D3.2

Question 1

Mendelian Crosses

Purebred?

Answer 1

• Mendel used this term for plants with a lineage of a single physical characteristic (e.g., tall plant rising from a crop of tall plants)
• We often use the term homozygous, however usually is a presumed genotype based on phenotype of related organisms.

Question 2

Mendelian Crosses

Heterozygous?

Answer 2

• Refers to having two different alleles for a single gene
• Also referred to as hybrid (coming from two different purebred lineages)
• The assumption - got genetic matieral from each lineage and therefore is heterozygous for that trait

Question 3

Mendelian Crosses

Genotype?

Answer 3

• Refers to the two alleles that an individual has for a gene
• Represented by letters, each white indicates an allele.
• Genotypes can be determined from an organism’s appearane (phenotype) but not often.
• Often, those with a recessive phenotype are known to be homozygous recessive, but those with the dominant phenotype may be homozygous dominant/ reciessive so genotype is unknown.

Question 4

Mendelian Crosses

Monohybrid Cross?

Answer 4

• When we consider the likely outcomes of two parents producing offspring while considering only one trait (only one gene).
• Zooming in on the allelic phenotypes for a single gene locus
• Use punnet squares for this with 4 boxes

Question 5

Mendelian Crosses

Mendel’s Pea Plant Experiments

Answer 5

• He conducted research into genetics by crossing over purebred peas
• DNA had not yet been discoerverd, so he called genes ‘factors’
• He used artifical pollination by placing pollen from one flower onto another plant’s stigma to control parental phenotypes to see what patterns would occur in offspring.
• He first cross two differen purebred phenotypes and then cross their offspring.
• He discovered that while F1 had one phenotype consistant with on of the parents, F2 often had a 3:1 ratio with both phenotypes.

Question 6

Mendelian Crosses

Dominant vs Recessive Alleles

Answer 6

• The version that is visable in the heterozygotes is the dominant allele
• The version that requires two copies to be visable is the recessive allele

Question 7

Mendelian Crosses

Genetic Generations: P, F1, F2

Answer 7

• P-Generation: The PARENTAL Generation = the first two organisms crossed (Mendels: first two purebred organisms)
• FI Generation: The offspring of the P generation so the first generation to be produced in the experiment (Mendels: the hybrids)
• F2 Generation: When two plants from the F1 generation are crossed with each other & their offspring observed.

Question 8

Mendelian Crosses

Steps in Creaing a Punnet Grid: STEP 1

Answer 8

• Select a letter (or letters) to represent the alleles you’ll be using.
• If completely dominant, with one dominant and one recessive alleles, dominant is capital and lowercase is recessive.

Question 9

Mendelian Crosses

Steps in Creaing a Punnett Grid: STEP 2

Answer 9

• Determine the parent’s genotypes.
• Often described in words in the question prompt & requires you to know your vocabularly (heterozygous, homozygous & carrier)
  1. Parent has the recessive phentoype/appearence –> homozygous reciessive.
  2. Parent has dominant phenotype –> you need more info.
• Could be told if they have a parent of child who has the recessive phenotype –> if so, they are a heterozygot.e

Question 10

Mendelian Crosses

Steps in Creating a Punnett Grid: STEP 3

Answer 10

• Determine what gametes each parent could pass on.
• IF heterozygous - can pass on either and if homozygous - only pass on the one they have.

Question 11

Mendelian Crosses

Steps in Creating a Punnett Grid: STEP 4

Answer 11

• Draw the punnett square, should have four offspring boxes & the parental gametes above & beside the boxes.
• Each offspring box will have two letters, representing parent above’s gamete and the parent to the side’s gamete.

Question 12

Mendelian Crosses

Steps in Creating a Punnett Grid: STEP 5

Answer 12

• Determine the genotype and phenotype ratios based on the offspring boxes.
• The genotype ratios look at how many of each allele combination would be expected.
• For phenotype ratio, need to consider what the phenotype will be based on the genotypes –> then state that as the ratio.
• The two ratios can be the same but often aren’t

Question 13

Mendelian Crosses

The Determinants of Phenotype

Answer 13

• Environment – smoking, bacteria, virus, environemental toxins, languages spoken
• Genotype – mutations, traits that are solely genetic (blood type)
• Epigenetics – DNA methylation, height

Question 14

Mendelian Crosses

Autosomal Recessive Disorders

Answer 14

• Disoders caused by a singular gene.
• If said gene is on a normal/autosomal chromosome (not sex chromosome) and when the disorder is recessive to ‘normal’ –> autosomal recessive disorders.
  1. Albinism
  2. PKU
  3. Tay-Sachs Disease
  4. Cystic Fibrosis

Question 15

Non-Mendelian Patterns of Inheritance

Single-Nucelotide Polymorphism?

(Another term for the result of a point or subsitution mutation)

Answer 15

• Refers to when one nucleotide in the genetic code has been replaced with another nucelotide.
• A single gene may have several SNPs (at different nucleotides) that give rise to different alleles - often with similar impact on protein.
• E.g., ability to taste the chemical PTC.

Question 16

Non-Mendelian Patterns of Inheritance

What does ‘Multiple Alleles’ mean?

Answer 16

• More than two genetic sequences in the population for that gene.
• When there are more than two different phenotypes that result from the different genetic combinations (e.g., ABO blood types, controlled by 3 diff alleles)

Question 17

Non-Mendelian Patterns of Inheritance

Co-Dominant Alleles?

Answer 17

• Simply: when both alleles are expressed and recognized in the phenotype
• Co-Dominance refers to a situation in which two alleles have phenotypes that are BOTH present in the heterozygote, often in some sort of pattern/patching for external traits (like a red AND white flower)
• For blood –> both antigens are on the surface
• Different from incomplete dominance, where the heterozygote has a blend of the two phenotypes (pink flowers over red or white)

Question 18

Non-Mendelian Patterns of Inheritance

Incomplete Dominance?

Answer 18

• Neither allele is able to show its full phenotype with only one copy , AKA the heterozygote shows neither phenotype but a blended phenotype (instead of blue or red, it’s purple)
• As genotype has its own phenotype, both ratios stay the same.

Question 19

Non-Mendelian Patterns of Inheritance

Sex-Linked Genes?

Answer 19

• One that is on the X or Y chromosome
• There two chromosomes (X and Y) determine biological sex but also have protein coding genes in them.
• Y chromosome is small, very few coding genes.
• X chromosome is large, contains many non-sex related genes.
• As females have two X chromosomes and males have X and Y, genes that are on sex chromosomes have different patterns on inheritance in male and female offspring.

Question 20

Non-Mendelian Patterns of Inheritance

Chromosomes and Biological Sex

Answer 20

• Biological sex is determined by the presence of the SRY gene on the Y chromosome
• All embryos default to developing female sex organs.
• If the fetus has a Y chromosome it contains the SRY gene that then drives the expression of genes that instead for male sex organs
• Biological sex of a baby is determined by whether the father’s sperm contains an X or Y (50/50 chance)

Question 21

Non-Mendelian Patterns of Inheritance

Genetic Causes & Symptons of Haemophilia

A sex-linked condition

Answer 21

• Sex-linked condition as the gene impacted is on the X chromosome
• A mutation in the F8 or F9 genes (both on X chromosome) that produces the protein clotting factors responsible for the signalling cascade that converts prothrombin into thrombin is the cause.
• As males only have one X chromosome and can’t therefore mask a recessive allele, they’re more likely to get haemophilia.
• For a daughter to have haemophilia her father would have to have the condition (and her mum would be a carrier

Question 22

Pedigrees

Pedigree Chart?

Answer 22

• The genetic family tree for one family for one single trait
• Indicates the phenotypes of individuals in a specific family
• Pattern on pedigree is then used to determine the likely pattern of inheritance and then to determine the genotypes of individuals
• Can be used to preodict carriers

Question 23

Pedigrees

Symbols for Sex and Trait on Pedigree

Answer 23

• Circles denote female biological sex
• Shaded indicates having the condition/trait often written as affected
• Carrier can be half shown/circle inside

Question 24

Pedigrees

Recessive Disorders on Pedigrees

Answer 24

• When the condition is recessive, it will often skip generations on a pedigree.
• This can be shown when when two unaffected parents have affected offspring.
• To check if autosomal or sex-linked, check the AFFECTED male to female ratio.
• If theres almost/an equal amount of males and females, likely autosomal
• Another check, if a shaded girl has an unshaded father, it can be confirmed as autosomal.

Question 25

# Pedigrees Dominant Disorders on Pedigrees

Answer 25

* If dominant, it's expected that **every affected offspring** has an **affected parent** * There should **not be generations skipped** * Two affected parents (if heterozygous) can **have an unaffected child** - NOT POSSIBLE if recessive. * Check for **even male and female affected ratio** to confirm if **autosomal**

Question 26

# Pedigrees Sex-linked Recessive Disorders on Pedigrees

Answer 26

* For **Sex-linked recessive traits** look for **more males affected than females** * In a family with **two unaffected parents** we would expect to see **ONLY MALES affected** * Sex lineage as a likely pattern if more affected males are seen

Question 27

# Pedigrees Sex-linked Dominant Disorders on Pedigrees

Answer 27

* **Sex-linked dominant traits** are rare, however look for **more FEMALES affected** in a family tree. * As only one copy of the mutated X is needed, and females **recieve two copes** they are **twice as likely to get the mutation** than males * Look for **an affected father** and an **unaffected mother** having **all affected daughters and no affected sons**, likely sex linked dominant.

Question 28

# Pedigrees Inductive vs Deductive Reasoning

Answer 28

* **Inductive**: looking for inheritance patterns on a pedigree is an example - begins with data, analyze it for patterns, and then from that arrive at a hypothethis/theory * **Deductive**: having decided on a likely pattern (as a hypothesis) and then going back through the pedigree & assigning possible genotypes, where the hypothesis guides the observation of data.

Question 29

# Continuous Variation (and Box & Whisker Plots) Phenotype Plasticity?

Answer 29

* Refers to the **capacity for phenotypes to change in response to environmental conditions** * Often achieved by **altering patterns of gene expression** * Example - **skin colour**: impacted by genes but also exposure to sunlight (expresses production of melanin) * Often, the phentoype plasticity is **adaptive** (the environment regulates gene expression in a beneficial way)

Question 30

# Continuous Variation (and Box & Whisker Plots) Polygenic Inheritance?

Answer 30

* Refers to when **a trait is produced from the additive effect of multiple genes** * The pattern of dominant & recessive alleles across the no. alleles gives rise to many different phenotypes - often **creating a continuous trait**

Question 31

# Dihybrid Crosses Dihyrbid Cross?

Answer 31

* Considers the probable **phenotypic outcome for TWO traits** from a cross between two parents. * Because there's two traits, there are **4 possible phenotypes**

Question 32

# Dihybrid Crosses Gene Loci? | Singular: Gene Locus

Answer 32

* A gene locus is the **'address'** of that gene - which **chromosomes it is mapped to** & as much further info as possible, like which arm or exact nucleotide position.

Question 33

# Dihybrid Crosses Mendelian Laws: Law of Segregation

Answer 33

* Mendele observed that when the **hybrid F1 offspring are crossed**, the **recessive phenotype re-emerged**, leading him the to understand that **only one allele is passed onto offspring from each parent** * This lead him to the LOS: **A parent has 2 alleles but passes on only one to their offspring**

Question 34

# Dihybrid Crosses Mendelian Laws: Law of Independent Assortment

Answer 34

* Mendel noticed that the inheritance of one trait **did not impact the inheritance of another**. * If F1 heterozygotes for both colour & size traits crossed, **the offspring could have the recessive colour but haw the dominant height** * This relates to the **chromome pairs lining up randomly at Metaphase 1** * Independant assortment only applies **if the traits/genes are on separate chromomes**

Question 35

# Dihybrid Crosses Using FOIL for Gamete Combinations

Answer 35

* Now looking at 2 different genes, the combinations of alleles able to be passed is more complciated * Work out the **allele combos using FOIL** * Where **F is first letter for each gene, O for outside two letters, I for inside two letters and L for last of each letter**

Question 36

# Dihybrid Crosses Steps for Dihyrbid Crosses: STEP 1

Answer 36

* Assign letters for all alleles * Two different alleles with distinct differences between lowercase & uppercase

Question 37

# Dihybrid Crosses Steps for Dihyrbid Crosses: STEP 2

Answer 37

* Write the genotype of each parent * Two alleles for each of the two traits, so a total of four letters * The two letters for one trait should be next each to each other but no space between letters * Either gene can go first, but be consistent.

Question 38

# Dihybrid Crosses Steps for Dihyrbid Crosses: STEP 3

Answer 38

* Work out what possible alleles combos each could pass on to their children * If the individual is homozygous for both genes than there may only be one combination (e.g., AABB only pass on AB) * But heterozygous individuals for one of both trais have more options

Question 39

# Dihybrid Crosses Steps for Dihyrbid Crosses: STEP 4

Answer 39

* Create a 16 box grid * Place the 4 possible gamete combos from one parents across the top (or if only two combos, write them each twice or just make a smaller grid) * Other parent down left side

Question 40

# Dihybrid Crosses Steps for Dihyrbid Crosses: STEP 5

Answer 40

* Fill in the genotypes for each offspring box * Use gametes above it and to the side * When writing the genotype, write the 2 alleles for the same gene next to one another (with the capital WITHIN the gene first) and then the two alleles for the other gene next to it

Question 41

# Dihybrid Crosses Steps for Dihyrbid Crosses: STEP 6

Answer 41

* Work out the phenotypes of each offspring * Use colours/symbols to indicate the phenotype for each box with a key to the side, so you don't get confused

Question 42

# Dihybrid Crosses Steps for Dihyrbid Crosses: STEP 7

Answer 42

* Work out any ratios that the question asks - often just a phenotype ratio * Make sure it adds up to 16 * Can memorize the most common ratios too, see next two slides

Question 43

# Dihybrid Crosses Phenotype Ratios: 9:3:3:1

Answer 43

* Two parents who **are BOTH heterozygous for BOTH traits** * **9** Dominant for both traits: **3** dominant for the first trait & recessive for the second: **3** recessive for first trait and dominant for the second: **1** recessive for both. * Most difficult dihbrid, so memorize!

Question 44

# Dihybrid Crosses Phenotype Ratios: 1:1:1:1

Answer 44

* Crossing of **one parent who is heterozygous for BOTH traits** with another parent who is **homozygous RECESSIVE for BOTH traits** * Cross with homozygous recessive individuals are called **test crosses** becayse the second parent is always masked, allowing us to determine the pattern with the dominant phenotype parent. * Result is a 1:1:1: (25% for all) ratio, often used to test for linkage

Question 45

# Gene Linkage with Chi Square Tests Linked Genes?

Answer 45

* Genes which are usually **inherited together** and which **fail to independantly assort** because they are on the **same chromosome** * Therefore, when chromosomes line up **randomly in meiosis**, these genes stay together. * BUT - they can be **separated by crossing over IF the chiamsa falls between them** * SO they are **generally only linked if they're CLOSE TOGETHER** on the chromosome * Genes far apart on the same chromosome are **separated by crossing over** so they behave like genes on separate chromosomes and aren't inherited together/linked.

Question 46

# Gene Linkage with Chi Square Tests Linkage Group?

Answer 46

* Refers to a **group of genes on the same chromosome** that tend to be inherited together * May be close together on the **same arm of the chromosome** (note that: in a big likage group, the top & bottom one may be separated, so it's not a perfect term)

Question 47

# Gene Linkage with Chi Square Tests Recombinants?

Answer 47

* Refers to **a new combination not seen before in the parents** * Often determined by the phenotypes, so look for trait combinations **not seen in either parent**. * Generally done with a **test cross** where **one parent has the dominant** (but heterozygous) **phenotypes** and the other parent is **recessive for both** * Recombination occurs at a **genotype level due to crossing over creating unqiue allele combinations** not originally found on either parental chromosome.

Question 48

# Gene Linkage with Chi Square Tests Denoting Linked Genes

Answer 48

* If writing two linked genes - indicate that the **parental alleles are likely to stay together** * Do this by showing them on a **line next to one another to represent them on the same chromosome** * Preferably **vertical lines** (better show concept of chromosomes) * So, if known to be linked, don't write as AaBb, rather AB on a vertical line next to ab on a vertical line.

Question 49

# Gene Linkage with Chi Square Tests Recombination Frequency and Map Distance

Answer 49

* The **number of recombinants between two linked genes** is an indication of **how far apart they are from one another on the same chromosome** * If close, crossing over will rarely separate them, so the no. recombinants is less. * If further away, the **chiasma falls between them** so they'll be more. * Hence, **recombination frequency (% of recombinants)** can be used to **map genes in relation to one another on a chromosome** *Won't have to calculate, just know conceptually*

Question 50

# Gene Linkage with Chi Square Tests Using Chi-Squared Tests to determine Linkage

Answer 50

* Tests to see if **genes assort independantly** (the expected) or not. * Determining if the **number of offspring with each phenotype** differs too much from what we would expect if the were **independently assorting/unlinked**

Question 51

# Gene Linkage with Chi Square Tests The Null Hypothesis in Chi Square Linkage Test

Answer 51

* The genes are **UNLINKED** and assorting **independently** (most likley situation). * "There is no statistically significant difference between the observed phenotypes and those expected for two genes that are assorting independently"

Question 52

# Gene Linkage with Chi Square Tests Calculating Expected Values in a Chi Square Linkage Test

Answer 52

* For a goodness of fit (in a contingency table where you do Row Total X Colum total/TOTAL) you use the **MODEL/THEORY** to determine the expected. * In this case that is what we would expect for **independent assortment**- so this is done by using a **DIHYBRID CROSS, determing the phenotype ratio** and then **multiplying the ratios by the no. organisms** (For 1:1:1:1 ratio, multiply 0.25 by total number, for 9:3:3:1, multiply 9/16 by total number then 3/16...etc)