Evans 2C03

chpts 1-9,12,13

What is genetics

sub-field of biology thatinvestigates genotypicand phenotypic variationamong organisms, howthis variation is inherited,how they are linked toeach other, and how theyevolve

Why is Genetics Important?

Genetics is fundamental tounderstanding and treatmentof disease; biotechnology;drug design, development, &production•Many applications to agriculture, domestic animals, invasive species,conservation biology,criminology• Crucial insights into evolutionof humans and beyond

Mendelian genetics

investigates the transmission oftraits in successive generations

Molecular genetics

studies the inheritance, expression,and variation of nucleic acids and proteins

Evolutionary genetics

examines the origins of andgenetic relationships among organisms and theevolution of genes and genomes

Gene

A region of DNA with some biological function

Allele

One of two or more alternative forms of a gene

Locus

Specific place on a chromosome occupied by anallele (sometimes used synonymously with "gene")

Genotype

Combination of alleles at one or more locipossessed by an individual organism

Heterozygote

An individual organism possessing two differentalleles at a locus (for diploid or higher ploidyorganism)

Homozygote

An individual organism possessing the same allelesat a locus

Phenotype or Trait

physical form of a biological characteristicresulting from the interaction between a genotypeand the environment

• Jim's blood genotype is AA• Jill's blood genotype is AB• Jack's blood genotype is AO• Joanne's blood genotype is OO
- Whose blood genotype(s) is homozygous?- Which combination of genotypes would produce the mostgenotypic variation in offspring (and how many possiblegenotypes)?- If alleles A and B are co-dominant, which combination ofgenotypes would produce the most phenotypic variation inoffspring (and how many phenotypes would there be)?

a) Jim, Joanne
b) Jill x Jack; 4 genotypes (AA,AO,AB,BO)
c)Jill xJack; 3 phenotypes: A, AB, B

How long have humans used genetics?

Knowledge and use ofGenetics is ancient
• Humans have been awareof genetics, via selectivebreeding, for \>10,000years
• Selective breeding of rice,maize, wheat, anddomesticated animals wasused to enhancementdesirable traits

Developments in 'Modern' Genetics
1900s -?

Early 1900s and earlier: Localization of geneticmaterial (visualization of chromosomes, developingconcept of a gene and inheritance, understanding ofvariation in ploidy, identification of organelles,understanding cell division - meiosis and mitosis)• Mid 1900s: Identification of DNA, understandingDNA structure and replication• Mid to late 1900s until the present: Understandinghow genetic information is processed (transcription,translation, genetic regulation); advent of geneticengineering• Last few decades: Genomics era (sequence andanalysis of complete genomes, advances in geneticmanipulation; CRISPR!!!)

Overview of Molecular Genetics- who discorvered DNA structure

Watson and Crick in 1953
Changes(mutations) in DNAsequence are linkedto phenotypicvariation6

DNA Structure

nucleotides in DNA - A,C, G, T
Site of phosphodiester bond - 3' OH group and 5' phosphate group
Strands have polarity and areantiparallel
Complementary base pairs - AT, CG
purines - adenine, guanine (2 rings)
pyrimidines - cytosine, thymine, uracil (1 ring)

Chargaff's rule

percentages of adenineand thymine areapproximately equal andthe same for cytosine andguanine

What is semi-conservative DNA?

Two complementarystrands separate and eachacts as a template for thesynthesis of a newcomplementary strand

practice problem
What is the difference between polarity andantiparallel with respect to the structure of DNA?a. Polarity refers to DNA being negativelycharged and antiparallel refers to theinteractions with transcription factors
b. Polarity refers to the 5' to 3' structure of DNAwhereas antiparallel refers to the hydrogenbonds being perpendicular to thephosphodiester bonds
c. Polarity refers to the orientation of the 3' and5' carbons of DNA whereas antiparallel refersto the double strands having opposite polarity

c

Central Dogma of Molecular Biology

doesn't really flow back and forth and redo between DNA, RNA, and protein
DNA --\> RNA --\> ProteinDNA replication --\> RNA transcription --\> protein translation
special- RNA replication viruses (RNA recreates itself)- Prions, inteins, posttranscriptional modification (protein remakes itself)- Reverse trancription (RNA into DNA)

Transcription

one strand of DNA to directsynthesis of a single-stranded RNA
5' to 3' direction
U in mRNA replace T
Some RNA is translated into protein; other RNA isnot translated and has enzymatic or regulatoryfunction as RNA - without encoding protein

Regulation of transcripton
(hint: promoters, exons, introns)

Promoters do not get transcribed - theycontrol the transcription of downstreamregions•In Bacteria and Archaea, one promotor canregulate transcription of multiple genes
eukaryotes, genes may have exons and introns;introns are removed before translation (splicing)In most genes in Bacteria and Archaea, there is onlyone exon (no splicing).Some exons contain "UTRs" (untranslated regions).Exons may be completely or partially translated

Translation

Nucleotides have a non-overlapping, triplet codonthat encodes the sequence of amino acids in proteins

Practice questionsWhich of these examples of informationtransfer between information containingbiomolecules are uncommon or nonexistent inmost organisms? Please choose more thanone if needed.a. DNA to proteinb. DNA to RNAc. RNA to proteind. Protein to DNAe. Protein to RNA

a.d.e.

What are the three major types of information-carrying biopolymers?

DNA, RNA, protein

What are the three major types of informationexchange between these information carryingbiopolymers? What does each one mean?

Replication, transcription, translation

Do all exons encode protein?

No, some exons have 5'UTRs or 3'UTRs

Are all enzymes made up of amino acids?

No, there are also RNA enzymes

Theory of Evolutionby Natural selection

to occur youneed: (1) variation, that is (2) heritable, and (3)influences fitness
If certain heritablecharacteristics lead toincreased success inproducing offspring, thenthese traits becomemore common in thepopulation over time

Major Forces Impacting Evolution

sources of genetic variation to population-environment interaction leads to allele frequenices changed (evolution)
sources of genetic variation - mutation, recombination, gene flow (migration, lateral gene transfer)
population-environment interaction - natural selection (adaptive) and genetic drift (non-apative)

Mendelian Genetics
How does inheritance of one phenotype that is governed by one genework?

recessive and dominant
mendel studied seed with 7 traits with 2 states (dichotomous states). either dominant or recessive phenotypes so easy to distinguish.
start with 'pure breed' strains (self-pollination). then cross-pollinate.
P - parents, F1 generation (self-fertilized) F2 - (self-fertilized)
phenotypic ratio varied among generations• This was used to demonstrate segregation of alleles

Mendel's Results for one gene

monohybrid cross isa cross between twoorganisms withdifferent phenotypescontrolled by onegenetic locus ofinterest.The parentalindividuals arehomozygous fordifferent alleles ("purebreeding")
When two purebreeding lines arecrossed, 100% of theresulting F1 generationhas the dominantphenotype• When individuals fromthe F1 generation self-fertilized, thephenotypic ratio of theF2 generation is ~3:1
test cross is when anindividual with a dominantphenotype is crossed witha homozygous recessiveindividual in order todetermine whether thedominant phenotype isdue to a homozygous orheterozygous genotype (hetero parent if offspring is 50:50 hetero and recessive)
If the dominant phenotype is due to a heterozygousgenotype, the phenotypicratio of the test cross is 1:1

What proportion of thetest cross offspring wouldhave the dominantphenotype of the parentwere due to a homozygous genotype?

100% - each offspring is heterozygous with dominant and recessive allele, and only dominant trait would show

Mendel's law of segregation:

alleles of an individual separate during theformation of gametes
Diploid individuals have two versions of eachgene (alleles)Each gametes contain sonly one of these alleles

How does inheritance of multiple phenotypes that are each governedby different geneswork?

some inhibit each other
epistatsis

What if a phenotype that Mendel studied weredetermined by two genes instead of one? Howwould this affect the offspring phenotypeproportions?

The short answer is that it could make theoffspring ratios different from ratioscontrolled by one gene
The two gene offspring ratio would dependon how the genes interacted.
epistasis

Mendel's results for two genes

A dihybrid cross is across between parentsthat are heterozygous attwo different genes thatcontrol two differentphenotypes.
The doubleheterozygotes aregenerated by crossingtwo lines that are purebreeding for two traits
A dihybrid cross can alsooccur via self-fertilizationof an individual that isheterozygous at twogenes

Why are 9 different genotypes expectedfrom a dihybrid cross?

RrGg - RRGG, RrGG, RRGg, RrGg, rrGG, rrGg, RRgg, Rrgg, rrgg
expected phenotypic ratio of a dihybridcross is 9:3:3:1R-G-: R-gg: rrG-: rrgg

Mendel's law ofindependent assortment

he allelesof two (or more)different genes getsorted into gametesindependently of oneanother*
* This is only true of the genes are"unlinked" - i.e., on differentchromosomes or far enough away fromeach other on the same chromosome thatrecombination makes their inheritanceindependent

ractice questionConsider a dihybrid cross between twoindividuals with this genotype: AaBb, where A isdominant over a and B is dominant over b. Howmany individuals with the AABb genotype wouldyou expect?
a. 25%b. 12.5%c. 6.25%d. This genotype is not possible in the offspring

b.
This is because the probability of the AA genotype from Aa x Aaparents is 25% and the probability of a Bb genotype Bb x Bbparents is 50%. Thus the probability of AABb is 0.25*0.50 = 12.5

In the previous question, would the answer differif a were dominant over A instead of vice versa?

No; dominance affects phenotypes, notgenotypes and the question asked aboutgenotypes only

Probability Theory Predicts Mendelian Ratios

Product rule and sum rule

Product Rule

If two or more events are independent of oneanother, the probability of both of them occurringsimultaneously or consecutively is the product oftheir individual probabilities

Sum Rule

If two or more events are independent of oneanother and can not both occur at the same time(they are mutually exclusive), then theprobability of one of them occurring is the sum oftheir individual probabilities

practice problem
What is the probability that a couple will havetwo daughters in a row? What rule are you usingfor this question?

= probability of first child being a daughter ANDprobability of second child being a daughter= probability of first child being a daughter *probability of second child being a daughter= 0.5 * 0.5= 0.25

What is the probability of getting an odd numberwhen you roll a six-sided dice? What rule areyou using for this question?

= probability of 1 OR 3 OR 5= probability of rolling a 1 +probability of rolling a 3 +probability of rolling a 5= 1/6 + 1/6 + 1/6 = 0.5Sum Rule

What is the probability of an offspring from a dihybridcross having a homozygous recessive genotype atboth loci? What rule are you using for this question?

= probability of a recessive allele at the first genefrom the first parent *probability of a recessive allele at the first genefrom the second parent *probability of a recessive allele at the secondgene from the first parent *probability of a recessive allele at the secondgene from the second parent
= 0.5 * 0.5 * 0.5 * 0.5 = 0.0625
Product Rule

What is the probability of an offspring from a dihybridcross having homozygous genotypes at both genes(either both homozygous dominant or bothhomozygous recessive)? What rule are you using forthis question?

= 0.0625 + 0.0625
Product Rule to get probability of each double homozygous genotype, then the Sum Rule to getthe probably of either double homozygous genotype

How can we evaluate Mendel's interpretation when the offspringnumbers are not exactlypredicted?

chi square test
provides a way to test whether observed countdata depart significantly from expectations

Chi-Square Analysis Tests the Fit between Observed and Expected Outcomes
whats the formula

chi-square (X2) test was developed to compare experimental observation with anexpected outcome
X^2 = sum of(O-E)^2 / E
O = observed valuesE = expected values

How to use a chi-square table?

determine whether our observed values depart significantly from the expected values, we compare the X2 value calculated from the formula to a "critical value" that is obtained from a statistical table.
critical value" is based on (1) the degrees offreedom and (3) the probability threshold (a) for the null hypothesis to be true. Below this probability we favour the alternative hypothesis. (a is often set at 0.05)

Interpreting Chi-Square Test Results

probability (P) value depends on X2 value and degrees of freedom
X2 value; higher X2 values mean the null hypothesis of no difference between observed and expected is less likely, so P is lower(accept null hypthesis if X2 value is less than P value (not significantly different), accept alternative hypthesis if X2 is greater than P value)
degrees of freedom (df); this is thenumber of independent values in the data;more degrees of freedom means the c2 valuemust be higher to reject the null hypothesis
degrees of freedom = \# outcomes - 1

example.monohybrid cross (Rr ́ Rr), where the Rallele is dominant for round seeds and the r allele isrecessive for wrinkled seeds, Mendel observed atotal of 7324 seeds: 5474 round and 1850 wrinkled

ratio expected by the law of segregation forthe proportions of round (RR or Rr) and wrinkled (rr)phenotypes is 3:1
Thus, the expected counts are:(7324)(3/4) = 5493 round (7324)(1/4) = 1831 wrinkled
X^2 = (5474 - 5493)^ 2/5493 + (1850 - 1831)^2/1831 = 0.263
degrees of freedom (df) equals 1 becausethere are two possible outcomes anddf = \# outcomes -1
a (propability threshold) =0.05
df = 1, and a = 0.05, is 3.84X^2 = 0.263 < 3.84
P value falls between a = 0.50 and 0.70, well above the critical value of 0.05. Thus, we are unable to reject the expectationassociated with the "law of segregation"

practice problem:Hypothesis:• Yellow seed colour (G) is dominant over green(g) in peas• During gametogenesis of a heterozygote Gg,alleles G and g segregate in equal frequenciesin gametes• During fertilization, G and g gametes fertilizeeach other randomly
observedyellow - 5448green - 1881total = 7329
• What is the expected phenotype ratio?• What are the expected counts (E)• What is the Chi-square value?• What is the degree of freedom?• What is the P value?

expectedyellow - 7329 * (3/4) = 5497green - 7329 * (1/4) = 1832
3:1(5448-5497)^2/5497+(1881-1832)^2/1832 = 1.77
df= 1
~0.15 (not significantly different)
P value falls between 0.20 and 0.10, which is above the critical value of 0.05• Thus, again we are unable to reject the expectationassociated with the "law of segregation"

Where are the genes controlling traitsof Mendel's peas located?

on the same chromosome

Two phenotypes are controlled by genes onchromosome 1 and three are controlled by geneson chromosome 4... why then didn't Mendel see anon-random association between the alleles ofthese different genes (genetic linkage)? In otherwords, why did Mendel observe "independentassortment" of alleles at these genes?

The reason is that these genes are sufficiently farapart on the same chromosome thatrecombination occurs frequently enough that thealleles on each gene are not associated.

why do alleles of Mendel's peas have different phenotypes.

Seed shape - dominant allele produces enzyme, mutant recessive allele can't produce enzyme (loss of function)
seed colour - dominant allele has enzyme that that catalyzes yellow colour, mutant recessive allele prevents cataclusis so it maintains green colour

human karyotype

humans - 22 autosome chromosomes and 1 sex chromosome

Autosomal Inheritance in Humans

ransmissionof genes carried on autosomes -chromosomes found in both males andfemales in equal numbers and representations
In humans, there are 22 pairs of autosomes.A 23rd pair of chromosomes is the sex chromosomes (females are XX, males XY)

pedigree symbols

circle - femalesquare - male
white - do not express trait (could still be carriers though)black - express trait

Pattern of Inheritance for Autosomal Dominant Traits

Equal or similar frequency in males and females• Each individual with the trait has at least one parent with thetrait• Either sex can transmit the trait to an offspring• If neither parent has the trait, none of their offspring will• Even if both parents have the trait, they may produceoffspring who do not have it

black circle and and square produce white shaped kids, how?

Parents with a dominant phenotype that produce offspringwith a recessive phenotype must be heterozygous

Pattern of Inheritance forAutosomal Recessive Traits

Equal frequency in males and females• If both parents have the trait, all offspring also will have it• The trait is often not seen every generation but frequentlyseen among siblings in the same generation

Different ploidy levels have different chromosomal complements (Hint: diploid and haploid life, blend of dominance)

humans have 23 chromosomes, and we are 2N : 2 copies of genetic material subdivided into chromosomes
homologous chromosomes contain same genes in the same order
humans spend their life mostly as diploid, BUT for short period we are haploid (sperm and egg - between meiosis and fertilization)
Most fungi and some unicellular eukaryotes have a haploid-dominant life cycle, in which the mature, ecologically importantform—is haploid

Meiosis vs. Mitosis

Somatic cells are diploid (2n), and replicate by mitosis
• Gametes are haploid (n), produced from germ-line cellsthrough meiosis• Gametes have half the number of chromosomes as theoriginal cell• Meiosis produces gametes that are not geneticallyidentical to one another (because of chromosomalsegregation and recombination)

cell division

tightly regulated process
Too little cell division preventsappropriate development and growth• Too much leads to cancer, morphologicalanomalies, and death• Cell division consists of sequentialstages called the "cell cycle"

Mitotic Cell cycle

somatic cells
M phase: cell division occurs (mitosis or meiosis)• Interphase: longerperiod between celldivisions, includingchromosome replication• G0 : cell division isarrested; cell remainsspecialized but no longerdivides and eventuallydies (apoptosis)

interphase: G1

active gene expression and cell activity

interphase - s

DNA replication and chromosome duplication

interphase - G2

preparation for cell division

how does mitosis divide somatic cells

The nucleolus is where ribosome subunits are assembled
• The centrosome is an organelle where spindle fibers form that contains two microtubule structures called centrioles
• The kinetochore is a disc-shaped structure where spindle fibers attachto pull sister chromatids apart
chromosomes align on metaphase plate
sister chromatids seperate during anaphase

What is a chromosome?

telomeres at the end.
centromere connects the short and long leg.
1 chromsome can include a single chromatid or sister chromatids
spindle microtubles connects at the kinetochose at the centromere.

nuclear content of human cell in MITOTIC cell cycle (G1, S, Mitosis)

\# of chromsomes: throughout is 46
\# of chromatids. G1 - 46, S - 92, Mitosis - 46

Cell cycle checkpoints

crucial to ensure the cell contains the necessary requirements. if failed that cell death - apoptosisif it doesnt function can lead to cancer

metaphase checkpoint

pass if all chromosomes are attached to mitotic spindle

G1 checkpoint

pass if cell size is adequate, nutrient availability is sufficient, and growth factors (signals from other cells) are present

S phase checkpoint

Pass if DNA replication is complete and has been screened to remove base-pair mismatch or error

G2 checkpoint

pass if cell size is adequate and chromosome replication is successfully completed

meiosis

Gametes (sperm, eggs) are created by aspecial type of cell division
gametogenesis undergoes meiosis twice
begins with a diploid precursor cell that was generated by mitosis.Chromatids are then duplicated, but remain connected to each other at centromere.The first round of cell divisionoccurs (Meiosis I), whichresults in each homologouschromosome becomingisolated in a different cell.The second round ofcell division occurs(Meiosis II), whichresults in eachchromatid becomingisolated in a differentcell. This cell is a gamete.

Meiosis 1

1. Homologous chromosomes pair2. Crossing over (recombination) occurs3. Homologous chromosomes separate to daughter cells

Meiosis 2

separates sister chromatidsinto separate daughter cells

Practice problem
Which of the following is true regarding meiosis I andmitosis? Select more than one if appropriatea. The daughter cells of meiosis I and mitosis arethe same; the main difference between meiosisand mitosis is that meiosis has another celldivision (meiosis II)b. The daughter cells of meiosis I have similar allelicdiversity as the daughter cells of mitosisc. Cells that under go meiosis were generated bymitosis

c.
The first response is incorrect; daughter cells of meiosis I do not contain pairs ofhomologous chromosomes whereas the daughter cells of mitosis do contain pairs ofhomologous chromosomesThe second response is also incorrect; daughter cells of meiosis I usually have less allelic diversity (sister chromatids of same gene)compared to daughter cells of mitosis , except in chromosomal regions whererecombination occurred.

When does recombination occur?

prior to homolog separation during meisosis 1during metaphase 1 the chiasma overlaps and moves apart
occurs between non-sister chromatids of homologous chromosomes

Nuclear contents of human cell through meiosis cell division

Number of chromosomes:G1 - 46, S - 46, Meiosis 1 - 23, Meiosis - 23
Chromatids - G1 - 46, S - 92, Meiosis 1 - 46, Meiosis - 23

What is the biological mechanism behind Mendel's laws of segregation and independent assortment?

Meiosis

What is the basis of segregation?

Homolog separation (at meiosis 2 the gametes each allele has equal frequency.

Through meiosis and law of independent assortment, what combination and percentage would each gamete have?

From metaphase 1, 2 arrangments can occur.The gameres can be, AB, Ab, aB, ab. 0.25 chance

Mitosis - purpose

produce genetically identiacal cells for growth and maintenance

Mitosis - location

somatic cells

Mitosis - mechanics

1 round of division following 1 round of DNA replication

Mitosis - homologous chromosomes

do not pair, rarely undergo recombination

Mitosis - sister chromatids

attach to spindle fibers from opposite poles in metaphase. separate and migrate to opposite poles at anaphase

Mitosis - product

2 genetically identical diploid daughter cells that continue to divide by mitosis

Meisois - purpose

produce gametes for sexual reproduction that are genetically different

Meisois - location

germ-line cells

Meisois - mechanics

2 rounds of division (meiosis 1 and meiosis 2) following a single round of DNA replication. the mechanical basis of Mendel's laws of heredity.

Meisois - homologous chromosomes

synapsis during prophase 1, crossing over during prophase 1, separation at anaphase 1

Meisois - sister chromatids

attach to spindle fibers from the same pole in metaphase 1, migrate to same pole in anaphase 1, attach to spindle fibers from opposite poles in metaphase 2, separate and migrate to opposite poles in anaphase 2

Meisois - product

4 genetically different haploid cells that mature to form gametes and unite to form diploid zygotes