BIOL214 Exam 2 - Heritable Variation (ch 5+6)

Important Molecules for Evolution

• 3 kinds of molecules are important for evolution

  • proteins

  • DNA

  • RNA

Proteins

• chains of amino acids

• can act as enzymes, structural support, regulate passage of substances across cell membrane, immune function, and coordinate signaling pathways

Organelles Involved in Protein Manufacture

• ribosomes

• golgi apparatus

• endoplasmic reticulum

Protein Production

• transcription: in the nucleus results in DNA → RNA

• translation: at the ribosomes results in RNA → proteins

After Transcription…

• RNA travels from nucleus → ribosome

• proteins are made in ribosomes (some bound to rough ER, some float in the cytoplasm)

Endoplasmic Reticulum

• filled with membranes

• smooth ER: contains enzymes that produce lipids

• rough ER: contains ribosomes that produce many types of proteins

Golgi Apparatus

• proteins are finalized and packaged in the golgi apparatus

• proteins are finished in vesicles (small bubbles of membrane)

Deoxyribose Nucleic Acid (DNA)

• holds instructions for all living things

• double helix with two strands of nucleotide strings

• each nucleotide contains a sugar, a phosphate, and a base

DNA Bases

• Adenine (A) = Thymine (T)

• Guanine (G) = Cytosine (C)

• hydrogen-bonding

Eukaryotic DNA is Organized into Chromosomes

• DNA is organized into chromosomes in which the molecule is wound around histones (proteins)

• the winding and unwinding of DNA around histones can expose or hide genes

  • regulation of gene expression

Ploidy

• number of copies of unique chromosomes in a cell

• haploid (n)

  • 1 copy of each chromosome

• diploid (2n)

  • 2 copies of each chromosome

• triploid (3n)

  • 3 copies of each chromosome

• tetaploid (4n)

  • 4 copies of each chromosome

Sex Chromosome

• a chromosome that pairs during meiosis but differs in copy number between males and females (X and Y)

Autosome

• a chromosome that does not differ between sexes

Gene

• segment of DNA whose nucleotide sequences code for proteins/RNA or regulates the expression of other genes

Gene Expression

• process by which information of a gene is transformed into a product

RNA Polymerase

• the enzyme that builds the single-stranded RNA molecule from the DNA template during transcription

Transcription

• the process that takes place where RNA polymerase reads a coding sequence of DNA to the ribosome where it can be translated into protein

Translation

• the process that takes place when a strand of mRNA is decoded by a ribosome to produce a protein

Ribosomes Translate mRNA into Protein

• each mRNA acts as a template for building a protein

• the ribosome reads 3 bases at a time (codon)

• tRNA adds the correct amino acid

Hormones

• molecular signals that flow through the body that can alter the expression of genes

Upstream and Downstream

• upstream: → 5’ end of RNA/DNA

• downstream: → 3’ end of RNA/DNA

Gene Control Region

• an upstream section of DNA that includes the promoter region and other regulatory sequences that influence transcription of DNA

Repressor

• protein that binds to a sequence of DNA or RNA and inhibits the expression of one or more genes

Transcription Factor

• protein that regulates the expression of a gene by binding to a specific DNA sequence in association with the gene sequence

Enhancer

• short sequence of DNA within the gene control region where activator proteins bind to initiate gene expression

MicroRNA

• group of RNAs that act as post-transcriptional regulators of gene expression

• bind to complementary sequences on specific mRNAs and can enhance or silence gene translation

Introns

• non-coding sequences

• longer than exons

• removed during RNA splicing

Exons

• coding sequences

RNA Splicing

• spliceosome: group of proteins that removes introns from transcripts

• occurs after transcription

Alternative Splicing

• creating multiple proteins from a single gene

Prokaryotic Gene Expression

• primarily controlled at the level of transcription

• translation and transcription occur simultaneously in the cytoplasm

Eukaryotic Gene Expression

• controlled at the levels of epigenetics, transcription, post-transcription, translation, and post-translation

• regulated during transcription and RNA processing (nucleus), protein translation (cytoplasm)

• further regulation can occur through post-translational modifications of proteins

Mobile Genetic Element

• type of DNA that can move around in the genome and plasmids

Plasmid

• a molecule of DNA found most often in bacteria that can replicate independently of chromosomal DNA

Vertical Gene Transfer

• receiving genetic material from an ancestor

Horizontal Gene Transfer

• transfer of genetic material between organisms without reproduction

  • can be inherited once added to genome

Pseudogenes

• nonfunctional

• often form after a gene has been duplicated and one or more of the redundant copies lose their function

Types of Mutation

• point mutation

• insertion

• deletion

• frameshift

• duplication

• inversion

• chromosome fusion

• aneuploidy

• genome duplication

Point Mutation

• a single base changes from one nucleotide to another (substitution)

Insertion

• a segment of DNA is inserted into the middle of an existing sequence

Deletion

• a segment of DNA is deleted

Frameshift Mutation

• insertion of 1 or 2 bases changes the codon, modifying all amino acids coded downstream

Duplication

• a segment of DNA is copied a second time

Inversion

• a segment of DNA is flipped around and inserted backwards into its original position

Chromosome Fusion

• two chromosomes are joined together

Aneuploidy

• chromosomes are duplicated or lost

Genome Duplication

• leads to increased ploidy

Cis-Acting Element

• a stretch of DNA located near a gene that influences the expression of that gene

Trans-Acting Element

• sequence of DNA located away from a gene (e.g. on another chromosome) that codes for a protein, microRNA, or other diffusible molecules that they influence gene expression

Somatic Mutation

• mutation that affects cells in the body of an organism

• not passed down to offspring in animals

Germline Mutation

• mutation that affects the gametes of an individual and can be transmitted from parents to offspring

• results in heritable genetic variation

Coding Region

• Type of Mutation

  • substitution, insertion, deletion, duplication

• Consequences for Gene Action

  • alter the product of the gene and thus its function or activity

Cis-Regulatory Regions

• Type of Mutation

  • substitution, insertion, deletion, duplication that alters the binding affinity of promoters, activators, repressors, etc.

• Consequences for Gene Action

  • alters the timing, location, or level of expression of the gene. Alters the developmental or environmental context in which the gene is expressed

Trans-Regulatory Regions

• Type of Mutation

  • mutation to coding regions of trans-acting factor

  • mutatiion to cis- or trans-regulatory regions of trans-acting factors

• Consequences for Gene Action

  • alters the binding affinity and thus the activity of a promoter, activator, repressor, etc.

  • alters where, when, or to what extent inhibitory, activating, or other trans-acting regulatory factors are expressed

Physiological Pathways (ex. Hormones)

• Type of Mutation

  • mutations altering where, when, or how much an endocrine signal is produced

• Consequences for Gene Action

  • alters the timing, location, or level of expression of the gene.

  • alters the developmental or environmental context in which the gene is expressed

Albinism is an example of what mutation?

point mutation

Independent Assortment

• ensures novel combinations of alleles

• genes are inherited independently of each other

Genetic Recombination

• generates variation

• during the production of gametes, each pair of chromosomes crosses over and exchanges segments of DNA

Genotype

• the genetic makeup of an individual

Phenotype

• an observable, measurable characteristic as the manifestation of the genotype of an organism

Polyphenic Trait

• single genotype produces multiple phenotypes depending on environment

Quantitative Traits

• have a continuous distribution of phenotypic variation

• influenced by multiple genes

• normal distribution

Quantitative Trait Locus (QTL)

• the analysis of such can help discover genes influencing quantitative traits

Environmental Influences on Gene Expression

• during development, cells respond to a multitude of signals from their environment

  • morphogen

  • phenotypic plasticity

Morphogen

• signaling molecule that flows between nearby cells

• alters the expression of target genes

Phenotypic Plasticity

• changes in phenotype produced by a single genotype in different environments

  • tailors organism to environment

Population Genetics

• the study of the distribution and frequencies of alleles in populations

• how and why allele frequencies change

Genetic Locus

• location of a specific gene or sequence of DNA on a chromosome

Homozygous

• individual carries two copies of the same allele at a locus

Heterozygous

• individual carries different alleles at a locus

Hardy-Weinburg Conditions

• no mutations

• mating is random

• no selection (equal survival)

• very large population size

• no gene flow in or out

Hardy-Weinberg Equation

Alleles:

• p = frequency of dominant allele

• q = frequency of dominant allele

• p + q = 1

Genotypes:

• p² + 2pq + q² = 1

• p² = frequency of homozygous dominant genotype

• 2pq = frequency of heterozygous genotype

• q² = frequency of homozygous recessive genotype

Microevolution

• an evolving population is one that is showing genetic change over generations

• Hardy-Weinberg lets us detect microevolution

Hardy-Weinberg Equilibrium Assumptions

• allele frequencies of a population will not change if:

  • population is infinitely large

  • genotypes do not confer differences in fitness

  • there is no mutation

  • mating is random

  • there is no migration

Are the Hardy-Weinberg Equilibrium assumptions reasonable?

• population is infinitely large

  • populations are always finite, but some are large enough to function nearly as though they are infinite

• genotypes do not confer differences in fitness

  • natural selection imposes differential survival and reproduction

• there is no mutation

  • mutation rates have been studied and are known

• mating is random

  • mating is assumed to be random at specific loci of interest

• there is no migration

  • this may occasionally be true but not often

What results in genetic drift?

• random sampling error

  • higher in a smaller sample

Genetic Drift Reduces Genetic Variation

• small populations experience strong drift

• some alleles become fixed in the population

• some alleles disappear

Bottlenecks

• reduce genetic variation

• results in nonrepresentative set of alleles for subsequent populations

  • even after population size rebounds

• rare alleles more likely to be lost during bottleneck event

Founder Effect

• a type of bottleneck resulting from a small number of individuals colonizing a new, isolated habitat

Fitness

• the survival and reproductive success of an individual with a particular

• components:

  • survival to reproductive age

  • mating success

  • fecundity

Relative Fitness (w)

• contribution of individuals with one genotype compared with the average contribution of all individuals in the population

Contribution of Alleles to Fitness

• fitness is a product of an organism’s entire phenotype, but this is difficult to assess

Average Excess Fitness

• difference between the relative contribution of individuals with one genotype and the average fitness of the population as a whole

• Δp = p x (a_A1/ϖ)

  • Δp = change in allele frequency due to selection

  • p = frequency of the A1 allele

  • ϖ = average fitness of the population

  • a_A1 = average excess of fitness for the A1 allele

In what kind of population is natural selection more effective in?

Large populations

Pleiotropy

• mutation in a single gene affects more than one phenotypic trait

• may constrain evolution

Antagonist Pleiotropy

• beneficial effects for one trait but detrimental effects for other traits

• net effect on fitness determines outcome of selection

Pesticide Resistance and Pleiotropy

• the frequency of the Ester¹ (resistance to pesticides) gene increased in response to the use of pesticides in coastal areas

• mosquitoes with this gene are more susceptible to predation by spiders

Pesticide Resistance and Antagonistic Pleiotropy

• Ester¹ raised the fitness of carriers in coastal areas because of insecticide use

• carrying this allele farther inland proved detrimental in escaping predation

Negative Selection

• alleles that lower fitness experience negative selection

Positive Selection

• alleles that increase fitness experience positive selection

What model is useful for running evolution experiments and why?

• bacteria

• haploid genetics are easier to study

• diploid genetics are more complex due to interactions between two alleles

Additive Alleles

• homozygous condition yields twice the phenotypic effect for the gene as compared with heterozygotes

Dominance

• dominant allele masks presence of recessive in heterozygote

Mutations Generate Variations in Populations

• mutation rates for any given gene are low

• per genome and population, many new mutations arise each generation

• source of variation upon which selection and drift act

Mutation-Selection Balance

• equilibrium frequency reached through “tug-of-war” between negative selection on deleterious alleles and new mutations

• explains persistence of deleterious mutations in populations

Balancing Selection

• selection that favors more than one allele

• maintains genetic diversity in a population by keeping alleles at frequencies higher than would be expected by chance or mutation alone

Negative Frequency-Dependent Selection

• common phenotypes are selected against

• rare phenotypes are favored

• heterozygote advantage

  • malaria and sickle-cell anemia

Inbreeding Coefficient (F)

• F = probability that two alleles at any locus of an individual are identical by descent

Inbreeding Depression

• results in reduced fitness

• rare recessive alleles are expressed in homozygous state

• high inbreeding associated with low infant survival rates

Population Subdivision

• depends on landscape features and the relative degree of motility of individuals in the population

• subdivided populations show distinct genetic structure (heterogeneity in allelic frequencies)