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FTIB > fundamental molecular biology > Flashcards

fundamental molecular biology Flashcards

1
Q

mutations are usually dominant/recessive

A

recessive

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2
Q

mutations are usually silent or advantageous/ deleterious

A

deleterious

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3
Q

what is a mutation

A

a change in the genetic material of a virus or cell

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4
Q

what process are mutations essential for and why

A

evolution - new genetic material creates variation which is needed for evolution

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5
Q

which mutations are heritable

A

mutations which arise in the germ line

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6
Q

which mutations are not heritable

A

mutations which arise in the soma

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7
Q

describe germ line cell mutations in terms of mutation rate and heritability

A

they have a low mutation rate

the mutations are passed on to the next generation

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8
Q

describe somatic cell mutations in terms of mutation rate and heritability

A

they have high mutation rate

the mutations are not heritable (genetic dead end)

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9
Q

what are germ line cells

A

Cells that become gametes are referred to as germ line cells

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10
Q

what are somatic cells

A

any biological cell forming the body of an organism, any cell other than a gamete, germ cell, gametocyte or undifferentiated stem cell.

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11
Q

name some origins of mutation

A

replication and repair errors

DNA damaging agents - mutagens

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12
Q

give examples of mutagens (DNA damaging agents)

A

by products of metabolism - ROS
ionizing radiation
UV light

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13
Q

DNA damage – repair =??

A

mutation

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14
Q

DNA repair works to lower what

A

net mutation rate

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15
Q

mutation rate increases with decreasing/increasing rate of repair

A

decreasing

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16
Q

mutation rate increases with decreasing/increasing DNA damage

A

increasing

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17
Q

describe what happens to DNA when exposed to UV light

A

exposure to UV light causes thymine dimers to form (covalent bonding between thymine bases) which lead to frameshift mutations. RNA polymerase can’t access the DNA to make mRNA

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18
Q

what is Xeroderma pigmentosum

A

a condition where thymine dimers cannot be repaired. it is caused by mutations in excision repair machinery causing extreme UV light sensitivity.

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19
Q

what happens when someone with Xeroderma pigmentosum is exposed to UV light

A

basal cell carcinoma
metastatic malignant melanoma
squamous cell carcinoma

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20
Q

what are induced mutations

A

mutations that are brought on by mutagens

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21
Q

can all mutagens damage DNA

A

yes

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22
Q

can all mutagens cause cancer

A

yes

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23
Q

what are the 4 categories of chemical mutagens

A
  1. base modifiers
  2. base analogues
  3. intercalating agents
  4. deaminating agents
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24
Q

what is a base modifier

A

a chemical mutagen that reacts directly with nucleotide bases altering their structure and causing point mutations

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25
Q

give an example of a base modifier

A

EMS

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26
Q

what are base analogues

A

chemical mutagens that have very similar structures to DNA bases and cause point mutations

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27
Q

give an example of a base analogue

A

5BU

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28
Q

what are intercalating agents

A

chemical mutagens that can insert themselves between successive bases in DNA which causes a frameshift mutation

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29
Q

give as example of an intercalating agent

A

arcidine dyes

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30
Q

what is a deaminating agent

A

they cause point mutations (substitutions) for example by converting cytosine to uracil.

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31
Q

give an example of a deaminating agent

A

nitrous acid

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32
Q

what are the 4 types of chromosome mutation

A

inversion
translocation
duplication
deletion

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33
Q

what are the 3 types of point mutation

A

insertion
deletion
substitution

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34
Q

most random mutations affect important/unimportant regions

A

unimportant - between genes, between exons

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35
Q

in which regions are mutations not silent

A

if they affect key functional residues (protein coding regions) or regulatory regions (gene expression/translation)

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36
Q

why are mutations usually silent

A

because exons take up such little space in the genome the mutations very rarely fall in them. most of the genome is empty space

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37
Q

what are the 3 possible consequences of point substitution mutations

A

missense
nonsense
silent

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38
Q

what are conservative mutations

A

when the amino acid produced after mutation has a very similar structure to the amino acid in the absence of the mutation (polar aa –> polar aa)

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39
Q

what are non conservative mutations

A

when the amino acid produced from the mutated area has a completely different structure to the amino acid in the absence of the mutation (polar aa –> non polar aa)

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40
Q

what is a point mutation

A

a mutation affecting only one base pair

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41
Q

what is a frameshift mutation

A

a mutation that causes a change in the reading frame (insertions and deletions)

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42
Q

what is a missense mutation

A

when a mutation causes a different amino acid to be made

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43
Q

what is a nonsense mutation

A

when a mutation causes an early stop codon so the resulting polypeptide chain is cut short and often results in a non functional protein

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44
Q

what do rare recessive mutations require to affect phenotype

A

inbreeding - in order to get a person who is homozygous - these mutations have high incidence in isolated communities

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45
Q

what are the 4 conditions caused by mutations in the albinism pathway

A
  1. albinism
  2. alkaptonuria
  3. cretinism
  4. phenylketonuria
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46
Q

what causes albinism

A

a mutant tyrosinase enzyme cannot convert tyrosine –> melanin so melanin is absent or in very little quantities

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47
Q

what are the symptoms of albinism

A

lack of melanin form skin, hair and eyes

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48
Q

what are the 4 oculocutaneous albinism genes

A

oca1
oca2
oca3
oca4

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49
Q

what do mutations in the oca1 gene result in

A

mutation in tyrosinase enzyme - severe albinism

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50
Q

what do mutations in the oca2 gene result in

A

mutation in P protein (tyrosinase helper) - mutants have mild albinism

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51
Q

what do mutations in the oca3 gene result in

A

mutation in tyrosine related gene - mutants have weak albinism

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52
Q

what do mutations in the oca4 gene result in

A

mutation in tyrosinase helper protein - mutants have mild albinism

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53
Q

mutations in which oca genes result in weak/mild albinism

A

oca2
oca3
oca4

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54
Q

which oca gene causes severe albinism

A

oca1

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55
Q

what is alkaptonuria an what causes it

A

recessive condition
sufferers have black urine
it is caused by a mutation on chromosome 3 which encodes mutant homogentisate 1,2 -dioxygenase which results in homogentisic acid (HA) NOT being converted to maleylacetoacetic acid. HA is expelled in the urine

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56
Q

what is phenylketonuria and what causes it

A

recessive condition
mutation causing enzyme phe hydroxylase being unable to convert phenylalanine to tyrosine.
high levels of phenylalanine leads to high levels of phenylpyruvic acid which leads to progressive brain dysfunction dues to it acting as a neurotoxin
treatment – low phenylalanine diet

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57
Q

what is cretinism

A

recessive condition

mutation causes tyrosine not to be converted into thyroxine which causes mental retardation

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58
Q

what happens to substrate and product levels when enzymes fail to function

A

substrate level builds up and there is a lack of product

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59
Q

which of the albinism pathway conditions is caused by lack of product

A

albinism

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60
Q

which of the albinism pathway conditions is caused by build up of substrate

A

alkaptonuria
phenylketonuria
cretinism

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61
Q

what is the genotype

A

the internally encoded inheritable information (the DNA)

62
Q

what is the phenotype

A

the outward physical manifestation of the organism - anything that is an observable function, structure or behaviour

63
Q

what is epigenetics

A

changes dues to gene expression rather than changes in genetic code

64
Q

what affects phenotypes

A

gene products - proteins

65
Q

what determines dominance/recessiveness

A

it is determine by how the pool of products (protein) of the 2 alleles functions in a heterozygote

66
Q

most recessive/dominant mutations are GAIN OF FUNCTION

A

dominant - more of a normal function or gain of a new function

67
Q

most recessive/dominant mutations are LOSS OF FUNCTION

A

recessive

68
Q

what are null alleles

A

completely non functioning allele - no protein is produced

69
Q

describe the yellow pigment in fruit flies

A

WT and heterozygotes convert yellow pigment to black

homozygous recessive mutants cannot convert pigment

70
Q

why are most mutations recessive

A

it is easier to damage something than to make it work better or differently

71
Q

how could a recessive condition be treated by gene therapy

A

by introducing a WT copy of the gene

72
Q

how could a dominant condition be treated by gene therapy

A

inactivating the gene - stopping the new function

73
Q

what is incomplete dominance

A

when the heterozygote has an intermediate phenotype

74
Q

what are oncogenes

A

genes which transfer cells into tumour cells

75
Q

give examples of conditions caused by autosomal recessive mutations

A

albinism
alkaptonuria
cretinism
phenylketonuria

76
Q

give examples of conditions caused by autosomal dominant mutations

A

achondroplasia

Huntington’s disease

77
Q

what is achondroplasia

A

the most common form of dwarfism caused by an autosomal dominant mutation

78
Q

what causes achondroplasia

A

achondroplasia is caused by an autosomal dominant mutation. It is caused by one of 2 point mutations in the gene for the FGFR3 receptor which is a transmembrane protein kinase

79
Q

what happens in achondroplasia sufferers by comparing sufferers and non sufferers

A

NORMAL
FGF is a signalling protein which binds to FGFR receptor
this causes phosphorylation by kinases which results in the molecules of the receptor coming together
this conformation of the receptor inhibits limb growth
ACHONDROPLASIA
We see phosphorylation and the molecules of the receptor coming together in the absence of the FGF signal
the mutant receptor is locked in a more active state so limbs do not grow normally

80
Q

doe the achondroplasia mutation confer the same function as the wild type but more of it or does it result in a new function

A

the same function but more of it - in WT limb growth is inhibited, just not all the time

81
Q

of those affected with achondroplasia, how many have a parent with achondroplasia

A

20%

82
Q

80% of the achondroplasia mutations are generated in the parents germline as ……………………………….

A

de novo mutations

83
Q

what are de novo mutations

A

from new mutations - arise during our lifetime - we all get approximately 200 de novo mutations

84
Q

what do two heterozygous parents for achondroplasia give offspring in ratios of

A

normal and achondroplasia children in a 1:2 ratio. would be 1:3 but homozygous embryos for achondroplasia die in utero
from this we can infer that achondroplasia shows incomplete dominance since homozygous and heterozygous people show different phenotypes

85
Q

give an example of an autosomal dominant condition that results in gain of new function

A

huntiinton’s disease

86
Q

what does huntington’s disease cause

A

causes progressive neurodegeneration

- loss of limb control

87
Q

does huntington’s disease show complete or incomplete dominance

A

complete

88
Q

if huntington’s is a dominant lethal mutation then how is it present in the population

A

because it is late onset - doesn’t start till 30-50s

89
Q

does the huntington’s phenotype skip generations

A

no - child of affected parent has 50% chance of being affected

90
Q

what mutation causes huntington’s disease

A

it is caused by an autosomal dominant mutation in the HDD1 gene which encodes the huntingtin protein
the mutation is found in the glutamine triplet in DNA which causes the glutamine section to repeat (microsatellite), expanding the genome. the large polyglutamine tract formed is toxic in some neurons

91
Q

what is ncRNA

A

non coding RNA that does not code for proteins but do code for other functional RNA

92
Q

what 2 things do genes encode for (as well as all the other things it contains LINEs, LTRs etc)

A

mRNA which codes for proteins

ncRNA which codes for other functional RNA

93
Q

what methods could we use to find a protein coding gene

A

proteomics - look for protein and work back to sequence on DNA
transcriptomics - look for mRNA and work back to sequence
look at DNA sequence directly - predict exons, ORF (open reading frame), start/stop codon - use homology

94
Q

how to find an ncRNA gene

A

look for RNA using transcriptomics and work back to find gene sequence
look at sequence directly - predict exons and use homology

95
Q

what percentage of RNA is coding and non coding

A

coding - 4%

non-coding - 96%

96
Q

what are LINES

A

long interspersed nuclear elements

97
Q

what are SINEs

A

short interspersed nuclear elements

98
Q

what are transposons

A

DNA that can translocate

99
Q

what are LTRs

A

long terminal repeats

100
Q

what can indicate the function of a gene

A

where ii is expressed - organ
when it is expressed - age
inactivate the gene - knockout, CRISPR, RNAi tech
activate the gene - over expression
find mutations in the population and study them
study other genomes and look for homology

101
Q

what are taste receptors

A

proteins found on the cell surface of the tongue, lungs and gut and affect taste perception

102
Q

what genomes is the human genome closely related to which can be tested ethically? (model organisms)

A 
mouse 
fly
worm
yeast 
e.coli
103
Q

what are orthologs

A

genes in different species that evolved from a common ancestral gene and normally retain the same function. they can be used to infer roles in other species where iit is not ethical to study them

104
Q

what are paralogs

A

genes resulting from gene duplications, probably with diverged role or function

105
Q

the more closely related species are, the more genes are .…………….. and may have similar/identical roles

A

conserved

106
Q

in distantly related species less of the genome is …………….and may have similar/related roles

A

conserved

107
Q

provide the percentage of orthologs of human diseases in mice, flies, worms, yeast

A

mice - 90%
fly - 70-80%
worm - 60-70%
yeast - 30-40%

108
Q

human CDK1/yeast cdc2 homology spiel

A

47% identity in protein sequence between yeast and human gene. a pair of genes that have very similar sequences and the same function.

109
Q

define co-dominance

A

contributions from both homozygous parents are present in the offspring phenotype e.g. red and white spot flowers

110
Q

ancestor calculation

A

look in notes

111
Q

if there is a new generation every 25 years, how many ancestors does one have after 500 years

A

2^20

112
Q

if there is a new generation every 25 years, how many ancestors does one have after 1000 years

A

2^40

113
Q

what is a polymorphism

A

common genetic differences between people

114
Q

what percentage of identity do humans generally show at sequence level

A

99.5%

115
Q

what is a microsatellite

A

repeating sequence of DNA that is 2-6bp long with 5-200 repeats - huntington’s

116
Q

what is a minisatellite

A

repeating sequences of DNA that are 10-100bp long with 10-1500 repeats

117
Q

provide a practical application for microsatellites

A

DNA fingerprinting

118
Q

provide a practical application for minisatellites

A

paternity testing because they occur in family groups

119
Q

what are indels

A

insertions and deletions in the genome which can vary in size

120
Q

how can indels have an effect on proteins

A

they can result in frameshift mutations if they occur in the ORF of a protein coding gene

121
Q

apart from proteins what other parts of the genome are effected by indels

A

ncRNA and regulatory regions

122
Q

why are most indels silent

A

because they occur outside the coding region

123
Q

what are CNVs

A

copy number variants - they are chromosomal deletions or duplications that involve large stretches of DNA which can span many genes

124
Q

are CNVs inherited or de novo

A

they can be both

125
Q

how long ar CNVs

A

500- 1 million bp long

126
Q

why don’t all CNVs have an effect

A

they often occur in unimportant parts of the genome so are silent but they can have drastic effects if the sections duplicated or deleted involve important genes

127
Q

what are SNPs

A

single nucleotide polymorphism -a substitution of a single nucleotide that occurs at a specific position in the genome where each variation is present to some appreciable degree within a population e.g. >1%

128
Q

what % of the population have rare SNPs

A

between 1 and 4.9%

129
Q

what % of the population have common SNPs

A

5% allele frequency or more

130
Q

if SNPs occur in the OFR what are the 3 possible outcomes

A

missense - different amino acid
nonsense - early stop codon
silent - same amino acid

131
Q

can SNPs affect ncRNA

A

yes if they occur in those regions

132
Q

can SNPs affect regulatory regions of the genome

A

yes, if they occur there

133
Q

what is the affect of most SNPs

A

silent or they occur outside of genes

134
Q

every how many bp does a common SNP occur

A

every 100bp approximately - common variant among the population

135
Q

do many SNPs have an effect

A

no most are silent but those within a gene or regulatory region can have a role in disease by affecting a gene’s function

136
Q

what are point mutation

A

mutations that only affect a single base - insertion, deletion, substitution

137
Q

what is a private point mutation

A

a de novo mutation - we each get around 200 of these

138
Q

what is the frequency of a fairly common point mutation

A

allele frequency is less than 1% - variant

139
Q

what is the allele frequency of a very common point mutation

A

allele frequency greater then 1% - polymorphism

140
Q

most SNPs only have two alleles but for a single SNP there can be up too 4 different alleles, why is this

A

because there are only options of A, T, C, G

141
Q

how can eye colour have more than 4 colours if there are only 4 bases for a polymorphism

A

eye colour involves interactions between more than one gene so there are a greater number of polymorphism combinations

142
Q

how do you calculate allele frequency

A

no. allele of interest/total no. alleles

143
Q

if we have a two allele system what equation can we use to describe their frequency

A

p+q=1 where p and q are the frequencies of allele one and two respectively

144
Q

what is evolution

A

the change in allele frequency of a gene pool over time

145
Q

why are most new mutations lost in the gene pool

A

they are either detrimental or cause no advantage - soo the organisms either dies or does not pass on the mutation to offspring

146
Q

what is the hardy Weinberg equilibrium

A

the equilibrium predicts that the allele and genotype frequencies in a population will remain constant from one generation to the next - there is no evolution
p^2 +2pq +p^2=1
if the equation equals 1 then the population is in hardy Weinberg

147
Q

when is a population considered to be in hardy Weinberg equilibrium

A

when the observed genotype frequencies equal the expected genotype frequencies

148
Q

Are most SNPs in hardy Weinberg

A

yes they are, there is no evolution because there is no change in frequency

149
Q

what are the 5 conditions for a population to be in hardy Weinberg equilibrium

A
  1. random mating
  2. large population
  3. no change in allelic frequency due to mutation
  4. no immigration or emigration (no gene flow)
  5. no natural selection
150
Q

what are the differences in the TAS2R38 taste receptor caused by

A

SNPs - there are 3 SNPs that are strongly linked

151
Q

what is epistasis

A

interaction of genes that are not alleles, in particular the suppression of the effect of one such gene by another

152
Q

what is epigenetics

A

changes caused by gene expression

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