A2 Biology, topic 7

• Gene- sequence of nucleotide bases on a DNA molecule that normally code for a polypeptide, resulting in a characteristic. Genes exist in at least 2 forms; alleles
• Allele-one of the different forms of a gene- most plants and animals carry 2 alleles of each gene (although there can be more). As the order of bases in each allele is slightly different, they code for different versions of the same characteristic. Only one allele of a gene can occur at the locus of any one chromosome. But, diploid organisms have homologus chromosome pairs, meaning that there are two loci, so potentially (up to) 2 different alleles, but no more than two alleles can be present at any one time, as there are only 2 homologus chromosomes, so only 2 loci
• Genotype- the genetic constitution of an organism in terms of the alleles they have. This determines the limits within which the characteristics of an individual may vary
• Phenotype- the expression of genetic constitution (genotype) and its interaction with the environment. This is the observable characteristics of an organism
• Dominant- an allele whose characteristics always appear in the phentotype, even if there's only one copy. Shown with a capital letter
• Recessive- allele whose characteristic only appears in phenotype if there's two copies present; shown with a lower case letter. Needs to be a homozygous recessive (organism with 2 identical recessive alleles

• Codominant- alleles that are both expressed in phenotype; neither one is recessive. This means both alleles contribute to the phenotype. This results in the phenotype being a blend of the two alleles, ot having both features represented (e.g. the presence of both A and B antigens in blood group AB)
• Locus- the fixed position of a gene on a chromosome- alleles of a gene are found in the same locus on each chromosome in a pair
• Homozygous/homozygote- a pair of two of the same alleles/an organism that carries two copies of the same alle
• Heterozygous/Heterozygote- a pair of two different alleles/an organism that carries two different alleles
• Carrier- a person who is carrying an allele that is not expressed in their phenotype, but can still be passed onto their offspring

• Humans are diploid, so have 2 sets of chromosomes, with two alleles for each gene. Gametes only have one allele per gene, so that when 2 parent gametes fuse together, the alleles they each contain can form the genotype of the offspring. At each locus, this genotype can be homozygous or hetrozygous.
• Genetic diagrams, often displayed as punnet squares, can be used to predict the genotypes and phenotypes produced when two parents are (crossed) bred. 
• Genetic diagrams can demonstrate monohybrid inheritance, in which the inherited characteristic is controlled by a single gene, as well as dihybrid crosses. Here, the diagram looks at the chances of offspring inheriting certain combonations of characteristics, i.e. looking at how two different genes are inherited at the same time.
• The diagrams then allow phenotypic ratios to be predicted, with this being 3:1 for monohybrid crosses, 9:3:3:1 for dihybrid crosses and 1:2:1 for codominant crosses

• Whilst expected ratios are able to be worked off for the characteristics of offspring during genetic crosses, it is common that these will not always be achieved due to mutations, environment and developmental factors. This is true of Mendel's classic pea experiment, in which he bred together 2 heterozygous pea plants for colour and shape. 
• It is chance that determines which gametes fuse together, and therefore which characteristics the offspring will have. During mendel's experiment, the ratios that were the closest to the theoretical values were during the experiments with the largest sample sizes, where the ratios furhest from it were in the smallest sample sizes
• In order to test whether these results hold any statistical significance, the Chi-Squared test can be used. This compares the expected frequency of phenotypes in a population with the observed actual characteristics to see if there's a significant difference between the two. The test can only be used with measurements relating to the frequency of individuals in defined, discrete characteristics, only use raw counts of data (not percentages, rates etc) and requires at least 20 data sets in the sample size
• Once calculated, the Chi-Squared value is compared to the critical value for the degree of freedom (-1 set of data); if it is equal to or larger than the critical value, the results are statistically significant, and the null hypothesis can be rejected. 

Sometimws, alleles show co-dominance in that both alleles share dominance of the characteristic, so are both expressed in the phenotype. This means that neither is recessive. One example of this is with a heterozygous cross between co-dominant red and white flowers. If such a cross occured, all the potential offspring would have pink petals, as this is a combination of both the red and white petal traits.

Some genes have multiple alleles (more than 2), however only 2 can be present in an individual. This is exemplified in the ABO blood group gene in humans. A and B are co-dominant and O is recessive to both, making the possible combinations group A, B, O and AB.

This describes an interaction between genes where one gene can impact the presentation of another- one gene needs to not be expressed in the phenotype in order for the other to be observable. This is because many different genes can control the same characteristic, e.g. hair colour, with them interacting to form phenotype. Due to this, it is possible that one can block another. For example, if a man had genes for both baldness and brown hair, the baldness gene would evetually block the brown hair one, as if he has no hair left, you can't see what colour it is; i.e. the trait isn't expressed in the observale phenotype. 

• Genetic information for gender is carrued on one chromosome pair (2 'sex chromosomes'); in mammals this is the 23rd pair of chromosomes. Therefore, a trait is 'sex linked' when the allele that codes for the trait is located on a sex chromosome.
• In mammals, females have two X chromsomes, and men have XY. The Y chromosome is smaller than the X, so carries less genes. As a rest, most alleles that're sex-linked are found on the X chromosome
• As males only have one X chromosome, they often have only 1 allele for sex-linked genes, meaning they'll always express the characteristics of the allele, even if it's recessive. This makes males more likely than females to show recessive phenotypes for genes that're sex-linked.
• Genetic disorders caused by faulty alleles on sex chromosomes include colour blindness and haemophilia. Both of the disoders are 'X-linked', as the alleles that code for them are carried on the X chromosome. This means that men have a higher chance of developing them than women, as women need 2 copies of each recessive allele to suffer from the condition, but men only need 1.

• Autosomes are the chromosomes that are not concerned with sex determination/characteristics. So, in humans, this includes pairs 1-22. Autosomal genes are the genes located on the autosomes, with any genes located on the same autosome (chromosome) being 'linked'.
• During meiosis, genes located on separate homologus chromosomes are independently segrated. If two alleles are on the same autosome, they're less likely to be separated during this process, so are 'linked'. This means the alleles will be passed on to offspring together, as long as the crossing over of chromatids doesn't split them up. The closer together 2 genes are on an autosoe, the more closely linked they are.
• If autosomal linkage occurs, a dihybrid cross of 2 heterozygotes results on 3/4 of the offspring having both dominant characteristics amd 1/4 having both recessive characteristics. This changes the expected phentotypic ratio from 9:3:3:1 to 3:1 and is due to the fact that the 2 autosmally linked genes are inherited together, so a higher proportion of the offspring will have the parents' heterozygous genotype and phenotype. Because of thus, we can use the predicted phenotypic ratio to identify autosomal linkage

• A species is a group of similar organisms that're able to reproduce to give fertile offspring
• A population is a group of organisms of the same species living in a particular area at a particular time, meaning they have the potential to interbreed. Species can exist as one or more population(s)
• The gene pool is the complete range of alleles of breeding individuals present in a population at a given time
• Allele frequency refers to how often an allele occurs in a population; it's usually given as a percentage of the whole population

• This is a mathematical model that predicts the frequency of alleles in a population won't change from one generation to the next. However, this prediction is only true when based on a large population where there's no immigration, emigration, mutations or natural selection. There also needs to be random mating- all possible genotypes can be breed with all others.
• The HW equations can be used to calculate the frequency of particular alleles, genotypes and phenotypes and also test whether frequencies do change between generations in a large population when there is an influence of some kind.

1st Equation- predicting allele frequency: p + q= 1. p is the frequency of the dominant allele and q the frequency of the recessive one. The frequency of an allele has to be between 0 and 1, with 0 meaning that nobody has the allele and 1 meaning that everyone in the population has it

2nd Equation- predicting genotype of phenotype frequency: p squared+ 2pq+ q squared= 1. This allows the frequency of one genotype to be calculated if you know the frequencies of the the others, where p squared is the frequency of the homozygous dominant genotype, 2pq is the frequency of the heterozygous genotype, and q squared is the frequency of the homozygous recessive genotype. Genotype frequencies can then be used to calculate phenotype frequencies.

It can predict the percentage of a population that has a certain genotype: e.g. the frequency of people with cystic fibrosis (genotype ff) in the UK is 1 in every 2500. This allows us to calculate the percentage of CF carriers (Ff) in the UK by finding the frequency of the heterozygous genotype Ff (2pq). First calculate q: ff=q sqaured. 1/2500 = 0.0004. Square root this value to find 'q', which is 0.02. Then, use p+q=1 to find p; 1-0.02 is 0.98; this is p. Then, calculate 2pq- 2 x (0.98 x 0.02)= 0.039. So 3.9% of the UK population is a carrier of CF

It can show if external factors are affecting allele frequency: if the CF frequency is measueed 50 years later, it might be found to e 1 in 3500- from this info, you can calculate that the recessive allele is now 0.017, comapred tp 0.02 currently. As the frequency has changed between generations, the HW principle doesn't apply here, so there must have been some factors affecting allele frequency, e.g. mutations or natural selection

• Directional selection- where individuals with alleles for a single extreme phenotype are more likely to survive and reproduce. Could be in response to an environmental change
• Stabalising selection- where individuals with alleles for characterisics towards the middle of the range are more likely to survive and reproduce. This occurs when the environment isn't changing
• Disruptive selection- individuals with alleles for extreme phenotypes at either end are more likely to survive and reproduce. This occurs when the environment favours more than one phenotype
• Sexual selection- natural selection that occurs through preference by one sex for certain characteristics in individuals of the other sex
• Artificial selection- when organisms are bred by farmers (etc) in order for the most desirable traits to be reproduced

Speciation is the devlopment of a new species from an existing one- it occurs when populations of the same species become reproductively isolated. Changes in allele frequency cause changes in phenotype, meaning organisms can no longer mate to produce fertile offspring. This can occur if there's a physical barrier, so some individuals are separated from the main population. This is geographical isolation, and leads to allopatric speciation; this is when separated populations experience different conditions, so experience different selection pressures. This means different alleles will be directionally selected until they've changed so much, they become reproductively isolated. Selection can also occur when a population becomes reproductively isolated without any physical separation. This is called sympatric speciation; random mutations can occur in the population, preventing members of that population breeding with other members of the species. 

Reproductive isolation occurs because changes in alleles and phenotype in some individuals prevent them from breeding successfully- these changes include seasonal, mechanical and behavioural aspects.

• Evolution can also occur by genetic drift- when chance, rather than environmental factors dictates which individuals survive, breed and pass on their alleles. If by chance the alleles for one genotype are passed on to offspring more often than others, meaning the number of individuals with that allele increases
• Natural selection and genetic drift work alongside each other to drive evolution. Evolution by genetic drift usually has greater impact on smaller populations, where chance has a greater influence

• The niche a specues occupies within its habitat includes its biotic interactions- the organisms it eats + those it's eaten by and its abiotic interactions- the oxygen an organism breathes in + the carbon dioxide it breathes out. A niche can only be occupied by 1 species- if 2 species try to occupy the same niche, they'll compete with each other until only one species is left.
• Adaptations are physiological, behavioural or anatomical. Natural selection ensures that organisms with better adaptations are more likely to survive and pass on their alleles. Every species us adapted to use an ecosystem in a way that no other species can. The organisms are adapted to both the abiotic conditions and biotic conditions in their ecosystem.
• The carrying capacity varies as a result of both abiotic and biotic factors. Abiotic factors inc the amount of light, water, space and temperature; if they're optimum, organisms will grow and reproduce more successfully. 
• Interspecific competetion is between species- as resources decrease, the species that're better adapted to its surrounding will be more likely to claim the niche
• Intraspecific competition is within species- a smaller population means there's less competition, which is better for growth and reproduction
• Predation is when an organism eats and kills another. The population sizes of predators and prey atr interlinked

• Primary succession happens on land that's been newly formed or exposed. Seeds and spores are blown in by the wind and begin to grow. The pioneer species must be specially adapted to these hostile conditions to survive. When they die and microorganisms decompose the dead material, a basic soil is formed, making the conditions less hostile and plants can start to grow
• Seconadry succession happens on land that's been cleared of all plants, but where the soil remains, with the pioneer species being larger plants. As succession goes on, the ecosystem becomes more complex and biodiversity increases. The final stage of succession is called climax community- the ecosystem is supporting the largest and most complex community it can.
• The species that make up the climax community depends on the climate of the community- if there's not much change between seasons, the climax will contain large trees, if there is, it'll only contain herbs and shurbs.
• Human activities can prevent succession (e.g. regularly mowing grassy fields), stopping a climax community from developing- it's called a plagoclimax when this occurs

Conservation sometimes involves preventing succession to preserve an ecosystem in its current stage of succession, as otherwise there could be a loss of some of the plants and animals that currently live there. Conservation is the protection of ecosystems in a sustainable way- i.e. enough resources are taken to meet the needs of people today, without reducing the ability of people in the future to meet their own needs.

There's often a conflict between human needs and conservation, so a balance needs to be found between the two in order to maintain the sustainability of natural resources.