Genomics/genome Project

Question 1

Gene sequences can be identified for chromosome maintenance what does this mean

Answer 1

Eg sequences which attach chromatids to spindle fibres. Mutations in these cause trisomy etc

Question 2

How is dna sequenced

Answer 2

Broken into small fragments

Overlaps in sequences are used for computer to reconstruct the dna

Question 3

Why is dna broken into fragments for analysis

Answer 3

Dna easier sequenced if it’s fragmented

Question 4

Why is dna harder to to reconstruct in human genome sequencing

Answer 4

Many repeats so computer can’t determine fragment ends

Question 5

Why are model organisms used

Answer 5

Smaller genome = saves cost

Less repeats = easier to reconstruct

No splicing usually = orf easier to find

Easy to manipulate after sequence is found

Question 6

What makes human sequencing time consuming

Answer 6

4000 genes

Also 3 reading frames for each strand

Question 7

Can computers detect sn rna splice sites

Answer 7

No

Question 8

Why can sequencing eg yersinia pestis plague pathogen important

Answer 8

Identify the strain
Insight into their antibiotic resistance
Insight into how they infect

Question 9

Why eukaryotic genome was first sequences

Answer 9

Cerevisiae

Question 10

Why is genome sequencing of children in Ic unit important

Answer 10

Found 1/4 have undiagnosed genetics disorders hard to identify with symptoms alone

Question 11

What 4 aspects of proteins is found by computer analysis

Answer 11

Function
Localisation
Modification
Domains

Question 12

Why are model organisms good in predicting gene function

Answer 12

30% of cerevisiae are complete homologs to humans

Question 13

Which mutated gene was sequenced in colon cancer cells

Answer 13

Msh2

Question 14

What is the blast p value

Answer 14

Probability homology is by chance. If low then they are homologs

Question 15

What function did msh2 have in yeast

Answer 15

Dna repair (explains cancer)

Question 16

How can we identify cellular effects of msh2 mutation via model organisms and what was found

Answer 16

Mutate it same place as colon cancer cells

Found it affects protein protein interactions and has a reduced steady state

Question 17

Why is it important to understand cell effects of mutations using models like msh2

Answer 17

For targeted medicine

Question 18

How is computer analysis/genome project able to produce personalised medicines (pharmacogenetics)

Answer 18

It detects genetic variability in a population and can see how responsive people would be to eg diet supplements through sequencing

Question 19

Which program predicts protein localisation

Answer 19

Psort 2

Question 20

Why is p sort 2 beneficial

Answer 20

Localisation of protein can determine its function eg yox1 was localised in nucleus = regulator/tf

Question 21

Because p sort 2 isnt 100% what is done to detect localisation

Answer 21

Gfp

Question 22

Which program detects domains

Answer 22

Blast

Question 23

why is identifying domains through blast beneficial and example

Answer 23

Tells you likely function

Yox1 has a homeodomain which is dbd suggesting it’s a tf

So now can find genes it regulates

Question 24

Which program identifies potential modifications (phosphorylation)

Answer 24

Net phos

Question 25

What can you do with detecting phosphorylation activity

Answer 25

Test effect it has on genes eg yox1 cell activity
Test if it’s true by phosphorylation of same residue in vivo

Test kinases

Question 26

Which residues mimic phosphorylation

Answer 26

Aspartic acid and glutamic acid (both -ve)

Question 27

Why can’t you fully use sequencing of tf bs yox1 to advantage

Answer 27

Because you can’t be sure all genes with the sequence are regulated by it

Question 28

Which enzyme family can be analysed as a whole on whole genome

Answer 28

Kinase family