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Genetics for A2

Covering the genetics section of the AQA Biology course.
by

Alex Van Dijk

on 5 November 2015

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Transcript of Genetics for A2

Genetics
Definitions
Gene
Allele
Dominant
Recessive
Codominant
Sex-linked
Locus
Homozygous
Heterozygous
Genotype
Phenotype
A gene is a unit of inheritance. It will code for the production of a specific mRNA which will be translated into a specific protein sequence.
An allele is a particular form of a gene, with a different sequence. Everyone has two copies of each gene, but these might be different alleles of the same gene.
The locus of a gene is the location of the gene on a particular chromosome. You might say that a gene has a locus on the short arm of chromosome 4 for example.
A dominant allele is an allele whose phenotype is shown even if only one copy of the allele is present in the organism
A recessive allele is an allele whose phenotype is only seen when both copies of the gene are this allele.
An organism's genotype is homozygous for a particular gene when both alleles are the same.
The phenotype of an organism is the physical manifestation of its genotype and the effect that the environment has on the organism. (think eye colour, height, the presence or absence of cystic fibrosis etc.)
The genotype of an organism is the collection of all alleles at all loci. The genotype for a particular locus is the combination of alleles present at this locus.
An organism is heterozygous at a particular locus when it has two different alleles of the gene at this locus.
Codominant alleles will both have an effect on the phenotype if the organism is heterozygous at this locus.
The locus of the gene is on the one of the sex chromosomes (X or Y).
Genetic crosses
Rules
Monohybrid
Recessive/Dominant
Codominant
Sex-linked
Dihybrid
Allelic Frequency and Population Genetics
Definitions
Hardy-Weinberg
Selection and Speciation
Types of Selection
Types of Speciation
Genetic crosses are shown in a form of shorthand. Knowing this, and using it at all the times, will allow you to minimise mistakes.
A genetic feature is represented by a single letter. Look at the features you are making the cross for and pick a letter that suits it. Make sure the upper - and lowercase of the letter are different when you write it, to avoid confusion.
Use an upper case letter to represent a dominant allele and a lower case letter for a recessive allele. In a situation of codominancy use two different upper case letters.
Represent the parents with their appropriate letters. Each parent has two alleles, so should be represented by two letters. Label the parents clearly.
Write down the possible gametes produced by each parent below the parent, and circle them. Each gamete will only have 1 allele as meiosis has occurred.
Example:
A cross between pea plants with green and yellow pods.
Choose G and g rather than Y and y which look too similar.
Example:
Green is dominant over yellow so a Green allele is represented as G and a Yellow allele as g.
Parents
Phenotype Pure-Breeding Pure Breeding
Green pod x Yellow Pod
Genotype GG x gg
Gametes
G
G
g
g
male gametes
G
G
female gametes
g
g
Gg
Gg
Gg
Gg
Use a Punnet square (matrix) to show the possible outcomes of the random cross between the two parents.
Write down the genotypes and phenotypes of the possible outcomes
Genotypes: all Gg
Phenotypes: all Green pods
Different alleles will result in different protein products. In general a recessive allele will produce a faulty gene product, and is therefore not visible in the phenotype when heterozygous. A dominant allele will produce a working product, and so its effect will be seen when heterozygous
Most genetic disorders are linked to recessive alleles.
Why?
Not many genetic disorders are linked to dominant alleles, though some do exist, such as Huntington's. Most of these lead to the accumulation of the product because it cannot degrade.
When an organism is pure-breeding for a particular characteristic, all of its offspring (when bred with another pure-breeding individual for that characteristic) will show that characteristic. The organism is homozygous at this locus.
Let's go back to our peas...
We saw that the F1 (first filial) generation was all of the genotype Gg and the phenotype Green Pod.
Work out the genotypes and phenotypes of the second filial generation (F2).
G
g
G
g
GG
gg
Gg
Gg
male gametes
female gametes
F1 Green Pod x Green Pod
Gg Gg
F1 Gametes
G
G
g
g
cross:
phenotype: 3/4 Green pod 1/4 Yellow pod
genotypes: 1/4 GG, 2/4 Gg, 1/4 gg
Breeders are interested to know whether their plants are pure-breeding or heterozygous for a particular characteristic. How could they find out if a particular pea plant with green pods was homozygous or heterozygous?
You would carry out a "test cross". This means that you would cross your unknown plant with a known pure-breeding plant with the recessive characteristic.
Work out the genotypes and phenotypes of a cross between:
a homozygous dominant plant with the pure-breeding recessive
a heterozygous plant with the pure-breeding recessive
How could the breeder tell what plant he had?
Try to answer question 1 and 2 pg 116 and questions 2 and 3 on page 117
Keep in mind the following ratios (for a monohybrid recessive/dominant cross):
homozygous dominant x homozygous recessive -> all dominant phenotype
heterozygous x heterozygous
-> 3/4 dominant phenotype, 1/4 recessive
heterozygous dominant x homozygous recessive
-> 1/2 dominant phenotype, 1/2 recessive phenotype
A sex-linked characteristic is a characteristic for which the gene has a locus on one of the sex chromosomes.
Any species with a distinct difference between the sexes will have sex chromosomes.
In humans this is chromosome 23. Women will have two X chromosomes, whereas men will have a X and a Y chromosome.
Women are homogametic, men are heterogametic.
As the X chromosome is much larger than the Y chromosome, many more genes will be
found on it than on the Y chromosome.
We describe these genes as X-linked.
We will use the following notation for X-linked genes
X
N
X
Y
n
X-linked Dominant
X-linked Recessive
Y
Most sex-linked disorders are caused by a recessive X-linked allele.
Why do men have a higher prevalence of these disorders than women?
male gametes
X
Y
female gametes
X
X
N
n
N
Imagine a sex-linked disorder such as red-green colour blindness.
Let's call X the normal gene and X the recessive gene causing the disorder.
If we cross a female carrier with a non-colour blind male what would happen?
N
n
X
X
X
X
X
X
N
N
N
Y
Y
N
n
n
Phenotypes:
50% of the female children will be a carrier, the other 50% will not have the allele at all.
50% of the male children will only have the recessive allele, and be colour blind, the other 50% will be "normal".
What is the only way that you could get an affected female child?
This means that the incidence of sex-linked recessive characteristics is far higher in men than in women.
For a non-fatal disorder the prevalence in the population of women will be the square of the proportion of men in the population with the disorder. Eg if 1/30 men are colour blind, then 1/900 (1/30 * 1/30) women will be.
You need to be aware of the notation rules for pedigree charts, tracking a particular gene through a population.
Affected Male
Unaffected Male
Unaffected Female
Carrier Female
Affected Female
Multiple Alleles
Sample Pedigree Chart
Do the application questions on page 120
Codominance is when two alleles are equally dominant.
An organism that is heterozygous will show a different phenotype than organisms that are homozygous for either allele.
In a genetic cross the alleles will be represented as an uppercase letter representing the characteristic with a superscript uppercase letter representing the allele.
Example:
A white flowering plant has the genotype
C
C
W
W
A red flowering plant has the genotype
C
C
R
R
A pink flowering plant has the genotype
C
C
R
W
Draw a cross for a F1 from a white flowering plant and a red flowering plant.
Then cross two F1 plants.
male gametes
C
C
female gametes
C
C
W
R
R
C
C
C
C
C
C
W
R
W
C
C
W
W
R
Parent
Phenotype white x red
Genotype C C x C C
W
W
R
R
W
R
R
F1
Phenotype Pink
Genotype C C x C C
w
w
R
R
male gametes
C
C
female gametes
C
C
W
R
W
C
C
C
C
C
C
W
W
W
C
C
W
R
R
R
R
R
F2
Phenotype 1/4 White, 2/4 Pink, 1/4 Red

Genotype 1/4 C C , 2/4 C C , 1/4 C C
w
w
w
R
R
R
Ratios:
100% of the offspring from a cross between two pure-breeding individuals of a codominant characteristic will show the intermediate value.
25% of the offspring of two individuals with the intermediate value will show one of the extreme values, 25% the other and 50% the intermediate value.
Many genes have more than 2 different alleles at any one locus.
The alleles will need to be assessed for the dominance over each of the other alleles to allow you to carry out your genetic cross. This is called the construction of a dominance hierarchy.
Example 1:
Human blood groups is a multi-allelic characteristic controlled by 3 possible alleles: I , I and I
A
B
o
As in codominance you will use a capital letter for the characteristic and then in superscript for the allele.
I
A
I
o
is dominant over
I
B
is dominant over
o
I
A
I
is codominant with
B
I
I
A
I
A
I
A
I
A
I
B
I
B
I
B
I
B
I
o
I
o
I
o
I
o
Phenotypes
and
and
lead to Blood group A
lead to Blood group B
leads to Blood group AB
leads to Blood group O
Exercises:
What phenotypes might the children be:
if one parent is blood group AB and other O
If one is blood group A and the other O
If one is blood group A and the other B
Coat colour in rabbits is controlled by 4 alleles.
In order of dominance they are:
C
A
agouti coat
C
Ch
Chinchilla
C
H
Himalayan
C
a
Albino
List the genotypes that give:
an agouti coat
a chinchilla coat
a Himalayan coat
an albino coat
Draw genetic diagrams for:

1a)i Albino and chinchilla (all offspring are chinchilla)
ii Offspring cross from 1a)i (producing 4 chinchillas, and 2 albino)
b) Agouti and himalayan (producing 3 agouti and 3 himalayan)

2. Two agouti rabbits produce a litter of 5 young. 3 are agouti and 2 are chinchilla. The 2 chinchilla are crossed producing 4 chinchilla and 1 himalayan
Extension (not needed for exam):
A dihybrid cross is a cross that takes into account two characteristics at different loci.
For example you could be breeding a pure-breeding pea plant with tall stem and green peas, with a pure-breeding variety with a short stem and yellow peas.
All of the F1 are tall stemmed with green peas.
This means that tall is dominant over short and green peas over yellow peas.
We have two loci, so we need to assign two letters.
Let's say that tall = T, short = t
and green = G and yellow = g
The pure-breeding tall plant with green peas will have the genotype TTGG and the pure-breeding short plant with yellow peas, ttgg.
All the gametes from the tall, green plant will be TG, and all the gametes from short, yellow plant tg.
All F1 will have the genotype TtGg, showing the tall and green phenotype.
What would the ratio of phenotypes be in the F2 generation?
The possible gametes for the F1 generation, if independently assorted, are TG, Tg, tG, tg.
You now need to draw a punnet square of 4x4 squares.
Female gametes
Male Gametes
TG
TG
Tg
Tg
tG
tG
tg
tg
TTGG
TTGg
TTGg
TtGG
TtGG
TtGg
TtGg
TTgg
Ttgg
Ttgg
TtGg
TtGg
ttGG
ttGg
ttGg
ttgg
Female gametes
Male Gametes
TG
TG
Tg
Tg
tG
tG
tg
tg
TTGG
TTGg
TTGg
TtGG
TtGG
TtGg
TtGg
TTgg
Ttgg
Ttgg
TtGg
TtGg
ttGG
ttGg
ttGg
ttgg
The phenotypes are: 9/16 tall green (dark blue) , 3/16 tall yellow (light blue), 3/16 short green, and 1/16 short yellow.
1
2
3
4
Gene Pool
The total of all alleles of all the genes of all the individuals in a population.
Allelic Frequency
The number of times a particular allele occurs within the gene pool, typically expressed as a number between 0 and 1.
For any one gene, the number of alleles in a population of diploid organisms is twice the number of individuals in the population.
The total number of alleles is taken to be 1.0. If everyone in a population was homozygous for the same allele then the frequency of that allele is 1.0. If everyone was heterozygous with the same two alleles the frequency would be 0.5 for both alleles.
The Hardy-Weinberg principle provides an equation that allows you to calculate the frequencies of the alleles of particular genes in a population
The principle predicts that the proportion of recessive and dominant alleles of any gene in a population is constant if:
no mutations arise
the population is isolated
there is no selective pressure
the population is large
mating is random
You might argue that this is not very realistic, which is why population genetics involves far more complicated equations as well, which you don't need to know...
Worked example:
A specific recessive disorder is caused by having the genotype aa.
The dominant allele will be A
The frequency of A = p
The frequency of a = q

There are no other alleles so

p + q = 1.0
There are four possible genotype combinations:
AA, Aa, aA and aa.

Therefore

AA + Aa + aA + aa = 1.0

Using our frequencies this would be:

p + 2pq + q = 1.0
2
2
Let's say that the disorder represented by aa is seen in 1/10000 people. What is the allelic frequency of a and A?
aa = 1/10000 = 0.0001

aa = q

q = 0.0001

q = sqrt 0.0001 = 0.01
2
2
p + q = 1.0

p = 1.0 - q

p = 1.0 - 0.01

p = 0.99
Frequency of carriers of a is

2pq = 2 * 0.99 * 0.01

= 0.0198
This means that out of every 10000 people, 198 people (or 1.98%) will be carriers for the recessive allele.
The AA genotype will be seen in (10000-198-1) people, or 9801/10000.
Exercises:
1. What is the frequency of the heterozygous genotype if the dominant allele has a frequency p of 0.850?
2. Calculate the allele frequencies and the frequency of carriers for cystic fibrosis which shows up in 1/3200 of Caucasians.
In most natural situations the 5 pre-requisites for the Hardy-Weinberg principle will not be met. This means that the frequency of alleles in the gene pool will change.
This might be because of:
migration
changes in the environment
new allele formation due to mutation
interbreeding with other populations
one allele causing a difference in reproductive success in individuals compared to other individuals.
A change in allele frequency can be seen as a result of differences between individuals because:
All organisms produce more offspring than can be supported by the environment
Populations generally remain constant
Therefore not all members of a population will survive
Those individuals with a set of alleles that makes them fitter than other individuals have a higher probability of passing on their genes.
Those alleles that made them fitter are present in a higher frequency in the next generation.
This continues generation after generation, raising the frequency of "advantageous alleles" and lowering the frequency of "disadvantageous alleles".
Example 1: Warfarin Resistance in rats
Warfarin is a chemical that was used to kill rats. It is not used much anymore as most rats are now resistant to its effects.
Warfarin was used to poison bait grain. The rats would accumulate the toxin over time and eventually die from its effects.
Some rats had an allele that protected them from the effects of warfarin.
Rats with this mutation were more likely to survive in areas with warfarin use.
They passed the allele on to their offspring, increasing the frequency of the resistant allele in the population.
Over a number of generations most rats in the populations were resistant to warfarin.
There are a number of types of selection that can occur:
stabilising selection
directional selection
disruptive selection
In stabilising selection the extremes are selected against, removing them from the gene pool and creating a more homogenous population when conditions remain the same. An example of this is birth weight in babies, where low birth weight results in loss of heat and increased risk of infection, whereas large babies will often cause complications at child birth as they do not fit through the pelvic canal.
Directional selection selects
against one extreme of a trait.
This means that the mean
population value will move
towards the other extreme.
An example might be short
fur length in a cold climate.
Directional selection often happens
when environmental conditions
change. For example as an
environment gets colder, individuals with longer fur are more likely to reproduce than individuals with shorter fur. This will increase the frequency of the genes resulting in longer fur in the population, with the mean shifting towards longer fur.
Disruptive selection is when the middle value is selected against. This causes the population to move towards both extremes, and might lead to speciation if the populations become isolated (geographically or reproductively). An example is the beak shape of finches on the Galapagos.
We have mostly looked at characteristics that are controlled by the expression of a single gene. However, many biological characteristics are controlled by multiple genes (polygenes).
A characteristic that is controlled by many genes will give a normal distribution curve when the characteristic is plotted against the frequency of individuals with a particular value for this characteristic.
Stabilising selection occurs when the environment is constant and the mean value is better suited than either extreme.
As the finches adapted to different niches, the beak sizes and shapes that best fitted the new niche were selected for. Beaks that were neither very good at eating seeds, nor at eating insects were selected against in favour of beaks that were very good at eating seeds, but bad at eating insects, or beaks that were very good at eating insects, but bad at eating seeds.
Speciation is the evolution of new species from existing species. A species is a group of individuals with similar genes that can produce fertile offspring. All members of a species belong to the same gene pool.
A species can consist of more than 1 population. Often these populations will still interbreed. If they are both exposed to the same selective pressures, a single gene pool will continue to exist.
If the two populations become separated the flow of alleles between them ceases. If they are then exposed to different selective pressures, the frequency of various alleles will differ in each population.
As the genetic differences between the two populations increase it becomes ever more likely that the two populations will no longer be able to interbreed. They have become 2 different species.
The main type of speciation you need to be aware of is speciation through geographical isolation (also known as allopatric speciation).
You can also see speciation in populations that are near each other but are occupying different niches or populations that start to become isolated through reproductive selection even if the populations are overlapping.
Geographical isolation
Imagine a lake with a population of a particular fish.
Species X lives and breeds in the lake.
As the environment gets more arid, the water level of the lake drops
This causes the lake to split into two smaller lakes, each containing some individuals of species X.
These populations will no longer be able to share alleles.
Over time the environment changes in the two lakes.
Let's say the water in this lake is having more particulates washed into it, making it cloudier. There's also more of a current in the water. Fish with larger eyes that can let in more light will do better than the smaller eyed fish. Fish with larger fins will also be able to swim against the stream better and as such are more likely to survive
The conditions in the other lake stay the same, so stabilising selection retains the original dominant phenotype
The fish now look markedly different, and will start to develop different gene pools
When the environment becomes wetter again, the two lakes become one again.
The larger-eyed fish and the smaller-eyed fish are sufficiently different that they will not interbreed. The larger-eyed fish is predominant in the depths of the lake.
And the smaller-eyed fish in the shallows.
Chi-Squared
C
C
R
W
or
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