forensic molecular biology ch 7-9

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polymerase chain reaction

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63 Terms

1

polymerase chain reaction

the exponential amplification of specific sequences of DNA to yield sufficient amplified product for downstream applications

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2

0.5 ng

PCR can amplify fragments as small as _______

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3

primer sets

the component of PCR that determines what area of DNA will be copied

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4

forward primer

the primer for PCR that is complementary to the 5' to 3' strand

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5

reverse primer

the primer for PCR that is complementary to the 3' to 5' strand

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6

double stranded

taq polymerase can only attach to ___________ DNA

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7

thermus aquaticus

taq ploymerase is named after...

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8

processivity

the number of bases taq polymerase can add before it falls off

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9

fidelity

the accuracy of taq polymerase

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10

5' to 3'

taq polymerase only has proofreading capability in the ______ direction

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11

hot start PCR

when taq polymerase isn't added until the first annealing step

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12

taqgold

a form of taq polymerase that has been modified and can only be activated once activated at 95ºC

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13

tris buffer

the buffer used that is pH sensitive with temperature variation

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14

multiplex kits

PCR kits that simultaneously amplify 2 or more regions of DNA

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15

94

the denaturation step of PCR is done at _____ºC

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16

60

the annealing step of PCR is done at _____ºC

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17

72

the extension step of PCR is done at _____ºC

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18

95

the pre-incubation step of PCR is done at ____ºC

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19

final extension

the stage of PCR in which taq polymerase adds an extra adenine to each strand

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20

amp+

control sample that ensures the amplification components and thermocycler are working properly

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21

amp-

control sample that ensures purity of amplification components

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22

reagent blank

control sample that ensures the purity of extraction components

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23

stochastic effect

when two alleles in a heterozygous individual are unequally detected, resulting in allele dropout

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24

inhibitors

things that interfere with or prevent the DNA amplification process from occurring properly

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25

inhibitors

heme, melanin, and indigo dyes are examples of _______

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26

BSA

protein from cows that improves the activity of enzymes

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27

staff elimination database

a database in which workers are typed at the same loci as samples to identify the source of contamination

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28

micro-satellite regions

another name for STRs/SSRs

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29

highly variable

STRs are good for human identity purposes because they are highly variable

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30

tetranucleotides

the type of STR repeat unit that is analyzed in forensic applications

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31

stutter

caused by taq polymerase slipping off while extending a region and joining back on in the wrong place

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32

degraded

shorter allele lengths in shorter nucleotide patterns are better for _________ DNA

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33

5' to 3'

STR nomenclature is designated by the number of repeat units on the ______ strand

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34

non-consensus alleles

STR alleles that contain an incomplete repeat unit that fall in between alleles with a full repeat unit. ex.) (GATA)(GAT-)(GATA)

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35

compound repeats

comprise of two or more adjacent simple repeats. ex.) (GATA)(GATA)(GACA)

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36

complex repeats

contain several repeat blocks of variable unit length. ex.) (GATA)(GACA)(CA)(CATA)

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37

THO1

an example of a non-consensus allele, which contains of nine tetranucleotide repeats with one trinucleotide sequence

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38

native electrophoresis

electrophoresis that is done while the DNA is in double stranded form

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39

denaturing electrophoresis

electrophoresis that is done while the DNA is in single stranded form

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40

resolution

denaturing electrophoresis can provide better _________ due to increased flexibility of the single stranded molecule

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41

formamide or urea

in denaturing electrophoresis, ________ is added to denature the DNA. A hydrogen bond is formed with each strand of DNA so the DNA strands do not rejoin. The sample is heated at 95ºC and then the sample is snap cooled.

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42

agarose

electrophoresis gel that has larger pores, separates molecules with sizes of 600-23,000 nucleotides

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43

acrylamide

electrophoresis gel that has smaller pores, separates molecules with sizes of 100-1000 nucleotides

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44

vertically

acrylamide gels are run __________

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45

horizontally

agarose gels are run ___________

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46

capillary

a length of glass filled with polymer that the sample is run through for CE

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47

polymer

what fills the capillary in capillary electrophoresis

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48

performance optimized polymer

POP stands for...

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49

POP4

the polymer used for fragment analysis is...

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50

electrokinetic injection

the sample enters the capillary via __________, where a voltage is applied while the end of the capillary is immersed in a sample. the current pulls negatively charged DNA into the capillary

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51

argon ion laser

the component of the capillary electrophoresis that excites the fluorescent dyes in the sample

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52

internal size standard

a molecular size marker that is added to the sample to permit calibration of sizing measurements

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53

fluorophore

molecule capable of fluorescence

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54

400-600

for DNA typing, dyes fluoresce in the visible range, which is ______ nm

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55

molar extinction coefficient

a fluorophore's ability to absorb light

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56

quantum yield

a fluorophore's efficiency with which it converts absorbed light to emitted light

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57

photostability

a fluorophore's ability to undergo repeated cycles of excitation without being degraded

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58

spectral calibration

accounts for spectral overlap of fluorescent dyes by subtracting out contribution of other dyes for each fluorescent dye, generating a matrix using standards

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59

allelic ladder

a sample containing a mixture of all of the common alleles in a population at specific loci

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60

allelic ladder

converts size of fragments into allele repeat number

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61

mobility modifying non-nt linkers

hexaethylenoxide imparts a shift of ~2.5 nucleotides for each unit, slowing down DNA fragments that may overlap otherwise

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62

amelogenin

an allele that identifies the gender of individual

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63

5 dye system

new identifiler technology that enables smaller PCR products to be generated instead of extending the size of the amplicons

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