APS 125: Genetics Flashcards
(125 cards)
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
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)
3
Q
What type of chromosome does anneuploidy have a different effect on?
A
Sex chromosomes, women can survive with only one X chromome
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
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
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
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
8
Q
What is Mendels second law
A
Alleles of different genes segregate independently of each other (except when on the same chromosomes)
9
Q
When was mendels work published?
A
1866
10
Q
In the 1900s mendels work lead to debate between biometricians and mendelians. Who wrote a paper that eneded this controversy
A
Fisher
11
Q
What is the scientific term for an inbred relationship?
A
Consanguineous
12
Q
What are the 5 basic mendelian possibilities?
A
Autosomal dominant Autosomal recessive X linked recessive X linked domimant Y linked
13
Q
Give some examples of autosomal dominant features
A
Achondroplasia - dwafism
Polydactyl
Widows peak
Hairy mid digit
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
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
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
17
Q
Why are drosophila useful for genetic studies
A
Easy to rear
Rapid generation time
Model organism - lots of genetic info about them
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
19
Q
How many genes are on humans 23 chromosomes? Comapred to that of drosophilas 4
A
20,000
14,000
20
Q
What is the main cause for genotypes to not meet the predicted values?
A
Recombination
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
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
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
24
Q
What does a recombination factor of 0.5 or above tell you ?
A
Two genes lie on seperate chromosomes
25
Describe the main evolutionary significance of recombination
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
26
What is a polymorphism
Where there is more than one form of a phenotype
27
Define evolution (in genetic terms)
The change in allele frequency over time
28
How do you work out if a population is in hardy Weinberg equilibrium ? (From raw data)
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
29
What are the HWE assumptions?
```
Random mating
No natural selction
Huge population size - infinite
No migration
No mutation
```
30
Heterozygote deficit is a sign of what?
Non random mating
31
Give Darwins definition of Natural Selection
This preservation of favourable variations and the rejection of injurious variation I call natural selection
32
Which form of the peppered moth is the melanic form?
The darker form
33
What is the selection coefficient and how do you calculate it?
It determines the speed at which natural selection occurs it is calculated by finding the difference between the two fitnesses
34
Explain HIV and 3TC in the context of natural selection
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
35
Why are sickle cell heterozygotes selected for in africa?
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
36
How do you calculate relative fitness?
Divide expected by observed
Highest value is the standard
Divide all others by the standard
37
Describe the heterozygote advantage involved in Kuru resistance
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
38
How many mass extinctions have there been?
5 currently in the 6th
39
Define genetic drift
The process of losing genetic variation by chance
40
On what does generic drift have more impact
Small populations
41
Describe the elephant seal case study for genetic drift
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
42
What is a microsatellite in genetics?
An area that has a very high mutation rate
43
Why is genetic variation important?
Species with lower genetic variation are far less likely to be able to adapt to overcome rapid changes e.g. Climate change
44
How do you measure inbreeding? Give some key values
Use wrights inbreeding coefficient
Siblings = 0.25
Cousins = 0.0625
Average in humans = 0.0088
45
What are the consequences of inbreeding
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
46
What has been the comsequence of the many gentic bottlenecks expericned by koalas ?
Many have missing testicles
47
What is the use of geologically or socially isolated populations of humans in Genetic studies?
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
48
How long ago did homosapienes diverge from apes
5-7 million years ago
49
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
30 million bp differnece
450,000 coding bp differneces
9 differences per gene
50
What is the first hominid species to arise in the fossil record? When was this? There were two species called?
Australopithecines
Anamensis (3.9-4.2MYA)
Afarensis (3-3.9MYA)
51
When did homo erectus appear in the fossil record? When and where did it last live?
2.5 million years ago
| Found in java dating 27,000 years old
52
When was the first out of africa hominid present ?
1.6 - 1.9 MYa
53
When was homo heidelbergensis present? Who was is a descendant of?
1 million years ago, descendant of homo erectus
54
When and where did homospaiens originate?
Ethiopia 154-160KYA
55
What is the other name for homo erectus?
Homo ergaster
56
Why is especially hard to find new species of hominid in the fossil record ?
Hard to tell if the phenotypic differneces are polymorphisms or a new species
57
What are the two different models for when and where modern humans came from?
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
What pieces of evidence can be used to conclude upon wether the out of africa or multiregional models of human life?
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
Why do autosomes not provide accurate results in molecular clock studies? What can be used instead to improve this?
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
Describe the results of both types of molecular clock study that have been done on hominids to shed light on their inital distribution.
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
How has it been suggesed that interbreeding between Neanderthals and humans didnt take place and why is this study flawed?
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
What evidence for human evolution comes from Head lice?
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
There are two distinct types of cattle what are they and what does this tell us about human evolution?
Indicus and taurus
| Tells us domestication of cattle occured twice
64
What can we learn about human evolution from melanin?
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
What is the heterozygous advantage for the cholera gene
Resistance to typhoid
66
What are the different types of variation?
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
Define quantitative trait locus
Genes close together that all contribute to one gene
68
Give some further complications in understanding the impact genes have in quantitative traits
Genes vary in size and effect
Allele frequency varies
Alleles can be dominant or codominant
Environment can also play a role
69
What is a monozygotic twin?
Identical twins
70
Define the following
Phenotypic variation
Genetic variation
Environmental variance
Phenotypic variation - total variation within a popukation for phenotype
Genetic variation - variation due to genotypic variance
Environmental variation - variation due to environmental effects
71
Phenotypic variation = ?
Genetic varaiance + environmental variance
72
What is broad sense heritability?
The proportion if phenotypic variation within a population that is due to genetics
73
How do you calculate broad sense heritabiltiy?
H^2 = VG/Vp
We know that Vp= Vg+ Ve
Therefore : H^2 = Vg / (Vg+Ve)
74
In cases of extreme inbreeding what will happen to broad sense heritabiltiy?
Becomes O becuase the variation due to genetics becomes O
75
What could cause Heritabiltiy to change?
Allele frequency change (genetic drift or evolution)
| This causes Vg values to change and hence hertiabiltoy changes
76
Define norm of reaction in quantitative genetics
Response of a single genotype to variation in an environmental parameter
77
What is needed in order for selection to be acting on a quantitative trait?
Heritable variation
Resource competition
Fitness differences dependant on the trait
78
Describe the effects of each of the types of variation on genetic variation
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
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?
Genetic variation starts to run out
| Natural selection is opposing artificial selection
80
Why may selection not cause a decrease in genetic variance?
Mutations
Migrations
Hidden genetic variance
Different forms of selection
81
Define narrow sense heritabiltiy is this usually greater or smaller than broad sense?
The proportion of variation that can be passed on to the offspring
Usually smaller than broad sense heritabiltiy
82
Give the equation for narrow sense heritabiltiy
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
How do you calculate the response to selection?
Mean of offspring of the selected variables - the mean of the original offspring
84
How do you calculate the selective differential?
Mean of selected individuals - mean of the offspring of selected individuals
85
Genotypic variance is made from three elements what are these? Which element do we look at in narrow sense heritabiltiy?
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
Define mutagen
Anything that increases chemical reactivity in the cells
87
What percentages of conceptions does polyploidy occur in?
1-3%
88
What is turners syndrome?
Female with only one X chromosome
89
What is cri duc chat syndrome? How does it occur?
Deletion on chromome 5, causes babies to cry like a cat and have a smaller head - microphaly. Prone to learning difficulties
90
What is the difference between paracentric inversions and pericentric?
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
How large is the human genome ? How many genes?
3 x 10^9 (3billion)
| 20,000-30,000 genes
92
What is the nucleotide change that causes sickle cell anaemia?
GTA --> GAA
93
How many SNPs are there?
12,000,000 (accounts for 0.3% of genome)
94
What is satellite DNA?
Often harmless tandem repeats that can be used to find disease genes
95
How did Mendel manipulate the reproduction of his pea plants?
Removed the anther of one plant, got pollen from another and add to it
96
If a disease isnt caused by mendelian traits what is it called?
Multifactorial
97
Give the symbols used in pedigrees
```
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
Give the characteristics of a autosomal dominant disease pedigree
Affected person has at least one affected parent
Affects either sex
Transmitted by either sex
99
What is achondroplasia ?
A form of dwafism
100
What mendelian pea features are dominant
Yellow dominat to green
Purple dominant to white
Smooth dominant to wrinkled
101
What are the characteristics of an autosomal recessive disorder
Affecteds can have unaffceted parents
Parents will be carriers
Either sex
102
Examples of autosomal recessive condtions
Albinism
Sickle cell
Cystic fibrosis
Attached ear lobes
103
What are the characteristics of an x linked resessive disorder?
Mainly males affected
50% male offspring of female carriers
Females only effected where mother is carrier and father is affected
104
Examples of x linked recessive disorders
Duchenne muscular dystrophy
Red green colour blindness
Haemophilia
105
Charcteristics of x linked dominant disorders
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
Charcteristics of a y linked disorder
Only males affected
All males of affected males are affected
Very few since Y chromosome is small, hairy ear rims
107
Describe morgans crosses with white and red eyed flies
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
Describe morgans experiment on independent assortment
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
What blood group is most common in east asia?
b
110
Describe the Fy1 and Fy2 genes as signals of genetic diversity
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
In peppered moth the melanic form is the dominant or recessive allele?
Dominant
112
What are the latin names for the two forms of peppered moth?
Typical - typica
| Melanic - carbonaria
113
Describe the case study involving the Mauritius kestrel and genetic drift
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
What is meant by identical by descent? How does this relate to the inbreeding coefficient
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
What lethal gene has risen to high levels in californian condors?
Chondrodystrophic dwafism they die at hatching
116
What predictions are made by both the out of africa model and the multiregional model?
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
What is an exception to the idea that african populations are more diverse? What could this be due to?
Beta globin gene in asian populations is more diverse, could be due to selection
118
What gene controls lactase persistance?
LCT*P dominat to introllerant LCT*R
119
What is meant by anagenesis? And cladogenesis?
Origin of a new species without branching - anagenesis
| Cladogenesis = branching of new species
120
What two problems are there we reproductive isolation as a means of speciation ?
New gene causing sterility will not spread
| New gene causing new mating signal unlikely to spread
121
There are two forms of stickleback fish what are they and where are they fitter
Limnetic - high fitness in open water
| Benthic - high fitness in lake margins
122
Describe the dobzhansky muller solution to sympatric speciation
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
What happens when D.simulans and D.Melanogastor try to interbreed? Why?
Females offspring are sterile and all males die in devolvement, harmless mutation in each species cause a defect when together
124
What are the two types of polyploidy?
Auto polyploidy- multiple chromosomes within a species
| Allopolyploidy - two species hybridise
125
How many speciation events does polyploidy account for?
5%
