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BIO235 > microsatellites and SNPs > Flashcards

microsatellites and SNPs Flashcards

1
Q

what are molecular markers

A

genetic markers
specific DNA sequences with a known location in the genome that show variation between individuals, populations or species

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2
Q

what is a locus

A

the fixed position where the allele is found on each chromosome

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3
Q

what is the genome and what is its role

A

DNA
store genetic material

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4
Q

what is the transcriptome and what is its role

A

RNA
message transmission

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5
Q

what is the proteome and what is its role

A

protein
enact cellular response

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6
Q

what is the possible result of a change in DNA sequence

A

change in amino acid sequence and protein structure

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7
Q

what were the first molecular markers

A

proteins

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8
Q

what are allozymes

A

variant proteins (enzymes) encoded by different alleles

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9
Q

what is important about the structure of allozymes

A

it varies

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10
Q

how can allozymes be separated

A

gel electrophoresis based on size / charge

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11
Q

what do different allozymes indicate

A

genetic variation in a population

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12
Q

what followed allozymes in use as a molecular marker

A

RFLP’s

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13
Q

what does RFLP mean

A

restriction fragment length polymorphisms

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14
Q

what are RFLPs and what do they do

A

restriction enzymes which recognise and cut short specific stretches of DNA sequence

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15
Q

what is the result of mutations on RFLPs

A

loss or addition of cut sites

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16
Q

how can the DNA fragments be separated in RFLP

A

using a gel, separate based on size

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17
Q

what can be used to hybridise fragments of interest

A

DNA probes

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18
Q

give an example of when RFLPs were used as molecular markers and how

A

detection of sickle cell disease
mutation caused loss of restriction site

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19
Q

what was used in 1st generation molecular markers

A

sequence data and microsatellites

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20
Q

what is used in 2nd and 3rd generation molecular technique

A

SNP’s, sometimes still microsatellites

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21
Q

what are 4 benefits of 2nd and 3rd generation molecular techniques

A

more sensitive,
greater genome coverage - whole genome sequencing,
high throughput,
cheaper

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22
Q

what does high throughput mean

A

lots of sequences produced at once

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23
Q

where does taq polymerase come from

A

isolated from heat tolerant bacterium

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24
Q

what is the benefit of using taq polymerase

A

can use higher temperatures = faster

25
Q

what are the PCR primers (how long are they)

A

18-20 base pair oligonucleotides

26
Q

what are the 3 steps of PCR and what temperatures do they occur

A
  1. denaturing, 96C
  2. annealing, 45-65C
  3. extension, 72C
27
Q

what happens during denaturation

A

heat denatures DNA strands (breaks H bonds) leaving a single-stranded template

28
Q

what happens during annealing

A

cooling allows primers to bind to complementary sequences

29
Q

what happens during extension

A

optimal temperature for Taq polymerase t0 synthesise new strands of DNA

30
Q

how many genes can be done in Sanger sequencing

A

1

31
Q

what is the cost of Sanger sequencing

A

low

32
Q

what type of DNA is Sanger sequencing more useful for

A

mitochondrial

33
Q

how does Sanger sequencing work

A

using dye-labelled deoxyribose nucleotides (ddNTP),
picked up by machine

34
Q

what is a neutral marker

A

infers no reproductive disadvantage or advantage

35
Q

where are neutral markers usually found

A

mitochondrial DNA

36
Q

how does DNA barcoding work

A

taxonomic identification based on sequence variation
reads are compared to existing databases

37
Q

what is a well known primer in DNA barcoding

A

CO1

38
Q

what are microsatellites

A

repetitive DNA, widespread in eukaryotic organisms

39
Q

what is another word(s) for microsatellites

A

short tandem repeats

40
Q

how many base pairs in a microsatellite

A

2-6

41
Q

where are microsatellites usually found

A

non-coding regions

42
Q

how does DNA fingerprinting work

A

sampling multiple markers simultaneously

43
Q

how much of the population will share one microsatellite allele

A

5-20%

44
Q

how many microsatellite markers are used in DNA fingerprinting in the UK

A

17

45
Q

what people can DNA fingerprinting not distinguish between

A

monozygotic twins

46
Q

what occurs in DNA fingerprinting after DNA has been extracted

A

PCR using specific set of primers to amplify microsatellite of interest

47
Q

how are the fragments from PCR separated

A

gel electrophoresis or capillary electrophoresis

48
Q

how are the results from DNA fingerprinting interpreted

A

unique set of DNA fragments is matched to database or family members

49
Q

how does next generation sequencing work

A

parallel sequencing of millions of DNA templates simultaneously

50
Q

what molecular marker is most often used in NGS

A

SNP’s

51
Q

what is a single nucleotide polymorphism (SNP)

A

a single base change in a DNA sequence

52
Q

SNP’s are biallelic, what does this mean

A

the base change / mutation occurs on both alleles of the chromosome

53
Q

where are SNP’s usually found

A

non-coding / regulatory regions

54
Q

what is an SNP chip and which animals have them

A

SNP chips hold up to 500k SNP probes allowing identification of individuals
most animals now have an SNP chip made

55
Q

what happens if there is no SNP chip for your species

A

whole genome must be sequenced

56
Q

how do we know what the faces of those that sunk on the Henry VIII flagship in 1545 look like

A

genotyping based on SNP’s
compare genotypes to databases of known traits e.g. height, weight, eye and hair colour, diseases

57
Q

why do SNP’s outperform microsatellites

A

clearer population delimitation and more populations identified

58
Q

what is the goal of Darwin’s tree of life programme

A

to sequence all described species in the UK

BIO235 (12 decks)

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