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chapter 5 Flashcards

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1
Q

**

what are genes on the same chromosome called?

A

syntenic genes

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2
Q

what can be quantified to map the positions of genes on chromosomes?

A

genetic linkage

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3
Q

what produced recombinant chromosomes?

A

when the alleles of syntenic genes can be reshuffled & crossing over occurs between them

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4
Q

what are chromosomes called that do not reshuffle alleles called?

A

parental chromosomes or non-recombinant chromosomes

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5
Q

what plots the position of genes on a chromosome

A

genetic linkage mapping

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6
Q

when does independent assortment of syntenic genes occur?

A

when they are far part on a chromosome

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7
Q

syntenic genes that are closer together will tend to ______ together

A

segregate

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8
Q

what occurs in prophase of meiosis 1?

A

crossing over that prevents linked genes from segregating together

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9
Q

linked genes are always syntenic to one another & always located near one another. T or F

A

True

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10
Q

what does genetic linkage lead to?

A

the production of significantly more gametes with parental allele combinations than nonparental combinations

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11
Q

T or F: If genes are linked, parental allele combinations will be observed at higher frequency than predicted by chance

A

True

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12
Q

complete genetic linkage is observed…

A

when no crossing over occurs between linked genes, only parental gametes are formed

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13
Q

what is an example of an organism that exhibits complete linkage?

A

drosophila males
-they have no crossing over
-biological bases for this is unkown

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14
Q

which is more common, incomplete linkage or complete linkage?

A

incomplete genetic linkage

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15
Q

what is recombination frequency?

A

a likely reflection of the physical distance between two genes

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16
Q

what type of test did morgan realize that the linkage of autosomal genes in Drosophila could be determined in?

A

two-point test-cross analysis

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17
Q

what type of relationship is genetic linkage?

A

a physical relationship among genes located near one another on a chromosome

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18
Q

what is crossover accompanied by?

A

chromosome breakage & rejoining in plants & animals

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19
Q

who was the first to demonstrate that genes are on chromosomes?

A

morgan

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20
Q

who created the genetic map for the five X-linked genes in drosophila?

A

Alfred Sturvant

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21
Q

what is a map unit (m.u), also called?

A

centiMorgan (cM)

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22
Q

where does recombination primarily occur?

A

at specific hotspots

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23
Q

what happened in mis-1980s

A

methods to identify polymorphic DNA sequences & improved-gene mapping software facilitated genome mapping efforts

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24
Q

what are the polymorphic DNA sequences called?

A

genetic markers

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25
Q

what lead to linkage groups?

A

the availibility of large numbers of DNA markers on each chromosome

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26
Q

what are linkage groups

A

clusters of syntenic genes that are linked to one another

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27
Q

where are genetic markers typically

A

in noncoding regions of the genome

28
Q

genetic markers include

A

-variable number tandem repeats (VNTRs)
-single nucleotide polymorphisms (SNPs)
-restriction fragment length polymorphisms (RFLPs)

29
Q

how long are VNTRs?

A

they are short- 3-20 bp

30
Q

VNTRs

A

-sequences repeat end-to-end in a chromosomal region
-different chromosomes can carry different repeat numbers of the sequence
-repeat length can vary

31
Q

how big are SNPs?

A

1 bp

32
Q

SNPs

A

-more commonly used markers than VNTRPs
-involve variants where one base pair is substituted by another base pair, typically in a noncoding region

33
Q

how many SNPs are there in the human genome?

A

3.3 million

34
Q

which marker is more common, VNTRs or SNPs?

A

-SNPs

35
Q

RFLPs

A

-changes in DNA sequence that are detected using DNA-cutting enzymes called restriction endonucleases (restriction enzyme)
-the restriction enzymes recognize & cut specific sequences of DNA
-peices of DNA resulting from restriction enzyme cutting are called restriction fragments

36
Q

what are the pieces of DNA resulting from restriction enzyme cutting called?

A

restriction fragments

37
Q

what is a haplotype?

A

-specific array of SNPs in a small region on a single chromosome
-they are closely linked variants & will tend to be passed on together during meisois

38
Q

when will haplotype SNPs be passed on?

A

these specific arrays of SNPs will be passed on together during meiosis

39
Q

what may haplotypes differ between?

A

members of a chromosome pair

40
Q

what is the first obstacle when happing human genes?

A

the difficulty in determining the allelic phase

41
Q

what is the allelic phase

A

the arrangement of alleles of linked genes on parental chromosomes

42
Q

when can allelic phase be determined?

A

when a disease-causing allele is seen to segregate along with a known genetic marker

43
Q

what does LOD score analysis do

A

compared the likelihood of obtaining the genotypes & phenotypes observed in the pedigree if two genes are linked versus the likelihood if they are unlinked

44
Q

what does LOD stand for?

A

the logarithm of the odds ratio

45
Q

what does the LOD score determine

A

the likelihood of linkage for many recombinant frequencies, called theta values

46
Q

if theta equals 0 LOD score

A

complete linkage

47
Q

if theta equals 0.5

A

not linked = independent assortment

48
Q

if theta equals 0.1, how many map units is that?

A

10 m.u.

49
Q

what does a LOD score of 3.0 or higher mean?

A

significant evidence in favor of linkage at the theta value

50
Q

what does a LOD score of less than -2.0 mean

A

significant evidence against genetic linkage

51
Q

LOD scores between 3.0 & -2.0 are what

A

inconclusive

52
Q

what does the Zmax value indicate?

A

the recombination frequency most likley to be correct

53
Q

what allows identification of the most likely recombination distance between genes?

A

the LOD score

54
Q

what does Genome-wide association studies (GWAS) do?

A

-it detects & located genes that influence traits as a group of multiple genes
-the influenced genes may be scattered through the genome
-identifies where in the genome the genes influencing a single trait are located

55
Q

what does GWAS look for?

A

-associtation between traits & groups of alleles in populations

56
Q

why are SNPs typical genetic markers used in GWAS and what type of SNPs does GWAS use?

A

due to their frequent distribution in most genomes
-uses closely linked SNPs in haplotype groups with known chromosome locations

57
Q

what are GWAS results represented in the form of?

A

a Manhattan Plot

58
Q

what does the manhattan plot indicate?

A

the locations of genes contributing to the development of traits & conditions

59
Q

reading a manhattan plot

A

-the higher the green bar, the stronger the association between a potential contributing gene & a chromosomal location

60
Q

disequilibrium

A

nonrandom distribution of alleles for linked genes

61
Q

linkage disequilibrium

A

when frequencies of haplotypes in a population deviate significantly from what is expected

62
Q

what does linkage disequlibrium reflect?

A

the NON-RANDOM relationship between alleles of closely linked genes
-means the gene are are studying is closely associated to the SNP haplotype

63
Q

how can linkage disequilibrium be separated?

A

by crossovers which are random & infrequent

64
Q

what must be identified if linkage disequilibrium is found in a SNP haplotype?

A

all genes located in that chromosome region
-then activites associated with the identified genes are then identified to determine if their action may contribute to the condition

65
Q

what gene was suggested to be associated to Crohn’s disease based of GWAS results?

A

CARD15 (recently named NOD2 gene)

genetics (37 decks)

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