Genes, Alleles, Genotype and Phenotype

• Genes are sections of DNA that contain coded information, in the form of a specific sequence of bases, which determine the sequence of amino acids in a protein
• A gene is a sequence of nucleotide bases on a DNA molecule that codes for a single polypeptide
• A gene occupies a fixed position, called a locus, on a particular DNA molecule

Alleles

• Different versions of a gene are called alleles
• In diploid organisms, the alleles at a specific locus may be the same (homozygous) or different (heterozygous)
• The order of bases in each allele is slightly different, and this results in a different amino acid sequence being coded for
• As a result, a different polypeptide is produced

Genotype and Phenotype

• Genotype describes the genetic constitution of an organism, specifically which alleles it possesses
• Phenotype describes the observable characteristics of an organism, which are determined by the interaction of the genotype and the environment

Dominant, Recessive, and Codominant Alleles

• Dominant alleles are always expressed in the phenotype, even if only one copy is present (heterozygous)
• Recessive alleles are only expressed in the phenotype if two copies are present (homozygous)
• Codominant alleles are both expressed in the phenotype when present in a heterozygote

Monohybrid Inheritance

• Monohybrid inheritance is the inheritance of a single gene
• A monohybrid cross involves crossing two parents and looking at a single characteristic which is controlled by one gene
• The expected ratios of genotypes and phenotypes in the offspring can be predicted using a Punnett square

Dihybrid Inheritance

• Dihybrid inheritance is the inheritance of two genes that reside on different chromosomes
• Dihybrid inheritance can also be influenced by the linkage of the two genes which are being investigated
• A dihybrid cross involves crossing two parents and looking at two characteristics which are controlled by two different genes
• When two genes are on different chromosomes, independent assortment of alleles occurs during gamete formation
• The expected phenotypic ratio in the F2 generation of a dihybrid cross (assuming no linkage) is 9:3:3:1

Autosomal Linkage

• Autosomal linkage occurs when two or more genes are located on the same autosome (non-sex chromosome)
• Linked genes are inherited together because they are located on the same chromosome
• The closer the genes are on the chromosome, the less likely they are to be separated during crossing over in meiosis
• Crossing over can produce recombinant gametes, which have different combinations of alleles than the parent chromosomes
• The frequency of recombination depends on the distance between the genes; the greater the distance, the higher the frequency of recombination
• A chi-squared test can be used to test the null hypothesis that there is no linkage between two genes

Sex-linked characteristics

• Sex-linked genes are genes located on the sex chromosomes (X and Y chromosomes)
• In mammals, the X chromosome is much longer than the Y chromosome and carries many more genes
• Most sex-linked genes are located on the X chromosome and are therefore called X-linked genes
• Males (XY) have only one copy of the X chromosome, so they are more likely to express X-linked recessive traits
• Females (XX) have two copies of the X chromosome, so they are less likely to express X-linked recessive traits because they would need to inherit two copies of the recessive allele, one from each parent, to display the trait
• Examples of X-linked recessive disorders include hemophilia and red-green color blindness
• Pedigrees can be used to track the inheritance of sex-linked traits in families

Epistasis

• Epistasis is the interaction of genes where the expression of one gene affects or masks the expression of another gene
• Epistasis is where one gene masks or suppresses the expression of another gene
• Epistasis can alter the expected phenotypic ratios in crosses
• In recessive epistasis, a recessive allele at one gene locus masks the expression of alleles at another gene locus
• In dominant epistasis, a dominant allele at one gene locus masks the expression of alleles at another gene locus

Population Genetics

• A population is a group of individuals of the same species that live in the same area and can interbreed
• The gene pool is the total collection of genes and their alleles in a population at a given time
• Allele frequency is the proportion of a specific allele in a population
• Allele frequencies can change over time due to various evolutionary factors such as mutation, gene flow, genetic drift, and natural selection

Hardy-Weinberg Principle

• The Hardy-Weinberg principle states that allele and genotype frequencies in a population will remain constant from generation to generation in the absence of other evolutionary influences
• The Hardy-Weinberg equation is used to calculate allele and genotype frequencies in a population
• The two equations are:
  • p + q = 1 (where p is the frequency of the dominant allele and q is the frequency of the recessive allele)
  • p^2 + 2pq + q^2 = 1 (where p^2 is the frequency of the homozygous dominant genotype, 2pq is the frequency of the heterozygous genotype, and q^2 is the frequency of the homozygous recessive genotype)
• The Hardy-Weinberg principle assumes the following conditions:
  • No mutations
  • Random mating
  • No gene flow
  • No natural selection
  • Large population size
• If the observed genotype frequencies in a population deviate significantly from the expected frequencies calculated using the Hardy-Weinberg equation, it suggests that one or more of the assumptions are not being met, and the population is evolving

Natural Selection

• Natural selection is the process by which individuals with certain heritable traits survive and reproduce at a higher rate than others because of those traits
• Natural selection leads to adaptation, where populations become better suited to their environment over time
• Variation exists within populations due to genetic mutations
• Mutations are spontaneous and random changes in the genetic material of a cell
• Selection pressure is an environmental factor that affects the survival and reproduction of individuals in a population
• Individuals with advantageous traits are more likely to survive and reproduce, passing on their genes to the next generation
• Over time, the frequency of advantageous traits increases in the population

Types of Selection

• Stabilizing selection favors intermediate phenotypes, reducing variation in the population
• Directional selection favors one extreme phenotype, shifting the population's genetic variance toward the new, favored phenotype
• Disruptive selection favors both extreme phenotypes, leading to increased variation and potentially the formation of two distinct groups within the population

Genetic Drift

• Genetic drift is the random change in allele frequencies in a population due to chance events
• Genetic drift has a greater effect on small populations
• Genetic drift can lead to the loss of alleles from a population, reducing genetic diversity
• The founder effect occurs when a small group of individuals establishes a new population, and the allele frequencies in the new population may differ from those in the original population
• The bottleneck effect occurs when a population undergoes a drastic reduction in size due to a chance event, and the surviving individuals may not represent the original genetic diversity of the population

Speciation

• Speciation is the process by which new species arise
• A species is a group of organisms that can interbreed and produce fertile offspring
• Reproductive isolation is the key to speciation, where different groups within a population become unable to interbreed

Types of Speciation

• Allopatric speciation occurs when populations are geographically isolated, preventing gene flow between them
  • Different selection pressures in the different environments can lead to the evolution of reproductive isolation mechanisms, resulting in the formation of new species
• Sympatric speciation occurs when new species arise within the same geographic area
  • Sympatric speciation can occur through mechanisms such as polyploidy (duplication of chromosomes), disruptive selection, and non-random mating

Evolution

• Evolution is the change in the heritable characteristics of biological populations over successive generations
• Evidence for evolution comes from various sources, including:
  • The fossil record shows the gradual change in organisms over time
  • Comparative anatomy reveals similarities and differences in the structures of different organisms, suggesting common ancestry
  • Comparative embryology shows similarities in the embryonic development of different organisms, suggesting common ancestry
  • Molecular biology provides evidence for evolution through the comparison of DNA and protein sequences, which show the degree of relatedness between different organisms
  • Biogeography shows the distribution of organisms on Earth, which reflects their evolutionary history and the movement of continents
• Evolution is not always a linear process, and it can involve periods of rapid change followed by periods of relative stasis

Learn about genes as sections of DNA containing coded information. Explore alleles, different versions of a gene, and their impact on amino acid sequences. Understand the concepts of genotype and phenotype and their relationship.