[Lec 14+15] Key Terms: Methods II and Methods III

Question 1

reverse transcription

Answer 1

a viral protein that can synthesize DNA from RNA templates

Question 2

dNTP

Answer 2

deoxynucleoside triphosphate

Question 3

plateau (qPCR)

Answer 3

reached when most of reagents are used up

Question 4

fluorescent (qPCR)

Answer 4

measured with each PCR cycle and can be used to quantify the amount of DNA used as a template

Question 5

Philadelphia chromosome

Answer 5

one chromosome infused together; usually chromosome 9 and chromosome 22

Question 6

annealing

Answer 6

DNA strands binding to each other

Question 7

denaturation

Answer 7

separation of DNA strands

Question 8

Florescent Labels

Answer 8

detecting by microscopy; multiple colors

Question 9

radioactive labels

Answer 9

detected by exposure of a film

Question 10

FISH

Answer 10

florescent in-situ hybridization is used to detect specific sequences in the context of cell or tissue

Question 11

Southern blots

Answer 11

rely on hybridization of probers and can be used to detect Philadelphia chromosomes; named after Edward Southern

Question 12

ddNTPs

Answer 12

lead to termination of the reaction

Question 13

Sanger’s sequencing

Answer 13

uses ddNTPs; separate fragments by gel electrophoresis; fragments ending where a ddGTP was incorporated is generated

Question 14

bioinformatics

Answer 14

used to align and analyze data

Question 15

hybridize

Answer 15

anneal

Question 16

delta G

Answer 16

only determines the direction of a reaction and not rate of the reaction; negative delta G means the reaction occurred spontaneously

Question 17

activation energy

Answer 17

determines the speed of the reaction

Question 18

catalysts

Answer 18

lower the activation energy by interacting with the transition state

Question 19

starch

Answer 19

a glucose polymer that is very stable in water

Question 20

enzyme

Answer 20

proteins that catalyze reactions

Question 21

substrate

Answer 21

a molecule that undergoes an enzyme catalyzed reaction

Question 22

products

Answer 22

differs from substrates by one or more covalent bond

Question 23

amylose

Answer 23

forms a helix into which iodine can intercalate and form a black/blue complex

Question 24

allosteric regulation

Answer 24

conformation of enzyme changes shapes upon binding a regulatory molecule ; can inhibit or activate

Question 25

activated intermediate

Answer 25

through transfer of high energy phosphate group or AMP from ATP

Question 26

ion-exchange chromatography

Answer 26

separates protein by charge

Question 27

gel-filtration chromatography

Answer 27

separates proteins by size

Question 28

affinity chromatography

Answer 28

separates proteins by specific interactions

Question 29

SDS PAGE

Answer 29

a strong ionic detergent; denatures proteins and coats proteins with overall negative charge

Question 30

beta-mercaptoethanol

Answer 30

reducing agent; removes disulfide bonds

Question 31

ATM

Answer 31

a kinase often mutated in Axtia telangietasia; a disease with high risk of cancer

Question 32

p53

Answer 32

is an important cell cycle regulator, its activity depends on phosphorylation on cellular stress and regulates function like DNA repair, cell cycle arrest, and apoptosis

Question 33

“gel shift” assay

Answer 33

identifies proteins that bind to DNA

Question 34

EMSA

Answer 34

electrophoretic mobility shift assay

Question 35

Mass spectroscopy

Answer 35

identifies protein by separating them out

Question 36

LC-MS/MS

Answer 36

liquid chromatography used to separate peptides and reduce complexity of mix

Question 37

MS 1

Answer 37

mass of peptide-select to fragment

Question 38

MS 2

Answer 38

fragmentation pattern of peptide-sequence specific

Question 39

Proteomics

Answer 39

1. compare proteins expression in diff. cell type, 2. correlate with transcription data, 3. compare protein interaction between in different cell types