Genetics and Evolution

Cellular Control

Mutations

A mutation is a change in the DNA and this could result in a non-functioning protein being created. However, some mutations result in the creation of a protein that provides an advantage to an organism. All alleles of genes are a result of a mutation.

Gene Mutations

A mutation in a gene is a change in the base sequence of the DNA. Gene mutations randomly occur during DNA replication. These random mutations are more likely to occur if you are exposed to mutagenic agents, which can interfere with DNA replication. These include high energy radiation (UV light), ionising radiation (Gamma rays and X rays) and chemicals (carcinogens such as mustard gas and cigarette smoke).

Because mutations alter the gene, they can result in a different amino acid sequence in the encoded polypeptide. If the amino acid sequence changes then when the protein is modified into the tertiary structure it will form hydrogen and ionic bonds in different places and fold differently. This will result in a different 3D shape, and therefore a non-functioning protein could be made. Not all mutations are harmful though. Sometimes the new protein that is made may be beneficial, such as the mutation that resulted in antibiotic resistance in bacteria. Some mutations are neutral, meaning that despite the change in DNA, the same protein is still made.

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A gene mutation could result in either a base being deleted or substituted for a different one e.g.:

TAC CCA AGT GGC__ - original DNA sequence__

TAC ACA AGT GGC__ - base substitution mutation__

TAC CAA GTG GC __- base deletion mutation__

A base substitution may be ‘silent’, meaning that the new codon still codes for the same amino acid. This is because the genetic code is degenerate (multiple codons can code for the same amino acid). Base deletions result in a frameshift. Removal one base changes all of the subsequent codons, as can be seen above, which is more harmful as multiple amino acids many be incorrectly coded for.

Addition

One extra base being added to the sequence:

Original: TAC TTC AGG TGG

Mutation: TAC ATT CAG GTG G

The impact of adding one base is that all subsequent codons are altered. This is known as a frame shift. This type of mutation can be very harmful because all the altered codons could potentially code for different amino acids and result in a very different sequence of amino acids resulting in a non-functioning protein.

Deletion

The deletion of a base in a sequence.

Original: TAC TTC AGG TGG

Mutation: ____TAC TCA GGT GG

This causes a frame shift to the left. This could result in a different polypeptide chain and a non-functioning protein.

Substitution

One bases has been changed for a different base, but the number of bases remains the same and there is no frame shift. This results in only one codon changing, and due to the genetic code being degenerate it may still code for the same amino acid and therefore have no impact.

Original: TAC TTC AGG TGG

Mutation: TAC ATC AGG TGG

High Energy and Ionising Radiation

These mutagenic agents include radiation such as α and β particles and x-ray and gamma rays. Ultraviolet light is not ionising, but it is still high enough so can cause damage and disrupt the structure of DNA.

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Carcinogens

This is the term given to chemicals that can alter the structure of DNA and interfere with transcription. These include chemicals in tobacco smoke, mustard gas and peroxides.

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Control of Transcription

In eukaryotes, transcription of target genes can be stimulated or inhibited when specific transcriptional factors move from the cytoplasm into the nucleus. Turning on/off particular genes in a cell is what enables them to become specialised. In prokaryotes the function is more to preserve resources, to ensure that not all proteins are being constantly produced.

The lac operon is found in E.coli and it is a sequence of 3 genes that collectively aid with lactose digestion. Bacteria require less energy to digest glucose, so this is favourable, but if it is not present then it will digest lactose. Therefore, the proteins produced by the lac operon are only needed if glucose is absent and lactose is present. This is how the transcription of these genes is regulated to match this demand.

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There are two molecules that can turn the operon on and off. Firstly, the lac repressor and secondly, the catabolite activator protein (CAP).

The lac repressor (shown as an orange square on the diagram) is able to sense if lactose is present. It is able to do this through the isomer allolactose. This molecule is usually bound to the operon to prevent transcription, but the lac repressor detaches when lactose is present so that transcription can occur. lactose is present normally blocks transcription of the operon, but stops acting as a repressor when lactose is present.

Catabolite activator protein (CAP) is able to sense the presence of glucose. When glucose levels are low it will initiate transcription of the lac operon. CAP is able to sense glucose through the molecule cAMP.

Transcriptional Factors

Transcription of a gene will only occur when a molecule from the cytoplasm enters the nucleus and binds to the DNA in the nucleus. These are called transcription factors and each one can bind to different base sequences on DNA, and therefore initiate transcription of genes. Once bound, transcription begins, creating the mRNA molecule for that gene which can then be translated in the cytoplasm to create the protein. Without the binding of a transcription factor, the gene is inactive, and the protein won’t be made.

Oestrogen

Oestrogen is a steroid hormone that can initiate transcription. It does this by binding to a receptor site of a transcriptional factor. When it binds to the transcriptional factor it causes it to change shape slightly, and this change in shape makes it complementary and able to bind to the DNA to initiate transcription.

Epigenetics

Epigenetics is how the environment interacts with the genome. Factors such as diet, stress and toxins can add chemical tags to the DNA and this can control gene expression in eukaryotes. In this way epigenetics involves heritable changes in gene function, without changes to the base sequence of DNA. Epigenetic inheritance, as well as DNA inheritance, takes place. The layer of chemical tags on the DNA is called the epigenome and this impacts the shape of the DNA-histone complex and whether the DNA is tightly wound so won’t be expressed or unwound so it will be expressed. If the DNA is tightly wound, then transcription factors cannot bind. Therefore the epigenome, which is due to changes in the environment, can inhibit transcription.

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Chemical Tags

Increased methylation of the DNA: when methyl groups are added to DNA, they attach to the cytosine base. This prevents transcriptional factors from binding and attracts proteins that condense the DNA-histone complex. In this way methylation prevents a section of DNA from being transcribed.

Decreased acetylation of associated histones: If acetyl groups are removed from the DNA then the histones become more positive and are attracted more to the phosphate group on DNA. This makes the DNA and histones more strongly associated and hard for the transcription factors to bind.

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Post-Transcriptional Changes

mRNA modification

The newly synthesized strand of mRNA is called pre-mRNA before it has been modified. The key modifications are the removal of the introns and protective caps added to protect the mRNA against degrading enzymes in the cytoplasm.

To provide protection the pre-mRNA has a 5’ cap added. This is a protective cap added to the 5’ end of mRNA. At the 3’ end a poly A tail is added. This is several adenine RNA nucleotides. Both of these modifications protect both ends of the mRNA from being hydrolysed by endonuclease enzymes.

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The second modification is the removal of the ‘junk DNA’ or introns. These are removed by a protein called a splicesome, therefore the removal is called splicing.

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The mRNA is spliced in many different ways, allowing a single gene to actually result in the creation of multiple proteins. This process is called alternative splicing. Humans have approximately 23,000 genes, but at least 90,000 so the creation of these extra proteins via alternative splicing of the introns is why the introns are important.

After translation, some proteins need to be activated by other molecules. Cyclic AMP is a molecule that can bind to certain enzymes, protein kinases, which then activates them to catalyse reaction. This is seen in the second messenger model for glucose regulation.

Homeobox Gene Sequence and Hox Genes

Plant, animals and fungi all have homeobox gene sequences to control the development of their body. These are sequences of genes which regulate the expression of other genes that are involved in the formation of the body in the early stages of develop as an embryo. Hox genes are a type of homeobox gene found in metazoan.

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Mitosis and apoptosis, programmed self-cell death, are important in the control of body form. The cell cycle can also be controlled by genes to ensure new cells are only made when they are needed for growth and repair to preserve energy and prevent tumour formation. The tumour suppressor gene is responsible for making proteins that stop the cell cycle continuing and proto-oncogenes are responsible for producing proteins that initiate the cell cycle. If an error is detected in a cell or if it is too old to function the apoptosis occurs, and this cell is destroyed and the resources are recycled. The control of mitosis and apoptosis are both in response to internal and external stimuli, such as stress.

Genetic Variation

The exact mechanisms of how genetic variation is introduced to a population through mutations and meiosis is introduced in topic 4. The first source of genetic variation is mutations, but meiosis and the random fertilisation of gametes during sexual reproduction result in more genetic variation.

Within a population there will be competition for resources, the impact of disease and predators results which results in the process of natural selection.

Natural selection is when individuals within a population show a wide range of variation in phenotype. This is due to genetic and environmental factors. The primary source of genetic variation is mutation. Predation, disease and competition result in selection pressures. Those organisms with phenotypes providing selective advantages are likely to survive. They are also likely to produce more offspring and pass on their favourable alleles to the next generation. The effect of this is a change in the allele frequency (evolution).

Artificial selection is when humans select plants or animals with favourable characteristics and deliberately breed these individuals together. This manipulates the gene pool so that the favourable allele becomes more common and less favourable alleles become less common. This was particularly prevalent in creating dog breeds with popular features, for example pugs. Pugs were bred to have features deemed cute, such as the flat squashed face. The ethical issue with this is that, due to these selected features, pugs haec many medical issues linked to breathing due to their flat nose structure.

Individuals within a population that have a phenotype that makes them more able to survive and pass on their alleles to their offspring are described as having the selective advantage. This is differential reproductive success, as not all individuals are as likely to reproduce, and this is results in changes in allele frequencies within a gene pool. Evolution is the term given to the change in the allele frequencies in a population.

Below is a recap of the impact directional and stabilising selection have on the allele frequency.

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The final type of selection is disruptive selection. This is when individuals which contain the alleles coding for either extreme trait are more likely to survive and pass on their alleles. As a result, the allele frequency changes and more individuals possess the allele for the extreme trait and the middling trait allele becomes less frequent. Continued disruptive selection can ultimately lead to speciation.

Patterns of Inheritance

Inheritance Key Terms

  1. Genotype__ __– The genetic constitution of an organism (the alleles is has for a gene).
  2. Phenotype__ __– The expression of the genes and its interaction with the environment.
  3. Homozygous- A pair of homologous chromosomes carrying the same alleles for a single gene.
  4. Heterozygous__ __– A pair of homologous chromosomes carrying two different alleles for a single gene.
  5. Recessive allele– An allele only expressed if no dominant allele is present.
  6. Dominant allele – An alleles that will always be expressed in the phenotype.
  7. Codominant__ __– Both alleles are equally dominant and expressed in the phenotype.
  8. Multiple Alleles– More than two alleles for a single gene.
  9. Sex-linkage__ __– A gene whose locus is on the X chromosome.
  10. AutosomalLinkage– Genes that are located on the same chromosome (not the sex-chromosomes).
  11. Epistasis– When on gene modifies or masks the expression of a different gene at a different locus.
  12. Monohybrid__ __– Genetic inheritance cross of a characteristics determined by one gene.
  13. Dihybrid__ __– Genetic Inheritance cross for a characteristic determined by two genes.

Inheritance Crosses and Examples

Test Cross

A test cross can be used to determine whether an organism displaying a dominant characteristic is due to a homozygous dominant or heterozygous genotype. To determine the genotype the organism in question is crossed with a member of its own species that is homozygous recessive for that trait. The offspring’s phenotypes are then analysed. If any of the offspring have the homozygous recessive trait then the original parent in question must have been heterozygous for the dominant trait.

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Dihybrid

Below is an example of a genetic cross showing the inheritance of two genes at the same time.

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Codominance and Multiple Alleles

Blood group is an example of both codominance and multiple alleles. The phenotype for blood group can be A, B, AB or O. These letters refer to which protein, or antigen, is found on the outside of red blood cells. Only one gene codes for this phenotype, but there are three alleles (multiple alleles). Allele IA codes for the A antigen and it is dominant. Allele IB codes for the B antigen and it is dominant. Allele IO codes for no antigen and it is recessive. As allele IA and IB are both dominant they will both be expressed to create the phenotype AB (a codominance example).

Genetics and Evolution, figure 3

Sex-Linkage Inheritance

The X chromosome is much larger than the Y chromosome, it contains a much larger non-homologous region that contains many non-sex-determining genes. For example, genes linked to haemophilia, Duchenne muscular dystrophy and red-green colourblindness.

Autosomal Linkage Inheritance

There are 23 pairs of chromosomes in humans on which there are many different genes. Autosomal linkage studies the inheritance of two genes located on the same chromosome, excluding the X and/or Y chromosome (the term autosomal refers to the non-sex-determining chromosomes). In this inheritance, assuming that crossing over did not occur to change the locus of the gene, the genes located on the same chromosomes cannot be separated during independent segregation and therefore have to be inherited together.

Epistasis

Epistasis is when the one genes masks the expression of another gene. Coat colour on Labrador retrievers is an example of epistasis. There are two genes that control coat colour, one gene codes for whether pigment is produced or not and the other gene codes for the concentration of the pigment.

__Gene 1 __– Pigment produced (Allele E) OR Pigment not produced (e)

Gene 2- High pigment concentration- black (allele B) OR lower concentration -brown (Allele b)

Gene 1 can mask the expression of gene 2 if the alleles inherited are e, coding for no pigment produced.

PhenotypeGenotypesExplanation
Yellow LabradoreebbeeBBeeBbGenotype for gene 1 is homozygous recessive, so gene 2 is masked because no pigment will be produced.
Chocolate LabradorEebbEEbbGenotype for gene 1 codes for making pigment so there must be at least one dominant E allele. The second gene must be homozygous recessive to code for brown.
Black LabradorEeBbEEBbEeBBEEBBGene 1 codes for making pigment so there must be at least one dominant E allele. For the Labrador to be black, the genotype for the second gene must contain at least one dominant B allele.

The Hardy–Weinberg principle

This is a mathematical model which can be used to predict the allele frequencies within a population. It assumes that there will be no change in the allele frequency between generations within a population (e.g. no deaths, births or migration), so it is not perfectly accurate.

The frequency of alleles, genotypes and phenotypes in a population can be calculated using the Hardy–Weinberg equation:

p2 + 2pq + q2 = 1

This equation needs to be used simultaneously with the following equation to help work out p or q first to then use the above equation.

p+q = 1

Where:

p =the frequency of one (usually the dominant) allele

q = is the frequency of the other (usually recessive) allele of the gene.

p2 = The frequency of the homozygous dominant genotype

2pq = The frequency of the heterozygous genotype

q2 = The frequency of the homozygous recessive genotype

Chi-Squared Statistic in Inheritance

All the above types of genetic inheritance can be used to determine as estimate of the expected frequency of each phenotype/genotype with certain parents. Chi-squared can be used to determine whether the frequency, or ratio, or phenotypes you expected is significantly different to the ratio you observe.

Two parents had three children. Two of the children had blood group AB and one child had blood O. Determine the genotypes of the parents have been?
Your answer should include: IAIO / IBIO
Red-green colour blindness is a sex-linked condition recessive. Work out the probably of a male that is not red-green colour blind and a mother who is colour blind having a child that has the condition.
Your answer should include: 50 / 50% / half / 1/2
What are all the possible genotypes for blood group?
Your answer should include: IAIO / IAIA / IBIB / IBIO / IAIB / IOIO
What does epistasis mean?
Your answer should include: Gene / Masks / Interacts
How does autosomal-linkage differ to sex-linkage?
Your answer should include: Somatic / Chromosomes / X / Y

Speciation

Speciation is the process the results in the creation of new species. This occurs when one original population of the same species becomes reproductively isolated. This isolation means that there are now two populations of the same species, but they cannot breed together. This can result in the accumulation of differences in their gene pools to the extent that the two populations would be unable to reproduce to make fertile offspring, and are therefore classed as two different species. There are two different ways that populations can become reproductively isolated, either geographically (allopatric) or because of changes in reproductive mechanisms (sympatric speciation).

Allopatric Speciation

Populations can become separated geographically leading to reproductive isolation. Within all populations there is genetic variation due to random mutations. A population could become geographically isolated over time by new mountain ranges or new bodies of water separating land masses for example. This separates the original population, which are now unable to reproduce due to the geographical barrier. Both separate populations will continue to accumulate different beneficial mutations over time to help them survive in their environments, which are likely to vary. Due to this accumulation of DNA differences over time the two populations become so genetically different that they would be unable to reproduce to create fertile offspring. They are therefore classed as two different species.

Genetics and Evolution, figure 1

Sympatric Speciation

Populations can also become reproductively isolated due to differences in their behaviour. Individuals of the same species may not be separated by geographical barriers, but are still unable to reproduce. This could be because a random mutation within the population could impact reproductive behaviour, for example it may cause individuals to perform a different courtship ritual or for individuals to be fertile at different times of the year. Due to this, these individuals will not reproduce together and there will be no gene flow between the two groups within the populations. Overtime these reproductively isolated populations will accumulate different mutations to the extent that their DNA is so different that they cannot reproduce to create fertile offspring. They are therefore classes are two different species.

Genetics and Evolution, figure 2

Genetic Drift

This is the change in the allele frequency within a population between generations. There will always be genetic drift from one generation to the next, but continual, substantial genetic drift results in evolution. The smaller a population is the bigger the impact allele frequency changes have proportionally and this is why evolution often occurs more rapidly in smaller populations.

Genetics and Evolution, figure 1

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Genetic Bottlenecks and the Founder Effect

These two processes have different causes but the same impact. Genetic bottlenecks is when an event occurs that kills almost all of the population, leaving only a few individuals left. Therefore the genel pool is very limited.

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The diagram above indicates the impact. Many alleles are lost and the remaining breeding population pass on the same alleles. This results in a lack of diversity and therefore genetic diseases that exist in the population and far more likely to be passed on.

The Founder Effect is when a few individuals from an existing population relocate to an isolated area, again resulting in a new population with a limited gene pool.

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An example on this is The Fugates in Kentucky. There is a rare genetic allele that produces a blue pigment and therefore blue skin. A small number of individuals in Kentucky isolated themselves who happened to be carriers for this allele. Due to the limited gene pool and number of breeding individuals, this recessive blue allele became widespread and now many individuals of this human population have blue skin!

Explain why individuals within a population of a species may show a wide range of variation in phenotype?
Your answer should include: Differences / DNA / Meiosis / Crossing / Over / Independent / Segregation / Mutations
Explain why genetic drift is important only in small populations:
Your answer should include: Rapid / Evolution
Explain how evolutionary change over a long period of time has resulted in a great diversity of species:
Speciation