btec 3301

ncbi - mrna sequences

ncbi nucleotide

ncbi - all amylase sequences

ncbi protein

you want to search pubmed for publications on bacteria that degrade toluene. which keyword search strategy will most likely give the most number of results and not so relevant results

- tolune degradation bacteria

- tolune or degradation or bacteria - TOO MANY

- "tolune degradation by bacteria" - FEW

- bacteria and "tolune degradation"

subset of pubmed where full contents of publications are freely available

pubmed central

MeSH is short for

Medical Subject Heading

Fruitfly.org - used to predict ___ upstream of open reading frames which RNA polymerase binds to during transcription initiation

promoter sequence

3 biggest sequence databases in the world. spell out the one under US NIH

- ncbi - nation center for biotechnology information

- ddbj

- embl-ebi

if the percent of cytosine in a double strnaded DNA molecule is 30%, what will be the percent adenine? show calculation

gc = 60%

at = 40%

%at= 40/2 = 20%

sequence accession numbers consist of 2 letters followed by a combination of numbers. the accession numbers of most curated, reference mRNA records from sweet pea would start with which two letters

NM

list 3 filters/fields you can use to narrow your search in pubmed database

date, author, journal, review, free

ncbi scientific name of organism and its lineage

ncbi taxoonomy

in jmol, which of the following components of a protein model is not considered as a ligand

peptide chain

(following ARE:

enzyme substrate

enzyme inhibitor

cofactors

carbohydrates

metal ion)

in ___, a pair of sequences with high similarity and about the same lengths are aligned and each residue of sequence A is compared with each residue in sequence B. end gaps may or may not be penalized

global alignment

the lac operon transciptional repressor, lacI, is a four peptide protein, with identical subunits. what do you call proteins that are made up of 4 peptides of the same kind

homotetramer

which protein feature refers to a small combination of a secondary structural elements, examples of which are helix-turn-helix and hairpins, and which are not able to function independently of the other parts of the protein

motifs

aside from ncbi protein, which other database can be searched to find "how many g-protein coupled receptors more than 600 nt in length hav been associated with disease in humans"

uniprot

BLOSUM62 substitution scores were calculated using closely related sequences which are at least 62% identical. Blosum is short fro

block substitution matrix

given a protein sequence, which tool will show domains, motifs, and other protein features that are identified by a collection of different feature-searching tools

interpro

in dotmatcher what two parameters can you change to reduce or filter out the background noise, to be able to more clearly see regions of similar sequences

window and threshold

TMHMM and Phobius are used mainly used to find alpha helices in proteins that may be embedded in

cell membranes

the signalP tool is used to

find sequences which get cleaved off in secreted proteins

the major driving force in 3d folding of globular proteins is believed to be

hydrophobic collapse

the sum of the substitution scores in the identity diagonal of a PAM matrix is highest

PAM30

two aligned protein sequences are considered homologous if their sequence identity is at least

35%

what is the correct arrangement of the matrices from the lowest to the highest degree of divergence of the sequences that were used to generate the pairwise scores in the matrices

pam10, blosum62, blosum30

which amino acid is invovled in the formation of intramolecular and intermolecular disulfide bonds

cysteine

which method is used is used to come up with 3d protein structures found in pdb or jmol

xray diffraction

which of the following is most likely to be a pdb accession number that can be used to search jmol for available structure

3aky