BIOL 2500 - Topic 3

Genetics

The study of inheritance

To understand biology, we often try to understand individual _________ properties

Biological

Individual biological properties we try to understand

1.) Characters

2.) Gene discovery

Characters

Aka traits, which are attributes of individual members of a species that is inherited and can be measured/defined

Character example

1.) Eye colour

2.) Blood type

Gene discovery

The process of determining which genes are responsible for any given trait

Method of gene discovery

Studying single-gene inheritance patterns

Single-gene inheritance patterns

1.) Refers to patterns where a single gene corresponds to a single trait/character.

2.) It analyzes heritable variants and compares it with the wild type

Wildtype

The most common form of the trait in nature

Mutant variants

Heritable variants that differ from the wild type, usually arising from mutations

Are wild types and mutants the same thing as dominant and recessive

No, they are not the same thing, because the wild type can be a recessive gene, while the mutant variant is the dominant gene.

Phenotypes

The physical alternative forms of a trait, including the wild type and all heritable variants

General steps of analyzing a trait

1.) Gather mutants

2.) Cross (mate) the mutant individuals to wildtype individuals

3.) Deduce the functions of genes at the molecular level and see how gene interactions contribute to the trait

Why cross mutant and wildtype individuals

To see if their offspring show the phenotypic ratios expected for single gene inheritance, which can potentially tell us if it is dominant or recessive

Different ways of studying genetics

1.) Genetic dissection

2.) Forward genetics

3.) Reverse genetics

Genetic dissection

1.) Produce mutants via irradiation (i.e. mutagens)

2.) Cross mutants with wild type to see if the offspring produce predictable phenotypic ratios

3.) Do this for a bunch of mutants for the trait in question

Forward genetics

Start with the phenotypic mutants and then look at the DNA sequence for differences, to see where the mutation is

Reverse genetics

1.) Start looking at DNA for candidate genes

2.) Then induce genetic changes (i.e. mutations) to see how it affects the phenotype

Who is Gregor Mendel

The father of genetics, born in the Czech republic

Story of Gregor Mendel

1.) He initially studied chemistry, but failed all his first year classes, then turned to priesthood

2.) They wanted him to teach, so they sent him back for a degree at the university of Vienna, where he studied plant physiology and plant biology

What did Gregor Mendel teach

Natural sciences at a middle school in the local town

What specific plant did Gregor Mendel study

Peas, which have dichotomous traits (i.e. all of its traits only have two forms)

What did Mendel’s research on peas show?

That inheritance was particulate and not blended.

Importance of Mendel’s experiments

It opened up the field of genetics

Mendel’s experiment (method)

He followed the standard scientific method:

Observation —> Hypothesis —> Quantitative test

Initial thoughts on Mendel’s experiment

People thought that it was too good to be true and that he faked it

Why did people think Mendel faked his experiments

He kept getting the same results over and over again

Why made Mendel’s experiments so effective

Everything was well thought out, with replicates and deliberate testable hypotheses, as well as multiple tests to confirm the results

What did Mendel do to confirm his results

1.) Controlled crosses

2.) Used pure-breeding strains, with dichotomous traits

3.) Quantified results

4.) Used replicates

5.) Did reciprocal crosses and test-crosses

Why did Mendel use peas?

1.) They have flowers that have both male and female structures (i.e. it is bisexual)

2.) It can self-fertilize

3.) But you can also do artificial cross-fertilization

4.) It has short life cycles

Artificial cross-fertlization

You can manually fertilize pea plants by removing the male anthers

Which characters did Mendel look at

1.) Round or wrinkled

2.) Seed colour

3.) Petal colour

4.) Ripe pods shape

5.) Unripe pods colour

6.) Flower position

7.) Stem length

Mendel starting lines

He used pure lines for each trait that he examined (aka true-breeding)

Pure lines

The genotype of the individual is homozygous

Mendel performing crosses

He performed crosses to produce various generations of plants

1.) The parental generation (P)

2.) First filial generation (F1)

3.) Second filial generation (F2)

Parental generation

1.) Cross pure-breeding parents with each other, with each parent having an alternative form of the trait

2.) The resulting progeny is the F1 generation

F1 generation

1.) The progeny produced from the parental cross

2.) They are then self-fertilized or crossed to produce the F2 generation

F2 generation

The progeny producing from the crossing of F1

What did Mendel do for the F1 and F2 that he did not do with the P generation

He measured the phenotypes of the resulting offspring, using multiple replicates

Mendel’s pure lines

He bred two pure-line parental plants, thereby forming a monohybrid cross:

Yellow seeded pea plants (AA) x Green seeded pea plants (aa)

Seed colour phenotype of F1 generation

They all had yellow colour seeds

Confirming the F1 results

He did reciprocal crosses to confirm his results, where he ended up getting the same thing.

Reciprocal crosses use

1.) It determines if the gene is autosomal or sex-linked

2.) If the gene is inherited equally in both males and females then it is autosomal

Generating the F2 generation

The F1 plants self-fertilized to obtain the F2 generation

F2 generation (phenotypes)

A 3:1 phenotypic ratio was seen (yellow:green)

Replicate crosses results

It produced hundreds of F1 plants and thousands of F2 plants

Reciprocal crosses

Plants with the same phenotypes were crossed, but the sexes of the donating parents were swapped, such that the plant donating the egg in one cross, donated the pollen in another and vice versa.

Test-crosses

1.) Crosses designed to identify the alleles carried by an organism whose genotype is unknown

2.) It is usually to determine whether it is homozygous or heterozygous, so you would cross AA and Aa with aa (the homozygous recessive)

AA x aa (phenotypic results)

100% A (it means the unknown genotype is homozygous dominant)

Aa x aa (phenotypic ratio)

1:1 (it means that the unknown genotype is heterozygous)

Heritable factors

1.) Mendel proposed that traits had heritable factors, otherwise known as genes

2.) In the case of the pea plant, which is diploid, it has a pair of each type of gene

The two different forms of genes are called

Alleles

If a plant has a pair of alleles, it has ___ alleles

2

Genotype alleles

YY, Yy, yy

/ between A/a

It signifies that the two alleles can be found on different homologs, but within the same homologous chromosome

Phenotype alleles

YY and Yy produces the dominant phenotype, while yy produces the recessive phenotype

Homozygous

Individuals with a pair of identical alleles

Heterozygous

Individuals with a pair of different alleles (the phenotype presents as the dominant trait)

Homozygous dominant

Both alleles are dominant alleles and present the dominant trait

Homozygous recessive

Both alleles are recessive alleles and present the recessive trait

Phenotypic ratio

The relative proportions between organisms with different phenotypes

ex.) Mendel’s yellow:green peas —> 3:1

Genotypic ratio

Relative proportions between organisms with different genotypes

ex.) Mendel’s peas —> 1:2:1

Mendel’s first law

Mendel’s law of segregation (aka the law of equal segregation), indicating that each gamete will only contain one member of the gene pair (either the one from dad or the one from mom)

What stage does the law of segregation come into play in meiosis?

Anaphase I, when the homologous chromosomes are being separated by the spindle fibers

Mitosis in haploid organisms vs. mitosis in diploids

They occur similarly

Can meiosis occur in haploids?

1.) Yes, it can, but it requires the fusion of 2 strains to create a temporary diploid cell

2.) It only takes place during a short part of the haploid organisms life cycle

Meiosis in haploid yeast

1.) Two haploid cells of opposite mating types fuse together, resulting in the formation of a diploid meiocyte

2.) The meiocyte will then undergo meiosis to produce haploid sexual ascospores

Alleles at the molecular level

They are different from each other in their DNA sequences, either by a single base-pair or a few nucleotides within the gene

What causes differences in alleles

1.) Mutations

2.) Recombination

Dihybrid crosses

Looks at two traits and how they are simultaneously inherited

Mendel’s dihybrid crosses

1.) He started with pure-breeding parents, either AABB + aabb OR AAbb + aaBB

2.) The resulting F1 generation are the heterozygous for both traits —> AaBb

A/a ; B/b

This indicates that the two genes are on separate chromosomes

AB/ab

This indicates that the two genes are on the same chromosome (aka syntenic)

A/a • B/b

This indicates that we do not know if the two genes are syntenic or not

General annotation for unlinked genes

AaBb (unlinked meaning on separate chromosomes)

Mendel’s 2nd law

Law of independent assortment

Law of independent assortment

Unlinked or distantly linked segregating gene pairs assort independently at meiosis (i.e. the inheritance of 2 separate traits is independent)

When does the law of segregation occur in meiosis?

Metaphase I

What did Mendel’s dihybrid experiment look at

1.) Seed colour: Y and y

2.) Seed shape: R and r

What did Mendel’s dihybrid experiment start with

He crossed two pure-breeding parents (RRyy and rrYY), such that each gamete will have one allele from each gene

Mendel’s dihybrid experiment F1 generation

They all produced one phenotype and they were all heterozygous (RrYy)

What did Mendel’s F1 from his dihybrid experiment show us

1.) It showed us which alleles were dominant (whichever phenotype was presented)

2.) It also showed that the dominance of one character was independent of the dominance of the other

Mendel’s dihybrid experiment F2 generation

1.) He crossed the heterozygous F1 plants to produce the F2 generation, which gave him four different phenotypes

2.) Two parental phenotypes and 2 recombinant phenotypes (i.e. different from the parents)

Resulting F2 phenotypic ratio of Mendel’s dihybrid experiment

9:3:3:1 (which is a typical pattern for Mendelian dihybrid crosses)

Using probabilities

It can be used to predict phenotypic ratios in dihybrid crosses and to predict gamete combinations

Predicting the phenotypic traits

You combine the probabilities for each trait to get the phenotypic ratio using the product rule and fork diagrams

What happens once we have the predicted gamete genotypes

We can set up a punnett square to perform the cross

Punnett squares

1.) It helps us summarize genotypic frequencies and genotypes

2.) It can also translate genotypes into phenotypes to get the phenotypic ratio

Inheritance of two genes on separate chromosomes or very apart on the same chromosome

The probability of them being inherited together is low

What two things are evidence of independent assortment

1.) Gamete ratio —> 1:1:1:1

2.) Phenotypic ratio —> 9:3:3:1

Punnett squares vs. fork diagrams

1.) Punnett squares are good for monohybrid, dihybrid, and sometimes trihybrid crosses

2.) Fork diagrams are more efficient when using increasing numbers of traits

Determining whether to use punnett squares or fork diagrams

1.) n = number of genes with 2 alleles

2.) 2ⁿ = The number of phenotypes

3.) 3ⁿ = The number of genotypes

Probability

The proportion of times a particular event/outcome is expected to occur

ex.) p(Heads) = 1/2

Independence

The probability of an outcome that does not depend on the outcome of another or previous outcome

ex.) p(Heads) is independent from the p(Heads) of the next toss

Product rule

Probability that 2 independent outcomes will BOTH occur (do this by multiplying the separate probabilities)

Sum rule

The probability that either one OR the other of two independent outcomes will occur, therefore making them mutually exclusive (usually do this by adding their individual probabilities)

Mutually exclusive

It means that you can’t have one if you have the other

Key words to know when you use the sum rule

1.) Either or

2.) No more than

3.) At least

Assuming independent assortment of genes when calculating the probability of getting a specific genotype

You can do separate monohybrids for each gene that encodes the trait

Conditional probabilities

Probability prediction that is dependent on another previous event that has taken place