Genetics Notes Bio 2C03

8/10/2019 Genetics Notes Bio 2C03

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Week 1: Gene to Protein (Sickle Cell Disease)

3.1. Basic principles of heredity

3.2. Monohybrid crosses and the Principle of Segregation

note: probability as a tool in genetics 3rd edition: pp.51-53; 4th edition: pp.52-55)

Chapter 6: Pedigree analysis, applications and genetics testing

6.1, 6.2. Pedigrees

Gregor Mendel - experimented with

peas, having the monastery garden and

greenhouse for use. Peas grow relatively

rapidly (compared to animals) and also

produce many offspring which made his

experiments less time consuming

In Mendel's crosses, seed shape

determined by gene that exists as 2

alleles (specific version for a gene)

Genotype is the set of alleles that an

individual organism possess

Phenotype is the manifestation or

appearance of a characteristic

o This characteristic can be either

physical, physiological,

biochemical, or even behavioural

Note that in Mendel's experiments,

the genotype largely determined the

shape of the seeds whereas in other

situations, environmental factors could

have a huge impact on phenotypic

characteristics (such as the height of a

tree)

Remember that only alleles are passdown (not the parent's phenotype)

Mendel realized that each variety of

peas he was studying was pure

breeding (homozygous) as all offspring

were the same as their parents


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o He then began to cross the different varieties

Mendel used monohybrid crosses - crossing two different pure breeding pea plants (round vs

wrinkled) - this is called the P (parental) generation

The offspring (F1 Generation) expressed only one of the phenotypes present in the parental

generation

The F1 generation was then self fertilized by each other - producing theF2generation in which he

discovered a 3:1 ratio of round to wrinkled

This lead to the idea that each plant must possess two genetic factors encoding a character

2nd conclusion - alleles separate when gametes are

formed by the parents (one from each)

3rd - the concept of dominance and recessiveness

4th conclusion - alleles separate with equal

probability

Principle of segregation - each individual diploid

organism has two alleles for any particular

characteristic which then segregate into gametes in

equal proportions

Punnett Squares:

Backcross - crossing a heterozygous F1 generation

with a homozygous parent

In the square, each cell contains an allele from each

of the corresponding gametes

Probability as a tool in genetics:

Multiplication rule: the probability of two or more

independent events occurring together is calculated

by multiplying their independent probabilities (eg.

Probability of rolling two 4's) - the key word is and

Addition rule: the probability of any one of two or

more mutually exclusive events is calculated by

adding the probabilities of these events (eg.

Probability of rolling either a 3 or a 4)

Binomial expansion and probability: sometimes we want to know the probability of several

different combinations of outcomes occurring


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Another way to determine the probability of any particular combination of events is to use the

following formula:

o

Where P equals the overall probability of event X with probability p occurring s times andevent Y with probability q occurring t times

The Testcross:

When one individual of unknown genotype is crossed with another individual with a known

homozygous recessive genotype for that trait

o In the instance that you have a tall pea plant but don't know it's genotype, you could

perform a testcross with a homozygous short plant

If the tall plant were homozygous: all progeny would be tall

If it were heterozygous, half would be tall and half would be short

Pedigree Analysis, Applications, and Genetic Testing

The study of human genetic characteristics presents some major obstacles:

o Controlled matings are not possible unlike with plants

o Humans have long generation times (geneticists would have to wait on average 40 years to

observe the F2 progeny

o Human family size is also generally small (not

enough sample size)

Instead, to study human inheritance, we use

pedigree charts which are pictorial representations

of a family history of the inheritance of traits

A son will always inherit his X chromosome from his

mother - if we observe that a trait is passed from


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father to son, it is certain that the trait is not X-linked

Mating between closely related people is called consanguinity

Autosomal recessivetraits appear with equal frequency in males and females. Affected children

are commonly born to unaffected parents who are carriers of the gene for the trait which tends to

skip generation. Traits are also more likely to appear among progeny of related parents

Autosomal dominant traits appear with both

sexes with equal frequency but usually does not

skip generations. Affected people have affected

parents. Unaffected persons cannot possibly

transmit the trait

X linked recessive Traits:

o Appear more frequently in males than in

females (males only have one X

chromosome)o

Affected males usually born to unaffected

mothers (tends to skip generations:

unaffected female to affected male to

unaffected female)

o Cannot be passed from father to son

(receives Y chromosome from dad)

o All daughters of affected man will be carriers

o Woman displaying trait must be homozygous


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Y linked Traits

o Only males are affected - passed from

father to son

o If the father is affected, all of his sons will

be affected

o

Do not skip generations

Class Example

Anemia is a clinical condition with signs of

abnormally low red blood cell count

RBCs contain haemoglobin which transports oxygen

Anemia can be chronic or temporary due to poor

nutrition

Hereditary anemia is due to abnormalities in

haemoglobin structure

Symptoms include:

o

Fatigue, pain crises (cells dying), swelling

and inflammation, splenic sequestration,

lung and heart injury, ulcers

Tissue is being deprived of oxygen


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Haemoglobin has 2 alpha and 2 beta subunits which

make up the protein tetramer

o

Thus the product of two protein coding genes

(alpha and beta globin)

The genetic cause is due to a single nucleotide base

pair substitution in the beta globin gene sequence (SNP)A is

replaced with T resulting in Valine amino acid rather than

Glutamine

o The consequence is the formation of long,

linear polymers of HG at low concentrations

o Lifespan of RBCs is reduced from 12 days to

10-20, cells are not being replaced enough

Sickle cell disease is inherited as a homozygous

recessive diseasetwo Beta-S alleles

Mendels first principle of segregation: TWO ALLELES

OF AN ALLELE PAIR SEGRAGATE APART DURING GAMETE FORMATION


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Basics of probability and inheritance:

o

Sum Rule: probability of the occurrence of any of several possible mutually exclusive

events is the sum of the probabilities of the individual events

For instance, the probability of rolling a 3 ORa 4 is 1/6 + 1/6 = 2/6

o

Product Rule: probability of two independent events happening simultaneously is the

product of their individual probabilities

for instance, probability of roll of a 6 AND THEN a 4 in two separate rolls is 1/6 x

1/6 = 1/36

o Another example:

the probability of having a boy and a girl can occur in two ways:

1st

child is a girl, 2nd

is a boy: x =

1stchild is a boy, 2ndis a girl: x =

The probability is the total of these two probabilities =

Genotypic/phenotypic ratios

can also be drawn out as branch

diagrams:

1: draw out the possible

alleles for one parent with their

probabilities

2: connect each allele

individually to the other parentspossible segregated alleles

3: multiple the connect

probabilities to get the probability of

getting that particular genotype in

the offspring


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With a western blot and densitometry, SCD can be distinguished by its expression of proteins

Vernon Ingram also studied SCD and found that a peptide (Valine) was substituted in place of

Glutamic acidfather of molecular genetics

Dominant and recessive are relative terms

dependent upon the level of analysis, we can

distinguish levels of phenotype in the context of

SCD

o

Physiologicalo Cellular

o Molecular

The phenotype can also be effected by

changes in the environment:

At normal altitudes, the

heterozygous carriers do not show symptoms of SCD


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However, at high altitudes, heterozygotes show a phenotype that is

intermediate between the two homozygousthis is phenotypic incomplete

dominance

Week 2: Population Genetics (Malaria and the B-globin allele)

Chapter 25: Population genetics

25.1. Genotypic and Allelic frequencies

25.2. Hardy-Weinberg principle

25.4 Forces that can change allelic frequencies

we are focusing upon the role of natural selection 3rd edition: pp.695 700 ; 4th edition: pp.709- 714.

Population genetics - studies the genetic makeup of groups of individuals and how its genetic

composition changes with time

o Focus attention on mendelian population which is a group of interbreeding sexually

reproducing individuals with a common set of genes (gene pool)

o Evolution is changes in a gene pool (frequency of different alleles)

o Mutations commonly appear in higher frequency due to a selective advantage

o Mechanisms of malaria:

Symptoms include headache, nausea, high fever, vomiting and flu like

symptoms Susceptible to other infections which may lead to death

Cause by protozoanplasmodium falciparumcarried by the mosquitolarvae

mature in the liver of the host animal and then RBCs

How do Sickle cells help against Malaria?

Sickled RBCs are fragile and how low lifespan in heterozygotes

This lifespan interrupts the development cycle of the plasmodium larvae, preventing

proliferation of malaria in the host

BsBs homozygous carriers would be resistant but still die early due to the detrimental effects of

SCD Therefore, BsBa carriers live on and pass their genes (gain of Bs and Ba allele in population)

natural selection maintains both alleles in populationhomozygous phenotypes are still

maintainedbalanced polymorphism

Allele frequency: frequency of a single allele of a gene within the whole population, to calculate

this, you first need genotypic frequencies

Remember that diploids carry two alleles per gene = 2N


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Genotypic frequencies:


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p + q = 1

frequency of two alleles in a population are unlikely to be the same

the recessive allele will never disappear from the gene pool of future generationsthey are

maintained

Mendel patterns of inheritance for a cross are based upon frequencies of alleles in individuals

Fitness: the relative reproductive success of one genotype compared to other genotypes

within a population

o Ex. Bb is only 80% as successful as Bb or BB at producing offspring

Fitness (W) of the recessive phenotype is 80% Wbb = 0.8

Selection coefficient(relative disadvantage ) intensity of selection against a

genotype = 1W = 10.8 = 0.2


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o We set the fitness of the genotype with highest reproductive success to 1, every other

fitness level is relative (divide number of offspring by most successful genotype)

o

o

Selection against a dominant allele will reduce frequency of the allele in the population

if selection coefficient is higher, frequency of alleles will decrease at a higher rate

If s=1.0, allele will be eliminated in one generation

o

o Selection against a recessive allele will also reduce frequency of the allele- very fast at

beginning, slows down, a proportion is still maintained in heterozygotescannot be

entirely eliminatedeven if lethal

o

To determine changes in allele frequency due to selection:

o


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Sickle cell anemia is an example of overdominance which results in a stable equilibrium

The frequencies change if the selective pressures change

o

Balanced polymorphismloss of an allele in one genotype is balanced by a selective

advantage in another genotype

Evidence for this advantage:

o Overlay of maps of malariahigher incidence of Bs allele

o Molecular evidence that Bs allele independently mutated

o Frequency of carriers increases with increasing age (live longer)

B^E and B^C allele variants were also found in Asian/pacific and west African populations as well

resistant to malaria

Linus Paulingpassionate about screening techniques to prevent sickle cell anemia:

o Heterozygotes should not marry each other and have children

o Heterozygotes marrying homozygotes should have few children

o Current screening techniques:

Blood smears

Protein electrophoresis

When more than 2 different types of alleles can exist at the loci (eg. 3 alleles):


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X-linked loci - supposed there are two alleles at an X-linked locus XA and Xa

Can also be calculated through

Hardy-Weinberg Principle (of equilirbrium): makes several simplifying assumptions about population

and provides two key predictions if these assumptions are met


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Assumption: population is large, randomly mating, not affected by mutation, migration, or natural

selection

Prediction 1: allelic frequencies of population do not change

Prediction 2: the genotypic frequencies will not change after one generation in the proportions p1,

2pq, and q2 (hardy weinberg equilibrium)

By adhering to the hardy weinberg principle, populations cannot evolve

When a population is not in hardy weinberg equilibrium, we have no basis for predicting the

genotypic frequencies

When in HW equilibrium, genotypic frequencies are determined by allelic frequencies

Single generation of random mating produces the equilibrium frequencies p2, 2pq and q2

HW law applied to multiple alleles and X-linked alleles


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Forces that can change allelic frequencies:

Mutation: before evolution can take place, genetic variation must exist which arises through

mutation

o

Allelic frequencies change with time as some alleles mutate into others, eventually reach

equilibrium (forward and reverse mutation rates)

Migration: the influx of genes from other populations (also known as gene flow)

o Causes gene pools of populations to become more similar

o Adds genetic variation to populations

Genetic Drift: usually due to small population size, a small deviation by chance can lead to changes

in allelic frequencies (random and unpredictable)

o Reduces genetic variation within populations, causes genetic divergence among populations

Natural selection: when individuals with adaptive traits produce a greater number of offspring

than that produced by others in the population

o

If genetic, they are inherited by the offspring, reproductive advantage allows populations to

become better suited (adapted) to their environments


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CHI SQUARE TESTS: a goodness of fit chi square test is used to determine whether the differences

between the observed and the expected numbers of each genotype arise through chance

25.4 Forces that change allelic frequencies:

Processes that bring about change in allelic frequency include mutation, migration, genetic drift, and

natural selection

Mutation:


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Allelic frequencies change with passage of time, eventually they reach equilibrium and are determined

by forward and reverse mutation rates

At equilibrium, Hardy-Weinberg law tells us that genotypic frequencies will remain the same

Long periods of time are required for population to reach mutational equilibrium

Migration: prevents populations from being genetically different from one another and introduces

genetic variation within populations


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Genetic Drift:

Because no population is infinitely large, allele frequency will deviate by chance

Limited sample size can be referred to as sampling error

Natural Selection: when individuals with adaptive traits produce a greater number of offspring than that

produced by others in the population

Fitness is the relative reproductive success of a genotype


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Week 3: Dihybrid patterns of inheritance

Multiple genes determine phenotypic traits (cats and humans are not peas)

Dihybrid ratio: 9:3:3:1

there can be multiple types of mutations at a single gene example: multiple alleles contributing to fur coloration in cats, different dominance

frameshift mutationdeletion of a nucleotide causes the reading frame to be read differently, often

results in a loss of function allele

number of alleles determines number of possible genotypes


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Wildtype allelefunctional proteinmost common phenotype

Loss of function allele: no longer produced, non functional, or produced at lower levels

Wiltype usually dominant

o

Half of protein is sufficient to achieve normal phenotype: happlosufficiency (ie tyrosinase)

o Or not sufficienthaploinsufficiency (tailless cats)

Dominant alleles can also be gain of function mutations (ie huntingtons disease)

Law of segregation: allele pairs separate independently during gamete formation

o Mendel proved this using monohybrid crosses

Law of independent assortment: inheritance pattern of one trait will not affect pattern of another

trait

For two alleles, the Mendelian ratio is 9:3:3:1


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Gene interactions may produce novel phenotypes that will modify the 9:3:3:1 ratio

epistasis: when one gene masks or modified the phenotypic expression of another gene

Complementation: 9:7 phenotypic ratio

o Mutations in two different genes product the same mutant phenotype

o Also a duplicate recessive epistasis

When a loss of function mutation leads to a lethal phenotype, we get a 2:1 ratio


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Week 4: Quantitative Genetics

Week 5: Chromosomal Theory of Inheritance

Studies reveal that multiple genes are on each chromosome

Haploid (N)one copy of genetic material

Diploid (2N)two copies of genetic material; homologous pair consists of a homolog from each

chromosome

Ploidynumber of complete chromosome sets

Eukaryotesgametes are haploid, adults are diploid

Chromosomes can be classified by their length and position of centromere (attaches to spindle

fibers during mitosis and meiosis)


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Painting probes or g banding can be used to distinguish the 23 pairs of chromosomes we have

Can also be separated into two categories:

Autosomes: present in the same copy number in both males and femalesnumber of

morphology is species specific Sex-chromosomes: different copies in males vs females

Chromosome number and structure varies between species:

Humans have 46 total chromosomes, as do sable antelopes

12 chromosomes in the Datura stramonium

12 variant phenotypes (arisen from different trisomies)

Sex chromosomes are represented differently in the two sexes

In the meiosis of grasshoppers, independent assortment was observed

Parallel to Mendels patterns of inheritance

Review of mitosis:

Def: replication of identical cellsone cell produces two genetically identical cells

All cells in body reproduce and multiply by mitosis

A failure to separate is called nondisjunction

Homologues: two chromosomes carrying the same gene sequences

Meiosis: germ line cells undergo meiosis in order to produce haploid gametes

1st

law: principle of equal segregation

2nd

law: principle of independent assortment

Anaphase 1: reductional divisionhomologues segregate (explains 1st

principle)


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Pairing permits exchange of DNA between homologous pair in prophase

Nonsister chromatids in bivalent undergo breakage and reunion at the chiasma (crossing

over)

Pairs attach to spindles independently of one another (independent assortment)

Anaphase 2: equational division, paired sister chromatids separate

Evidence that genes are transmitted on chromosomes:

Wild type flies have red eyes carrying w+ allele

o White allele is a mutationw

o

Red eyed female crossed with white eyed male

Observed 237 red eyes flies compared to 3 white eyed flies

o After F1 cross:

3470 red (1011 male, 2459 female) : 782 white (all males)

Morgan proposed that eye colour gene is on X chromosomemales are

only hemizygousone allele

If different ratios are seen for the two sexes, the gene is likely on a sex

chromosome

If reciprocal crosses give different results, the gene is likely on a sex

chromosome

Non-disjunction of X chromosome: homologues fail to segregate in meiosis 1 and/or sister

chromatids fail to segregate in meiosis 2

Week 6 Chromosome Structure and Gene Regulation

If genes are on chromosomes, then what exactly are chromosomes? Chromosomes are compacted and organized within the nucleusthis compaction/coiling changes in

different stages of the cell cycle and changes when genes are transcribed into RNA

Chromosomes consist of DNA and histone proteins

o In interphase, the chromosomes are unwound to allow transcription where in the

metaphase they are tightly coiled


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o

we see no transcription occurring at the telomere or centromeres which are tightly compacted

these are classified as heterochromatinhighly compact throughout cell cycle, low gene

expression, low gene density

o rather than constitutive, facultativeheterochromatin actually converts between the hetero

and euchromatin

o euchromatin composes most of the chromosomeis gene rich and relatively

transcriptionally active (turned on/off dependent on cell type)

histone tails are modified to alter chromatin structurechanges the ability of transcription

factors to access DNA

o may provide binding sites for other proteins

non-histone proteins are also important (scaffold proteins) - contain 20 000 to 100 000 bp

Under interphase:

o

1: chromatin structures changes to allow transcriptionchromosomal puff

o 2: when chromatin is in open conformationDNAse can cut DNA into small pieces

Sensitivity of DNA to digestion by DNase 1 is correlated with gene expression

Chromatin changes structure by relaxing decreased association with histone proteins

Modifications in the histone protein include:

o Acetylation

o Methylation


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o Phosphorylation

The centromere:

o Functional definitionattachment of microtubule spindle fibres for chromosome

movement in mitosis and meiosis

o Commonly see repeated sequencesnot protein coding, not exclusive to centromere

o

Centromeres are structurally important:

Lost centromeres results in degraded chromosome fragments

Too many may also result in a break in mitosis or meiosis

The telomere:

o Natural ends of linear chromosomesprevent chromatin degradation and

inappropriate attachment

o Also repeated sequences

In between: genes

o Unique sequence DNA: single copy genes, protein coding genes, only about 4-5% in

humans is actually protein coding

o

Lots of moderately and highly repetitive DNAie ribosomal DNA and tRNA genes

Rememberfemales have two x chromosomes whereas males only have one and a shorter y

chromosome

o dosage compensation - way to equalize gene expression

either increase expression from y chromosome, decrease the two x

chromosomes, or turn off expression from one X chromosome

involves modifications to chromosome structure and gene expression

o this demonstrates epigenetics - heritable changes in gene expression that does not

involve a change in DNA sequence

o Barr and Bertram found a condensed mass in the nuclei of female cells in cats, not males

Was suspected to be to the x chromosome

o Sometimes genes are on the X-chromosome

o Early in development, one X chromosome is randomly inactivated

Females that are heterozygous for X-linked traits are genetic mosaics

Xist RNA coats inactivated X chromosome which attracts protein modification

factors

Compaction occurs by modification of histones that is initiated by the

Xist RNA

In each cell of the embryo, number of Xics are counted

One of the X chromosomes is targeted for inactivation

Examples of mosaics in humans for X-linked genes include:

Red green colour blindness

Anhidrotic ectrodermal dysplasia

RememberRNA polymerase and general transcription factors initiate transcription

o Cis sequencesDNA sequences that bind to DNA such as enhancers and promoters

To inhibit - silencers


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o Trans factorsproteins that bind to DNA such as transcription factors, activator

proteins, mediators, etc

to inhibitrepressor proteins

o In a barr body, these proteins can not bind

The ability of protein binding is determined by chromatin structure

Modifications to histones:

o Methylation: may activate or repress gene transcription

o CpG islands are found in promoter sequences

Methylation inhibits the binding of an activator protein to the enhancer element

Methyl-CpG binding recruits other proteins that cause region to become more

compact

o

o Acetylation: usually stimulates gene transcription

o Deacetylation is associated with silencing (no transcription) as seen in heterochromatin

Genomic Imprintingthe expression of genes is determined by whether the gene is inherited

from the mother or the father

o Igf2mice inheriting the deletion from mother were normal, mice inheriting from

father were only 60% of normal birthweight


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Genetics Notes Bio 2C03