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GENETIC VARIATION Flashcards

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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
what effect do missense mutation have?
May or may not have an effect on protein function loss of function gain of function
26
what is nonsense mutation?
A change in the nucleotide sequence that results in a premature stop codon
27
what is nonsense mutation caused by?
by point mutations and frameshifts
28
what do nonsense mutation result in?
in a non-functional protein PAH, mutations in the BMPR2 gene Duchenne muscular dystrophy
29
how does Duchenne muscular dystrophy occur?
arises due to mutations that introduce a premature stop codon in the dystrophin gene
30
what are insertions/deletions?
Removal of one to several million nucleotides
31
how common are insertions/deletions?
5-10-% of all mutants
32
what do small insertions/deletion cause?
Small ones often cause frame shifts resulting in missense/ nonsense
33
give examples of haploinsufficient
Majority of α-Thalassemias | Associated with melanoma
34
what is an elctropherogram?
e
35
what are simple tandem repeats?
same bits of sequence repeated lots of times, one after the other throughout the human genome
36
what can happen to expanding trinucleotide repeats during replication?
these can increase in copy number
37
how many diseases are caused by expanding trinucleotide repeats?
around 17 diseases
38
give examples of diseases caused by expanding trinucleotide
Huntington’s Disease Fragile X syndrome Kennedy Disease Myotonic Dystrophy
39
when do CAG repeats occur?
in Huntington’s Disease
40
what do CAG repeats encode?
a poly-glutamine region in a number of proteins
41
what is Huntington's disease?
A genetic disease – involuntary muscle movements and dementia
42
what is transposons?
Sequences of DNA that can move around the genome
43
how common are transposons?
Often regularly repeated throughout the genome
44
what do transposons act as?
act as recombination hotspots
45
what is retrotransposons?
Analogous to a ‘copy and paste’ system | Exhibit an intermediate RNA stage, prior to insertion into the genome
46
what are DNA transposons
Simply ‘cut and paste’ the transposable element (TE)
47
what are Alu repeats ?
The most abundant mobile element in the human genome
48
what are SINEs?
short interspersed elements
49
what are LDL receptors?
removes ‘bad’ cholesterol from the body (FH, atherosclerosis)
50
what do LDL receptors contain?
has a large number of Alu repeats, which may be responsible for the large number of pathogenic deletions in this 45 kb gene
51
what is selective pressure?
s
52
what is the selective pressure for malaria?
SP for erythrocytes with sickle cell haemoglobin (Hb S) mutation – cause sickle cell anaemia but provide protection against malaria
53
what is normal Hb susceptible to?
to death from malaria
54
what effect does the Sickle cell trait have on malaria?
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
what effect does the Sickle cell diseases have?
susceptible to death - complications of sickle cell disease | but shows heterozygote advantage
56
how do cancers have an effect?
they acquire distinct characteristics during their evolution
57
what are tumours?
derived from a single ancestral cell that acquires more mutations to evolve from benign proliferation to malignant
58
how so tumours develop?
These mutations are selected as they proliferate more and also lead to genome instability (accelerated mutation rate)
59
what is haploinsufficiency?
when one copy is deleted, or inactivated by a mutation, so you only have one copy functioning
60
what does haploinsuffiecienct mean?
it means one functional gene on it’s own is not enough
61
is loss of function mutants recessive or dominant?
tend to be recessive
62
why does loss of function mutants tend to be recessive?
Feedback loops upregulate the production of the normal gene in heterozygotes 50% of the gene product is sufficient
63
what is dosage effect ?
d
64
what does dosage effect cause?
Gene product is part of a quantitative signalling system | Gene products compete to determine a metabolic or developmental switch
65
how do gene products combine in a fixed stoichiometry?
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
how much genetic variation do single nucleotide changes represent?
75%
67
how often do differences between parental genomes occur?
every 1000bp, but mostly are in non-coding regions
68
what do 25% of genetic variation represent?
structural changes mainly in copy number variation
69
how can genetic changes increase our risk of/susceptibility to disease?
Rare high risk variant and high penetrance Rare low penetrance mutation/variation and moderate risk Common low risk and low penetrance variant
70
what is penetrance?
how frequently the disease is manifested
71
how much of our DNA encodes for proteins?
1.2%
72
how much effect do most mutations have?
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
what other effects can mutations have?
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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