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Final Everything Flashcards

1
Q

normally, most of the DNA of human cells is in what form

A

antiparalllel double stranded

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2
Q

plant chloroplast DNA is inherited in a similar manner to that of one type of human DNA, and the two DNA sequences can be used to for similar purposes. What human DNA source is this?

A

mitochondria

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3
Q

what pH can be safely used to denature DNA

A

neither pH 10 nor 1

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4
Q

can DNA polymerase cope a template without a primer

A

no

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5
Q

what year was the daubert standard established

A

1993

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6
Q

significance of the daubert standard, what does it say, how does it affect forensic DNA evidence

A

sets a standard basic to test DNA evidence, scientific method applied in court

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7
Q

what year was the pitchfork case

A

1985

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8
Q

in what way is the amount of DNA available from crime scenes typically different from the amount in reference samples

A

crime scenes have less DNA than reference

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9
Q

in what way is the quality of DNA available from crime scenes typically different from the quality of reference samples

A

it is less abundant and can denature easily when out in the open

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10
Q

what is the charge of DNA

A

negative

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11
Q

which component of DNA carries the charge

A

phosphate

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12
Q

it is not possible for 2 pyrimidines to base pair with each other in normal DNA. what is at least one reason why

A

hydrogen bonding doesnt line up properly to form a double helix

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13
Q

the double helix is held by two interactions
hydrogen bonding
van der waals with hydrophobic effect
which is the strongest

A

van der waals with hydrophobic effect

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14
Q

how does the strength of the double helix relate to the sequence of bases ? is one stronger than the other?

A

G’s and C’s have three H bonds while A’s and T’s have two
G’s and C’s are stronger

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15
Q

what is meant by “high stringency” relative to DNA annealing

A

ability to be single stranded

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16
Q

how would you alter each of the following to increase stringency
temp
organic content
detergent
salt concentration

A

increase temp
increase organic content
increase detergent
decrease salt concentration

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17
Q

what is the probe made of

A

DNA

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18
Q

how is a locus different from an allele

A

locus: location on a chromosome expressing a gene
allele: individual gene that could be dominant/recessive

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19
Q

HW equilibrium is necessary to allow investigators to interpret DNA evidence using the product rule. this form is specifically required to interpret results at

A

any single locus

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20
Q

name and describe a factor or force that would disrupt HW

A

small population
nonrandom mating
mutation
natural selection
genetic drift

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21
Q

linkage equilibrium is necessary to allow investigators to interpret DNA evidence using the product rule. this form is specifically required to interpret results at

A

any pair of loci

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22
Q

name and describe a factor or force that would disrupt linkage equilibrium

A

how close the genes are on the chromosome

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23
Q

what is the cause of the polyionic effect on DNA

A

crowding of charges

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24
Q

what is the effect of the polyionic effect on DNA

A

local increase in salt concentration

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25
which quantity is the typical, recommended amount of starting DNA template for a modern multiplex STR kit
1 ng
26
1 mg is how much of a gram
1x10-3
27
1 pg is how much of a gram
1x10-12
28
most PCR reactions use two primers, what can be said about any such pair of primers
the Tm of the two primers must be quite close together
29
in the older organic method of DNA extraction, which component is used to denature and REMOVE protein from solution
phenol
30
in q-PCR what is initially the limiting supply
template
31
in the PCR cycle what determines the extension temperature used
the optimum temperature of the DNA polymerase used
32
in the PCR cycle what determines the annealing temperature used
the melting point of the primers (oligos)
33
stochastic effects in PCR are bad because they often lead to
false negatives (allelic drop out, missing alleles)
34
what kind of molecule is a nuclease
protein
35
what do nucleases do that is so bad
damage DNA
36
which type does not increase during the PCR process (2, 1 or 0 ends defined)
0
37
which type increases in a linear manner during the PCR process (0, 1 or 2 ends defined)
1
38
which type increases in an exponential manner during the PCR process (2, 1 or 0 ends defined)
2
39
quantitative PCR is also called real-time PCR. explain why it should not be called RT-PCR
RT-PCR stands for reverse transcript which is a different method that quantifies the DNA at the end of the reaction
40
how is it possible for the same amount of sample DNA to serve as a template for the production of more than twice as many different products
additional primers are added to different areas of the DNA template and different chromosomes
41
what happens at 94C during PCR
denaturation DNA bonds break apart from double to single stranded
42
what happens at 55C during PCR
annealing primers bind to DNA
43
what happens at 72C during PCR
extension DNA polymerase creates new DNA
44
why would a crime lab use differential extraction for a sample containing sperm and what is the property of the sperm
be able to separate a mixture of male and female DNA to aid cases in common victim/perpetrator assaults
45
what does stochastic mean when very low amount of template DNA is used for PCR
random results from high amplification of a low template strand concentration
46
when may it be an advantage to know both values of the total and male DNA
sexual assault cases victims vs perpetrator/murder
47
explain the FTA paper method for separating DNA
DNA is put on a piece of paper for later extraction
48
how are sperm cells different from other cells that may be present and allows differential extraction to be based on
the DNA lyse with the addition of DTT unlike other cells
49
what is a staff elimination database and why do forensic DNA labs maintain them to be used for
databases with the staff's DNA to prevent false data if contamination were to occur with a sample
50
agarose is a
carbohydrate
51
which type of DNA best corresponds to ALL satellite DNA
repeated
52
which type of DNA is most likely used for small DNA fragments
polyacrylamide
53
more complex genetic analyzers can detect a fifth color, called orange. what is it really
far red
54
what do degenerate primers mean in terms of mutations common in primer binding areas
intact, but a mixture of different sequences
55
which is true about the amelogenin locus
it is not an STR locus but generally included in STR profiles
56
in capillary gel electrophoresis, how are fluorescent bands detected
as they pass a fixed point near the end of the capillary
57
which is not a main manufacture of commercial STR kits in north american forensic labs
NIST
58
gel electrophoresis is noncovalent or covalent linked
non covalently linked
59
an agarose gel is either native or denaturing
denaturing
60
explain the difference between native and denaturing
native is dsDNA denaturing is ssDNA
61
two methods to prevent STR products from overlapping
different molecular weights fluorescent labels
62
how would a procedure be manipulated to maximize the addition of an allele
increase the elongation time to ensure the extra nucleotide gets added every time
63
what is the mechanism of stuttering
DNA polymerase slippage
64
what is the effect of stutter
a smaller repeated peak 1 base pair away
65
what is the fifth color orange used for
molecular weight standard
66
an off ladder allele is detected in an autosomal STR profile, but is in between alleles on the ladder and can be identified as ten and a half repeats, what is the correct name
10.2
67
how is the DNA from each sample loaded int0 a capillary
the negative DNA enters the positive capillary tube and a negative rod repeals the DNA towards it
68
ogston sieving
common form of DNA like a ball trying to go through the gel high molecular weight and won't be able to go through as easily
69
reptation or repetition
rare form of DNA a snake of DNA is able to slide through the gel low molecular weight can reach closer to the end of the gel
70
what is the purpose of formamide in the sample loading buffer and urea in the matrix
to denature the DNA enough to pass effectively
71
linkage disequilibrium relates to which aspect of the inheritance of autosomal STR loci
the inheritance of different loci
72
which of a mans grandparents contributed to his autosomal profile
all made a major contribution
73
which of a mans grandparents contributed to his mtDNA
maternal grandmother
74
which of the methods is generally used to calculate the probability of a random match between mtDNA profile and a randomly chosen, unrelated member of the population
counting method
75
how is the probability of calculated of the mtDNA profile
database value of allele/total allele
76
why are investigators almost always going to prefer autosomal STR over a mtDNA profile
autosomal is the only type of profile that is unique to one person
77
what procedure detail is involved in LCN protocols
large number of cycles
78
why do they sequence the HV regions instead of some other area of similar size
this region has the most variation
79
why dont they sequence the wholw mtDNA
leads to error and high cost so much more to the genome than just the HV regions
80
heteroplasmy
1 person has more than 1 profile, usually mtDNA
81
in both autosomal and Y-STR a single mismatch between a reference and evidence sample will lead to exclusion. what does this mean
they cant be the same person
82
why is the standard relaxed in mtDNA cases being viewed as inconclusive, and not grounds for exclusion
mtDNA has a higher error rate
83
list and describe two ways in which mtDNA is different than nuclear DNA
small size circular
84
what is the primary reason that the mitochondrial chromosome is a better target in degraded and low concentration DNA samples
cell has a lot of copies, more copies
85
a higher value for theta might be required 100 years ago than today. why? what makes it different?
theta is a correction for population studies and a factor for inbreeding, which was higher 100+ years ago than it is now
86
why would you expect the autosomal STR amplified to generally be the smallest
some amplify and others dont big loci generally degrade and disappear faster than smaller loci
87
why would you expect a mtDNA sequence to work in terms of a partial autosomal profile
overall autosomal X mtDNA probability
88
the ends of the Y chromosome are called pseudo-autosomal regions, what is their function
regions match X chromosome to synapse during meiosis and mitosis
89
why would Y-STR profile not be any better than a crime scene sample containing DNA of a male perp. and no female DNA because of degradation
same technology is used same number of copies
90
despite the fact that mini-STR and LCN theoretically address different problems, a crime scene sample will often benefit from both. why?
mini STR solves degradation LCN solves low concentrations many scenes have both issues
91
why does the Jefferson's case Y chromosome profile not necessarily prove he was the father of his slaves children
couldve also been his brother, following the male line
92
describe one of the two differences between sequencing and PCR that prevent sequencing from being PCR
only one primer for sequencing chain terminators are used in sequencing
93
why do profiles sometimes match up with ethnic groups, while autosomal do not
no recombination in STR alleles
94
how do the beads manage to bind DNA
DNA binds silica, glass beads have a silica coating
95
how is the magnetic nature of the beads useful
able to be pulled to the side

Forensic DNA (1 decks)

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