Genotype to Phenotype Notes

Phenotype

  • Phenotype is the observable characteristics of an organism for a given trait.

Trait

  • A trait is a characteristic of an organism.
  • The phenotype is what the organism looks like for that trait.
  • Examples:
    • Trait: Height (phenotype: 5’11”)
    • Trait: Eye color (phenotype: brown)
    • Trait: ‘risk for heart disease’ (phenotype: ‘high’)

Examples of Traits & Phenotypes

  • Traits can include physical appearance:
    • Trait: Height (possible phenotypes: 5’1”, 6’0”, 3’11”)
    • Trait: Hair color (possible phenotypes: brown, black, blonde)
  • Traits can include behavior:
    • Trait: Depression (possible phenotypes: not depressed, mildly depressed)
    • Trait: Sociability (possible phenotypes: extroverted, introverted)
  • Traits can include development:
    • Trait: Lifespan (possible phenotypes: 67 years, 91 years)
  • Traits can include internal properties of the organism:
    • Trait: Estrogen levels (possible phenotypes: 10 pg / mL, 3 pg / mL)
    • Trait: Cholesterol levels (possible phenotypes: 200 mg / dl, 150 mg / dl)
    • Trait: Red blood cells shape (possible phenotypes: round, sickle-celled)
    • Trait: Cell growth (possible phenotypes: non-cancerous, cancerous)

Nature vs. Nurture

  • Nature vs. nurture asks how much of our phenotypes are because of our genetics (nature) vs. our environment (nurture)?
  • Almost all phenotypes are the result of both nature AND nurture.

Phenotypes, Genotypes, and the Environment

  • Phenotypes are the result of your genotypes and the environment.
  • Genotype is your genetic makeup.
  • The environment includes:
    • Diet / nutrients
    • Climate
    • Exposure to bacteria / viruses / etc.
    • Stress
  • Both your current environment and your past environment matter to your phenotypes.
  • Example: Blocked arteries have genetic and environmental components (high-fat diet, not exercising, smoking).
  • Maternal stress during pregnancy can affect offspring phenotype (MacKinnon et al. 2018).
    • Kids born to moms experiencing high stress during pregnancy are twice as likely to have a behavioral disorder than moms who had low-stress pregnancies.

Continuous vs Discrete Traits

  • Discrete traits are traits where the phenotypes can be put into a few categories.
    • Example: flower color (purple or white), sickle cell anemia (you have it or you don’t).
  • Continuous traits are where there is a huge range of possible phenotypes.
    • Example: height, eye color, male baldness, depression, IQ, blood pressure.

Complex Traits

  • Almost all traits are continuous because most traits are complex.
  • Complex traits are those where many proteins interact to give rise to the trait.
  • This can result in a wide range of phenotypes for that trait, depending on how each protein is working.

How Genotype Affects Phenotype

  • Genotype can affect phenotypes if different alleles lead to different protein structures or different levels of gene expression.

Alleles and Mutations

  • Mutations create alleles (genetic diversity).
  • Alleles are different versions of the same gene.
  • One gene could have hundreds of alleles.
  • Different alleles SOMETIMES affect how the gene & its protein work.
  • Example: A gene involved in flower color can have one allele that leads to purple flowers, another that leads to white flowers, and others that lead to light purple flowers.

Phenotypic Effect of Mutations

  • Most mutations DO NOT affect phenotype because they occur in non-functional parts of the genome or don’t affect the gene.
  • Some mutations DO affect phenotype.
  • Mutations can affect phenotypes in two main ways:
    • Change the structure of a protein (change in amino acids, affecting protein function).
    • Change gene expression (change when/where a gene is turned on, or how much protein is made).
  • Example: Hemoglobin gene mutation leads to mutant hemoglobin that clumps up, leading to abnormal red blood cells and sickle cell disease.

Mutation Effects on Protein Structure and Gene Expression

  • Mutations can affect protein structure through changes in the amino acid sequence (typically in the exon, or intron mutations that affect splicing).
  • Mutations can affect gene expression by changing how much protein is made and/or when the protein is made.

Gain-of-Function vs Loss-of-Function Mutations

  • Mutations that affect phenotypes can either be gain-of-function (gof) or loss-of-function (lof).
  • Gain-of-function (gof):
    • Mutation affecting gene expression: Increased gene expression.
    • Mutation affecting protein structure: New function for protein OR protein functions more.
  • Loss-of-function (lof):
    • Mutation affecting gene expression: Decreased gene expression.
    • Mutation affecting protein structure: Protein no longer functions at all OR protein functions less.

Dominant vs. Recessive Alleles

  • Gof mutations tend to lead to dominant alleles.
  • Lof mutations tend to lead to recessive alleles.
    • Dominant allele: shows its phenotype even if you just have one copy of the allele.
    • Recessive allele: shows its phenotype only if you are homozygous for the allele.
    • Homozygous: when you have identical copies of an allele at a given gene.
    • If gene alpha has three possible alleles A1, A2, and A3, homozygous genotypes are A1A1, A2A2 and A3A3.

Why Lof Mutations Tend to Be Recessive & Gof Mutations Dominant

  • Lof mutations tend to be recessive:
    • If a flower has a lof mutation in one copy of the purplase gene, the other “normal” allele is still making purplase, so the flower will still have enough purplase enzyme to turn purple.
    • But, if the flower has a lof mutation in BOTH copies of the purplase gene, the flower will have no purplase enzyme & will stay white.

Why Gof Mutations Tend to Be Dominant

  • Gof mutations tend to be dominant:
    • If a flower has a gof mutation in one copy of the purplase gene, this gof mutation changes the enzyme so now it makes even MORE purple color.
    • The “normal” copy will still make the “normal” enzyme.
    • The mutated copy will make the mutated enzyme.
    • Because the mutated enzyme is around … you will see even MORE purple color.
    • It only takes one copy of the gof mutation to see its phenotype.

Exception 1: Haploinsufficiency

  • Haploinsufficiency is when having one copy of the “normal” allele is not enough to produce the “normal” phenotype.
  • In this case, a lof mutation leads to a dominant allele.
  • Example: the colorase gene makes the colorase protein, which makes brown pigment and brown dogs.
    • A dog has a lof mutation in the colorase gene, so it makes less colorase protein.
    • Only having 50% of colorase isn’t enough!
    • Because 50% colorase isn’t enough, and the dog cannot make the brown pigment.
    • So, the dog will stay white even though it only has one lof mutation.

Exception 2: Antimorphic Mutations

  • Antimorphic mutations are lof mutations that lead to a defective protein that interferes with the “normal” protein.
  • Example: Marfan syndrome is caused by a lof mutation to the fibrillin-1 gene (FBN1).
    • FBN1 is a protein that makes up our connective tissue.
    • The lof mutation leads to a shortened version of FBN1 with a different structure.
    • Normally, fibrillin-1 assembles into long chains (microfibrils) that bundle together to form our connective fibers.
    • Defective fibrillin-1 proteins mess up the chains, even though the normal fibrillin-1 is around.
    • This leads to the connective tissue getting all messed up.

Complexity of Genotype-Phenotype Connection

  • Organisms are complicated.
  • Even seemingly "simple" traits are complicated.
    • At least 400 genes are involved in partially determining human skin color.
    • More than 700 genes are involved in partially determining human height.
    • More than 100 genes are involved in partially determining risk for coronary heart disease.
  • Each of these genes makes a protein that somehow affects the trait!

Biochemical Pathways

  • Genes interact to give rise to a trait.
  • Ethanol breakdown:
    • Alcohol dehydrogenase converts ethanol into acetaldehyde.
    • Aldehyde dehydrogenase converts acetaldehyde to acetate.

Key Vocabulary

  • Epistasis is when multiple genes interact to give rise to the same trait.
  • Pleiotropy is when one gene affects multiple traits.
  • Redundancy is when multiple genes are redundant with each other, or when they play similar roles in the organism.

Made Up Biochemical Pathway Example: Epistasis

  • Imagine the organism was homozygous for lof mutations in the Gamma gene.
  • This would mean no working protein Gamma!
  • No working protein Gamma would mean no chemical D would be made.
  • Even though protein Theta works, there is no Chemical D to turn into Chemical E.
  • So, the organism wouldn’t be able to turn green.
  • Being green depends on BOTH protein Gamma and protein Theta working.

Made Up Biochemical Pathway Example: Redundancy

  • Imagine that an organism is homozygous for a lof mutation in gene Alpha.
  • This would mean no working Protein Alpha.
  • No working protein Alpha means no chemical C, right?
  • No! Protein Beta to the rescue!
  • Protein Beta is still around, so it can convert Chemical B into chemical C.
  • Protein Alpha and Beta both make chemical C, so they are redundant with each other.

Made Up Biochemical Pathway Example: Pleiotropy

  • Now, protein Theta can do two reactions in the cell.
  • Protein Theta can convert Chemical D into Chemical E (which makes you green).
  • And, protein Theta can convert Chemical F into Chemical G (which makes you glow).
  • Protein Theta affects two traits (color & glowing).

Connecting Genotype to Phenotype

  • To make this connection, you have to think about the protein’s function and how the mutation affects its function.

Protein Functions

  • Catalyze reactions (enzymes).
  • Give our body structure (structural proteins).
  • Regulate how energy, chemicals, water etc. move in a cell (membrane-transport and carrier proteins).
  • Regulate when other genes turn on or off (transcription factors, activators, repressors).

Wild-Type

  • Wild-type is used for both alleles and phenotypes.
  • Wild-type is the most common allele in the natural population.
  • Wild-type is the most common phenotype in the natural population.
  • Wild-type is not better than mutant!
  • Wild-type is not worse than mutant!

Alcohol Intolerance Example

  • Mutation in the gene aldehyde dehydrogenase (ALDH) leads to alcohol intolerance in people of Asian descent.
  • When you drink alcohol, the ethanol is first broken down into acetaldehyde by alcohol dehydrogenase.
  • ALDH is an enzyme that then breaks down acetaldehyde into acetate.
  • Many people of Asian descent have a substitution mutation in an exon of the ALDH gene.
  • The mutation leads to an amino acid change in the ALDH enzyme.
  • This amino acid change disrupts the active site of the enzyme.
  • This is a lof mutation.
  • The enzyme no longer works as well, meaning it does not break down acetaldehyde well.
  • Because ALDH doesn’t work, acetaldehyde doesn’t get converted into acetate. So, the acetaldehyde just builds up in the cell!
  • So, when people with the ALDH mutation drink alcohol, acetaldehyde builds up in their liver.
  • Acetaldehyde is toxic, so their bodies then have a negative reaction to acetaldehyde.
  • Negative reaction includes getting a flushed & red face.

“Butterfly Disease” (Junctional Epidermolysis Bullosa) Example

  • Caused by mutations in the laminin gene.
  • Laminin proteins make up basement membranes.
  • Basement membrane is a tissue that separates the lining of our body (i.e., skin) from connective tissue (i.e., the dermis).
  • Some people have a lof mutation in laminin.
  • This mutation leads to splicing of the premature laminin mRNA going wrong.
  • Because the splicing of the mRNA goes wrong, the mature mRNA sequence is wrong.
  • So the laminin protein made has the wrong amino acid sequence.
  • So the laminin protein cannot be incorporated into the basement membrane properly.
  • This leads to the skin not holding together properly.
  • A slight touch to the skin can lead someone with this disease to blister.
  • Scientists developed a technique to help treat this disease:
    • They took healthy skin cells from the sick patient.
    • Used a virus to introduce the wild-type laminin sequence into the cells.
    • Then transplanted these cells back into the patient.
    • The patient soon had healthy skin

SLC24A5 Example

  • The SLC24A5 (solute carrier family 24 member 5) gene makes a protein involved in transport of ions in the cell.
  • By helping move ions, the protein SLC24A5 helps produce melanin.
  • Melanin is a pigment that determines the skin color of humans & and other animals.
  • The wild-type allele of SLC24A5 leads to high melanin production and dark skin.
  • A substitution mutation in an exon of SLC24A5 leads to an amino acid change in the SLC24A5 protein (alanine to threonine).
  • The amino acid change leads to the protein no longer working well.
  • So, this mutation is a lof.
  • Because people with the lof mutation don’t have working SLC24A5, melanin production goes down.
  • So, people with this mutation have lighter skin.
  • This mutation explains 30% of the variation in skin color among human populations.
  • Mutations to SLC24A5 in zebrafish also affect zebrafish color.

Sonic Hedgehog (SHH) Example

  • Sonic hedgehog (SHH) is a gene that makes a transcription factor (sonic hedgehog, or SHH).
  • SHH plays a big role in limb development.
  • SHH regulates (i.e., turns on or off) many genes that are involved in limb development in vertebrates.
  • Snakes have multiple deletions in the enhancer sequence for SHH.
  • Because of these mutations, activators cannot turn on SHH.
  • And SHH expression is low in snakes.
  • Because there is no SHH (transcription factor), the genes that SHH regulates never get turned on, so no limbs ever develop in snakes.

Overall Considerations

  • When you are trying to understand the effect of a mutation on the phenotype, think about:
    • Where is the mutation in the gene (i.e., in the enhancer, exon, intron …)?
    • What kind of change is it (i.e., substitution, deletion, insertion)?
    • Does it affect gene expression or protein structure?
    • What kind of protein does the gene make?
    • What role does the protein have for the organism?

Study Guide

  • phenotype
  • trait
  • nature vs. nurture
  • environment
  • continuous traits
  • discrete traits
  • complex traits
  • gain-of-function
  • loss-of-function
  • dominant allele
  • recessive allele
  • haploinsufficiency
  • antimorphic mutations
  • epistasis
  • pleiotropy
  • redundancy
  • wild-type