcards
Gene sequences can be identified for chromosome maintenance what does this mean
Eg sequences which attach chromatids to spindle fibres. Mutations in these cause trisomy etc
How is dna sequenced
Broken into small fragments
Overlaps in sequences are used for computer to reconstruct the dna
Why is dna broken into fragments for analysis
Dna easier sequenced if it’s fragmented
Why is dna harder to to reconstruct in human genome sequencing
Many repeats so computer can’t determine fragment ends
Why are model organisms used
Smaller genome = saves cost
Less repeats = easier to reconstruct
No splicing usually = orf easier to find
Easy to manipulate after sequence is found
What makes human sequencing time consuming
4000 genes
Also 3 reading frames for each strand
Can computers detect sn rna splice sites
No
Why can sequencing eg yersinia pestis plague pathogen important
Identify the strain
Insight into their antibiotic resistance
Insight into how they infect
Why eukaryotic genome was first sequences
Cerevisiae
Why is genome sequencing of children in Ic unit important
Found 1/4 have undiagnosed genetics disorders hard to identify with symptoms alone
What 4 aspects of proteins is found by computer analysis
Function
Localisation
Modification
Domains
Why are model organisms good in predicting gene function
30% of cerevisiae are complete homologs to humans
Which mutated gene was sequenced in colon cancer cells
Msh2
What is the blast p value
Probability homology is by chance. If low then they are homologs
What function did msh2 have in yeast
Dna repair (explains cancer)
How can we identify cellular effects of msh2 mutation via model organisms and what was found
Mutate it same place as colon cancer cells
Found it affects protein protein interactions and has a reduced steady state
Why is it important to understand cell effects of mutations using models like msh2
For targeted medicine
How is computer analysis/genome project able to produce personalised medicines (pharmacogenetics)
It detects genetic variability in a population and can see how responsive people would be to eg diet supplements through sequencing
Which program predicts protein localisation
Psort 2
Why is p sort 2 beneficial
Localisation of protein can determine its function eg yox1 was localised in nucleus = regulator/tf
Because p sort 2 isnt 100% what is done to detect localisation
Gfp
Which program detects domains
Blast
why is identifying domains through blast beneficial and example
Tells you likely function
Yox1 has a homeodomain which is dbd suggesting it’s a tf
So now can find genes it regulates
Which program identifies potential modifications (phosphorylation)
Net phos
What can you do with detecting phosphorylation activity
Test effect it has on genes eg yox1 cell activity
Test if it’s true by phosphorylation of same residue in vivo
Test kinases
Which residues mimic phosphorylation
Aspartic acid and glutamic acid (both -ve)
Why can’t you fully use sequencing of tf bs yox1 to advantage
Because you can’t be sure all genes with the sequence are regulated by it
Which enzyme family can be analysed as a whole on whole genome
Kinase family
