Microbiology Chapter 5: Genetics – Structured Study Notes

Genotype Determines Phenotype

Genetics and Genomes

Genetics is the study of genes, their functions, and how variations arise in genomes. The genome is the entire collection of genetic material in a cell or virus, acting as an instruction manual for all cellular features.

• Gene: Heritable unit of genetic material determining a specific trait.

• Genotype: The genetic makeup of an organism.

• Phenotype: The observable physical and physiological traits influenced by genotype.

• Example: A gene coding for pigment affects the color phenotype of a cell.

Genome Basics

Organization and Complexity

Organisms vary in gene number, but chromosome count does not determine sophistication. Genomes are organized into chromosomes, which are carefully packaged DNA strands with organizational proteins.

• Eukaryotes: Multiple linear chromosomes in the nucleus, organized by histones.

• Prokaryotes: 1-3 circular chromosomes in the nucleoid, organized by histone-like proteins.

• Plasmids: Extra-chromosomal DNA pieces, often conferring survival advantages (e.g., antibiotic resistance).

DNA Structure

Nucleotides and Double Helix

DNA is composed of nucleotides, each with a phosphate group, a sugar (deoxyribose), and a nitrogen base. Nitrogen bases are classified as purines (A, G) or pyrimidines (C, T).

• Purines: Adenine (A), Guanine (G)

• Pyrimidines: Cytosine (C), Thymine (T)

• Base Pairing: A pairs with T, G pairs with C

• Double Helix: Two antiparallel strands forming a twisted ladder, with phosphodiester bonds linking the sugar-phosphate backbone.

• Directionality: DNA strands run 5’ to 3’ and 3’ to 5’.

Table: DNA and RNA Nitrogen Bases

Nitrogen Base	Family	Pairs with	Found in
Adenine (A)	Purine	Thymine (T)	DNA and RNA
Guanine (G)	Purine	Cytosine (C)	DNA and RNA
Cytosine (C)	Pyrimidine	Guanine (G)	DNA and RNA
Thymine (T)	Pyrimidine	Adenine (A)	Only DNA
Uracil (U)	Pyrimidine	Adenine (A)	Only RNA

RNA Structure

Differences from DNA

RNA nucleotides contain ribose sugar and uracil (U) instead of thymine (T). RNA is usually single-stranded and can form helical and loop structures.

• Ribonucleotides: Phosphate group, ribose, nitrogen base (A, G, C, U)

• Directionality: 5’ to 3’

• Single-stranded: Allows folding into complex shapes

Central Dogma of Molecular Biology

Information Flow

The central dogma describes the flow of genetic information: DNA directs the production of RNA, which directs the assembly of proteins.

• Transcription: DNA to RNA

• Translation: RNA to protein

DNA Replication

Process Overview

DNA replication is the process by which a cell copies its genome before division. It is fast and accurate, involving several enzymes.

• Unwinding: Helicase unwinds DNA

• Copying: DNA polymerase III synthesizes new DNA

• Rewinding: Ligase seals nicks in the backbone

• Semiconservative: Each new DNA helix contains one original and one new strand

Table: Key Enzymes in DNA Replication

Enzyme	Function
Helicase	Unwinds DNA helix
Primase	Builds RNA primers
DNA polymerase III	Main enzyme that copies DNA
DNA polymerase I	Replaces RNA primers with DNA
Ligase	Seals nicks in the DNA backbone
Gyrase and Topoisomerases	Relieve torsion stress ahead of helicase

Transcription

RNA Synthesis

Transcription is the process of synthesizing RNA from a DNA template. It occurs in the nucleus of eukaryotes and the cytoplasm of prokaryotes.

• RNA polymerase: Binds promoter, unwinds DNA, synthesizes RNA

• Base pairing: U pairs with A, G pairs with C

• Termination: RNA polymerase falls off at termination sequence

Types of RNA

• Messenger RNA (mRNA): Contains codons for amino acids or stop signals

• Transfer RNA (tRNA): Anticodon loop, carries amino acids to ribosome

• Ribosomal RNA (rRNA): Combines with proteins to form ribosomes

RNA Splicing (Eukaryotes)

RNA splicing removes introns (non-coding regions) and joins exons (coding regions) to produce mature mRNA.

Genetic Code

Codons and Redundancy

The genetic code consists of 64 codons (triplets of nucleotides), encoding 22 amino acids, start, and stop signals. The code is redundant; multiple codons can specify the same amino acid.

• Start codon: AUG (methionine)

• Stop codons: UAA, UAG, UGA

Translation

Protein Synthesis

Translation is the process by which ribosomes synthesize proteins using mRNA as a template. Ribosomes consist of large and small subunits.

• Initiation: Ribosome binds mRNA, initiator tRNA enters P site

• Elongation: tRNA brings amino acids, peptide bonds form

• Termination: Stop codon signals release of completed protein

Controlling Protein Synthesis

Gene Expression Regulation

Protein synthesis is resource-intensive, so cells regulate gene expression. Housekeeping genes are constitutively expressed, while facultative genes are expressed in response to environmental changes.

• Housekeeping genes: Always expressed

• Facultative genes: Expressed as needed

Mutations

Types and Effects

Mutations are changes in genetic material. They can be insertions, deletions, or substitutions, and their effects range from silent to detrimental.

• Silent: No change in amino acid sequence

• Reversion: Mutation corrected by another mutation

• Nonsense: Codon changed to stop signal

• Missense: Codon changed to encode a different amino acid

• Frameshift: Insertion/deletion alters reading frame

Causes of Mutations

Spontaneous and Induced

Mutations can occur spontaneously during DNA replication or be induced by mutagens (chemical, physical, or biological agents). Carcinogens are mutagens that promote cancer development.

• Spontaneous: Natural errors in replication

• Mutagens: Increase mutation rate (e.g., UV light, chemicals, viruses)

• Carcinogens: Mutagens causing cancer

Changes to DNA

DNA Repair and Gene Transfer

Cells have mechanisms to repair DNA, such as proofreading by DNA polymerases and excision repair. Genetic information can be transferred vertically (parent to offspring) or horizontally (between cells).

• Excision repair: Enzymes remove damaged DNA, DNA polymerase I fills gaps, ligase seals backbone

• Vertical gene transfer: Through cell division

• Horizontal gene transfer: Conjugation, transformation, transduction, transposons

Horizontal Gene Transfer Mechanisms

• Conjugation: Transfer via pilus and fertility plasmid

• Transformation: Uptake of environmental DNA

• Transduction: Transfer by bacteriophage (virus)

• Transposons: "Jumping genes" move within genome

Summary Table: Types of Mutations

Type	Description	Effect
Silent	Base change, no amino acid change	Neutral
Missense	Base change, wrong amino acid	Variable
Nonsense	Base change, stop codon	Usually detrimental
Frameshift	Insertion/deletion, alters reading frame	Often devastating

Practice Questions

• What are the four types of DNA nucleotides? A, T, C, G

• Match each enzyme involved in DNA replication with its function.

• Why is DNA replication called semiconservative?

• In which direction is DNA synthesized? 5′ → 3′

• Which type of RNA contains hairpin loops and carries amino acids? tRNA

• Which horizontal transfer mechanism involves bacteriophage? Transduction

• Which mutation is most devastating? Frameshift mutation

• Which molecule is inherited by daughter cells? DNA

• Which is not a method of horizontal gene transfer? Binary fission

• Transfer of DNA as naked DNA in solution is called? Transformation