Population Genetics

Question 1

Gene

Answer 1

A sequence of DNA nucleotides that codes for a particular characteristic or trait

Question 2

Allele

Answer 2

Slight variations in the code of a gene can result in different forms of that trait

Question 3

How are individuals the same and how do they differ?

Answer 3

Individuals within a species share the same genome but possess different combinations of alleles and different unique combinations of their Introns

Question 4

What is a population?

Answer 4

An interbreeding group of organisms of the same species in the space region a the same time.

Question 5

What is Gene pool?

Answer 5

> Is the total genetic information present in a given population of individuals ( genes + alleles).
Each individual has 2 copies of each genes in the form of alleles (maternal & paternal)

Question 6

Homozygous

Answer 6

Dominant & Same Copies
eg. AA

Question 7

Heterozygous

Answer 7

Different Copies
eg Aa
-> Express the dominant allele (A)

Question 8

Homozygous

Answer 8

Recessive & Same Copies
eg. aa

Question 9

Allele Frequency

Answer 9

Is the number of times an allele occurs in a gene pool.

Question 10

Factors concerned to maintain a constant allele frequency

Answer 10

> Large population
Random Mating
No mutations ( changes in DNA)
No migration- closed population
No Selection Pressures- natural or artificial

Question 11

Factors concerned to change the allele frequency

Answer 11

> Small population
Non-random mating
Mutations
Migration- open population
Selection Pressures- natural or artificial +

Question 12

Genotype?

Answer 12

> Various combinations of alleles in an individual

Question 13

Phenotype

Answer 13

> Observable traits
Genotype + environment determine phenotype

Question 14

Genetic Diversity

Answer 14

In a large gene pool, there is likely to be a greater number of different alleles, and therefore more genetic diversity, while in a small gene pool, there is likely to be less genetic diversity

Question 15

Evolution

Answer 15

When allele frequencies in a population changes over many generations, the population is said to be evolving
> Evolution is defined as the change in the allele frequencies of a population over time

Question 16

Mutations

Answer 16

> Are changes in the nucleotide sequence of DNA and are detected and repaired by enzymes.
Responsible for all genetic variation between species and between individuals of the same species
Are a source of new alleles and contribute to changes in allele frequency
Occur randomly during the DNA replication OR as a result of mutagens( factors that induce mutation)
May affect a single or multiple genes or an entire chromosome

Question 17

3 types of mutations that cannot be repaired?

Answer 17

> Neutral Mutations: Have no effect on survival. EG. ( colour blindness, chin dimple, green eyes)
Beneficial Mutations: Increase the likelihood of survival. EG (bacteria that develop antibiotic resistance)
Harmful Mutations: Decrease the likelihood of survival. EG ( sickle cell anaemia)

Question 18

Locations of Mutations

Answer 18

> Where the mutations occurs will determine whether the mutation can be inherited by offspring
1. Somatic Mutations: Occurs in body cells and only affect that individual
2. Germline Mutations: Affects gametes and are therefore heritable. May bring a new allele into a gene pool, influencing the allele frequencies

Question 19

Types of Mutations

Answer 19

1. Point
   > Substitution -> (silent, missense & nonsense)
   > Frameshift -> (insertion & deletion)
2. > Block -> deletion, duplication, inversion and translocation

Question 20

Point Mutations

Answer 20

> Describe changes to ONE nucleotide in a gene.
Base substitutions create silent, missense or nonsense mutations, while insertions and deletions cause frameshift mutations

Question 21

Point Substitution Mutations

Answer 21

> Is where one nucleotide is replaced by another type of nucleotide

Question 22

Point Substitution Silent Mutations

Answer 22

> Occurs when a substitution of a nucleotide results in a new codon that still codes for the same amino and therefore does not have any effect on the final polypeptide. Relates to the degenerate nature of the genetic code

Question 23

Point Substitution Missense Mutations

Answer 23

> Occurs when a substitution of a nucleotide results in an amino acid replacement, altering the primary structure of the polypeptide. This in turn affects the folding of the polypeptide and could affect the function of the entire protein

Question 24

Point Substitution Nonsense Mutations

Answer 24

> When a substitution of nucleotide results in the creation of a stop codon. Prematurely end the transcription of a gene resulting in a polypeptide that is too short which can have severe effects

Question 25

Point Frameshift Mutations

Answer 25

> Involved one or two nucleotides being either added or removed from a nucleotide sequence, altering every codon in that sequence from that point onwards
Cause a shift in the reading frame, resulting in an incorrect reading of the codons
Can have significant effects on the polypeptide as every codon & amino acid is altered ( results in the loss of protein function)

Question 26

Point Frameshift Insertion Mutations

Answer 26

> Adds one/ two nucleotides into the sequence and pushes the rest of the nucleotides back one or two places

Question 27

Point Frameshift Deletion Mutations

Answer 27

> Removes one/ two nucleotides into the sequence and pushes the rest of the nucleotides forwards one or two places

Question 28

Block Mutations (chromosome
mutations)

Answer 28

> Mutations that affect large sections of a chromosome, typically multiple genes
Occur during meiosis in eukaryotic cells
The effects are serious and can be lethal

Question 29

Block Duplication Mutations

Answer 29

> Involves the replications of a section of a chromosome that results in multiple copies of the same genes on that chromosome.
Lengthens the DNA
Often increases gene expression, which can be harmful of beneficial depending on the gene involved

Question 30

Block Deletion Mutations

Answer 30

> Involves the removal of a section of a chromosome.
Shortens the DNA
Leads to disrupted or missing genes which can have serious effects on growth and development and are often fatal

Question 31

Block Inversion Mutations

Answer 31

> Involves of a section of DNA having its sequence reversed ( removed, 180º rotation and reattached in reverse order)
May involved as few as two bases or may involve several genes

Question 32

Block Translocation Mutations

Answer 32

> When two sections of DNA on different chromosomes switch places
Typically interrupt normal gene regulation and are the cause of some forms of cancer

Question 33

Chromosomal Abnormalities

Answer 33

> Genomes can change through addition or subtraction of a chromosome or set of chromosomes
Detected with a karyotype ( technique of staining/ photographing chromosomes )
Two forms: Aneuploidy and Polyploidy

Question 34

Aneuploidy

Answer 34

> Is the presence of an abnormal number of a particular chromosome: EITHER with a missing or extra chromosome
Usually caused by nondisjunction during meiosis : ( when two homologous chromosomes do not separate)

Question 35

Polyploidy

Answer 35

> Is the condition that results from cells and organisms that contain more than two full sets of chromosomes
Caused by errors during meiosis and results in diploid gametes ( if one of these gametes is fertilised, it will result in a zygote with more than the usually two sets of chromosomes

Question 36

Genetic Diveristy

Answer 36

> Mutations introduce new alleles into a population gene pool and increase genetic diversity ( for this to occur, the mutation must occur in germ-line cells ( gametes). Somatic mutations are not passed down to future offspring

Question 37

Selection pressures?

Answer 37

> Conditions/ factors influencing allele frequencies in a population, contributing to the selection of which phenotypes survive in an environment
Two forms of selections pressures: Natural environment pressures (natural selection) and Artificial pressure brought by humans (artificial selection)

Question 38

Environmental Selection Pressures

Answer 38

> Factors that influence allele frequency in a population
Cause struggle for survival by impacting an individual’s ability to survive
Is a mechanism for evolution in which the individuals best adapted to the selection pressures in their environment survive, reproduce and pass on their alleles

Question 39

Environmental Selection Pressures ( Selective Agents)

Answer 39

> Physical: Climate ( extreme temps, droughts). Competition (food, water, shelter, mates)
Chemical: Infectious Disease and predation
Biology: Pollutant in soil or water (pesticides)

Question 40

PANDA PAW

Answer 40

> Density Dependent Factors:
Predators
Availability of resources
Nutrient Supply- food source
Disease/ pathogenic spread
Accumulation of wastes
Density Independent Factors:
Phenomena ( natural disasters)
Abiotic factors ( temp or CO2 levels)
Weather conditions ( floods, storms)

Question 41

Survival of the Fittest?

Answer 41

> Refers to some phenotypes having a higher adaptive value and giving the individual an advantage over other individuals without phenotypes of lower adaptive value
Having an advantageous trait means the individual is more likely to survive to reproduce and pass their alleles on to the next generation

Question 42

What is the Natural Selection Process?

Answer 42

> Physical, biochemical and/or behavioural variation in phenotypes between individuals in a population
Variation is heritable
A specific selection pressure exists resulting in some individuals survive and reproduce better, as they have an advantageous phenotype that helps them over the selection pressure
Organisms with the fitter (advantageous) phenotype pass their alleles onto the next generation. This changes the allele frequencies in the population as the trait becomes more common
Alleles of the advantageous trait tend to increase in frequency in the gene pool, while alleles of less advantageous traits tends to decrease.
Overtime the population evolves and adapts to its environment

Question 43

Extinction Risk:

Answer 43

> Species with large amounts of genetic variation are less likely to go extinct
Species with more variation in alleles has a higher chance of possessing a favourable genetic trait that will help it survive if a new selection pressure arises
Small population are more likely to have low genetic variation than large populations: have a higher risk of extinction
Extremely low genetic variation or diversity between members of a species puts the species at high risk of extinction because it is less likely that there is an allele that offers a survival advantage if selection pressure or the environment change

Question 44

Gene Flow

Answer 44

> Introduction or removal of alleles from a population due to migration
Gene pools can change when new individuals join the population from difference gene pool or when some individuals leave a population

Question 45

What does gene flow result from?

Answer 45

> Immigration (into) or emigration ( out of) a population for animals
For plants, the movement of seeds and pollen

Question 46

What can gene flow cause?

Answer 46

> Increase in genetic diversity
Or decrease the variability between two populations involved, making then more similar
When gene flow is not possible between populations, the gene pools are said to be isolated

Question 47

Two ways genetic drift can occur

Answer 47

> Founders Effect
Population Bottleneck

Question 48

What is genetic drift?

Answer 48

> Refers to the random change in a population’s allele frequencies as a result of random or chance events
-> No allele is favoured, they are all equally subject to being affected and results in the loss of genetic diversity as alleles are lost from the gene pool

Question 49

Genetic drift’s effects

Answer 49

> The smaller the population, the greater the potential impact
As time progresses alleles may be lost from the gene pool or fixed as the only allele present for the gene

Question 50

Founder Effect

Answer 50

> Occurs when a small group of individuals from a larger population move to a new location and colonise, are isolated from the main group and establish a new population
This new colony’s small size means a smaller gene pool which means their allele frequency is not representative of the original population

Question 51

The new environment of Founder Effect

Answer 51

> In the new environment, the environmental pressures on the founder population are likely to be different from those experienced by the original population
These differences in environmental pressures drive further changes in allele frequencies and ultimately evolution

Question 52

Population Bottleneck

Answer 52

> Occurs when there is a large reduction in the population size, due to a catastrophic chance event
The phenotype of an individual will not increase its chances of survival, so individuals that do survive do so by chance
Results in alleles within the surviving population being unrepresentative of the original population
Loss of so many individuals in a population means many unique alleles are lost

Question 53

The surviving population of Population Bottleneck

Answer 53

> The surviving population has lower genetic diversity than the pre disaster population causing changes in the allele frequency of the gene pool, and thus the population is evolving.
The reduced population size limits the possible reproductive pairings which may result in inbreeding ( when organisms that are closely related to each other mate and produce offspring)&raquo_space; resulting in reduced genetic variation in the population and an increase in the numbers of homozygous individualsm

Question 54

Population Bottleneck: a smaller population

Answer 54

> The smaller the population the greater the bottle neck effect of genetic drift: alleles may be lost from the gene pool immediately after the natural disaster or be ‘bred out’ in only a few generations
The lowered variation may make the population more vulnerable to environmental change

Question 55

Lowered Adaptive Potenial

Answer 55

> Populations affected by genetic drift are vulnerable to new selection pressures that could challenge and potentially wipe out an entire population because the population is less likely to have allele that will help individuals survive under new selection pressures

Question 56

Artificial Selection (selective breeding)

Answer 56

> Occurs when humans deliberately intervene in the reproductive process
Organisms that have the desired phenotypic characteristics are selected by humans to reproduce and pass on their alleles while those with undesired characteristics are prevent from reproducing
Breeders manipulate the gene pool and keep the desired features ( and their alleles) in a population that are economically beneficial or aesthetically pleasing, this process reduces the genetic diversity of the breeding population and consequently increases their vulnerability to selection pressures

Question 57

Artificial Selection in Plants

Answer 57

> Produces disease resistance, increased crop yield, drought tolerance, sweeter tasting fruit and larger or more colourful flowers.
Seeds are collected from the individuals with the desirable phenotype and planted. The new generation is cross-pollinated with other individuals with similar traits.

Question 58

Artificial Selection Effects:

Answer 58

> Reduces genetic variation: Although selective breeding increases the allele frequency of the desired trait, it also decreases the frequency of other alleles for this trait, reducing genetic variation within a gene pool and increases the incidence of homozygosity
Increases presence of undesirable linked alleles: Genes do not exist in isolation but are carried on chromosomes with other characteristics. Gene linkage means that selecting for one allele may result in the selection of several other traits. The success of selective breeding of both plants and animals may be limited by the presence of undesirable linked alleles.
Reduces resistance to environmental change
A population with low genetic variation is one in which all the individuals are very similar.
If the alleles in the gene pool have a high adaptive value for the environmental conditions, the species will persist.
Should the environmental conditions change, and the resulting selective pressures change, it is unlikely that the same alleles will still have the same adaptive values.
A single disease could potentially wipe out entire populations if none of the individuals are resistant.
Reduces biodiversity
Selectively bred species are replacing wild varieties, reducing biodiversity.
Combined with low genetic variation within the selectively bred populations, this puts global food security at great risk, especially with climate change.
This has led to the construction of seed banks around the world, where the seeds of both heirloom and modern varieties are stored.

> Can increase genetic abnormalities
Many purebred dogs, for example, have congenital problems including hip dysplasia, deafness and an increased risk of cancers, heart diseases and neurological diseases.
Other less detrimental traits, such as an underbite, are rare in wild dog populations but relatively common in domesticated dog breeds.
Many of these problems are recessive conditions.
Means an individual needs two copies of the same allele for the condition to be present.
Inbreeding and small gene pools greatly increase the frequency of these particular alleles.

Question 59

Bacterial Evolution

Answer 59

> A random mutation might cause some bacteria to become resistant to an antibiotic.
Bacteria only have one chromosome, and they have plasmids, but they only have one copy of each gene, so this means the impact of a mutation is immediate.
Bacteria may become resistant to an antibiotic in many ways.
Over time, the whole population becomes antibiotic resistant because the resistant strains are best suited to their environment.
This happens quickly as bacteria reproduce every 20 minutes.
This is an example of natural selection.

Question 60

Transfer of Resistance

Answer 60

> Genes for antibiotic resistance often occur on plasmids.
Plasmids can be transferred from one bacterium to another, even between different species, through conjugation.

Question 61

Conjugation

Answer 61

> Occurs when a tube forms between two bacteria to allow the movement of a plasmid from a donor bacterium to a recipient, passing on the allele for resistance.

Question 62

Challenges for Treatment

Answer 62

> Increasing numbers of antibiotic-resistant bacteria in the population means that infections and diseases caused by such bacteria are becoming harder to control.
It is increasingly difficult to find antibiotics that these strains of bacteria are not resistant to.
Consequently, the effects of bacterial infections are becoming more severe, longer lasting and more expensive, and often resulting in death.

Question 63

Antibiotic Alternatives ( CRISPR)

Answer 63

> An emerging tool particularly valuable in combating bacterial resistance by altering the allele for resistance, is CRISPR.
CRISPR: Disables the gene that makes bacteria antibiotic resistant.
Works by editing its target rather than destroying them.
Means the edited plasmid is still able to replicate and spread to other bacteria but is no longer able to produce antibiotic resistance.

Question 64

CRISPR-CAS9

Answer 64

> Disables the gene that makes bacteria antibiotic resistant.
Works by editing its target rather than destroying them.
Means the edited plasmid is still able to replicate and spread to other bacteria but is no longer able to produce antibiotic resistance.
Another approach is to program Cas9 to view itself as an enemy and therefore to make cuts in its own genome.
An advantage of this technology is that it can be programmed to destroy only specific pathogenic bacteria and leave the other, healthy microbes untouched.

Question 65

Cas9 programming

Answer 65

> Encoding a plasmid with instructions for CRISPR enzymes designed to disable Salmonella DNA
Placing the plasmid inside E.coli bacteria
Allowing the engineered plasmid to be transferred from the E.coli to Salmonella through conjugation
Activating the CRISPR system to destroy the Salmonella bacteria, leaving the E coli undamaged

Question 66

Influenza A

Answer 66

> Are divided into subtypes based on two glycoproteins
: > Haemagglutinin (H) > is an attachment protein that mediates the entry of the virus into a host cell
: > Neuraminidase (N) > is an enzyme that facilitates the release of the virus from the host cell after replication

Question 67

Antigenic Drift

Answer 67

> Occurs when mutations (gene change) in the genes of viruses leads to changes in the surface proteins of the virus.
Changes accumulate over time.
Results in viruses that are closely related to one another, meaning they also have similar antigenic properties.
Means that antibodies created by the immune system against one virus may recognise and respond to similar flu viruses.

Question 68

Antigenic Drift- Influenza

Answer 68

> The RNA in the influenza virus is more prone to mutations than genes made of DNA due to the virus’s replication machinery not having a proofreading mechanism
Over time, mutations accumulate
When a mutation alters a gene coding for either or both of the surface proteins, the shape of these molecules changes affecting whether specific antibodies can bind to these antigens.
E.g. The specific antibodies created to bind to haemagglutinin may be unable to recognise the shape of this viral antigen, however, antibodies specific for neuraminidase are unaffected.
Can result in an epidemic occurring.
That is more than the expected number of cases of disease occurring (e.g. the flu) in a particular community or region, during a given period of time.

Question 69

Antigenic Shift

Answer 69

> Involves reassortment (gene swapping).
Is the mixing of RNA in the virus genome which occurs when several different viruses infect the same host cell at the same time.
Leads to a new virus strain (subtype).
Changes occur abruptly, less frequently and at unpredictable intervals.

Question 70

Antigenic Shift - Influenza A

Answer 70

> Typically occurs when a human flu virus crosses with a flu virus that usually affects animals (such as birds or pigs).
Segments of their genetic material may recombine to produce viruses that have entirely new H or N surface proteins.
Can mean that the antibodies made by the host’s immune system in response to the previous subtypes don’t recognise the new subtype, so a large portion of the human population is vulnerable to infection by the new strain.
If this new virus causes illness in infected people, and can spread easily from person to person, an influenza pandemic can occur.

Question 70

Antigenic Drift vs Shift

Answer 70

Antigenic Drift
> Caused by the accumulation of point mutations
> Gradual change
> Continually occurring
> Minor changes in the virus
> Same subtype
> Causes epidemic
Both
> Affect whether specific antibodies can bind to viral antigens
Antigenic Shift
> Caused by the reassortment of genes
> Sudden change
> Less frequent
> Major changes in the virus
> New subtype created
> Causes pandemic

Question 71

Antiviral Medication

Answer 71

> Antiviral drugs are recommended only for people who are very sick, immunocompromised, pregnant or at high risk of serious complications.
A key reason why their use is limited in this way is to decrease the chance that a virus will exist that has resistance to the drug.
Neuraminidase inhibitors (NAIs) are the most commonly used antiviral medication.
Their mechanism of action is to prevent the liberation of the virions from the host cell.
To combat future influenza virus epidemics (evolution due to antigenic drift) and pandemics (evolution due to antigenic shift) we need medication that can replace or work in combination with the neuraminidase inhibitors.

Question 71

Two key approaches to preventing and treating influenza viruses

Answer 71

> Medication : Successful antiviral medication will interfere with the life cycle of a virus.

> Vaccination

Question 72

Medication Challenges

Answer 72

> One ongoing challenge in the design of novel antiviral medication is to ensure that the drug targets a process or structure that is unique to the virus.
Given that viruses use host cells to multiply,it is difficult to destroy viruses without killing the host cells as well.

Question 73

Vaccination Programs

Answer 73

> Every year, a slightly different version of the Influenza A virus emerges because of antigenic drift.
This means that every time the virus evolves, the vaccine for influenza A must be updated so that the antibodies it induces are specific to the antigens of the new strains.

Question 74

Universal Vaccine

Answer 74

> Finding a universal vaccine is the challenge of defending against evolving viruses.
One way of finding a universal vaccine is to target a conserved area of the virus - this is an area of its structure that doesn’t change despite antigenic drift and shift.