forensic molecular biology ch 7-9

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63 Terms
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polymerase chain reaction
the exponential amplification of specific sequences of DNA to yield sufficient amplified product for downstream applications
0.5 ng
PCR can amplify fragments as small as _______
primer sets
the component of PCR that determines what area of DNA will be copied
forward primer
the primer for PCR that is complementary to the 5' to 3' strand
reverse primer
the primer for PCR that is complementary to the 3' to 5' strand
double stranded
taq polymerase can only attach to ___________ DNA
thermus aquaticus
taq ploymerase is named after...
the number of bases taq polymerase can add before it falls off
the accuracy of taq polymerase
5' to 3'
taq polymerase only has proofreading capability in the ______ direction
hot start PCR
when taq polymerase isn't added until the first annealing step
a form of taq polymerase that has been modified and can only be activated once activated at 95ÂșC
tris buffer
the buffer used that is pH sensitive with temperature variation
multiplex kits
PCR kits that simultaneously amplify 2 or more regions of DNA
the denaturation step of PCR is done at _____ÂșC
the annealing step of PCR is done at _____ÂșC
the extension step of PCR is done at _____ÂșC
the pre-incubation step of PCR is done at ____ÂșC
final extension
the stage of PCR in which taq polymerase adds an extra adenine to each strand
control sample that ensures the amplification components and thermocycler are working properly
control sample that ensures purity of amplification components
reagent blank
control sample that ensures the purity of extraction components
stochastic effect
when two alleles in a heterozygous individual are unequally detected, resulting in allele dropout
things that interfere with or prevent the DNA amplification process from occurring properly
heme, melanin, and indigo dyes are examples of _______
protein from cows that improves the activity of enzymes
staff elimination database
a database in which workers are typed at the same loci as samples to identify the source of contamination
micro-satellite regions
another name for STRs/SSRs
highly variable
STRs are good for human identity purposes because they are highly variable
the type of STR repeat unit that is analyzed in forensic applications
caused by taq polymerase slipping off while extending a region and joining back on in the wrong place
shorter allele lengths in shorter nucleotide patterns are better for _________ DNA
5' to 3'
STR nomenclature is designated by the number of repeat units on the ______ strand
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)
compound repeats
comprise of two or more adjacent simple repeats. ex.) (GATA)(GATA)(GACA)
complex repeats
contain several repeat blocks of variable unit length. ex.) (GATA)(GACA)(CA)(CATA)
an example of a non-consensus allele, which contains of nine tetranucleotide repeats with one trinucleotide sequence
native electrophoresis
electrophoresis that is done while the DNA is in double stranded form
denaturing electrophoresis
electrophoresis that is done while the DNA is in single stranded form
denaturing electrophoresis can provide better _________ due to increased flexibility of the single stranded molecule
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 95ÂșC and then the sample is snap cooled.
electrophoresis gel that has larger pores, separates molecules with sizes of 600-23,000 nucleotides
electrophoresis gel that has smaller pores, separates molecules with sizes of 100-1000 nucleotides
acrylamide gels are run __________
agarose gels are run ___________
a length of glass filled with polymer that the sample is run through for CE
what fills the capillary in capillary electrophoresis
performance optimized polymer
POP stands for...
the polymer used for fragment analysis is...
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
argon ion laser
the component of the capillary electrophoresis that excites the fluorescent dyes in the sample
internal size standard
a molecular size marker that is added to the sample to permit calibration of sizing measurements
molecule capable of fluorescence
for DNA typing, dyes fluoresce in the visible range, which is ______ nm
molar extinction coefficient
a fluorophore's ability to absorb light
quantum yield
a fluorophore's efficiency with which it converts absorbed light to emitted light
a fluorophore's ability to undergo repeated cycles of excitation without being degraded
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
allelic ladder
a sample containing a mixture of all of the common alleles in a population at specific loci
allelic ladder
converts size of fragments into allele repeat number
mobility modifying non-nt linkers
hexaethylenoxide imparts a shift of ~2.5 nucleotides for each unit, slowing down DNA fragments that may overlap otherwise
an allele that identifies the gender of individual
5 dye system
new identifiler technology that enables smaller PCR products to be generated instead of extending the size of the amplicons