Unit 3: Genetics

3.1 Genetic Materials

Introduction to Genetics

Genetics is the branch of biology that studies heredity (the transmission of traits from parents to offspring) and variation (differences among individuals). It provides the framework for understanding how genetic information is stored, expressed, and passed on.

Genetic Materials: DNA as the Genetic Material

Early experiments identified DNA as the molecule carrying genetic information.

• Avery‑MacLeod‑McCarty experiment (1944): Treated heat‑killed Streptococcus pneumoniae with enzymes that destroyed proteins, lipids, carbohydrates, and RNA. Only DNase abolished the transforming activity, indicating DNA is the transforming principle.
• Hershey‑Chase experiment (1952): Used bacteriophage T2 labeled with radioactive ³²P (in DNA) and ³⁵S (in protein). After infection, only ³²P entered bacterial cells, showing DNA, not protein, is the genetic material.

Composition of DNA

DNA is a polymer of nucleotides. Each nucleotide consists of:

• A deoxyribose sugar (5‑carbon)
• A phosphate group
• A nitrogenous base (adenine, thymine, guanine, or cytosine)

The nucleotides link via phosphodiester bonds between the 3′‑OH of one sugar and the 5′‑phosphate of the next, forming a sugar‑phosphate backbone.

Structure of DNA: Watson‑Crick Model

James Watson and Francis Crick proposed the double‑helix model in 1953.

• Antiparallel strands: One strand runs 5′→3′, the complementary strand runs 3′→5′.
• Base pairing: Adenine (A) pairs with thymine (T) via 2 hydrogen bonds; guanine (G) pairs with cytosine (C) via 3 hydrogen bonds.
• Major and minor grooves: The twisting of the helix creates asymmetric grooves that allow proteins to bind specifically to DNA sequences.

"It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material." – Watson & Crick, 1953

Function of DNA

• Storage of genetic information: The sequence of bases encodes instructions for protein synthesis.
• Replication: DNA duplicates itself prior to cell division, ensuring each daughter cell receives an identical copy.
• Transcription: A segment of DNA is transcribed into RNA, which serves as a template for translation.

Composition and Structure of RNA

RNA differs from DNA in three key ways:

• Contains ribose sugar (with a 2′‑OH group) instead of deoxyribose.
• Uses uracil (U) in place of thymine.
• Typically exists as a single‑stranded molecule, though it can fold into complex secondary structures.

Types of RNA

mRNA (messenger RNA)

Carries the genetic code from DNA to the ribosome; each codon specifies an amino acid.

tRNA (transfer RNA)

Adaptor molecule; anticodon loop pairs with mRNA codon, acceptor stem carries the corresponding amino acid. Often depicted as a clover‑leaf secondary structure.

rRNA (ribosomal RNA)

Structural and catalytic component of ribosomes; forms the core of the small and large subunits.

DNA Replication

DNA replication is semi‑conservative: each new DNA molecule consists of one parental strand and one newly synthesized strand.

Meselson‑Stahl Experiment (1958)

E. coli grown in ¹⁵N (heavy) medium then transferred to ¹⁴N (light) medium. After one generation, DNA showed an intermediate density; after two generations, both light and intermediate bands appeared, confirming semi‑conservative replication.

Steps of Replication

1. Unwinding: Helicase separates the two strands, creating a replication fork.
2. Priming: Primase synthesizes a short RNA primer (≈10 nucleotides) to provide a 3′‑OH for DNA polymerase.
3. Elongation:
   • DNA polymerase III adds nucleotides in the 5′→3′ direction.
   • Leading strand: synthesized continuously toward the fork.
   • Lagging strand: synthesized away from the fork in short segments called Okazaki fragments (≈100‑200 nt in eukaryotes).
4. Removal of primers: DNA polymerase I replaces RNA with DNA.
5. Ligation: DNA ligase seals the nicks between Okazaki fragments, forming a continuous strand.

Key enzymes: Helicase, primase, DNA polymerase III, DNA polymerase I, ligase, topoisomerase (relieves supercoiling), single‑strand binding proteins (stabilize unwound DNA).

Introduction of the Genetic Code

The genetic code translates nucleotide sequences into amino acid sequences.

• Triplet code: Three nucleotides form a codon that specifies one amino acid.
• 64 codons: 4³ possible combinations.
• 61 sense codons: encode amino acids.
• 3 stop codons: UAA, UAG, UGA (no amino acid; signal termination).
• Start codon: AUG encodes methionine and initiates translation.
• Properties:
  • Universal: nearly all organisms use the same code.
  • Degenerate: most amino acids are specified by more than one codon (e.g., Leu = UUA, UUG, CUU, CUC, CUA, CUG).
  • Non‑overlapping: each nucleotide belongs to only one codon.
  • Comma‑free: no punctuation; codons are read sequentially.

3.2 Mendelian Genetics

General Terminology

Term	Definition
Trait	A characteristic that can be inherited (e.g., flower colour).
Character	The specific attribute of a trait (e.g., purple vs. white flower).
Allele	Alternative form of a gene occupying the same locus.
Homozygous	Two identical alleles (e.g., AA or aa).
Heterozygous	Two different alleles (e.g., Aa).
Genotype	Genetic makeup of an organism (e.g., Aa).
Phenotype	Observable expression of the genotype (e.g., purple flower).
Dominant	Allele that masks the effect of another allele in a heterozygote.
Recessive	Allele whose effect is hidden in the presence of a dominant allele.
F1	First filial generation – offspring of the parental cross.
F2	Second filial generation – offspring of self‑crossing F1 individuals.

Mendel's Experiments

Gregor Mendel (1856‑1863) performed systematic crosses using the garden pea (Pisum sativum). He selected true‑breeding lines for seven characters (seed shape, seed colour, flower colour, pod shape, pod colour, flower position, plant height).

Monohybrid Cross

Cross between parents differing in a single trait.

Example: Purple flower (PP) × white flower (pp).

Punnett Square for Monohybrid Cross (Pp × Pp)

	P	p
P	PP	Pp
p	Pp	pp

Expected F₂ phenotypic ratio: 3 purple : 1 white (3:1).

Dihybrid Cross

Cross between parents differing in two traits.

Example: Seed shape (round R, wrinkled r) and seed colour (yellow Y, green y). Parental genotypes: RRYY × rryy.

Punnett Square for Dihybrid Cross (RrYy × RrYy)

	RY	Ry	rY	ry
RY	RRYy	RRYy	RrYY	RrYy
Ry	RRYy	RRyy	RrYy	Rryy
rY	RrYY	RrYy	rrYY	rrYy
ry	RrYy	Rryy	rrYy	rryy

Expected phenotypic ratio: 9 round‑yellow : 3 round‑green : 3 wrinkled‑yellow : 1 wrinkled‑green (9:3:3:1).

Laws of Inheritance

1. Law of Dominance: In a heterozygote, the dominant allele determines the phenotype while the recessive allele remains masked.
2. Law of Segregation: During gamete formation (meiosis), the two alleles for a gene separate so that each gamete receives only one allele. This explains the 3:1 ratio in monohybrid crosses.
3. Law of Independent Assortment: Alleles of different genes assort independently into gametes, provided the genes are located on different chromosomes (or far apart on the same chromosome). This yields the 9:3:3:1 ratio in dihybrid crosses.

Gene Interactions

When alleles of a single gene or multiple genes interact, phenotypic ratios may deviate from Mendelian expectations.

Incomplete Dominance

The heterozygote exhibits an intermediate phenotype between the two homozygotes.

Example: Snapdragon flower colour.

• Red (RR) × White (rr) → F₁ all pink (Rr).
• F₂ cross (Rr × Rr) yields genotypes: 1 RR (red) : 2 Rr (pink) : 1 rr (white). Phenotypic ratio: 1 red : 2 pink : 1 white.

Punnett Square for Incomplete Dominance (Rr × Rr)

	R	r
R	RR	Rr
r	Rr	rr

Co‑dominance

Both alleles are fully expressed in the heterozygote, producing a phenotype that shows both traits simultaneously.

Example: Human ABO blood group.

• Alleles: I^A (adds N‑acetylgalactosamine), I^B (adds galactose), i (no addition).
• Genotype I^AI^B expresses both A and B antigens → blood type AB.
• Genotype I^Ai or I^AI^A → type A; I^Bi or I^BI^B → type B; ii → type O.

Punnett Square for Co‑dominance (I^Ai × I^Bi)

	IA	i
IB	IAIB	IBi
i	IAi	ii

Phenotypic ratio: 1 AB : 1 A : 1 B : 1 O (1:1:1:1).

Summary of Key Concepts

• DNA is the hereditary material; its double‑helix structure enables accurate replication and transcription.
• RNA serves as the functional intermediary (mRNA, tRNA, rRNA) in translating genetic code into proteins.
• The genetic code is a universal, degenerate, triplet system linking codons to amino acids.
• Mendelian genetics provides the foundation for predicting inheritance patterns through segregation and independent assortment.
• Gene interactions such as incomplete dominance and co‑dominance modify simple Mendelian ratios, illustrating the complexity of genetic expression.