Biology - Mendel

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Alleles

• Different forms of a gene that exist at a locus.

• Wild type allele is typically the most commonly found allele in a population.

Variant/Mutant Allele

• Different from wildtype allele.

• May or may not adversely affect gene product.

• May or may not result in detectable phenotype.

Homozygous

• If identical alleles are present on both homologous chromosomes, the organism/cell is said to be _________ for that allele.

• Two wild type alleles on tow mutant alleles highlight the same allele, so _____ can be used for both.

• FC/FC and fc/fc.

Heterozygous

• If one allele is wild type* and the other allele is not (i.e., a mutant allele), the organism/cell is said to be HETEROZYGOUS for that allele. 

• FC/fc.

Allelic Series

• The known mutant alleles for a given gene plus its wild-type allele.

• All alleles of the same gene. 

Wild-Type

• Most common allele in a population and functionally normal. 

Flower Colour (FC) Gene

• Purple flowers: functional protein produced.

• White flowers: no functional protein (absence of pigment).

• Gene named FC for “Flower Color.”

• Functional allele = FC; non-functional allele = fc (both listed when referred to).

Alleles on Structural & Functional Levels

• Different alleles can arise from mutations in various regions of a gene (e.g., promoter, coding region, or intron).

• Structural changes in DNA (mutations) can affect whether a functional protein is produced.

Null Mutations

• No functional protein produced; gene “OFF.”

• m1, m2, m3, and m6. 

Leaky Mutation

• Produces reduced protein activity; gene partially “ON.”

• m4.

Synonymous Mutation

• DNA change does not alter amino acid; no effect on protein function.

• m5.

Silent Mutation

• Mutation with no functional consequence.

• m7. 

FC / FC and fc / fc

• Example of homozygous wild-type and mutant genotypes. 

+/+ and -/-

• General symbols for wild-type and mutant alleles.

FC⁺ / FC⁺ and fc⁻ / fc⁻: “+” and “−”

• Denote wild-type and mutant forms of a specific gene.

• “-” would suggest a complete loss of function.

FC⁺ / FC⁺ and fc¹ / fc¹

• Superscripts identify specific alleles.

• Has partial function and is specified in the scientific paper. 

Uppercase/Lowercase Allele

• Uppercase indicates a dominant allele; lowercase indicates a recessive allele.

Heteroallelic

• Two different mutant alleles. 

• What if an individual has two mutant alleles that are different from each other.

• Also called transheterozygous or compound heterozygotes

Hemizygous

• (A situation where a cell/organism has only one copy of a gene/locus/chromosomal region).

Hemizygous

• A condition where a cell or organism has only one copy of a gene, locus, or chromosomal region.

• Example 1: Deletion — the corresponding gene or region is missing on the homologous chromosome.

• Example 2: Naturally single-copy genes — common for genes on X or Y chromosomes in XY individuals.

True-Breeding (Flower Ex)

• When plants consistently produce offspring with the same trait when self-crossed (e.g., white × white → white).

• Occurs when individuals are homozygous for the allele(s) controlling the trait.

Flower Colour Determination

• May depend on one gene (FC) or multiple genes (FC, W, GD, HE).

  • Monogenic traits. 

  • Polygenic traits. 

Monogenic Traits

• Controlled by a single gene (often with multiple alleles). 

Polygenic Traits

• Controlled by multiple genes, producing more complex variation.

Dominant Allele

• In a heterozygous organism, its phenotype is expressed even when a recessive allele is present.

• Typically represented by uppercase letters (e.g., A).

• Dominance is relative — it may be observed at the organismal level but not always at the molecular or cellular level.

Recessive Allele

• Its phenotype is masked by the dominant allele in a heterozygote.

• Example: If A is dominant, a is the recessive allele.

• Typically represented by lowercase letters (e.g., a).

• The terms dominant and recessive are always defined in relation to each other.

Complete Dominance

• The dominant allele (FC) completely masks the recessive allele (fc) in heterozygotes.

• Both FC/FC and FC/fc produce the same phenotype (purple petals).

• The fc allele is fully recessive when paired with FC.

• Wild-type alleles are often dominant over their mutant counterparts.

Haplosufficient

• A single functional copy of a gene is enough to produce the wild-type phenotype.

• Deals with a molecular mechanistic view. 

• In FC/fc plants, one working FC allele provides sufficient gene product for normal color (purple petals).

Incomplete Dominance

• Not all alleles show simple dominant/recessive relationships.

• The heterozygote displays an intermediate or blended phenotype between the two homozygotes.

• One functional copy is NOT sufficient for a wild type phenotype.

Four-o’clock Plants

• Cᴿᴱᴰ / Cᴿᴱᴰ: Red petals.

• Cᵂᴴᴵᵀᴱ / Cᵂᴴᴵᵀᴱ: White petals.

• Cᴿᴱᴰ / Cᵂᴴᴵᵀᴱ: Pink petals (intermediate phenotype).

• Heterozygotes show a phenotype midway between both homozygous parents.

Haploinsufficiency

• One functional copy is NOT sufficient for a wild type phenotype.

• One wild type copy is not sufficient to produce a wild type phenotype. Could result in complete or incomplete dominance. 

• More phenotypic difference. 

Codominance I

• Both alleles in a diploid organism show phenotypic effects.

• Hbᴬ / Hbᴬ: Normal red blood cells.

• Hbˢ / Hbˢ: Severe anemia, sickled cells.

• Hbᴬ / Hbˢ: Some sickling under low oxygen, generally no anemia.

Sickle Cell Anemia

• Caused by a point mutation in hemoglobin.

• Missense mutation: A → T at position 6 of the beta-globin chain.

• Too inflexible and cannot go through capillaries/BVs.

Hemoglobin A

• Tetramer.

• Two different gene that encode β-chain and α-chain.

Hb^s

• Hbˢ differs from Hbᴬ by a missense mutation substituting Valine for Glutamic Acid at position 6 of the β-chain.

• Hbᴬ / Hbˢ: No anemia; some sickling under low oxygen.

• Common in parts of Africa; one Hbˢ allele gives malaria resistance.

• This selective benefit is a heterozygous advantage.

Codominance (II)

• Genotypes & Phenotypes: Hbᴬ / Hbᴬ = normal RBCs; Hbˢ / Hbˢ = severe anemia, sickled RBCs; Hbᴬ / Hbˢ = no anemia, some slightly sickled RBCs.

• Cause: Sickle Cell Anemia — point mutation in hemoglobin (Hbˢ vs Hbᴬ).

• Dominance: Organism level — Hbᴬ is dominant; cellular level — incomplete dominance (some sickled cells).

• Protein level: Both Hbᴬ and Hbˢ produced equally → codominance.

Dominant Negative Effect

• The gene product from the mutant allele interferes with the gene product from the wild type allele (see also Muller’s morph “Antimorph” and next slide), blocking the wild type function.

Gain-of-Function Effect

• The mutant allele acquires a new property not present in the wild type allele, and this new property causes a phenotype (see also slides on Muller’s morph “Hypermorph” and “Neomorph”).

Dominance of a Mutant Allele Ex. 1

• A mutant protein interacts with the normal protein it can render the protein as non-functional.

  • The shape is altered. 

• Mutant affects the function by b/e non-functional or reduce its function. 

• This can be diver, tetranometer, etc. 

Dominance of a Mutant Allele Ex. 2

• The normal protein is affected by binding to the mutated protein.

• As a result, the dimer is non-functional.

Mutant Allele Classification

• Dominance/recessive describes relationships between alleles, not individual alleles themselves.

• A more useful system classifies alleles based on the type of genetic defect.

• H.J. Muller (Nobel Prize, 1946) designated five classes of mutant alleles called “morphs” (meaning “form”).

• These classifications are still used today, sometimes alongside modern equivalents.

Amorph (Null) Mutations

• “A” = absence; complete loss-of-function; also called null mutation.

• Caused by deletions, missense mutations that inactivate protein, or nonsense mutations.

• Classification is based on phenotype, not the type of molecular change.

• Any mutation causing total loss-of-function is an amorphic allele.

Hypomorphs

• “Hypo” = reduced; allele is partially functional but below wild-type levels.

• Most commonly used term in Muller’s system; modern equivalents: partial loss-of-function or leaky.

• Mutation may affect a regulatory element (reducing gene expression).

• Or a point mutation may reduce the activity of the gene product.

Hypomorphs

• Mutation in the regulatory region. 

• mRNA stability, doesn’t interact as good with a protein partner, etc. 

• All can lead to hypomorphism.

Porphyrias

• Porphyrias affect heme biosynthesis (8 genes).

• Most disease-causing alleles are amorphic or hypomorphic; patients usually heterozygous or heteroallelic.

• Heme precursors build up in the mitochondria.

• Complete loss of heme is lethal.

Porphyrias - Symptoms & Treatment

• Light sensitivity, gum recession, extreme neuropathic pain.

  • Sensitivity in UV.

• Heme or glucose injections can reduce symptoms.

Hypermorph (Increased Function)

• “Hyper” = increased; gene is more active than wild type.

• Modern equivalent: gain-of-function (but distinct from neomorphs).

• Cause: regulatory mutations increasing expression or coding mutations making protein more active; normal product, just more or more active.

• Gene product is produced in normal cellular context (unlike neomorphs).

Antimorphs

• “Anti” = against; mutant gene product antagonizes wild-type function (in a heterozygous setting).

• May dimerize with wild-type protein and inactivate it.

• Can also compete for substrate or binding partner.

• Usually dominant in inheritance.

Myostatin Mutations

• Function: Myostatin represses muscle growth; loss-of-function increases muscle mass.

• Cattle: Stop mutation → amorph (no myostatin).

• Sheep: Point mutation in non-coding mRNA creates microRNA binding site → hypomorph.

• Outcome: Reduced myostatin activity increases muscle; mutation type determines amorph vs hypomorph.

Neomorphs

• “Neo” as in “new.”

• The mutant gene product acquires a new function not found in the wild type protein.

• This could involve new interactions, new substrates, or expression in the wrong cell type or developmental stage.

• Neomorphs are generally dominant or semidominant.

Oncogenes - Relocation

• Example: Burkitt lymphoma caused by relocation of MYC oncogene next to a new regulatory element.

• MYC: normally important for cell proliferation.

• Mechanism: Recombination with chromosome 14 places MYC under incorrect regulatory control.

• Result: gain of new function leading to abnormal cell proliferation (neomorph).

Oncogenes - Hybrid

• Disease: Chronic Myelogenous Leukemia (CML).

• Mechanism: Translocation between chromosome 9 (ABL) and chromosome 22 (BCR1).

• Result: Formation of BCR-ABL fusion gene → hybrid oncogene.

Proto-Oncogene

• The wild-type version of the oncogene.

Mutation Classification

• Classification schemes are not mutually exclusive; they describe mutations at different levels:

  • DNA/chemical level: e.g., frameshift.

  • Gene product level: e.g., functional vs nonfunctional.

  • Phenotypic level: mutant vs wild type.

Allelic Interactions

• Dominant vs recessive, incomplete (semi-) dominance, codominance.

• Patterns depend on perspective, e.g., cell vs organism

Muller’s Morphs

• Classify all types of mutations.

  • Amorph, hypomorph, hypermorph, neomorph, and antimorph. 

Complementation Tests

• Used to determine if mutations are in the same or different genes.

• Mutations that complement: occur in different genes → non-allelic mutations.

• Mutations that fail to complement: occur in the same gene → allelic mutations.

Complementation in Genetic Screens

• Complementation tests help identify new mutants.

• After a genetic screen, we may have multiple mutants but don’t know if the same gene is affected more than once.

• Complementation allows us to group mutants by gene.

• Understanding this requires knowing how genetic screens are conducted.

Chemical Mutagenesis (Classic Approach)

• Method: Feed a chemical mutagen, usually to males, to mutagenize sperm.

• Efficiency: More efficient than X-rays; one male can fertilize many females.

• Common mutagen: EMS (ethylmethane sulfonate).

• Effect: Mostly G→A and T→C transitions; used in Drosophila, C. elegans, Arabidopsis.

EMS-Induced Mutations

• EMS (ethylmethane sulfonate, C₃H₈SO₃) is an alkylating agent that adds ethyl groups to nucleotides.

• Causes mispairing during DNA replication → point mutations.

• Commonly used in genetic screens.

• Efficient for creating G→A and T→C transitions.

Mutant Hunts = Genetic Screens

• Animals are mutagenized and thousands of progeny are examined to isolate new mutants.

• Heidelberg Screen (1979–1980, Drosophila): analyzed abnormal larval cuticle patterns.

• Isolated 600 mutants representing 120 genes using complementation tests.

• One of the most famous mutant hunts in developmental biology.

Heidelberg Screen Impact

• Revolutionized understanding of developmental processes.

• Many genes discovered are conserved in humans.

• Genes serve as models for human diseases.

• Nobel Prize 1995 awarded to Eric Wieschaus & Christiane Nüsslein-Volhard.

Preaxial Polydactyly

• Can be caused by mutation in the regulatory region of the human sonic hedgehog gene, which is important for limb development.

Mutagenesis & Screening (EMS Example)

• Procedure: Feed EMS → establish heterozygous +/m stocks → test homozygous m/m flies for a phenotype (e.g., inability to fly to light).

• Selection: Keep stocks where homozygotes show the phenotype.

• Example Outcome: Suppose we now have 20 different stocks.

• Question: How many different genes are affected?

Mutagenesis Scenarios (EMS Example)

• Extreme possibility I: 20 mutations are in 20 different genes.

• Extreme possibility II: 20 mutations are in the same gene.

• Use complementation tests to determine which scenario is correct.

• This helps map mutations to specific genes in genetic screens.

Complementation Tests - Mutant Collection (1)

• 20 mutants labeled m1…m20, all fully recessive.

• Homozygotes (m1/m1, m2/m2) show the mutant phenotype (cannot fly to light).

• Heterozygotes with wild type (m1/+, m2/+) show wild type phenotype.

Complementation Tests - Concept (2)

• If m1 and m2 are in the same gene, m1/m2 heteroallelic flies fail to complement → mutant phenotype.

• If m1 and m2 are in different genes, double heterozygotes (m1/+ ; +/m2) complement → wild type phenotype.

Complementation Concept - Purpose (3)

• Complementation tests determine if two mutations are alleles of the same gene.

• Helps map mutations to specific genes in a collection.

Crossing Homozygous Alleles

• Take two homozygous recessive mutants with the same phenotype and cross them.

• Wild type offspring: Alleles complement each other → mutations are in different genes.

• Mutant offspring: Alleles fail to complement → mutations are in the same gene.

Complementation in a Two-Gene Pathway (1)

• Example: Purple flower pigment requires two genes: A (first step) and B (second step).

• True-breeding lines homozygous for either A or B produce red pigment.

• Often only the phenotype (white or red) is known, not the underlying genotype.

• Consider four true-breeding white-petal lines; genotype unknown, only phenotype observed.

Complementation in a Two-Gene Pathway Purpose (2)

• Complementation tests determine whether mutations in different lines affect the same or different genes in the pathway.

• Mutations in the same gene fail to complement → offspring show mutant phenotype.

• Mutations in different genes complement → offspring show wild-type phenotype.

• Helps map which gene is mutated even when phenotype alone is insufficient.

Complementation in a Two-Gene Pathway - Case 1

Complementation in a Two-Gene Pathway - Case 2

Complementation Groups Setup (1)

• Six true-breeding white-petal mutant lines: a, b, c, d, e, f.

• Pairwise crosses performed; offspring scored as w = white (mutant) or p = purple (wild type / complemented).

Complementation Groups Results (2)

• Group I: b, c, f (all fail to complement each other).

• Group II: d, e (fail to complement each other).

• Group III: a (no complementation partner among these lines).

Complementation Groups Interpretations (3)

• Each complementation group = mutations in the same gene.

• Different groups = mutations in different genes (they complement).

• Conclusion: these six mutants represent 3 genes affecting pigment.

Distinct Mechanisms for Blonde Hair

• Phenotypic similarity: Solomon Island blond hair (Melanesia) and Swedish blond hair (Northern Europe) look alike.

• Different genetic causes: Each form of blond hair is due to a mutation in a different gene.

Solomon Island Blond Hair

• Gene: TYRP1 (Tyrosinase-related protein 1).

• Genotype: Homozygous recessive (TYRP1⁻ / TYRP1⁻).

• Inheritance: Must inherit the blond variant from both parents.

Swedish Blond Hair

• Gene: KITLG (KIT Ligand).

• Genotype: Homozygous recessive (KITLG⁻ / KITLG⁻).

• Inheritance: Must inherit the blond variant from both parents.

F₁ Hybrid Cross Blonde Hair

• Genotype: TYRP1⁻ / TYRP1⁺ ; KITLG⁻ / KITLG⁺.

• Phenotype: Not blond—likely darker hair.

• Interpretation: The wild-type alleles (TYRP1⁺, KITLG⁺) are dominant over the blond variants.

• Concept: Example of complementation — two mutations in different genes restore the wild-type phenotype.

Spirit Bear

• Blonde, not albino.

• Point mutation in melanocortin 1 receptor (Mc1r) affects melanocyte pigment production.

Rescue by Complementation - Problem

• A mutant line from a genetic screen may contain multiple mutations (e.g., m₁ in gene 1 and m₂ in gene 2).

• Even if m₁ is identified, it’s uncertain whether additional mutations contribute to the phenotype.

• Goal: Determine which mutation actually causes the observed defect.

Rescue by Complementation - Solution

• Introduce a wild-type copy of the suspected gene (m₁⁺) into the mutant.

• The added gene may integrate into the genome (transgenic) or remain independent (transformant, e.g., plasmid).

• If phenotype is rescued, the defect was caused by m₁.

• If not rescued, another gene (e.g., m₂) likely contributes to the phenotype.

Complementation Test - Host Cell [Control] (1)

• Genotype: Mutant allele ura3.

• Phenotype: Cannot synthesize uracil → fails to grow without added uracil.

• Interpretation: Mutation in ura3 disrupts pyrimidine (uracil) biosynthesis.

• Result on Minimal Medium (–Uracil): No colony growth.

Complementation Test - Experimental (2)

• Genotype: ura3 host transformed with plasmid carrying URA3⁺ (wild-type).

• Mechanism: Functional URA3⁺ complements the defective ura3 allele.

• Phenotype: Regains ability to synthesize uracil autonomously.

• Result on Minimal Medium (–Uracil): Colonies grow → phenotype rescued.

Complementation Test - Transformant [Negative Control] (3)

• Genotype: ura3 host transformed with plasmid carrying unrelated gene (e.g., Leu2⁺).

• Phenotype: Still unable to grow without uracil—mutation unrescued.

• Control Purpose: Confirms that complementation is gene-specific, not due to plasmid presence.

• Result on Minimal Medium (–Uracil): No colony growth.