Chapter 7

Question 1

single stranded 18 to 30 bases in length DNA fragments complementary to sequences flanking the region to be Amplified

Answer 1

PCR primers

Question 2

what do primers do

Answer 2

determines specificity, and the distance determine size of product

Question 3

technique used in molecular biology to amplify a single copy or a few copies of a segment of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence

Answer 3

polymerase Chain Reaction PCR

Question 4

PCR products that are just double the size of the primers. Result from binding of primers on to each other through short homologies after three prime ends and copying each primer sequence

Answer 4

primer dimers

Question 5

design to add or alter sequences to one or both ends of the PCR product

Answer 5

tailed primers

Question 6

heat stable polymerase isolated from thermus aquaticus

Answer 6

Taq polymerase

Question 7

taq polymerase lacking 289 n terminal amino acids

Answer 7

stoffel fragment

Question 8

product of PCR reaction

Answer 8

amplicon

Question 9

making copies of a Target sequence to such a level that they can be detected in vitro

Answer 9

amplification

Question 10

short oligonucleotide primers, nucleotides, polymerase, buffers

Answer 10

components of PCR DNA template

Question 11

what are the three cycles of PCR

Answer 11

denaturation, annealing, extension

Question 12

fluorescent detectors measure PCR product as the reaction proceeds

Answer 12

real-time PCR

Question 13

small sample volumes in Chambers that can be heated and cooled quickly by changing the air temperature surrounding sample

Answer 13

rapid PCR

Question 14

withstand the repeated high denaturation temperature

Answer 14

thermostable polymerase

Question 15

changes temp in a block or chamber holding the sample

Answer 15

thermal cycler

Question 16

what PCR cycle is where double-stranded DNA is denatured into two single strands by heating the sample at 90 - 96 degrees C for 20 minutes

Answer 16

denaturation

Question 17

what PCR cycle is the most critical step where primers determine the specificity of the amplification at 50-70 degrees C for 20 seconds

Answer 17

annealing

Question 18

what PCR cycle is where DNA is synthesized at 68 - 75 C for 30 seconds

Answer 18

extension

Question 19

what may occur due to non-specific hybridization of primers

Answer 19

Misprime’s

Question 20

isothermal, probe amplification, probes bind immediately adjacent to one another on template, ligated and become templates for The Binding of more probes. For chlamydia gonorrhea and sickle cell

Answer 20

ligase chain reaction

Question 21

isothermal, signal amplification, series of hybridisations attaches multiple signals to each Target molecule. HPV, HCV, HIV 1

Answer 21

branched DNA

Question 22

isothermal, signal amplification, immobilized DNA probe binds to RNA targets. RNA DNA hybrids are bound by LABELED monoclonal antibodies. HPV, HBV, CMV

Answer 22

hybrid capture

Question 23

isothermal, Target amplification as RNA, cDNA is made from RNA Target adding RNA polymerase promoter, RNA synthesis from cDNA template and can serve as a source of new cDNA. Tuberculosis, chlamydia, HIV, CMV

Answer 23

TXN- mediated amplification (TMA)

Question 24

two probes, one has donor five prime one has acceptor 3 Prime Vines two adjacent Target’s Fluoroscein-rhodamine

Answer 24

FRET

Question 25

Quencher and reporter together, broken when amplification occurs signal on

Answer 25

TaqMan

Question 26

binds minor groove of double-stranded DNA

Answer 26

SyBr Green

Question 27

what is the purpose of an amplification control in PCR

Answer 27

to distinguish true negatives from false negatives

Question 28

what is the most dangerous contaminant in PCR

Answer 28

carryover PCR product from previous reaction

Question 29

what is a way to avoid Misprimes, use the sequestered enzyme, keep everything on Ice, use a preheated cycler

Answer 29

Hot Start

Question 30

uses RNA as a Target. DNA is synthesized from Target RNA then transcription of DNA produces copies of RNA

Answer 30

TAS transcription based amplification systems

Question 31

measures the accumulation of product at annealing step in PCR cycle

Answer 31

molecular beacons

Question 32

bind fluoresce double-stranded DNA

Answer 32

DNA specific dyes

Question 33

bind and fluoresce intended PCR product

Answer 33

hybridization probes

Question 34

label the PCR product

Answer 34

primer Incorporated probes

Question 35

amplifying multiple Targets on the same strand of DNA at the same time

Answer 35

Multiplex PCR

Question 36

what control is run to detect contamination in PCR

Answer 36

reagent blank

Question 37

nonspecific extra PCR products can result from

Answer 37

Mispriming

Question 38

method for purifying PCR product

Answer 38

put the reaction mix through a spin column

Question 39

what enzyme system is used to avoid contamination in real-time PCR

Answer 39

dUTP - UNG

Question 40

sybr green fluorescence is detectable at which stage of the PCR amplification process

Answer 40

primer annealing and extension

Question 41

what PCR controls ensures that the enzyme is active, the buffer is optimal, and the primers are priming the correct Target sequence and must have a PCR product detected in order to be valid

Answer 41

positive control

Question 42

Taq-Man, molecular beacons, and Scorpion type primers are all used in which procedure

Answer 42

quantitative PCR

Question 43

complimentary of primer pairs at the 3’ end will result in what artifacts

Answer 43

primer dimers

Question 44

what amplification procedure uses an RNA polymerase to generate amplicons

Answer 44

Q beta replicase

Question 45

Target amplification

Answer 45

TMA - RNA is synthesized from cdna template. TB, C. trachmatis, HIV, CMV

Question 46

probe amplification

Answer 46

ligase chain reaction - ligate adjacent primers together requires a thermal cycler to change temp. chlamydia, gonorrhea, Sickle Cell mutation

Question 47

signal amplification

Answer 47

branched DNA - short oligomer probes used to capture Target nucleic acid. Hbv, hcv, hiv-1.

Question 48

hybrid capture

Answer 48

detection and characterization of HPV. HPV, hbv, CMV. four recognized by antibodies. bound to single stranded RNA probes