bio Genetics & Evolution

genes

which are DNA sequences that code for heritable traits that can be passed from one generation to the next.

Chromosomes

- contain GENES in a linear sequence

Alleles

• what are they

• what are different types

• what does each type mean/ connote

- alternative forms of a gene

- DOMINANT allele: requires only 1 copy to be expressed (capital letter)

- RECESSIVE allele: requires 2 copies (both) to be expressed (lowercase letter)

Genotype

• types of alleles

- combination of alleles one has at a given genetic LOCUS

refers to recessive genes which require two copies:

- HOMOZYGOUS: having 2 of the same allele

- HETEROZYGOUS: having 2 difft alleles

- HEMIZYGOUS: having only 1 allele (e.g. male sex chromosomes)

Locus

- the location of a gene on a chromosome

- normal locus of a particular gene is consistent among humans; a gene can be described by its location

Phenotype

- observable manifestation of a genotype, observable trait

Homologues

• relation to human beings

- copies of the same chromosome

- humans posses 2 copies of each chromosome (except male sex chromosomes -> one X and one Y)

Patterns of dominance

- COMPLETE DOMINANCE

- CODOMINANCE

- INCOMPLETE DOMINANCE

Complete dominance

- has 1 dominant allele & 1 recessive allele

When only one dominant and one recessive allele exist for a given gene, there is said to be complete dominance

- presence of 1 dominant allele will mask recessive allele, if present

Codominance

- has more than 1 dominant allele— think of it as they are BOTH dominant, hence co-dominace,both are present

. When more than one dominant allele exists for a given gene, there is codominance. For example, a person with one allele for the A blood antigen and one allele for the B blood antigen will express both antigens simultaneously.

e.g. AB blood type -> express both antigens stimultaneously

Incomplete dominance

- has no dominant alleles

- heterozygotes have intermediate phenotypes (mixture)

e.g. snapdragon flowers -> red + white = pink flower (RR x rr = Rr for all offspring, all pink)

Penetrance- 2 definitions

• what are the types of penetrance

- proportion of a population with a given genotype who actually express the phenotype i.e. probability that, given a particular genotype, a person will express the phenotype

- a population parameter

e.g. Huntington's disease

Full penetrance

- 100% of individuals with the allele show symptoms of the disease/phenotype

High penetrance

- most but not all with the allele show symptoms of the disease/corresponding phenotype

Less penetrance

- REDUCED PENETRANCE

- LOW PENETRANCE

- NONPENETRANCE

Expressivity

• what is it

• what are the types

- varying phenotypic manifestations of a given genotype

- if it's CONSTANT, then all individuals with the given genotype express the same phenotype

- if it's VARIABLE, then individuals with the same genotype may have difft phenotypes

- considered mostly at the individual level

e.g. disease -> range of phenotypic presentations btwn no clinical effect & severe disability

Mendel's Laws

• what do they do

- help explain the inheritance of genes from parent to offspring

Mendel's First Law (of segregation)

- an organism has 2 alleles for each gene, which segregate during meiosis, resulting in gametes carrying only 1 allele for a trait

- key: separation of homologous chromosomes during anaphase I of meiosis

1) genes exist in alternative forms called ALLELES

2) an organism has 2 alleles for each gene, one inherited from each parent

3) the 2 alleles segregate during meiosis, resulting in gametes that carry only 1 allele for any inherited trait

4) if 2 alleles of an organism are difft, only 1 will be fully expressed & the other will be silent -> the expressed allele = dominant; silent allele = recessive (codominance or incomplete dominance = exceptions)

Mendel's Second Law (of independent assortment)

- the inheritance of one allele does not influence the probability of inheriting a given allele for a difft trait

- RECOMBINATION results in novel combinations of alleles that were not present in original chromosomes

- thus, inheritance of one gene = independent of inheritance of others

problem: LINKED GENES

Recombination

- due to crossing over, a combining of genes or characters different from what they were in the parents

Key concept about Mendel's Laws

- segregation & independent assortment allow for greater genetic diversity in the offspring!!

Support for DNA as genetic material

3 experiments!

- GRIFFITH EXPERIMENT

- AVERY-MACLEOD-MCCARTY EXPERIMENT

- HERSHEY-CHASE EXPERIMENT

Griffith experiment

- demonstrated the TRANSFORMING PRINCIPLE: mouth injected with live nonvirulent bacteria + dead virulent bacteria => the live nonvirulent bacteria converted into virulent bacteria by exposure to dead virulent bacteria -> the live, nonvirulent bacteria must have acquired ability to form smooth capsules from the dead virulent bacteria

Transforming principle

- substance responsible for transformation

- DNA is the transforming principle

Transformation

- process in which one strain of bacteria is changed by a gene or genes from another strain of bacteria

Avery-MacLeod-McCarty experiment

- demonstrated that DNA = genetic material b/c degradation of DNA led to cessation of bacterial transformation

• declared that the transforming substance was DNA. this was NOT determined by the previous experiment

Hershey-Chase experiment

- confirmed that DNA = genetic material b/c only radio-labeled DNA could be found in bacteriophage-infected bacteria

What does it mean for an allele to be dominant? Recessive?

Dominant: requires only 1 copy for expression

Recessive: requires 2 copies for expression

What does it mean for a genotype to be homozygous? Heterozygous? Hemizygous?

Homozygous: 2 of the same allele

Heterozygous: 2 difft alleles

Hemizygous: only 1 allele is present for a given gene (e.g. X/Y male sex chromosome)

What is the difference btwn complete dominance, codominance, & incomplete dominance?

Complete dominance: gene has only 1 dominant allele & 1 recessive allele

Codominance: gene has more than 1 dominant allele & 2 difft dominant alleles can be expressed simultaneously (e.g. AB blood type)

Incomplete dominance: gene has no dominant alleles; heterozygotes = intermediate/mixture of homozygous phenotypes

What is the difference btwn penetrance & expressivity?

Penetrance: proportion of population with a particular genotype to actually express the phenotype; a population parameter (%)

Expressivity: the differences/variations in phenotypic expression (severity, location, etc.) across those with a particular genotype; more focused on individual level

With what phase of meiosis does each of Mendel's laws most closely correlate?

1st law: anaphase I of meiosis -> segregation of homologous chromosomes

2nd law: prophase I of meiossi -> crossing over of segments on homologues -> independent assortment of alleles

Gene pool

- all of the alleles (different versions of genes that exist) in a given population

- when mutations or genetic leakage occurs, new genes are introduced into gene pool

Mutations

Wildtype

- changes in DNA sequence that results in a mutant allele

- variety of causes: ionizing radiation (UV rays), chemical exposures, etc.

-. Mutant alleles can be contrasted with their wild-type counterparts, which are alleles that are considered “normal” or “natural”

Mutagens

- substances that cause mutations

Transposons

- chromosomal elements that can insert & remove themselves from the genome -> can disrupt genes

Nucleotide mutations

- POINT MUTATIONS (substituting of one nucleotide for another)

- FRAMESHIFT MUTATIONS (moving the 3-letter transcriptional reading frame) -> more severe usually

Point mutations and types

- substituting of one nucleotide for another

- e.g. SILENT, MISSENSE, NONSENSE

Silent mutation and how does it usually occur

- has no effect on the protein's amino acid sequence/structure/function

- most common when the changed nucleotide = 3rd nucleotide in a codon (DEGENERACY/WOBBLE)

• In genetics, degeneracy refers to the phenomenon where multiple codons (three-nucleotide sequences in mRNA) can code for the same amino acid. Wobble describes the ability of a single tRNA molecule to recognize more than one codon due to relaxed base pairing rules at the third position of the codon (the "wobble position").

Missense mutation

- substitution of one amino acid for another in the final protein

Nonsense mutation

- substitution of a stop codon for an amino acid -> translation terminates early (premature truncation of protein)

Frameshift mutations

• occur due to what

• what is the result

- occur due to insertion/deletion of nucleotide(s) from the genome -> shift in READING FRAME

- moving the 3-letter transcriptional reading frame

Insertions & deletions

- result in a shift in the READING FRAME, leading to changes for all downstream amino acids

- cause frameshift mutations

Chromosomal mutations

- much larger-scale mutations affecting whole segments of DNA

e.g. DELETION, DUPLICATION, INVERSION, INSERTION, TRANSLOCATION

Deletion mutations

- when a large segment of DNA is lost from a chromosome

Duplication mutations

- when a segment of DNA is copied multiple times in the genome

Inversion mutations

- when a segment of DNA is reversed within the chromosome

Insertion mutations

- when a segment of DNA is moved from one chromosome to another

Translocation mutations

- when a segment of DNA on one chromosome is swapped with a segment of DNA from another chromosome

Consequences of mutations

- ADVANTAGEOUS (positive selective advantage)

- DELETERIOUS (defect -> can cause disease)

- INBORN ERRORS OF METABOLISM= defects in genes required for metabolism -> can cause buildup of metabolites, causing serious health concerns

Genetic leakage

- flow of genes btwn species through HYBRID offspring

Hybrid offspring

- individuals from different but closely related species can mate and form this

e.g. the mule (hybrid of male horse & female donkey) -> not able to reproduce, but in some cases, hybrid can reproduce with members of one species or the other

Genetic drift

- occurs when the composition of the gene pool changes due to chance

- random change in allele frequencies that is more pronounced in small populations

- decreases genetic diversity

e.g. the last green-eyed person in a small town dies, leaving only brown-eyed and blue-eyed people

Founder effect

- extreme case of genetic drift

- a small population of a species finds itself in reproductive isolation from other populations as a result of natural barriers, catastrophes, or other BOTTLENECKS that drastically & suddenly reduce the size of the population available for breeding -> leads to INBREEDING (mating btwn 2 genetically related individuals) -> inbreeding leads to increased prevalence of homozygous genotypes (both dominant & recessive)

- genetic drift, founder effect, & inbreeding => reduction in genetic diversity -> this is why a small population may have increased prevalence of certain traits & diseases -> may cause reduced fitness of population, known as INBREEDING DEPRESSION

Inbreeding

- mating btwn closely related people or animals

Outbreeding

- introduction of unrelated individuals into a breeding group -> increases variation of gene pool and fitness of the population

Bottlenecks

- drastically and suddenly reduce the size of the population available for breeding

What are the 3 main types of point mutations? What change occurs in each?

1) Silent

2) Missense

3) Nonsense

What are the 2 main types of frameshift mutations

1) Insertion

2) Deletion

What are the 3 main types of chromosomal mutations that do NOT share their name with a type of frameshift mutation? What change occurs in each?

1) Duplication: segment of DNA copied multiple times

2) Inversion: segment of DNA inverted

3) Translocation: segment of DNA one chromosome swapped with that of another chromosome

Why would genetic leakage in animals be rare prior to the last century?

- genetic leakage requires formation of a hybrid organism that can then mate with members of one or the other parent species

- while hybrids exists historically (esp. mules), fertile hybrids were certainly rare before more modern understanding of genetics (& a commercial, financial, or academic impetus to create these organisms)

unlikely for animals to choose mates outside of their species

Why is genetic drift more common in small populations? What relationship does this have to the founder effect?

- genetic drift occurs due to change, so its effects will be more pronounced with a smaller sample size (in smaller populations)

- the founder effect occurs when a small group is reproductively isolated from the larger population, allowing certain alleles to take on a higher prevalence in the group than the rest of the population

Punnett squares

- visually represent the crossing of gametes from parents to show relative genotypic & phenotypic frequencies

Parent generation (P generation)

- represented by P

Filial (offspring) generations (F generation)

- represented by F1, F2, & so on

Monohybrid cross

- accounts for 1 gene

Key concept about monohybrid crosses with complete dominance

- Crossing 2 heterozygotes for trait with complete dominance: 1:2:1 ratio of genotypes (homozygous dominant:heterozygous dominant:homozygous recessive) & 3:1 ratio of phenotypes (dominant:recessive)

- the more offspring that parents have, the closer their ratios will be to expected ratios

Test cross aka back cross

- used to determine an unknown genotype

- organisms with an unknown genotype is crossed with an organism known to be homozygous recessive

- if offspring all dominant, unknown genotype = likely homozygous dominant

- if offspring is 1/2 dominant, 1/2 recessive, unknown genotype = likely heterozygous

Dihybrid cross

- accounts for 2 genes

- rmbr Mendel's 2nd law (of independent assortment): inheritance of one gene = independent of inheritance of the other -> holds true for UNLINKED GENES

- creates 4 x 4 Punnett Square

Key concept about dihybrid crosses with complete dominance

- 9:3:3:1 distribution phenotype

• each individual trait will have the 3:1 phenotypic ratio from before

e.g. tall (dominant) vs. short, purple (dominant) vs. white

- 9 tall, purple

- 3 tall, white

- 3 short, purple

- 1 short, white

If we cross two plants that are heterozygous for both traits, then the offspring have a phenotypic ratio of 9:3:3:1 (9 tall and purple:3 tall and white:3 dwarf and purple:1 dwarf and white). Note that the 3:1 phenotypic ratio still holds for each trait (12 tall:4 dwarf and 12 purple:4 white), reflecting Mendel’s second law.

Sex-linked

• what chromosome are they usually on and what is the memory device

• how many of this chromosome do men have? how many do women have? what is the relevance

• how to indicate sex-linked traits

• what is a carrier

• On the MCAT, sex-linked is X-linked. Further, unless told otherwise, assume that sex-linked traits are recessive.

• women have two x chromosomes, men have one x chromosome, sex-linked traits are much more common in males; having only one recessive allele is sufficient for expression of the recessive phenotype.

• When writing genotypes for sex-linked traits, we use X and Y to symbolize normal X and Y chromosomes. An X chromosome carrying a defective allele is commonly given a subscript, such as X_h, to indicate the presence of the disease-carrying allele.

• an individual who has one copy of a mutated gene responsible for a genetic condition but does not exhibit the condition themselves

Key concept about sex of children

- b/c egg necessarily carries an X chromosome, it is the sperm that determines sex of child

- men with a sex-linked trait will have daughters who are all either carriers of the trait or who express the trait (if partner also has an affected allele), but the man can never pass down a sex-linked trait to his son—- a man’s x chromosome comes from his mother, only get Y from his dad— draw out the punnett square and see

Hemophiliac

- X-linked disease -> those who have it suffer from a disease that causes uncontrolled bleeding

Recombination frequency

- likelihood of 2 alleles being separated during crossing over in meiosis -> proportional to the distance btwn the genes on the chromosome

- the further apart 2 genes are, the more likely that there will be a CHIASMA (point of crossing) btwn them

- strength of linkage btwn genes based on recombination frequency: tightly linked genes have recombination frequencies approaching 50%, as expected from independent assortment

- the proportion of recombinant individuals: 50% for unlinked genes; < 50% for linked genes.

Genetic maps

- made using recombination frequency as the scale

- represents relative DISTANCE btwn genes on a chromosome

- maps units: CENTIMORGANS

- can be used to approximate order of genes in chromosome (since map units = roughly additive)

Centimorgan

- in genetic mapping, a map unit (centimorgan) = a recombinant frequency of 0.01: a 1% chance of recombination occurring btwn the 2 genes

- a MAP UNIT

- roughly additive

e.g. if genes were 25 map units apart, we expect 25% of the total gametes examined to show recombination somewhere btwn the 2 genes

Allele frequency

- how often an allele appears in a population

Hardy-Weinberg principle

- if a population meets certain criteria (aimed at a lack of evolution), then the ALLELE FREQUENCIES will remain constant (HARDY-WEINBERG EQUILIBRIUM)

- in a stable environment, the allele and genotype frequencies of a population will remain constant

5 criteria must be met:

1) population is very large (no genetic drift)

2) no mutations that affect the gene pool

3) mating btwn individuals in the population is random (no sexual selection)

4) no migration of individuals into or out of population

5) genes in the population are all equally successful at reproducing

Hardy-Weinberg equation

2 possible alleles: T and t

p = frequency of dominant allele T

q = frequency of recessive allele t

- b/c there are only these 2 choices at the same gene locus: p + q = 1 (combined allele frequencies of T & t must = 100%)

- squaring both sides: p^2 + 2pq + q^2 = 1

p^2 = frequency of TT (homozygous dominant) genotype

2pq = frequency of Tt (heterozygous hominant)

q^2 = frequency of tt (homozygous recessive)

note: p^2 + 2pq = frequency of dominant PHENOTYPE

p + q = 1

- tells us about the frequency of the ALLELES in the population

p^2 + 2pq + q^2

- tells us about the frequency of GENOTYPES & PHENOTYPES in the population

- rmbr that there will be twice as many alleles as individuals in a population - b/c each individual has 2 autosomal copies of each gene

- these equations also can tell us when evolution is NOT occurring in a population

All 5 characteristic of Hardy-Weinberg principle are required to imply what characteristic of the study population?

- no evolution

Natural selection

- chance variations exist btwn individuals & advantageous variations (those that increase an individual's FITNESS for the envt) afford the most opportunity for reproductive success

- "survival of the fittest"

- organisms that possess FAVOURABLE adaptations pass them on to the next generation

Key concept on evolution vs. natural selection

- EVOLUTION is not equivalent to NATURAL SELECTION

- natural selection is simply a MECHANISM for evolution

- natural selection is equivalent to SURVIVAL OF THE FITTEST

Modern synthesis model (neo-Darwinism)

- theory that combines Darwinism and genetics

- when MUTATION or RECOMBINATION results in a change that is favourable to the organism's reproductive success, that change is more likely to pass on to the next generation

- accounts for mutation & recombination as mechanisms of variation

- considers DIFFERENTIAL REPRODUCTION as mechanism of reproductive success

NOTE: gene pool changes over time -> it is populations that evolve, not individuals

Differential reproduction

- organisms with the best adaptations are most likely to survive and reproduce

Inclusive fitness

- measure of an organism's success in the population

- based on the # of offspring, success in supporting offspring, & ability of the offspring to then support others

- survival of offspring or relatives ensures continuation of genes in subsequent generations

- takes into account benefits of certain behaviours on the population at large e.g. altruism, protecting the offspring of the group at large (even by sacrificing themselves)

Punctuated equilibrium

- considers evolution to be a very slow process with intermittent rapid bursts of evolutionary activity

Difft types of selection lead to changes in phenotypes:

- STABILIZING SELECTION

- DIRECTIONAL SELECTION

- DISRUPTIVE SELECTIVE

- ADAPTIVE RADIATION

Stabilizing selection

- keeps phenotypes in a narrow range, excluding extremes

- natural selection that favours intermediate variants by acting against extreme phenotypes

e.g. human birth weight

Directional selection

- moves the avg phenotype toward one extreme

e.g. a plate of bacteria -> a few bacteria that have resistance to antibiotics -> only they will survive once antibiotic is introduced to plate -> new standard phenotype emerges as result of differential survivorship

Disruptive selection

- moves toward 2 difft phenotypes at the extremes

- can lead to SPECIATION

e.g. Darwin's finches on Galapagos Islands -> beaks either large or small (no intermediate) -> reasons: sizes of seeds on island (food source for finches) either quite large or quite small

Adaptive radiation

- related concept to disruptive selection

- rapid emergence of multiple species from a common ancestor, each of which occupies its own ecological NICHE -> decreases competition for limited resources

Niche

- role of how an organism fits into its habitat

- specific way of life, including habitat location & utilization of resources

Species

- group of organisms capable of breeding to form fertile offspring

- species are REPRODUCTIVELY ISOLATED from e/o by PRE- or POSTZYGOTIC MECHANISMS

Speciation

- formation of a new species through evolution

Reproductive isolation

- when the progeny of separated populations (which were originally same species) can no longer freely interbreed

- we would then consider the 2 groups separate species

Prezygotic mechanisms

- prevent formation of zygote completely

e.g. temporal isolation (breeding at difft times), ecological isolation (living in difft niches in same territory), behavioural isolation (lack of attraction btwn members due to differences in pheromones, courtship displays, etc.), reproductive isolation (incompatibility of reproductive anatomy), or gametic isolation (intercourse can occur, but fertilization cannot)

Postzygotic mechanisms

- allow for gamete fusion but yield either nonviable or sterile offspring

e.g. hybrid inviability (zygote cannot develop to term), hybrid sterility (hybrid offspring cannot reproduce), hybrid breakdown (forming first-generation hybrid offspring that are viable & fertile, but 2nd-generation are inviable/infertile)

e.g. mules (sterile)

Patterns of evolution (3)

- similarities btwn 2 species -> may be due to sharing a common ancestor or sharing a common envt with same evolutionary pressures

1) DIVERGENT EVOLUTION

2) PARALLEL EVOLUTION

3) CONVERGENT EVOLUTION

Divergent evolution

- occurs when 2 species sharing a common ancestor become more difft

- independent development of dissimilar characteristic 2 or more lineages sharing a common ancestor

e.g. seals & cats are both mammals in the order Carnivora -> these two species live in very difft environments & adapted to difft selection pressures while evolving

Parallel evolution

- occurs when 2 species sharing a common ancestor evolve in similar ways due to analogous selection/environmental pressures