L9: Bioinformatics

Question 1

what is bioinformatics?

Answer 1

field that uses computational tools for understanding biological data

Question 2

what is proteomics? what is a proteome?

Answer 2

the study of proteins

the entire set of proteins produced by an organism

Question 3

over time, a protein’s structure is more highly ?

Answer 3

conserved than its sequence

by studying proteins you can establish evolutionary relationships

Question 4

how can sequences be used to id evolutionary relationships?

Answer 4

by comparing sequences to identify alignments

and testing for presence of homologs/paralogs/orthologs

Question 5

what is angiogenin

Answer 5

a signal molecule that stimulates BV growth

structurally similar to ribonuclease

Question 6

define homologous proteins

Answer 6

2 proteins derived from a common ancestor

is evident in aa sequence

Question 7

what is medical informatics?

Answer 7

field that uses computers, info technology to gain, store, analyze, communicate, and display medical info and knowledge

aids in understanding and evaluation of clinical info
–to improve proper, quick decision making

main goal is to reduce medical risks, improve patient care, cut costs of treatment

Question 8

what is ClinPhen?

Answer 8

database used to expedite the process of checking DNA for genetic disease risk

can do the work of one week for a person in 10 minutes

Question 9

How is ClinPhen used?

Answer 9

extracts and prioritizes phenotypes directly from medical records to expedite genetic disease diagnosis

Question 10

how do we detect homologs?

Answer 10

using statistical analysis of sequence alignments

and must compare sequences to rule out chance

Question 11

what is the purpose of GARD?

Answer 11

apart of NIH – national center for advancing translational sciences

used for quick access to genetic and rare diseases

Question 12

explain how statistical significance of alignments can be estimated by shuffling?

Answer 12

computer ‘shuffles’ one of the sequences that is being compared
then find a new score

if new score is not sufficiently different from original alignment – than the similar alignments could just be chance

Question 13

define conservative substitution

Answer 13

replacing one aa w/ a similar one

Question 14

define nonconservative substitution

Answer 14

replaces aa w/ one w/ dif chemical properties

Question 15

how are aa substitutions classified?

Answer 15

by the fewest number of nucleotide changes to achieve the aa substitution

Question 16

what is a substitution matrix

Answer 16

a scoring system that awards pts for substitutions that are commonly found in nature

substracts pts for one that only rarely occur

ex Blosum-62 test

Question 17

substitution matrices can reveal ?

Answer 17

homologs not found thru alignments only

Question 18

substitution matrices can reveal ?

Answer 18

homologs not found thru alignments only

Question 19

BLAST

Answer 19

basic local alignment search tool

Question 20

what is BLAST used for?

Answer 20

in order to detect sequence similarities between proteins or nucleic acids

Question 21

how is BLAST used?

Answer 21

enter your sequence under investigation

database will yield a list of close alignments and estimate of probability of chance

Question 22

since tertiary structure is closer to function than primary structure of proteins. on the basis of 3d structure, actin and Hsp70 ?

Answer 22

proteins w/ dif functions

but almost identical structure

thus considered paralogs

Question 23

convergent evolution

Answer 23

some proteins have common structural and functional features but do not share a common ancestor

thus a result of convergent evolution

Question 24

convergent evolution is an example of proteins from different ________ pathways, arriving at the same solutions to ?

Answer 24

ancestor pathways

biochemical problem

ex. serine proteases

Question 25

relate evolutionary tree diagrams to alignments

Answer 25

length of the limbs are proportional to number of differences between the 2 aa sequences

Question 26

horizontal gene transfer

Answer 26

the exchange of DNA between species that confers selective advantage on the recipient

common in prokaryotes