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Forensic DNA > Final Everything > Flashcards

Final Everything Flashcards

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Biology 101 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
Q

which quantity is the typical, recommended amount of starting DNA template for a modern multiplex STR kit

A

1 ng

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26
Q

1 mg is how much of a gram

A

1x10-3

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27
Q

1 pg is how much of a gram

A

1x10-12

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28
Q

most PCR reactions use two primers, what can be said about any such pair of primers

A

the Tm of the two primers must be quite close together

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29
Q

in the older organic method of DNA extraction, which component is used to denature and REMOVE protein from solution

A

phenol

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30
Q

in q-PCR what is initially the limiting supply

A

template

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31
Q

in the PCR cycle what determines the extension temperature used

A

the optimum temperature of the DNA polymerase used

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32
Q

in the PCR cycle what determines the annealing temperature used

A

the melting point of the primers (oligos)

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33
Q

stochastic effects in PCR are bad because they often lead to

A

false negatives (allelic drop out, missing alleles)

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34
Q

what kind of molecule is a nuclease

A

protein

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35
Q

what do nucleases do that is so bad

A

damage DNA

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36
Q

which type does not increase during the PCR process (2, 1 or 0 ends defined)

A

0

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37
Q

which type increases in a linear manner during the PCR process (0, 1 or 2 ends defined)

A

1

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38
Q

which type increases in an exponential manner during the PCR process (2, 1 or 0 ends defined)

A

2

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39
Q

quantitative PCR is also called real-time PCR. explain why it should not be called RT-PCR

A

RT-PCR stands for reverse transcript which is a different method that quantifies the DNA at the end of the reaction

40
Q

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

A

additional primers are added to different areas of the DNA template and different chromosomes

41
Q

what happens at 94C during PCR

A

denaturation
DNA bonds break apart from double to single stranded

42
Q

what happens at 55C during PCR

A

annealing
primers bind to DNA

43
Q

what happens at 72C during PCR

A

extension
DNA polymerase creates new DNA

44
Q

why would a crime lab use differential extraction for a sample containing sperm and what is the property of the sperm

A

be able to separate a mixture of male and female DNA to aid cases in common victim/perpetrator assaults

45
Q

what does stochastic mean when very low amount of template DNA is used for PCR

A

random results from high amplification of a low template strand concentration

46
Q

when may it be an advantage to know both values of the total and male DNA

A

sexual assault cases
victims vs perpetrator/murder

47
Q

explain the FTA paper method for separating DNA

A

DNA is put on a piece of paper for later extraction

48
Q

how are sperm cells different from other cells that may be present and allows differential extraction to be based on

A

the DNA lyse with the addition of DTT unlike other cells

49
Q

what is a staff elimination database and why do forensic DNA labs maintain them to be used for

A

databases with the staff’s DNA to prevent false data if contamination were to occur with a sample

50
Q

agarose is a

A

carbohydrate

51
Q

which type of DNA best corresponds to ALL satellite DNA

A

repeated

52
Q

which type of DNA is most likely used for small DNA fragments

A

polyacrylamide

53
Q

more complex genetic analyzers can detect a fifth color, called orange. what is it really

A

far red

54
Q

what do degenerate primers mean in terms of mutations common in primer binding areas

A

intact, but a mixture of different sequences

55
Q

which is true about the amelogenin locus

A

it is not an STR locus but generally included in STR profiles

56
Q

in capillary gel electrophoresis, how are fluorescent bands detected

A

as they pass a fixed point near the end of the capillary

57
Q

which is not a main manufacture of commercial STR kits in north american forensic labs

A

NIST

58
Q

gel electrophoresis is noncovalent or covalent linked

A

non covalently linked

59
Q

an agarose gel is either native or denaturing

A

denaturing

60
Q

explain the difference between native and denaturing

A

native is dsDNA
denaturing is ssDNA

61
Q

two methods to prevent STR products from overlapping

A

different molecular weights
fluorescent labels

62
Q

how would a procedure be manipulated to maximize the addition of an allele

A

increase the elongation time to ensure the extra nucleotide gets added every time

63
Q

what is the mechanism of stuttering

A

DNA polymerase slippage

64
Q

what is the effect of stutter

A

a smaller repeated peak 1 base pair away

65
Q

what is the fifth color orange used for

A

molecular weight standard

66
Q

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

A

10.2

67
Q

how is the DNA from each sample loaded int0 a capillary

A

the negative DNA enters the positive capillary tube and a negative rod repeals the DNA towards it

68
Q

ogston sieving

A

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
Q

reptation or repetition

A

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
Q

what is the purpose of formamide in the sample loading buffer and urea in the matrix

A

to denature the DNA enough to pass effectively

71
Q

linkage disequilibrium relates to which aspect of the inheritance of autosomal STR loci

A

the inheritance of different loci

72
Q

which of a mans grandparents contributed to his autosomal profile

A

all made a major contribution

73
Q

which of a mans grandparents contributed to his mtDNA

A

maternal grandmother

74
Q

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

A

counting method

75
Q

how is the probability of calculated of the mtDNA profile

A

database value of allele/total allele

76
Q

why are investigators almost always going to prefer autosomal STR over a mtDNA profile

A

autosomal is the only type of profile that is unique to one person

77
Q

what procedure detail is involved in LCN protocols

A

large number of cycles

78
Q

why do they sequence the HV regions instead of some other area of similar size

A

this region has the most variation

79
Q

why dont they sequence the wholw mtDNA

A

leads to error and high cost
so much more to the genome than just the HV regions

80
Q

heteroplasmy

A

1 person has more than 1 profile, usually mtDNA

81
Q

in both autosomal and Y-STR a single mismatch between a reference and evidence sample will lead to exclusion. what does this mean

A

they cant be the same person

82
Q

why is the standard relaxed in mtDNA cases being viewed as inconclusive, and not grounds for exclusion

A

mtDNA has a higher error rate

83
Q

list and describe two ways in which mtDNA is different than nuclear DNA

A

small size
circular

84
Q

what is the primary reason that the mitochondrial chromosome is a better target in degraded and low concentration DNA samples

A

cell has a lot of copies, more copies

85
Q

a higher value for theta might be required 100 years ago than today. why? what makes it different?

A

theta is a correction for population studies and a factor for inbreeding, which was higher 100+ years ago than it is now

86
Q

why would you expect the autosomal STR amplified to generally be the smallest

A

some amplify and others dont
big loci generally degrade and disappear faster than smaller loci

87
Q

why would you expect a mtDNA sequence to work in terms of a partial autosomal profile

A

overall autosomal X mtDNA probability

88
Q

the ends of the Y chromosome are called pseudo-autosomal regions, what is their function

A

regions match X chromosome to synapse during meiosis and mitosis

89
Q

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

A

same technology is used
same number of copies

90
Q

despite the fact that mini-STR and LCN theoretically address different problems, a crime scene sample will often benefit from both. why?

A

mini STR solves degradation
LCN solves low concentrations
many scenes have both issues

91
Q

why does the Jefferson’s case Y chromosome profile not necessarily prove he was the father of his slaves children

A

couldve also been his brother, following the male line

92
Q

describe one of the two differences between sequencing and PCR that prevent sequencing from being PCR

A

only one primer for sequencing
chain terminators are used in sequencing

93
Q

why do profiles sometimes match up with ethnic groups, while autosomal do not

A

no recombination in STR alleles

94
Q

how do the beads manage to bind DNA

A

DNA binds silica, glass
beads have a silica coating

95
Q

how is the magnetic nature of the beads useful

A

able to be pulled to the side

Forensic DNA (1 decks)

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