lecture 9 - intro to bioinformatics

Question 1

why do we need bioinformatics? (3)

Answer 1

(1) to determine 3D structure
(2) to study evolutionary relationships - relating to structure and function, sequence conservation implies importance for function
(3) can use sequences to guide experiments - can make mutations to test role in structure and function

Question 2

is DNA sequencing easier or harder? faster or slower?

Answer 2

-easier, faster

Question 3

what are the post translational modifications by DNA sequencing? (5)

• what are they
• what aa do they apply to
• what does it do

Answer 3

(1) phosphorylation: ser, thr, tyr, adds 2 neg charges
(2) methylation: lys, adds methyl groups (nh3+ to nh2+ –ch3 OR to nh+–(ch3)2 OR to n+–(ch3)3)
(3) glycosylation: ser, thr, asn, adds complicated structure
(4) hydroxylation: pro, adds polar OH
(5) acetylation: lys, removes pos charge from nh3+ (nh3+- to nh-)

Question 4

are post-translational modifications reversible or irreversible? what do they reflect?

Answer 4

• reversible

- reflect the metabolic state of a cell

Question 5

what is a possible non-reversible modification?

Answer 5

proteolytic processing

Question 6

what is proteolytic processing?

Answer 6

• cleavage of a protein by an enzyme
• e.g. to convert a precursor to an active form
• e.g.2 removal of a single sequence

Question 7

why is DNA sequencing useful? (3)

Answer 7

• partial protein sequences allow for the location genes
• allows for post-translational modifications
• can use the sequence to identify bands on an SDS-PAGE or 2D electrophoresis gel

Question 8

what are 2 methods of DNA sequencing?

Answer 8

(1) chemical: Edman degradation

2) mass spectometry: Tandem MS (MS/MS

Question 9

what are the limitations to chemical and mass spectometry DNA sequencing? what is done to account for this?

Answer 9

• limited in the length of sequence
• most often cleave a protein first into fragments using proteolytic enzymes
• consider disulphide bonds