Bioinformatics Lecture 2

Question 1

problem with blast

Answer 1

rather old

Question 2

homologous

Answer 2

same evolutionary ancestor

earlierst: cytochrome c (protein)

Question 3

blast seeps

Answer 3

input query sequence
search in data base
output hits
some partial hits, some non hits

Question 4

PSSM

Answer 4

type of profile
two-dimensional matrix
positive score: more than random
negative score: less than random
assumes positions are independent

Question 5

PSI blast

Answer 5

runs blast
calculates blossom score about hits
positive is match
also how much protein matters in this position
stops when you start finding the same hits in new iteration

Question 6

determines function

Answer 6

structure, not sequence

Question 7

evolution and proteins

Answer 7

more variation indicates more evolution

Question 8

primary structure

Answer 8

raw amino strand

Question 9

secondary structure

Answer 9

beta sheet and alpha helix

hydrogens from peptide backbones bond two peptide strands together

Question 10

tertiary structure

Answer 10

multiple proteins coming together

start having typology

Question 11

quaternary structure

Answer 11

larger protein complexes

interactions with other molecules and peptide chains

Question 12

protein domains

Answer 12

functional components of proteins

Question 13

hydrophobic collapse

Answer 13

hydrophobic stuff wants to go to the inside

causes secondary structure

Question 14

ATPase

Answer 14

assembles ATP within the cell

has a homologue that destroys stuff

Question 15

when new protein in found

Answer 15

looking at already known proteins to determine function

compare by sequences

Question 16

homology modelling

Answer 16

= structure modelling