Chapter 1: Introduction, Mendelian and Particulate Inheritance
Reminders and Logistics
CINBio Assignment 2: Due tonight (Friday) at midnight for the on-time deadline. Submissions made through Sunday at midnight will incur a temporary deduction. No answers will be accepted after Sunday at midnight.
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Next Week's Schedule: The instructor will be absent.
Lectures: Lecture recordings for next week have already been posted online for review.
In-person sessions: Teaching Assistants will cover the classes:
Jaden: Monday and Wednesday
Cyrus: Friday
Students are welcome to attend to ask TAs questions.
Instructor Availability: Still reachable by email. Office hours moved to the weekend due to an upcoming exam (not this Monday, but the following one).
Introduction to Mendelian and Particulate Inheritance
Today's Topic: Mendelian and particulate inheritance, focusing on Punnett Squares.
Connection to Previous Material: This topic connects the laws of segregation and independent assortment (learned with mitosis and meiosis) to the actual inheritance of traits.
Scope: We will cover simple dominant-recessive particulate inheritance today. A follow-up lecture on Monday will delve into more complex details.
Resources: Practice problems and an answer key are posted under "Particular Inheritance" (covering material from both lectures).
Pre-Mendelian Understanding of Inheritance
Darwin's Observations: Charles Darwin recognized that parents and offspring share traits, implying a mechanism for inheritance, but he did not understand how.
Blending Inheritance: The prevailing theory before Mendel was "blending inheritance." This analogy, like mixing paints, suggested that paternal and maternal characteristics simply combined in an equal mix to determine offspring traits.
Conflict with Darwin's Theory: Blending inheritance created a problem for Darwin's theory of natural selection. Natural selection relies on variation and the presence of extremes in populations for adaptation and evolution. Blending would continuously reduce variation by averaging traits in each generation, limiting the raw material for selection.
Gregor Mendel's Pivotal Experiments
Pioneer: Gregor Mendel, through his experiments with pea plants, established the foundational principles of inheritance.
Experimental Design: He also introduced rigorous experimental design for studying inheritance patterns.
Key Contribution: Particulate Inheritance: Mendel's most significant finding was demonstrating that inheritance is particulate, meaning there is no blending of traits.
Instead, inheritance involves receiving discrete "packets" of information (what we now call genes/alleles).
Each offspring receives half of these packets from the mother and half from the father.
This combination is random, and further randomness occurs during fertilization, contributing significantly to genetic diversity in sexual reproduction.
The outcome of traits depends on which specific alleles are received (e.g., dominant vs. recessive).
Advantages of Pea Plants and Key Terminology
Why Pea Plants?: Mendel chose pea plants strategically because:
They exhibit very simple inheritance patterns, often involving only two clear traits for a given character.
They grow relatively quickly, allowing for observation of multiple generations.
Seven Traits Studied: Mendel investigated characters such as flower color, plant height, pea color, pea texture, pod shape, pod color, and flower position.
Definitions:
Characters: Observable physical features (e.g., flower color, seed shape, plant height).
Traits: The specific forms or variations of a character (e.g., for flower color, the traits might be white or purple; for plant height, tall or short).
This parallels the concept where characters are the product of genes, and traits are the specific versions (alleles) of those genes.
Monohybrid Crosses and Generations
Blending Prediction vs. Mendel's Results: If blending inheritance were true, crossing a purple flower with a white flower should yield light purple flowers. Mendel found that all F1 generation flowers were purple.
Monohybrid Cross: A cross between two individuals that differ in only one specific trait.
Generations in Breeding Experiments:
Parental (P) Generation: The initial individuals chosen for the first cross.
F1 Generation: The first filial generation, consisting of the offspring from the P generation cross.
F2, F3, etc., Generations: Subsequent generations of offspring, typically produced by self-pollinating or intercrossing individuals from the preceding F generation.
Mendel's F2 Observations: Mendel often self-pollinated the F1 generation.
A remarkable finding was that the white trait, which had seemingly disappeared in the F1 generation, reappeared in the F2 generation.
Across all seven traits, the disappearing trait in F1 consistently reappeared in F2.
The F2 generation consistently showed a 3:1 ratio of the F1 trait (dominant phenotype) to the reappearing trait (recessive phenotype).
Mendel conducted these experiments in large quantities, observing these ratios reliably (e.g., observing 705 purple and 224 white in one experiment, close to 3:1).
Mendel's Explanations and Laws of Inheritance
Particulate Inheritance (Revisited): Mendel concluded that characters are determined by discrete, individual units of inheritance (which we now call genes).
Genes: Segments of DNA that code for specific proteins, which usually have important functions.
Alleles: Different versions or variants of a particular gene (e.g., the allele for purple flower color vs. the allele for white flower color).
Relevance of Meiosis: The patterns Mendel observed are fully explained by the processes of meiosis, specifically the laws of segregation and independent assortment.
Law of Dominance: One allele in a pair (the dominant allele) can mask or override the effect of the other allele (the recessive allele) when both are present.
Example: In pea plants, the purple allele for flower color is dominant over the white allele. If a plant has at least one purple allele, its flowers will be purple.
Mechanism: Often, dominant alleles produce a functional pigment or protein, while recessive alleles produce a non-functional or absent product. If any pigment is produced (e.g., purple), it will typically determine the color.
Real-world Analogy: Eye color. Blue eyes result from an absence of pigment in the iris. Brown pigment, if present, covers up the blue (recessive absence of pigment), making the eyes brown.
Exceptions: Some traits exhibit incomplete dominance or codominance, where blending or co-expression occurs (discussed in a later lecture).
Law of Segregation: During gamete formation, the two alleles for a heritable character (from each parent) separate or "segregate" from each other, so that each gamete receives only one allele for each gene.
This means a gamete (sperm or egg) cannot contain both alleles from a parent for a given gene. It receives either the maternal or the paternal allele.
This ensures that offspring inherit one allele from each parent, restoring the diploid condition.
Law of Independent Assortment: Alleles for different genes (located on different chromosomes or far apart on the same chromosome) assort independently of one another during gamete formation.
This occurs during meiosis I when homologous chromosomes line up randomly at the metaphase plate and then separate.
The orientation of one pair of homologous chromosomes does not influence the orientation of other pairs.
This randomness in chromosome sorting leads to many possible combinations of alleles in the gametes, generating significant genetic diversity.
Alleles, Genotypes, and Phenotypes in Detail
Notation for Alleles: We use letters to represent alleles:
Uppercase letter: Denotes a dominant allele (e.g., P for pink).
Lowercase letter: Denotes a recessive allele (e.g., p for purple).
Selection: Typically, one chooses a letter related to the dominant trait (e.g., 'P' for purple, if purple is dominant, or 'R' for round if round is dominant).
Convention: Letters where uppercase and lowercase forms are visibly distinct are preferred (e.g., 'A/a' over 'S/s').
Example: Flamingo Color: If crossing pink and purple flamingos results in pink offspring, pink is the dominant allele. Offspring will have alleles for purple but express pink.
Question: Can both alleles be dominant? Yes, this describes codominance or incomplete dominance, which are more complex patterns of inheritance discussed later. Simple Mendelian inheritance, as covered today, assumes one allele is clearly dominant.
Question: Hybridization between different species (e.g., lions and tigers)? This relates to species concepts and barriers to reproduction. Usually, if species can interbreed (e.g., if they have similar chromosome numbers and evolutionary history), Mendelian patterns can apply to shared genes.
Genotype: The specific combination of alleles an individual possesses for a given gene or genes.
Homozygous Dominant: Two identical dominant alleles (e.g., PP).
Homozygous Recessive: Two identical recessive alleles (e.g., pp).
Heterozygous: One dominant and one recessive allele (e.g., Pp).
Convention: The dominant allele is always written first in a heterozygous genotype (e.g., Pp, not pP).
Phenotype: The observable physical or biochemical trait expressed by an individual, resulting from their genotype and environmental influences (e.g., pink flower, attached earlobes).
Punnett Squares: Predicting Offspring
Purpose: A Punnett square is a diagram used to predict the possible genotypes and phenotypes of offspring from a genetic cross.
Information Required: To construct a Punnett square, you need:
The genotypes of both parents.
Knowledge of which traits are dominant and recessive.
Mechanism: The squares visualize all possible combinations of alleles that the parents can contribute through their gametes.
For example, if two heterozygous parents (Aa imes Aa) breed:
Each parent can produce two types of gametes: A or a.
The 2 imes 2 Punnett square will show four possible combinations.
Outcome of a Heterozygous Cross (Aa imes Aa):
Genetic Ratio (Genotypes): 1 AA : 2 Aa : 1 aa (or 25 ext{% } AA, 50 ext{% } Aa, 25 ext{% } aa).
Phenotypic Ratio: 3 individuals exhibiting the dominant trait (AA and Aa) to 1 individual exhibiting the recessive trait (aa).
This 3:1 phenotypic ratio is a hallmark of Mendelian monohybrid crosses where both parents are heterozygous.
Probability: This means a 25 ext{%} chance for any single offspring to have the recessive phenotype and a 75 ext{%} chance to have the dominant phenotype.
It's important to remember these are probabilities for each individual offspring, and actual observed ratios might deviate slightly in small sample sizes due to random chance (e.g., having 6 girls in a row, despite 50/50 chance of male/female).
Key Terminology for Genotypes:
Homozygous: An individual having two identical alleles at a specific gene locus (e.g., AA or aa). ("Homo" means same).
Heterozygous: An individual having two different alleles at a specific gene locus (e.g., Aa). ("Hetero" means different).
Dominant Trait: The trait that is expressed in heterozygous individuals.
Recessive Trait: The trait that is not observed in heterozygous individuals (masked by the dominant allele).
Monohybrid Practice Problems
Example 1: Earlobes
Character: Earlobes (attached vs. unattached).
Dominant Trait: Unattached earlobes (E).
Recessive Trait: Attached earlobes (e).
Cross: Two heterozygous parents (Ee imes Ee).
Punnett Square:
E
e
E
EE
Ee
e
Ee
ee
Outcomes:
Genotypes: 1 EE : 2 Ee : 1 ee
Phenotypes: 3 Unattached : 1 Attached
Probabilities: 25 ext{%} chance of a baby with attached earlobes (ee); 75 ext{%} chance of a baby with unattached earlobes (EE ext{ or } Ee).
Example 2: Determining Unknown Genotypes (Test Cross)
Problem: While the genotype of a white flower (recessive phenotype) is definitively homozygous recessive (aa), a purple flower (dominant phenotype) could be either homozygous dominant (AA) or heterozygous (Aa).
Solution: Test Cross: To determine the genotype of an individual with a dominant phenotype, cross it with a known homozygous recessive individual (aa).
Scenario 1 (Mystery is Homozygous Dominant): If the mystery purple flower is AA, then AA imes aa will produce all heterozygous (Aa) offspring. All offspring will express the dominant (purple) phenotype. Ratio: 1:0 (dominant:recessive).
Scenario 2 (Mystery is Heterozygous): If the mystery purple flower is Aa, then Aa imes aa will produce 50 ext{% } Aa (dominant phenotype) and 50 ext{% } aa (recessive phenotype) offspring. Ratio: 1:1 (dominant:recessive).
Conclusion: Observing a 1:0 ratio indicates the mystery parent was homozygous dominant. Observing a 1:1 ratio indicates the mystery parent was heterozygous.
Practical Use: Test crosses are crucial in agriculture and breeding programs to ensure "true breeding" (homozygous) parent lines for desired traits.
Example 3: Round vs. Wrinkly Peas (Test Cross Application)
Characters: Pea shape (round vs. wrinkly).
Dominant Trait: Round (R).
Recessive Trait: Wrinkly (r).
Cross: Unknown round pea plant to a wrinkly pea plant.
Given: The unknown round pea plant is heterozygous (Rr).
Cross Setup: Rr ext{ (unknown, heterozygous round)} imes rr ext{ (known, wrinkly)}.
Punnett Square:
R
r
r
Rr
rr
r
Rr
rr
Expected Ratio: 50 ext{%} round (Rr) and 50 ext{%} wrinkly (rr), or a 1:1 ratio.
In a large sample (e.g., 1000 peas), roughly 500 would be round and 500 wrinkly.
Dihybrid Crosses: Inheritance of Two Traits
Mendel's Next Question: Do different traits (e.g., pea shape and pea color) inherit together or independently?
Hypothesis: Being yellow should not make a pea more likely to be smooth, implying two separate gene locations that are not inherited together.
Dihybrid Cross Defined: A genetic cross between individuals that are heterozygous for two different traits.
Trait Examples:
Pea Shape: Round (R, dominant) vs. Wrinkly (r, recessive).
Pea Color: Yellow (Y, dominant) vs. Green (y, recessive).
Genotype Representation: Genotypes for both traits are written together (e.g., RRYY for a homozygous dominant round, yellow pea).
Crossing F1 Fully Heterozygous Individuals (RrYy imes RrYy):
Step 1: Determine Possible Gametes: Each parent can produce four types of gametes due to independent assortment. This can be visualized using the FOIL method (First, Outer, Inner, Last combinations of alleles).
For a parent with genotype RrYy, the possible gametes are: RY, Ry, rY, ry.
Step 2: Construct the Punnett Square: A 4 imes 4 grid (total of 16 squares) is needed to show all possible combinations of these gametes from both parents.
Convention: Alleles for the same gene are typically grouped together in the offspring genotype (e.g., RRYY).
Predicted Phenotypic Ratio (assuming independent assortment): The classic dihybrid cross of two fully heterozygous individuals always yields a 9:3:3:1 phenotypic ratio.
9 individuals with both dominant phenotypes (e.g., Round Yellow).
3 individuals with one dominant and one recessive phenotype (e.g., Round Green).
3 individuals with the other dominant and other recessive phenotype (e.g., Wrinkly Yellow).
1 individual with both recessive phenotypes (e.g., Wrinkly Green).
Mendel's Results: His experiments confirmed this 9:3:3:1 ratio, thus supporting the Law of Independent Assortment – that genes for different traits are inherited independently.
Exceptions: Genes located close together on the same chromosome (linked genes) do not assort independently and will result in different ratios (to be discussed in a later lecture).
Dihybrid Practice Problem
Scenario: From a dihybrid cross (RrYy imes RrYy) that follows the 9:3:3:1 ratio.
Question: What is the probability that a pea is smooth (round) and green?
Answer: According to the 9:3:3:1 ratio, 3 out of 16 offspring will exhibit the smooth (round) and green phenotype. So, the probability is rac{3}{16}.
Key takeaway: Students should know the 9:3:3:1 ratio for heterozygous dihybrid crosses and be able to interpret genotypes and phenotypes across multiple traits.
Trihybrid Crosses (Brief Introduction to Complexity)
Concept: Trihybrid crosses involve the inheritance of three different traits simultaneously.
Scaling Complexity:
If fully heterozygous (e.g., RrYyPp), an individual can produce 2^3 = 8 different types of gametes.
A Punnett square for a cross between two such individuals would be an 8 imes 8 = 64-square grid.
Typical Outcome: In such a cross, a vast majority of offspring will display dominant phenotypes. Only 1 out of 64 offspring, on average, will exhibit all three recessive phenotypes.
Note: Trihybrid crosses are presented to illustrate how genetic complexity scales up quickly but are not typically required for manual calculation in this course.
Studying Human Inheritance: Pedigrees
Challenges in Human Genetics:
Complex Traits: Many human traits are complex, controlled by multiple genes, or interact significantly with the environment.
Visibility: Some traits are not visible to the naked eye (e.g., blood type).
Long Generation Time: Human reproduction cycles span decades, making experimental breeding across generations impractical.
Ethical Constraints: Direct breeding experiments are ethically unacceptable.
Solution: Pedigrees: Geneticists use pedigrees, which are family trees that track the inheritance of specific traits (often diseases) across multiple generations.
Pedigree Symbols and Conventions:
Shapes: Squares represent males ( ext{ } ext{ }), circles represent females ( ext{ } ext{ }).
Shading: Filled shapes typically indicate individuals expressing the trait (affected phenotype). Unfilled shapes indicate unaffected individuals.
Lines: Horizontal lines connect mating pairs. Vertical lines lead to offspring. Siblings are connected by a horizontal line above them.
Sex Linkage: The inclusion of sex (male/female) in pedigrees is important because some traits are sex-linked (genes on sex chromosomes) and show different inheritance patterns in males vs. females (discussed later).
Inferring Genotypes and Dominance: Pedigrees allow for making inferences about genotypes and whether a trait is dominant or recessive, even without direct experimental crosses.
Example: Widow's Peak: If widow's peak is a dominant trait and no widow's peak is recessive:
If two parents with widow's peak (dominant phenotype) have a child with no widow's peak (recessive phenotype), then both parents must be heterozygous (e.g., Ww imes Ww
ightarrow ww).This pattern (affected parents having an unaffected child for a trait) is a strong indicator that the trait in question is dominant.
Conversely, if two unaffected parents have an affected child, it suggests the trait is recessive, and the parents were both heterozygotes carrying the recessive allele.
Pedigree Practice Problem
Scenario: A pedigree shows individuals with two different earlobe phenotypes. Let's assume white represents attached earlobes and purple represents free earlobes.
Question: Which trait (white or purple) is dominant?
Solution Strategy: Look for instances where two parents with the same phenotype have offspring with a different phenotype.
If two individuals with the purple trait produce offspring, and some of those offspring have the white trait, this is the key. The purple individuals must be heterozygous, carrying the allele for the white trait that occasionally expresses itself. Therefore, purple must be the dominant trait, and white is recessive.
Inferred Genotypes: If purple is dominant, then the two purple parents who had a white child must both be heterozygous (e.g., Pp). The white child would then be homozygous recessive (pp).
This pattern definitively establishes that the purple trait is dominant.