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ANBI 470 > Midterm 1 Key Concepts > Flashcards

Midterm 1 Key Concepts Flashcards

1
Q

3 types of tandem repeats

A

1) satellites
2) minisatellites
3) microsatellites

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2
Q

intron

A

functional part of gene, provides stability

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3
Q

promotor

A

RNA polymerases bind to initiate transcription (mRNA)

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4
Q

what 4 elements are taken out in non-coding sequences

A

introns, promotors, enhancers, silencers

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5
Q

list the 2 mutations in coding sequence

A

1) synonymous
2) non-synonymous
- missense
- nonsense
-frameshift

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6
Q

list the 2 mutations in coding sequence

A

1) synonymous
2) non-synonymous
- missense
- nonsense
-frameshift

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7
Q

4 types of DNA technologies

A

1) PCR
2) Gel electroporesis
3) DNA sequences
4) Array CGH

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8
Q

SSSSanger Sequencing

A

uses ddNTP which has hydrogen @ position 3 = stops chain
- fragments are read by fluorescence & built into a sequence

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9
Q

next generation sequencing

A

cuts whole genome + sequences all pieces @ same time

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10
Q

nanopore sequencing

A

uses nanopore to measure amount of electrical current produced when DNA molecules flows through it
- specific disruptions in current correlate to specific allele
- machine reads disruptions & sequences them all

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11
Q

1 advantage & disadvantage of nanopore sequencing

A

advantage: really long DNA reads
disadvantage: only 1 DNA molecule & can have errors so would need to use sanger sequencing to check

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12
Q

array CGH- usage & type of probe used

A

use to detect deletions & insertions
- oligonucleotide probe
- fluorescence intensities are plotted on graph
- red=subject DNA
- green=reference DNA
-yellow=both

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13
Q

oligonucleotide probe composition

A

short, single stranded DNA

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14
Q

what is mapping the genome

A

place genes on genome to specific location on chromosome

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15
Q

what is mapping a trait

A

associate trait to an area on genome

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16
Q

what is mapping a gene- what are you finding

A

find gene responsible to specific phenotype

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17
Q

2 types of genome mapping

A

1) physical
2) genetic

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18
Q

4 types of physical genome mapping

A

1) somatic cell hybridization
2) In situ hybridization
3) restriction mapping
4) genome sequencing

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19
Q

somatic cell hybridization

A

grow bovine fibroblast in culture, fuse cells with mouse tumor cell using sendai virus = heterokaryote
- then PCR DNA from heterokaryote to find chromosome
- disadvantage: takes a very long time

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20
Q

In situ hybridization

A

shows where on chromosome the area of interest is located
1) DNA will bind to chromosome where it matches up
2) use fluorescence to locate matching points
3) use banding to see location

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21
Q

restriction mapping

A

identifies where specific restriction enzyme sites are on small DNA molecule
- cuts fragments + adds enzymes then aligns all
- disadvantage: only uses small piece of DNA

22
Q

physical mapping

A

assign absolute position on chromosomes to identify chromosome location

23
Q

genetic mapping calculates ( ) based on…

A

distance based on frequency of recombination

24
Q

when does recombination occur?

A

during meiosis when homologous chromosomes meet up at spindle fibre & exchange genetic material (cross over event)

25
Q

linkage =

A

if recombination is < 50%

26
Q

how does linkage mapping work?

A

markers close together are likely inherited dependently

27
Q

T or F: must know location for linkage mapping

A

T

28
Q

what 2 things does mapping a trait require?

A

1) polymorphic traits
2) polymorphic markers
- SNPs
- microsatellites

29
Q

4 examples of SNPs

A

1) PCR-RFLP
2) sequencing
3) KASP
4) SNP array

30
Q

PCR-RFLP

A

restriction enzymes recognize a specific sequence & cut at that site
- if mutation at cut site = Eco R1 does not recognize sequence = no cut site = indication of mutation present

31
Q

why is gel electroporesis used

A

to show fragments

32
Q

disadvantage of sequencing

A

very expensive & slow if have to do for lots of animals

33
Q

KASPPP

A

uses fluorescence for allele specific PCR too determine genotype

  • amount of fluorescence is measured & plotted on graph
34
Q

SNP array

A

genotypes SNPs
1) microbeads are attached to short probe complementary to DNA sequence
2) machine reads signals & determines what SNP is present
3) probe stops right before SNP position & brings in fluorescence colour for whatever allele is next

35
Q

2 advantages & disadvantages of microsatellite markers

A

advantages:
1) easy to PCR
2) easy to compare
3) multi-allelic

disadvantages:
1) not as abundant as SNPs
2) is not causative mutation

36
Q

are SNPs or microsatellites more abundant?

A

SNPs

37
Q

PIC

A

value used to measure informativeness of a genetic marker for linkage studies

38
Q

marker assisted selection- uses a ( ) to select for ( )

A

use marker to select for specific trait

39
Q

T or F: marker assisted selection is used in humans & animals

A

F- only animals

40
Q

2 advantages & disadvantages of marker assisted selection

A

advantages:
- faster selection process
- ideal for traits difficult to measure

disadvantages:
- hitch hiking of undesired trait
- need large population

41
Q

what does the LOD score compare

A

the likelyhood for linkage vs non-linkage

42
Q

LOD > 3 =

A

proves linkage

43
Q

when is a physical, linkage, comparative map needed?

A

when species is not sequenced

44
Q

what is a SNP & what 2 things are involved?

A

simple substitution (A->G)
- transition (pyrimidine or purine substitution)
- transversion (purine replaced by pyrimidine)

45
Q

what is the recombination rate when they are all on different chromosomes unlinked?

A

25%
25%
25%
25%

46
Q

what is the recombination rate when they are all on the same chromosome unlinked?

A

25%
25%
25%
25%

47
Q

what is the recombination rate when they are all on the same chromosome linked?

A

48%
2% (recombination)
2% (recombination)
48%

48
Q

what are 2 types of genetic markers?

A

SNPs & microsatellites

49
Q

microsatellites have ( ) PICs than SNPs

A

higher

50
Q

what method is best for when traits are difficult to measure?

A

MAS

ANBI 470 (23 decks)

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