bioinformatics

Question 1

BLAST

Answer 1

basic local allignment search tool

Question 2

blastn/nucleotide blast

Answer 2

search all DNA sequences in database for

a significant match to the DNA sequence you are analyzing

Question 3

blastx

Answer 3

search all protein sequences in database for

a significant match does it code for protein

Question 4

for any given sequence there are _ possible reading frames

Answer 4

6, 3 on each strand of dna

Question 5

when you are using blast you input for dna in to the

Answer 5

query

Question 6

blastp/protein blast

Answer 6

input protein sequence and search protein
databases for significant match to any other known
protein sequences

Question 7

what can blastp help determine

Answer 7

if there is an ortholog for a gene

Question 8

what does % identities and % positives mean in blastp

Answer 8

% identities = % of amino acids that are in the same position
% positives includes exact matches and amino acids of similar chemical properties

Question 9

expression vector

Answer 9

cloning vector that contains a regulated bacterial promoter next to the cloning site

Question 10

what are the step to making recombinant proteinn

Answer 10

1)Isolate mRNA from 2)Treat with reverse transcriptase to
synthesize cDNA
3)Ligate cDNA’s into pUR expression
vector & transform E. coli to create
cDNA library
4)Sequence random clones until you findone that has an Open Reading Frame that matches the known protein sequence

Question 11

what is recomb. technology good for

Answer 11

making insulin, human groth factor safe virus for vaccines

Question 12

when making transgentic animals where do you inject the recombinant DNA

Answer 12

in the mothers oocyte (in vitro fertilization)

Question 13

what is the first step of creating a transgenic animal

Answer 13

clone cDNA into a expression vector

Question 14

Transgene =

Answer 14

a segment of DNA containing a gene sequence that has been isolated from one organism and introduced into a different organism.

Question 15

what are the main questions asked when looking at Gene Expression

Answer 15

(1) When during development is gene transcribed?
(2) In what tissues is the gene transcribed?
(3) In what cells is the gene transcribed?

Question 16

when using a northern blot you can determine

Answer 16

when during development is gene transcribed?

Question 17

what is the first step when doing a northern blot

Answer 17

Extract mRNA from each sample & run out on an agarose gel

Question 18

what is the order/components in a petri dish when making a northern blot filer

Answer 18

there is a buffer that the gel (from electroleysis ) sit in on top of the gel there is a nylon membrane, on top of the membrane are some paper towels for weight

Question 19

how does the RNA get transferred onto the membrane filter

Answer 19

As buffer is drawn up by capillary action, the paper towels soak up the buffer and the RNA in the gel is transferred

Question 20

after the RNA is on the filter paper what helps you find the gene of interest

Answer 20

a probe - made by recomb. dna w/t radioactive neucloides

Question 21

Now incubate membrane with _____ probe. Probe DNA

strands will to _______ complementary RNA on gel

Answer 21

denatured,hybridize

Question 22

Overlay northern blot filter with -________. Radioactivity will expose film and ______ will be seen

Answer 22

X-ray film,dark bands

Question 23

the techique that can best help you find out what tissues a gene is being expressed is

Answer 23

situ hybridization

Question 24

situ hybridization:

Answer 24

Make a labeled “probe” from the recombinant DNA plasmid and hybridize to embryos that have been fixed and permeablized.

Question 25

FISH = Fluorescence In Situ Hybridization is

Answer 25

technique is
to localize cloned DNA sequences to a specific
chromosomal site.
Mapping the gene sequence

Question 26

how does FISH work

Answer 26

fluorescent probes that
bind to only those parts of the chromosome with which they show a high degree of sequence
similarity