Genetics and Molecular Biology: Mendel, DNA, and Gene Expression

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Chapter 14: Mendel and the Gene

Heredity and Mendelian Genetics

Heredity is the passing of genetic traits from parents to offspring. Gregor Mendel used pea plants to uncover the basic principles of inheritance, which are foundational to modern genetics.

Trait: A specific characteristic, such as flower color or seed shape.
Genotype: The genetic makeup of an individual (the set of alleles).
Phenotype: Observable features or traits of an individual.
Pure lines: Populations that produce offspring identical to themselves when self-fertilized.
Hybrid: Offspring from the mating of two different pure lines.

Mendel's Experimental Design

Self-pollination: Pea plants can fertilize themselves because they have both male and female reproductive organs.
Cross-pollination: Mendel controlled pollination by removing male parts and transferring pollen.
Parental (P) generation: Pure-breeding parents.
F1 generation: First filial generation (offspring of P generation).
F2 generation: Second filial generation (offspring of F1 self-fertilization).

Genetic Terminology

Gene: Hereditary factor that influences a trait.
Allele: Different versions of a gene.
Dominant allele: Expressed when present (capital letter).
Recessive allele: Expressed only when two copies are present (lowercase letter).
Homozygous: Two identical alleles (RR or rr).
Heterozygous: Two different alleles (Rr).

Principles of Inheritance

Principle of Segregation: Each gamete receives one allele of each gene.
Principle of Independent Assortment: Alleles of different genes assort independently during gamete formation.
Dihybrid Cross: Mating between individuals heterozygous for two traits.
Test Cross: Used to determine the genotype of an individual with a dominant phenotype by crossing with a homozygous recessive individual.

Genetic Mapping and Chromosome Theory

Chromosome theory of inheritance: Genes are located on chromosomes.
Linkage: Genes located close together on the same chromosome tend to be inherited together.
Recombination: Crossing over during meiosis can separate linked genes.
Genetic map: Shows gene positions based on recombination frequencies.
Frequency of crossing over: Used to estimate genetic distances between genes.

Types of Dominance and Gene Interactions

Complete dominance: Dominant allele completely masks the recessive allele.
Codominance: Both alleles are expressed equally (e.g., ABO blood type).
Incomplete dominance: Heterozygotes have an intermediate phenotype.
Pleiotropy: One gene affects multiple traits.
Epistasis: One gene masks or modifies the effect of another gene.

Sex-Linked Inheritance

X-linked traits: Genes located on the X chromosome; males are more likely to express recessive X-linked traits.
Y-linked traits: Genes located on the Y chromosome; passed from father to son.
Examples: Color blindness (X-linked recessive), hemophilia (X-linked recessive), hypophosphatemia (X-linked dominant).

Pedigree Analysis

Pedigree: Diagram showing inheritance patterns in families.
Autosomal dominant: Affected individuals have affected parents; trait appears in every generation.
Autosomal recessive: Affected individuals may have unaffected parents; trait can skip generations.
X-linked recessive: More males affected; trait can skip generations.
X-linked dominant: Affected males pass trait to all daughters, not sons.

Chapter 15: DNA and the Gene: Synthesis and Repair

DNA Structure and Function

DNA is the hereditary material in most organisms. Its structure and replication are central to genetics.

Hershey-Chase experiment: Demonstrated that DNA, not protein, is the genetic material.
DNA structure: Double helix composed of nucleotides joined by phosphodiester bonds.
Phosphate group: Attached to the 5' carbon of deoxyribose sugar.
Base pairing: Adenine (A) pairs with Thymine (T); Guanine (G) pairs with Cytosine (C).
Antiparallel strands: DNA strands run in opposite directions (5' to 3' and 3' to 5').
Stability: Provided by hydrogen bonding and base stacking.

DNA Replication

Semiconservative replication: Each new DNA molecule consists of one old strand and one new strand.
Origin of replication: Specific sequence where replication begins.
Replication fork: Y-shaped region where DNA is being unwound and replicated.
Enzymes involved: Helicase (unwinds DNA), primase (synthesizes RNA primer), DNA polymerase (synthesizes new DNA), ligase (joins fragments), sliding clamp (holds polymerase).
Leading strand: Synthesized continuously.
Lagging strand: Synthesized discontinuously in Okazaki fragments.
Telomeres: Repetitive sequences at chromosome ends; telomerase extends telomeres.

DNA Repair Mechanisms

Proofreading: DNA polymerase checks and corrects errors during replication.
Mismatch repair: Enzymes correct errors missed by DNA polymerase.
Nucleotide excision repair: Removes damaged DNA segments (e.g., UV-induced thymine dimers).
XP (Xeroderma pigmentosum): Genetic disorder caused by mutations in nucleotide excision repair genes.

Chapter 16: How Genes Work

Gene Expression and the Central Dogma

Gene expression is the process by which genetic information is used to produce proteins, determining phenotype. The central dogma describes the flow of genetic information from DNA to RNA to protein.

Beadle and Tatum experiment: Showed that genes code for enzymes in metabolic pathways.
Central dogma:
Transcription: Synthesis of RNA from DNA template.
Translation: Synthesis of protein from mRNA template.
Messenger RNA (mRNA): Carries genetic information from DNA to ribosomes.
RNA polymerase: Enzyme that synthesizes RNA.
Codon: Sequence of three nucleotides in mRNA that specifies an amino acid.
Start codon: AUG (methionine); Stop codons: UAA, UAG, UGA.

Mutations and Their Effects

Point mutation: Change in a single base pair.
Missense mutation: Alters amino acid sequence.
Nonsense mutation: Creates a premature stop codon.
Silent mutation: No change in amino acid sequence.
Frameshift mutation: Addition or deletion shifts the reading frame.
Chromosomal mutations: Changes in chromosome structure (inversion, translocation, deletion, duplication).

Exceptions to the Central Dogma

Some RNAs (rRNA, tRNA) are never translated.
Some viruses use reverse transcriptase to convert RNA to DNA.

Additional Key Concepts and Definitions

Genetic Crosses and Predictions

Monohybrid cross: Mating between individuals heterozygous for one trait.
Dihybrid cross: Mating between individuals heterozygous for two traits; supports independent assortment.
Punnett square: Diagram used to predict genotype and phenotype ratios.
Testcross: Cross with a homozygous recessive individual to determine genotype.

Important Ratios and Equations

Monohybrid F2 ratio: 3:1 (dominant:recessive phenotype).
Dihybrid F2 ratio: 9:3:3:1 (phenotypes for two traits).

HTML Table: Types of Mutations and Their Effects

Mutation Type	Description	Effect on Protein
Missense	Change in one base pair	Alters one amino acid
Nonsense	Change creates stop codon	Premature termination
Silent	Change does not alter amino acid	No effect
Frameshift	Insertion/deletion shifts reading frame	Alters downstream amino acids

HTML Table: Types of Dominance

Type	Genotype	Phenotype	Example
Complete Dominance	RR, Rr	Dominant trait expressed	Purple flower color in peas
Incomplete Dominance	Rr	Intermediate phenotype	Pink snapdragon flowers
Codominance	IAIB	Both traits expressed	AB blood type

Additional info:

Some explanations and examples have been expanded for clarity and completeness.
Tables have been inferred and organized for comparison and classification.