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Semester 1 exams > APS 125: Genetics > Flashcards

APS 125: Genetics Flashcards

1
Q

Give three mutations that occur at the genome level

A

Polyploidy - 2 sperm fertilise one egg at excatly the same time, 3 sets of chromosomes have more than the normal number of chromosomes
Aneuploidy - one extra or one fewer single chromome
Translocation - exchange of parts of non-homologus chromosomes
Deletions - part of a chromome is deleted
Inversions - part of a chromome breaks off, repaired but the wrong around

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2
Q

There are three types of aneuploidy what are they

A

Nullisomy - both members missing
Monosomy - one member missing
Trisomy - one extra (e.g. Trisomy 21= Down syndrome)

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3
Q

What type of chromosome does anneuploidy have a different effect on?

A

Sex chromosomes, women can survive with only one X chromome

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4
Q

Gives reasons as to why the garden pea is a good organism for genetic studies

A 
Many easily identifiable binary traits
Easily available and very cheap
Short generation time 
Large number of progeny
Self fertilisation 
Easy to manipulate
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5
Q

What was mendels first cross with peas? And the second?

A

Crossed purple flowers with white flowers, all progeny were purple
Second cross he crossed this generation with each other. 705 purple to 224 white plants basically 3:1 ratio

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6
Q

What were Mendels reasonings for the results of his first genetic cross

A

There must be two versions of a gene which he called alleles
An organism must inheit two alleles
Alleles must be dominant or recessive
Alleles segregate during gamete production

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7
Q

What is mendels first law?

A

Two members of a gene pair segregate from each other during the formation of gametes. Half carry one other half carries the other

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8
Q

What is Mendels second law

A

Alleles of different genes segregate independently of each other (except when on the same chromosomes)

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9
Q

When was mendels work published?

A

1866

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10
Q

In the 1900s mendels work lead to debate between biometricians and mendelians. Who wrote a paper that eneded this controversy

A

Fisher

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11
Q

What is the scientific term for an inbred relationship?

A

Consanguineous

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12
Q

What are the 5 basic mendelian possibilities?

A 
Autosomal dominant 
Autosomal recessive 
X linked recessive 
X linked domimant 
Y linked
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13
Q

Give some examples of autosomal dominant features

A

Achondroplasia - dwafism
Polydactyl
Widows peak
Hairy mid digit

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14
Q

Describe the causes of the autosomal recessive disease cystic fibrosis

A

CFTR gene mutated a delta 508, 3bpndeletion causes a non function enzyme

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15
Q

Describe the spread of effect on different genders for an X linked domiant disease

A

Any child of an effected female has a 50% chance
All female offspring of a male with the disease will be effected
No male children of a male effected will be effected

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16
Q

Describe X chromosome inactivation

A

Y chromosome shorter than X
In females one X chromosome is inactivated (lyonization)
In each cell this occurs randomly
All daughter cells will have the same x inhibited

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17
Q

Why are drosophila useful for genetic studies

A

Easy to rear
Rapid generation time
Model organism - lots of genetic info about them

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18
Q

Describe the crosses done by morgans lab to work out ehich chromome the eye colour gene lies on

A

Red eyed male crossed with red eyed female - all red eyes
Therefore Red is dominant to white
Crossed F2 red eyed female with white eyed male
All females red eyes, 50:50 split between males for eye colour

2nd cross
White eyed female crossed with red eyed male, all males white eyed, all females red eyed

Crossed F2 red eyed female with white eyed male got a 1:1:1:1 ratio

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19
Q

How many genes are on humans 23 chromosomes? Comapred to that of drosophilas 4

A

20,000

14,000

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20
Q

What is the main cause for genotypes to not meet the predicted values?

A

Recombination

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21
Q

How do you work out a recombination factor? What is the measured and what does it work out?

A

Add up recombinants (i.e. Those with unexpected genotypes) and divide by total offspring. Measured in cM and measures the distance between genes

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22
Q

Describe how you build a genetic map using recombination factors

A

Calculate a recombination factor between gene 1 and 2
Repeat for gene two and 3
Then for 1 and 3
The recombination factors are additive hence draw on number lines and work out which one combination of distances is correct

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23
Q

What is an additional step that must be taken when building a genetic map of two genes that are far away from one and other?

A

Additive distances often greater than the real distance, this is due to double recombination
Square the probability of single recombination to work out the probability of a double recombination event
Subtract double recombination probability from recombination factor

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24
Q

What does a recombination factor of 0.5 or above tell you ?

A

Two genes lie on seperate chromosomes

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25
Q

Describe the main evolutionary significance of recombination

A

Two genes located on different homologus chromosome are both advantageous, without recombination an individual can only have one of the genes in its gametes

Recombination allows a gamete to have both advantegous traits, thus increasing fitness

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26
Q

What is a polymorphism

A

Where there is more than one form of a phenotype

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27
Q

Define evolution (in genetic terms)

A

The change in allele frequency over time

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28
Q

How do you work out if a population is in hardy Weinberg equilibrium ? (From raw data)

A

1) calculate allele frequency - multiply total population by 2 to get total number of alleles. Multiply homozygotes by 2 and add to heterozygotes (for each allele). Then divide by total allele number.
2) use the equation P^2 +2pq+q^2 = 1 to work out the expected values for each genotype
3) do a chi squared test (sum of: (observed-expected)^2/expected). If the value you get is below 3.84 then the population is in HWE

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29
Q

What are the HWE assumptions?

A 
Random mating 
No natural selction
Huge population size - infinite
No migration
No mutation
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30
Q

Heterozygote deficit is a sign of what?

A

Non random mating

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31
Q

Give Darwins definition of Natural Selection

A

This preservation of favourable variations and the rejection of injurious variation I call natural selection

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32
Q

Which form of the peppered moth is the melanic form?

A

The darker form

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33
Q

What is the selection coefficient and how do you calculate it?

A

It determines the speed at which natural selection occurs it is calculated by finding the difference between the two fitnesses

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34
Q

Explain HIV and 3TC in the context of natural selection

A

10,000bp genome of the the single stranded RNA virus, some of whicb codes for reverse transcriptase
3TC blocks reverse transcriptase working within 4 weeks 100% of a HIV strain will be resistant to 3TC this is because of:
1) only one bp change needs to happen
2) v high mutation rate 3.4x10^-5 comapred to humans 3x10^-8
3) rapid generation time
4) extremely large population size
One the mutation has occured it is hugely advantageous against 3TC

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35
Q

Why are sickle cell heterozygotes selected for in africa?

A

Sickle cell Homozygotes will die due to blood cells weakening
Non sickle cell homozygotes will be likely to get malaria
Heterozygotes red blood cells sickle in the presence of malaria, destroys the cell as well as the pathogen

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36
Q

How do you calculate relative fitness?

A

Divide expected by observed
Highest value is the standard
Divide all others by the standard

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37
Q

Describe the heterozygote advantage involved in Kuru resistance

A

Disease spread by the consumption of infected meat, when men died in some african tribes the women and children ate the flesh. Canabalism banned in 1950s.

PRNP gene is a defence against prion disease but may cause others

Before cannibalism banned the populations were not in hardy weinburg equilibrium. Heterozygotes were favoured, the PRNP gene is heterozygotes gives resistance but doesn’t cause the other diseases.

After the Ban the allele frequencies returned to HWE

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38
Q

How many mass extinctions have there been?

A

5 currently in the 6th

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39
Q

Define genetic drift

A

The process of losing genetic variation by chance

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40
Q

On what does generic drift have more impact

A

Small populations

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41
Q

Describe the elephant seal case study for genetic drift

A

Northern seal excessively hunted
Southern Seal always abundant

When hunting was banned in 1884 only 20-30 individuals survived in northern populations

Northern seal heterozygosity = 0.0026 in southern seals = 0.028
This acts as a measure of how genetically varied a population is

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42
Q

What is a microsatellite in genetics?

A

An area that has a very high mutation rate

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43
Q

Why is genetic variation important?

A

Species with lower genetic variation are far less likely to be able to adapt to overcome rapid changes e.g. Climate change

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44
Q

How do you measure inbreeding? Give some key values

A

Use wrights inbreeding coefficient
Siblings = 0.25
Cousins = 0.0625
Average in humans = 0.0088

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45
Q

What are the consequences of inbreeding

A

Inbred progeny have higher F values than outcrossed progeny

More are identical by decent so fewer heterozygotes therefore less heterozygotic advantage and more recessive diseases

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46
Q

What has been the comsequence of the many gentic bottlenecks expericned by koalas ?

A

Many have missing testicles

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47
Q

What is the use of geologically or socially isolated populations of humans in Genetic studies?

A

If they keep detailed pedigrees you can keep a track of diseases and learn about them. E.g. The armish have high frequencies of dwarfism and polydactyl

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48
Q

How long ago did homosapienes diverge from apes

A

5-7 million years ago

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49
Q

If chimps and humans differ by 1% of nucleotides how big of a difference is this in: BP, coding Bp, Bp differences per coding DNA

A

30 million bp differnece
450,000 coding bp differneces
9 differences per gene

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50
Q

What is the first hominid species to arise in the fossil record? When was this? There were two species called?

A

Australopithecines
Anamensis (3.9-4.2MYA)
Afarensis (3-3.9MYA)

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51
Q

When did homo erectus appear in the fossil record? When and where did it last live?

A

2.5 million years ago

Found in java dating 27,000 years old

52
Q

When was the first out of africa hominid present ?

A

1.6 - 1.9 MYa

53
Q

When was homo heidelbergensis present? Who was is a descendant of?

A

1 million years ago, descendant of homo erectus

54
Q

When and where did homospaiens originate?

A

Ethiopia 154-160KYA

55
Q

What is the other name for homo erectus?

A

Homo ergaster

56
Q

Why is especially hard to find new species of hominid in the fossil record ?

A

Hard to tell if the phenotypic differneces are polymorphisms or a new species

57
Q

What are the two different models for when and where modern humans came from?

A

Out of africa - less than 200kya H.sapiens emerged in africa then spread and replaced other hominids, predicts that diversity should decrease as you move away from Africa
Multi regional - transition from H.erectus to H.sapiens arose several times in different places suggests a much older common ancestor (1-2my older) no gradient of diversity

58
Q

What pieces of evidence can be used to conclude upon wether the out of africa or multiregional models of human life?

A

Genetic diversity - we are less polymorphic than recent ancestors, favours out of Africa since it suggests we originated from a small population

Diversity of African populations - there is consistent decline in genetic diversity when moving away from Africa, with most diverse populations in Africa

TMRCA - Time to most recent common ancestor, build a molecular clock. (Looks at how different two strands of DNA are and presuming constant mutation rates calculates their divergence) two types mtDNA and Y chromosome

59
Q

Why do autosomes not provide accurate results in molecular clock studies? What can be used instead to improve this?

A

They recombine which effects apparent rate of mutation

mtDNA - maternally inherited so easier to see linage as well as a high rate of mutation and no recombination

Y chromome - male specific again easier linaging, but also it wont redombine with X

60
Q

Describe the results of both types of molecular clock study that have been done on hominids to shed light on their inital distribution.

A

mtDNA - 4 branches 3 to africa 1 outside of africa with the out of africa event being 52+/-28 KYA

Y chromome - estimates we moved out of africa 40kya

61
Q

How has it been suggesed that interbreeding between Neanderthals and humans didnt take place and why is this study flawed?

A

mtDNA taken from Neanderthal fossils and comapred with humans. Humans have less than 10 pairwise differences, humans and chimps have 50. Humans and Neanderthals have 25.

Flawed becuase the mitochondria has a tiny genome - 17,000 base pairs

Also between 1% and 4% of eurasian human genome seems to come from neanderthals suggesting interbreeding on the move out of africa

62
Q

What evidence for human evolution comes from Head lice?

A

Two ancient linages of head lice, diverged 1 million years ago, one species found on many hominids whilst the other only found on new world hominids

Suggests they lived on homo erectus who was migrating and spread it to the new world. Suggests contact between hominids in the new world inc fighting and inbreeding

63
Q

There are two distinct types of cattle what are they and what does this tell us about human evolution?

A

Indicus and taurus

Tells us domestication of cattle occured twice

64
Q

What can we learn about human evolution from melanin?

A

Lighter skin is better at synthesising vitamin C
Darker skin is better at protecting from UV
Because its brighter in Africa UV protection is far more nessacary

MC1R controls the production of melanin either, Eumelainin (dark) or Pheomelanin (yellow)

African populations have far less mutations at the MC1R gene than eurasians - means europeans went from black (original state) to white. Further supports the out of africa model

65
Q

What is the heterozygous advantage for the cholera gene

A

Resistance to typhoid

66
Q

What are the different types of variation?

A

Discontinuous - simple genetics, phenotypes in discrete classes with no intermediates and follows mendelain ratios

Continuous - cannot be split into classes, offspring have an intermediate phenotype, no mendelian ratios, environmental basis as well as genetics

Threshold - appears discontinuous but is actually controlled continuous, the distribution is instead the liability for the individual to receive the characteristic. Phenotype is dependant on a crtical threshold once surpassed the phenotype is expressed

67
Q

Define quantitative trait locus

A

Genes close together that all contribute to one gene

68
Q

Give some further complications in understanding the impact genes have in quantitative traits

A

Genes vary in size and effect
Allele frequency varies
Alleles can be dominant or codominant
Environment can also play a role

69
Q

What is a monozygotic twin?

A

Identical twins

70
Q

Define the following
Phenotypic variation
Genetic variation
Environmental variance

A

Phenotypic variation - total variation within a popukation for phenotype
Genetic variation - variation due to genotypic variance
Environmental variation - variation due to environmental effects

71
Q

Phenotypic variation = ?

A

Genetic varaiance + environmental variance

72
Q

What is broad sense heritability?

A

The proportion if phenotypic variation within a population that is due to genetics

73
Q

How do you calculate broad sense heritabiltiy?

A

H^2 = VG/Vp
We know that Vp= Vg+ Ve
Therefore : H^2 = Vg / (Vg+Ve)

74
Q

In cases of extreme inbreeding what will happen to broad sense heritabiltiy?

A

Becomes O becuase the variation due to genetics becomes O

75
Q

What could cause Heritabiltiy to change?

A

Allele frequency change (genetic drift or evolution)

This causes Vg values to change and hence hertiabiltoy changes

76
Q

Define norm of reaction in quantitative genetics

A

Response of a single genotype to variation in an environmental parameter

77
Q

What is needed in order for selection to be acting on a quantitative trait?

A

Heritable variation
Resource competition
Fitness differences dependant on the trait

78
Q

Describe the effects of each of the types of variation on genetic variation

A

Directionals selection - no effect on variation because the whole population is shifted one way
Stabilising selection - reduces variation as extremes are removed
Divergent selection - increases genetic variation because extremes are favoured

79
Q

In an experiment where faster flies are artificially selected for the average speed rapidly increases at first but then starts to slow down why could this be?

A

Genetic variation starts to run out

Natural selection is opposing artificial selection

80
Q

Why may selection not cause a decrease in genetic variance?

A

Mutations
Migrations
Hidden genetic variance
Different forms of selection

81
Q

Define narrow sense heritabiltiy is this usually greater or smaller than broad sense?

A

The proportion of variation that can be passed on to the offspring
Usually smaller than broad sense heritabiltiy

82
Q

Give the equation for narrow sense heritabiltiy

A

h^2 = (mean of offspring of selected individuals - mean of original population) / (mean of selected offspring - mean of the offspring of selected individuals)

h^2 = Response to selection / selective differential

83
Q

How do you calculate the response to selection?

A

Mean of offspring of the selected variables - the mean of the original offspring

84
Q

How do you calculate the selective differential?

A

Mean of selected individuals - mean of the offspring of selected individuals

85
Q

Genotypic variance is made from three elements what are these? Which element do we look at in narrow sense heritabiltiy?

A

Additive genetic variance (Va)
Dominant genetic variance (Vd)
Interactive genetic variance (Vi) - epistasis

Only look at additive genetic variance in narrow sense heritabiltiy since it is the only type that responds rationally to selection

86
Q

Define mutagen

A

Anything that increases chemical reactivity in the cells

87
Q

What percentages of conceptions does polyploidy occur in?

A

1-3%

88
Q

What is turners syndrome?

A

Female with only one X chromosome

89
Q

What is cri duc chat syndrome? How does it occur?

A

Deletion on chromome 5, causes babies to cry like a cat and have a smaller head - microphaly. Prone to learning difficulties

90
Q

What is the difference between paracentric inversions and pericentric?

A

Pericentric inversions occur over the centromere, much worse can lead to problems in meiosis
Paracentric inversions exclude the centromere and hence arent as bad, often no effect on phenotype

91
Q

How large is the human genome ? How many genes?

A

3 x 10^9 (3billion)

20,000-30,000 genes

92
Q

What is the nucleotide change that causes sickle cell anaemia?

A

GTA –> GAA

93
Q

How many SNPs are there?

A

12,000,000 (accounts for 0.3% of genome)

94
Q

What is satellite DNA?

A

Often harmless tandem repeats that can be used to find disease genes

95
Q

How did Mendel manipulate the reproduction of his pea plants?

A

Removed the anther of one plant, got pollen from another and add to it

96
Q

If a disease isnt caused by mendelian traits what is it called?

A

Multifactorial

97
Q

Give the symbols used in pedigrees

A 
Squares for males
Circles for females
Diamonds for unknown sex 
Coloured squares/ circles is affected 
Dot in the middle meams a carrier
Line through means they are dead 
Line between is marriage
Double line is consanguineous marriage
98
Q

Give the characteristics of a autosomal dominant disease pedigree

A

Affected person has at least one affected parent
Affects either sex
Transmitted by either sex

99
Q

What is achondroplasia ?

A

A form of dwafism

100
Q

What mendelian pea features are dominant

A

Yellow dominat to green
Purple dominant to white
Smooth dominant to wrinkled

101
Q

What are the characteristics of an autosomal recessive disorder

A

Affecteds can have unaffceted parents
Parents will be carriers
Either sex

102
Q

Examples of autosomal recessive condtions

A

Albinism
Sickle cell
Cystic fibrosis
Attached ear lobes

103
Q

What are the characteristics of an x linked resessive disorder?

A

Mainly males affected
50% male offspring of female carriers
Females only effected where mother is carrier and father is affected

104
Q

Examples of x linked recessive disorders

A

Duchenne muscular dystrophy
Red green colour blindness
Haemophilia

105
Q

Charcteristics of x linked dominant disorders

A

Affects either sex
Child of affected female has a 50% chance of being affected
All female of affected males
No males of affected males affected

106
Q

Charcteristics of a y linked disorder

A

Only males affected
All males of affected males are affected

Very few since Y chromosome is small, hairy ear rims

107
Q

Describe morgans crosses with white and red eyed flies

A

Cross 1: crossed red eyed female (homozygote) with white eyed male
F1 : all red eyed, females were heterozygotes
F2: all females red eyed (50:50 hetero:homo) 50:50 males red and white eued

Cross 2: white eyed female (homozygote) and red eyed male
F1 females red eyed (heterozygotes) males white eyed
F2 1:1:1:1 of red eyed females, white eyed females, and same for males

Significant as it was the first demonstration that genes lied on chromosomes

108
Q

Describe morgans experiment on independent assortment

A

Purple eyes recessive to red eyes, vesigial wings recessive to normal wings

Crossed pRvN with ppvv, this cross should result in even numbers of each potential phenotype

It didn’t, two were far more common (RN and pv)

Therefore the chromosomes hadn’t assorted independently

109
Q

What blood group is most common in east asia?

A

b

110
Q

Describe the Fy1 and Fy2 genes as signals of genetic diversity

A

Europeans only have FY-1
Africans only have FY-2
African americans have a mixture
There is a gradient of the mix of white and black people with the heterozygosity of FY

111
Q

In peppered moth the melanic form is the dominant or recessive allele?

A

Dominant

112
Q

What are the latin names for the two forms of peppered moth?

A

Typical - typica

Melanic - carbonaria

113
Q

Describe the case study involving the Mauritius kestrel and genetic drift

A

Native forest destruction due to DDT insectisides used in 1940s
1974 only four remained with a single pair
1997 400-500 birds
Went through a bottle neck, heterozygosity was much lower in the restored speciemens than museum specimens or other kestrel species

114
Q

What is meant by identical by descent? How does this relate to the inbreeding coefficient

A

Trace ancestry back to the same ancestral allele
The inbreeding coefficient is the probability that the individual in question is identical by decent for the locus in question

115
Q

What lethal gene has risen to high levels in californian condors?

A

Chondrodystrophic dwafism they die at hatching

116
Q

What predictions are made by both the out of africa model and the multiregional model?

A

Multiregional predicts a large population therefore high genetic diversity should be seen in humans, whilst out of africa suggests the opposite

Out of africa suggests greater diversity in africa then elsewhere, whilst multiregional suggests no difference in diversity

multiregional model predicts tmrca is between 1-2 mya whilst out of africa suggests less than 200kya

117
Q

What is an exception to the idea that african populations are more diverse? What could this be due to?

A

Beta globin gene in asian populations is more diverse, could be due to selection

118
Q

What gene controls lactase persistance?

A

LCTP dominat to introllerant LCTR

119
Q

What is meant by anagenesis? And cladogenesis?

A

Origin of a new species without branching - anagenesis

Cladogenesis = branching of new species

120
Q

What two problems are there we reproductive isolation as a means of speciation ?

A

New gene causing sterility will not spread

New gene causing new mating signal unlikely to spread

121
Q

There are two forms of stickleback fish what are they and where are they fitter

A

Limnetic - high fitness in open water

Benthic - high fitness in lake margins

122
Q

Describe the dobzhansky muller solution to sympatric speciation

A

Negative epistasis between new alleles at 2 loci
E.g. Enzyme and substrate
In one population the enzyme changes
In another the substrate changes
If they hydrbrise the two are incompatible

123
Q

What happens when D.simulans and D.Melanogastor try to interbreed? Why?

A

Females offspring are sterile and all males die in devolvement, harmless mutation in each species cause a defect when together

124
Q

What are the two types of polyploidy?

A

Auto polyploidy- multiple chromosomes within a species

Allopolyploidy - two species hybridise

125
Q

How many speciation events does polyploidy account for?

A

5%

Semester 1 exams (4 decks)

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