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IMS > GENETIC VARIATION > Flashcards

GENETIC VARIATION Flashcards

1
Q

what is a mutation?

A

changes in the base sequence that typically occur very much less than in 1% of the population

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2
Q

how does genetic variation arise?

A

occurs at >1%, and presumably arose from a mutation that was positively selected during evolution

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3
Q

what is DNA variation described as?

A

as DNA polymorphism

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4
Q

how common are rare variants?

A

occur at less than 1% but are distinct from mutations

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5
Q

how so mutations arise/

A 
strand breakage
base loss
base change
DNA crosslinking
DNA replication error
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6
Q

what is strand breakage?

A

several nucleotides may be lost before end-joining (an error prone process)

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7
Q

what is base loss?

A

glycosidic bond is broken or enzymatically cleaved

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8
Q

what is base change?

A

guanine is oxidised to 8-oxoguanine and then base-pairs with adenine, cytosine loses an amine group to become uracil and base-pairs with adenine. Thymidine glycol just blocks replication. Polyaromatic carbons found in cigarette tar cause bulky DNA adducts

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9
Q

what is DNA cross linking?

A

UV light cause cyclobutane dimers, and anticancer agent cis-platinum causes adjacent guanines to cross link

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10
Q

what is DNA replication error?

A

some errors not corrected

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11
Q

what happens when DNA repair mechanism fail?

A

Lead to genetic damage that isn’t repaired or repaired inaccurately (change in DNA sequence)

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12
Q

what are the health consequences of genetic damage?

A

Cancer susceptibility
Progeria (accelerated ageing)
Neurological defects
Immunodeficiency

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13
Q

what does a mutation cause?

A

hereditable change in DNA sequence and chromosome number, form or structure

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14
Q

how do changes in DNA sequence arise?

A

due to errors in DNA replication

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15
Q

why is the mutation rate important?

A

too low and organisms cannot adapt, too high and information cannot be retained

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16
Q

how do genetic changes arise?

A

as a consequence of mutation

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17
Q

what is recombination?

A

crossover events in meiosis

has a huge impact on variation

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18
Q

what is a point mutation?

A

Changes to a single nucleotide (substitution)
Missense and nonsense mutations
Insertions and deletions

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19
Q

give examples of chromosome mutations

A

polyploidy
aneuploidy
chromosome rearrangement

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20
Q

what is polyploidy?

A

Multiple sets of chromosomes

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21
Q

what is aneuploidy?

A

abnormal number

Extra or missing chromosome

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22
Q

what is chromosome rearrangement?

A

Parts moved to other chromosomes

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23
Q

what is missense mutations?

A

A change in the nucleotide sequence that results in a change to the AA sequence

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24
Q

give examples of missense mutations

A

Includes point mutations and frameshifts

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25
Q

what effect do missense mutation have?

A

May or may not have an effect on protein function
loss of function
gain of function

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26
Q

what is nonsense mutation?

A

A change in the nucleotide sequence that results in a premature stop codon

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27
Q

what is nonsense mutation caused by?

A

by point mutations and frameshifts

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28
Q

what do nonsense mutation result in?

A

in a non-functional protein
PAH, mutations in the BMPR2 gene
Duchenne muscular dystrophy

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29
Q

how does Duchenne muscular dystrophy occur?

A

arises due to mutations that introduce a premature stop codon in the dystrophin gene

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30
Q

what are insertions/deletions?

A

Removal of one to several million nucleotides

31
Q

how common are insertions/deletions?

A

5-10-% of all mutants

32
Q

what do small insertions/deletion cause?

A

Small ones often cause frame
shifts resulting in missense/
nonsense

33
Q

give examples of haploinsufficient

A

Majority of α-Thalassemias

Associated with melanoma

34
Q

what is an elctropherogram?

A

e

35
Q

what are simple tandem repeats?

A

same bits of sequence repeated lots of times, one after the other throughout the human genome

36
Q

what can happen to expanding trinucleotide repeats during replication?

A

these can increase in copy number

37
Q

how many diseases are caused by expanding trinucleotide repeats?

A

around 17 diseases

38
Q

give examples of diseases caused by expanding trinucleotide

A

Huntington’s Disease
Fragile X syndrome
Kennedy Disease
Myotonic Dystrophy

39
Q

when do CAG repeats occur?

A

in Huntington’s Disease

40
Q

what do CAG repeats encode?

A

a poly-glutamine region in a number of proteins

41
Q

what is Huntington’s disease?

A

A genetic disease – involuntary muscle movements and dementia

42
Q

what is transposons?

A

Sequences of DNA that can move around the genome

43
Q

how common are transposons?

A

Often regularly repeated throughout the genome

44
Q

what do transposons act as?

A

act as recombination hotspots

45
Q

what is retrotransposons?

A

Analogous to a ‘copy and paste’ system

Exhibit an intermediate RNA stage, prior to insertion into the genome

46
Q

what are DNA transposons

A

Simply ‘cut and paste’ the transposable element (TE)

47
Q

what are Alu repeats ?

A

The most abundant mobile element in the human genome

48
Q

what are SINEs?

A

short interspersed elements

49
Q

what are LDL receptors?

A

removes ‘bad’ cholesterol from the body (FH, atherosclerosis)

50
Q

what do LDL receptors contain?

A

has a large number of Alu repeats, which may be responsible for the large number of pathogenic deletions in this 45 kb gene

51
Q

what is selective pressure?

A

s

52
Q

what is the selective pressure for malaria?

A

SP for erythrocytes with sickle cell haemoglobin (Hb S) mutation – cause sickle cell anaemia but provide protection against malaria

53
Q

what is normal Hb susceptible to?

A

to death from malaria

54
Q

what effect does the Sickle cell trait have on malaria?

A

one gene for haemoglobin A and one gene for haemoglobin S - greater chance of surviving malaria (do not suffer adverse consequences from the Hb S gene)

55
Q

what effect does the Sickle cell diseases have?

A

susceptible to death - complications of sickle cell disease

but shows heterozygote advantage

56
Q

how do cancers have an effect?

A

they acquire distinct characteristics during their evolution

57
Q

what are tumours?

A

derived from a single ancestral cell that acquires more mutations to evolve from benign proliferation to malignant

58
Q

how so tumours develop?

A

These mutations are selected as they proliferate more and also lead to genome instability (accelerated mutation rate)

59
Q

what is haploinsufficiency?

A

when one copy is deleted, or inactivated by a mutation, so you only have one copy functioning

60
Q

what does haploinsuffiecienct mean?

A

it means one functional gene on it’s own is not enough

61
Q

is loss of function mutants recessive or dominant?

A

tend to be recessive

62
Q

why does loss of function mutants tend to be recessive?

A

Feedback loops upregulate the production of the normal gene in heterozygotes
50% of the gene product is sufficient

63
Q

what is dosage effect ?

A

d

64
Q

what does dosage effect cause?

A

Gene product is part of a quantitative signalling system

Gene products compete to determine a metabolic or developmental switch

65
Q

how do gene products combine in a fixed stoichiometry?

A

Need both α and β globins to combine to make Hb in Thalassemia (anaemia)
If α-globin chain affected by mutation – α-thalassemia (same with β)

66
Q

how much genetic variation do single nucleotide changes represent?

A

75%

67
Q

how often do differences between parental genomes occur?

A

every 1000bp, but mostly are in non-coding regions

68
Q

what do 25% of genetic variation represent?

A

structural changes mainly in copy number variation

69
Q

how can genetic changes increase our risk of/susceptibility to disease?

A

Rare high risk variant and high penetrance Rare low penetrance mutation/variation and moderate risk
Common low risk and low penetrance variant

70
Q

what is penetrance?

A

how frequently the disease is manifested

71
Q

how much of our DNA encodes for proteins?

A

1.2%

72
Q

how much effect do most mutations have?

A

little effect as they are either silent mutations (don’t change the encoded amino acid) or are in regulatory regions with no discernable effect

73
Q

what other effects can mutations have?

A

Some are harmful and if reduce reproductive success will be gradually eliminated.
Some are beneficial and become prevalent by positive selection.

IMS (52 decks)

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