microsatellites and SNPs

Question 1

what are molecular markers

Answer 1

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

Question 2

what is a locus

Answer 2

the fixed position where the allele is found on each chromosome

Question 3

what is the genome and what is its role

Answer 3

DNA
store genetic material

Question 4

what is the transcriptome and what is its role

Answer 4

RNA
message transmission

Question 5

what is the proteome and what is its role

Answer 5

protein
enact cellular response

Question 6

what is the possible result of a change in DNA sequence

Answer 6

change in amino acid sequence and protein structure

Question 7

what were the first molecular markers

Answer 7

proteins

Question 8

what are allozymes

Answer 8

variant proteins (enzymes) encoded by different alleles

Question 9

what is important about the structure of allozymes

Answer 9

it varies

Question 10

how can allozymes be separated

Answer 10

gel electrophoresis based on size / charge

Question 11

what do different allozymes indicate

Answer 11

genetic variation in a population

Question 12

what followed allozymes in use as a molecular marker

Answer 12

RFLP’s

Question 13

what does RFLP mean

Answer 13

restriction fragment length polymorphisms

Question 14

what are RFLPs and what do they do

Answer 14

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

Question 15

what is the result of mutations on RFLPs

Answer 15

loss or addition of cut sites

Question 16

how can the DNA fragments be separated in RFLP

Answer 16

using a gel, separate based on size

Question 17

what can be used to hybridise fragments of interest

Answer 17

DNA probes

Question 18

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

Answer 18

detection of sickle cell disease
mutation caused loss of restriction site

Question 19

what was used in 1st generation molecular markers

Answer 19

sequence data and microsatellites

Question 20

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

Answer 20

SNP’s, sometimes still microsatellites

Question 21

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

Answer 21

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

Question 22

what does high throughput mean

Answer 22

lots of sequences produced at once

Question 23

where does taq polymerase come from

Answer 23

isolated from heat tolerant bacterium

Question 24

what is the benefit of using taq polymerase

Answer 24

can use higher temperatures = faster

Question 25

what are the PCR primers (how long are they)

Answer 25

18-20 base pair oligonucleotides

Question 26

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

Answer 26

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

Question 27

what happens during denaturation

Answer 27

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

Question 28

what happens during annealing

Answer 28

cooling allows primers to bind to complementary sequences

Question 29

what happens during extension

Answer 29

optimal temperature for Taq polymerase t0 synthesise new strands of DNA

Question 30

how many genes can be done in Sanger sequencing

Answer 30

1

Question 31

what is the cost of Sanger sequencing

Answer 31

low

Question 32

what type of DNA is Sanger sequencing more useful for

Answer 32

mitochondrial

Question 33

how does Sanger sequencing work

Answer 33

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

Question 34

what is a neutral marker

Answer 34

infers no reproductive disadvantage or advantage

Question 35

where are neutral markers usually found

Answer 35

mitochondrial DNA

Question 36

how does DNA barcoding work

Answer 36

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

Question 37

what is a well known primer in DNA barcoding

Answer 37

CO1

Question 38

what are microsatellites

Answer 38

repetitive DNA, widespread in eukaryotic organisms

Question 39

what is another word(s) for microsatellites

Answer 39

short tandem repeats

Question 40

how many base pairs in a microsatellite

Answer 40

2-6

Question 41

where are microsatellites usually found

Answer 41

non-coding regions

Question 42

how does DNA fingerprinting work

Answer 42

sampling multiple markers simultaneously

Question 43

how much of the population will share one microsatellite allele

Answer 43

5-20%

Question 44

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

Answer 44

17

Question 45

what people can DNA fingerprinting not distinguish between

Answer 45

monozygotic twins

Question 46

what occurs in DNA fingerprinting after DNA has been extracted

Answer 46

PCR using specific set of primers to amplify microsatellite of interest

Question 47

how are the fragments from PCR separated

Answer 47

gel electrophoresis or capillary electrophoresis

Question 48

how are the results from DNA fingerprinting interpreted

Answer 48

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

Question 49

how does next generation sequencing work

Answer 49

parallel sequencing of millions of DNA templates simultaneously

Question 50

what molecular marker is most often used in NGS

Answer 50

SNP's

Question 51

what is a single nucleotide polymorphism (SNP)

Answer 51

a single base change in a DNA sequence

Question 52

SNP's are biallelic, what does this mean

Answer 52

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

Question 53

where are SNP's usually found

Answer 53

non-coding / regulatory regions

Question 54

what is an SNP chip and which animals have them

Answer 54

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

Question 55

what happens if there is no SNP chip for your species

Answer 55

whole genome must be sequenced

Question 56

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

Answer 56

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

Question 57

why do SNP's outperform microsatellites

Answer 57

clearer population delimitation and more populations identified

Question 58

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

Answer 58

to sequence all described species in the UK