Mendelian Genetics and Gene Expression

Mendel's Principles of Heredity

Mendel's Study of Alternative Traits in Pea Plants

• Mendel inferred laws of genetics to predict trait appearance, disappearance, and reappearance.

• His paper "Experiments in plant hybrids" (1866) is a cornerstone of modern genetics.

• Peas were chosen for their pure-breeding lines, cross-fertilization capability, large offspring numbers in short time, and constant traits within lines.

• He studied inheritance of alternative forms of traits, which were "either-or" categorical traits (e.g., purple or white, yellow or green).

Keys to Mendel’s Experiments

• Pure-breeding lines of peas (Pisum sativum) allowed controlled crosses.

• Breeding could be done by cross-fertilization (selfing).

• Large numbers of offspring were produced within a short time.

• Traits remained constant in crosses within a line.

• Inheritance of alternative forms of traits

• “Either-or" (categorical) traits: e.g. purple or white, yellow or green (not continues traits, such as height)

Monohybrid Crosses and the Law of Segregation

• Mendel crossed pure-breeding lines differing in one trait (e.g., seed color).

• He examined the phenotypes of F1 and F2 progenies.

• F1 progeny had only one of the parental traits.

• Both parental traits reappeared in F2 progeny in a $3:1$ ratio/

1. Genes are the basic units of heredity.

   • Heredity transmits traits from parents to offspring.

   • Genes pass from one generation to the next.

2. Genes underlie every heritable trait (e.g., hair, skin, eye color).

   • $A, B, …$ = dominant

   • $a, b, …$ = recessive

Genotype vs. Phenotype

• A cross of $Yy \times Yy$ peas shows:

  • Genotypes in F2: $1:2:1$ ratio ($\frac{1}{4}YY$, $\frac{1}{2}Yy$, $\frac{1}{4}yy$).

  • Phenotypes in F2: $3:1$ ratio ($\frac{3}{4}$ yellow, $\frac{1}{4}$ green) (Fig. 2.13).

Testcross to Reveal Unknown Genotype

• Question: Is the genotype of an individual with a dominant phenotype heterozygous ($Yy$) or homozygous ($YY$)?

• Solution: Testcross to homozygous recessive ($yy$) and examine offspring phenotype.

Mendel's Proposal

• Each plant carries two copies of a unit of inheritance.

• Traits have two forms that can each breed true.

• Trait appearing in F1 is dominant; trait hidden is recessive.

• Progeny inherit one unit from each parent.

• Units of inheritance are now known as "genes".

• Alternative forms of a single gene are "alleles".

• Individuals with two different alleles for a single trait are "monohybrids".

The Blending Hypothesis

• Stated that inherited traits were determined randomly from a range between homologous traits in parents.

• Example: offspring height would be intermediate between parents' heights.

Definitions

• Phenotype: Observable characteristic (e.g., yellow or green pea seeds).

• Genes: Units of inheritance.

• Alleles: Alternative forms of one gene (e.g., A or a; Y or y).

• Dominant Allele: (A)

• Recessive Allele: (a)

• Genotype: Combination of alleles ($AA$ or $Aa$ or $aa$).

• Homozygous: Two identical alleles ($AA$ or $aa$).

• Heterozygous: Two different alleles ($Aa$).

• Heterozygous phenotype defines the dominant allele (e.g., $Aa$ peas are yellow, so yellow allele $A$ is dominant to green allele $a$).

Generations in Crosses

• P (Parents): $AA \times aa$.

• F1 (‘filial’ offspring 1): $Aa$. $Aa \times Aa$.

• F2 (‘filial’ offspring 2): $AA$ or $Aa$ or $aa$. *Another word for ‘offspring’ = progeny

Punnett Square

• A visual representation of possible genotypes from a cross.

Dihybrid Cross

• Cross between individuals who are heterozygous for two traits.

• Example: Seed shape and seed color.

• $RRYY \times rryy$ where R = round (dominant), r = wrinkled (recessive), Y = yellow (dominant), y = green (recessive).

• F1 generation: All $RrYy$.

• F2 generation phenotypic ratio: 9/16 round & yellow, 3/16 round & green, 3/16 wrinkled & yellow, 1/16 wrinkled & green.

Dihybrid Cross: Parental and Recombinant Types

• Each F1 dihybrid produces four possible gametes in a $1:1:1:1$ ratio: $Yy Rr \rightarrow \frac{1}{4}YR, \frac{1}{4}Yr, \frac{1}{4}yR, \frac{1}{4}yr$.

• Four phenotypic classes occur in the F2 progeny:

  • Two are like parents.

  • Two are recombinant.

Phenotype Ratio

• In F2 progeny, a $3:1$ phenotype ratio of dominant to recessive forms exists for both traits.

  1. Yellow to Green ratio ($3:1$)

  2. Round to wrinkled ratio ($3:1$)

Independent Assortment

• Independent assortment in crosses of F1 dihybrids produces a $9:3:3:1$ phenotype ratio.

Mendel's Law of Independent Assortment

• During gamete formation, different pairs of alleles segregate independently of each other.

  • $Y$ is just as likely to assort with $R$ as it is with $r$.

  • $y$ is just as likely to assort with $R$ as it is with $r$.

Mendel's Laws to Predict Offspring

• To calculate possible gamete genotypes from a hybrid, raise 2 to the power of the number of different traits:

  • $AaBbCcDd \rightarrow 2^4 = 16$ kinds of gametes.

  • $AaBbCcDd \times AaBbCcDd \rightarrow 16 \times 16 = 256$ genotypes.

• Break down polyhybrid cross into independently assorting monohybrid crosses as an easier method.

Example Cross

• Cross: yellow (heterozygous), short x yellow (heterozygous), tall (heterozygous): $Yytt \times YyTt$.

• Punnett Square setup with $Yt, YT, yt, yT$ gametes.

• Phenotypes:

  • Yellow & tall: 6/16 = 37.5% ($\frac{3}{8}$).

  • Yellow & short: 6/16 = 37.5% ($\frac{3}{8}$).

  • Green & tall: 2/16 = 12.5% ($\frac{1}{8}$).

  • Green & short: 2/16 = 12.5% ($\frac{1}{8}$).

Mendel’s 3 Laws Recap

1. Law of Dominance (‘3rd Law’): One allele is dominant, the other recessive. The dominant allele masks the effect of the other (e.g., $Yy$ = yellow, $Y$ dominant to $y$).

2. Law of Segregation (‘1st Law’): Two alleles ‘segregated’ (separated) during gamete formation, reunite at random during fertilization.

3. Law of Independent Assortment (‘2nd Law’): Alleles for different traits (on different genes) are distributed (‘assorted’) to gametes independently. Dihybrid cross (both parents are heterozygous for 2 traits): $AaBb \times AaBb$ . The alleles for separate traits are passed from parent to offspring independently of one another

Testcrosses on Dihybrids

• Testcross to individuals that are homozygous for both recessive traits.

• Determining genotype of a yellow and round pea:

  • Possible genotypes: $YYRR, YYRr, YyRR, YyRr$.

Single or Polygenic Traits

• Number of phenotypes depends on genes controlling the trait.

  1. Single gene traits (monogenic): Controlled by a single gene with two alleles (e.g., widow’s peak).

     • Only two phenotypes are possible (widow’s peak or no widow’s peak).

  2. Polygenic traits: Controlled by two or more genes with two or more alleles.

     • Many possible genotypes and phenotypes (e.g., height).

Single Dominant Traits

• Examples:

  • Dark hair ($LL, Ll$), light hair ($ll$).

  • Curly hair ($TT, Tt$), straight hair ($tt$).

  • Curl tongue ($CC, Cc$), cannot curl tongue ($cc$).

  • Mid-digital hair present ($MM, Mm$), mid-digital hair absent ($mm$).

  • Eyes not blue ($EE, Ee$), blue eyes ($ee$).

  • Widow's peak ($WW, Ww$), no peak ($ww$).

Human Disorders (Mendelian Fashion)

• Single gene disorders:

  1. Autosomal Dominant: Individuals have disorder if: $AA$ or $Aa$.

  2. Autosomal Recessive: Individuals have disorder if: $aa$.

  3. Sex-linked:

     • Y-linked: Disorder linked to Y chromosome, only males affected.

     • X-linked:

       • X-linked recessive: Male with disorder = $XY$, Female “carrier” = $XX$, Female with disorder = $XX$.

       • X-linked dominant

Single-Gene Traits caused by Recessive Alleles

• Examples:

  • Sickle-cell anemia: abnormal hemoglobin, anemia, blocked circulation, malaria resistance. 1/625 African-Americans

  • Cystic fibrosis: defective cell membrane protein, excessive mucus, digestive and respiratory failure. 1/2000 Caucasians

  • PKU(Phenylketonuria): missing enzyme, mental deficiency. 1/10,000 Caucasians.

Single-Gene Traits caused by Dominant Alleles

• Examples:

  • Huntington disease: nerve degeneration, neurological disorders by ages 40 - 70. 1/25,000 Caucasians

Pedigrees

• Orderly diagrams of a family's relevant genetic features.

• Includes multiple generations.

• Analyzed using Mendel's laws for single-gene traits, dominance.

Pedigree Analysis

• Symbols used in pedigree analysis (Fig. 2.20).

Pedigree Example

• Determining mode of inheritance: autosomal recessive or autosomal dominant.

• If autosomal dominant, possible genotypes listed for each individual in pedigree.

Autosomal Dominant Example: Huntington Disease

• Progressive nerve degeneration, results in severe physical and mental disability and death.

• Affects both sexes.

• Every affected person has an affected parent.

• $∼\frac{1}{2}$ the offspring of an affected individual are affected.

Dominant Traits in Pedigrees

• Key aspects:

  1. Affected children always have at least one affected parent.

  2. Dominant traits show a vertical pattern of inheritance.

  3. Two affected parents can produce unaffected children, if both parents are heterozygotes.

Autosomal Recessive Trait; e.g. Cystic Fibrosis

• Characterized mode of inheritance.

Recessive Traits in Pedigrees

• Key aspects:

  1. Affected individuals can be children of two unaffected carriers, often from matings between relatives.

  2. All children of two affected parents should be affected.

  3. Rare recessive traits show a horizontal pattern.

X-Linked Recessive Inheritance

• Unaffected father, carrier mother.

• Possible outcomes: unaffected son, unaffected daughter, carrier daughter, affected son.

Pedigree for X-Linked Recessive Trait: Hemophilia

Probability Calculations

1. Mother carrier of hemophilia?

   • Son: 50%, Daughter: 50%.

2. Mother not carrier, does not have hemophilia?

   • Son: 0%, Daughter: 0% (but 100% probability to be carrier).

3. Mother has hemophilia?

   • Son: 100%, Daughter: 100%.

4. Mother does not have hemophilia, carrier probability is 1/5000?

   • Son: $50\% \times \frac{1}{5000} = 0.01\%$, Daughter: $50\% \times \frac{1}{5000} = 0.01\%$.

VI DNA Structure, Replication, and Recombination

6.1 Experimental Evidence for DNA as the Genetic Material

Genes: DNA or Protein

• DNA is made of only four different subunits.

  • Too simple to specify genetic complexity?

• Protein is made of 20 different subunits.

  • More potential for creating different combinations?

• Chromosomes contain more protein than DNA.

Griffith's Experiment (1928)

• Used two strains of Streptococcus pneumoniae:

  • Smooth (S) strain: virulent.

  • Rough (R) strain: nonvirulent.

• R cells could be transformed by genetic material transferred from dead S cells.

Avery, MacLeod, and McCarty (1944)

• Provided evidence that DNA is the "transforming principle" of S cells.

GRIFFITH EXPERIMENT

• Rough strain: mouse lives (nonvirulent)

• Smooth strain: mouse dies (virulent)

• Heat-killed smooth strain: mouse lives

• Rough strain & heat-killed smooth strain: mouse dies

  • Also live bacteria found in blood of the dead mouse

• The DNA of the smooth bacteria was not destroyed by the heat and was taken up by the rough bacteria, allowing them to produce capsules that can infect the mouse.

Avery, MacLeod & McCarty

• Showed that DNA was the genetic material that caused the transformation

  • Living R form + protease => S cells (Transformation)

  • Living R form + RNase => S cells (Transformation)

  • Living R form + DNase => R cells (no transformation)

Hershey & Chase

• Showed that DNA was the genetic material that caused the transformation

• Used bacteriophages and E.Coli to prove that DNA, and not protein, is the genetic material of T2 bacteriophages (and probably most organisms)

• *Pellet is the dense part at the bottom of a tube after centrifugation.
  *The bacteria are heavier, denser, so they settle in the pellet.

6.2 The Watson and Crick Double Helix Model of DNA

• James Watson, Francis Crick and Rosalind Franklin resolved DNA structure in 1953.

• Strands are antiparallel.

• Sugar – phosphate backbone on the outside.

• Base pairs in the middle.

• Chains held together by H bonds between A-T and G-C base pairs.

DNA Chemical Constituents

• Deoxyribose, phosphate, four nitrogenous bases.

• Purines (Adenine, Guanine), Pyrimidines (Thymine, Cytosine).

• Attachment of base to sugar, addition of phosphate to nucleoside.

• Nucleoside, purine nucleotide, pyrimidine nucleotide.

• Phosphodiester bonds covalently join adjacent nucleotides