L9: Bioinformatics Flashcards
what is bioinformatics?
field that uses computational tools for understanding biological data
what is proteomics? what is a proteome?
the study of proteins
the entire set of proteins produced by an organism
over time, a protein’s structure is more highly ?
conserved than its sequence
by studying proteins you can establish evolutionary relationships
how can sequences be used to id evolutionary relationships?
by comparing sequences to identify alignments
and testing for presence of homologs/paralogs/orthologs
what is angiogenin
a signal molecule that stimulates BV growth
structurally similar to ribonuclease
define homologous proteins
2 proteins derived from a common ancestor
is evident in aa sequence
what is medical informatics?
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
what is ClinPhen?
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
How is ClinPhen used?
extracts and prioritizes phenotypes directly from medical records to expedite genetic disease diagnosis
how do we detect homologs?
using statistical analysis of sequence alignments
and must compare sequences to rule out chance
what is the purpose of GARD?
apart of NIH – national center for advancing translational sciences
used for quick access to genetic and rare diseases
explain how statistical significance of alignments can be estimated by shuffling?
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
define conservative substitution
replacing one aa w/ a similar one
define nonconservative substitution
replaces aa w/ one w/ dif chemical properties
how are aa substitutions classified?
by the fewest number of nucleotide changes to achieve the aa substitution
what is a substitution matrix
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
substitution matrices can reveal ?
homologs not found thru alignments only
substitution matrices can reveal ?
homologs not found thru alignments only
BLAST
basic local alignment search tool
what is BLAST used for?
in order to detect sequence similarities between proteins or nucleic acids
how is BLAST used?
enter your sequence under investigation
database will yield a list of close alignments and estimate of probability of chance
since tertiary structure is closer to function than primary structure of proteins. on the basis of 3d structure, actin and Hsp70 ?
proteins w/ dif functions
but almost identical structure
thus considered paralogs
convergent evolution
some proteins have common structural and functional features but do not share a common ancestor
thus a result of convergent evolution
convergent evolution is an example of proteins from different ________ pathways, arriving at the same solutions to ?
ancestor pathways
biochemical problem
ex. serine proteases
relate evolutionary tree diagrams to alignments
length of the limbs are proportional to number of differences between the 2 aa sequences
horizontal gene transfer
the exchange of DNA between species that confers selective advantage on the recipient
common in prokaryotes
