Genomes & Nucleic Acids: Microbiology Study Guide

Genomes & Nucleic Acids

Definition of Genetics

Genetics is the study of inheritance and heritable traits as expressed in an organism's genetic material. In microbiology, genetics forms the foundation for understanding how traits are passed and expressed in microorganisms.

• Genetics: Study of inheritance, structure/function of genetic material, mutations, and gene transfer.

• Microbial genetics: Cornerstone for general genetics knowledge.

What Geneticists Study

Geneticists investigate the structure and function of genetic material (DNA/RNA), mutations, and the transfer of genetic material among organisms (e.g., conjugation, transformation, transduction).

• Structure & function: DNA/RNA as carriers of genetic information.

• Mutations: Changes in genetic sequences.

• Gene transfer: Movement of genetic material between organisms.

Scope of Microbial Genetics

Microbial genetics applies genetic concepts specifically to microorganisms. These studies are foundational for understanding structure, function, mutation, and replication of genomes, and for comparison across domains of life.

• Comparison with eukaryotic and archaeal genomes.

Genomes

Definition & Types

A genome is the entire genetic complement of a cell or virus, including both coding (genes) and noncoding nucleotide sequences.

• Cellular genomes: DNA-based (e.g., bacteria, eukaryotes).

• Viral genomes: DNA or RNA-based.

Key Points

• Genome = all genetic material (coding + noncoding).

• Cells & DNA viruses use DNA; RNA viruses use RNA.

Nucleotides & Nucleic Acids

Nucleotides

Nucleotides are the building blocks of nucleic acids. Each nucleotide consists of a phosphate group and a nucleoside.

• Nucleoside = pentose sugar (ribose in RNA, deoxyribose in DNA) + nitrogenous base.

• Nucleotide = nucleoside + phosphate.

Nitrogenous Bases

Nitrogenous bases are classified as purines or pyrimidines:

• Purines: Adenine (A), Guanine (G)

• Pyrimidines: Cytosine (C), Thymine (T, DNA only), Uracil (U, RNA only)

Base Pairing Rules

• DNA: Adenine (A) pairs with Thymine (T) via 2 hydrogen bonds.

• RNA: Adenine (A) pairs with Uracil (U) via 2 hydrogen bonds.

• Both DNA & RNA: Guanine (G) pairs with Cytosine (C) via 3 hydrogen bonds.

Composition of Nucleic Acids

• Nucleic acids are polymers of nucleotides.

• DNA: Deoxyribose sugar, bases A, T, G, C.

• RNA: Ribose sugar, bases A, U, G, C.

DNA Structure

Double Helix & Antiparallel Strands

DNA is a double-stranded molecule with antiparallel strands. The strands are held together by hydrogen bonds between complementary bases.

• Strands run in opposite directions: 5'→3' vs 3'→5'.

• Sugar-phosphate backbone is on the outside (hydrophilic), bases are on the inside (hydrophobic).

Hydrophobic vs. Hydrophilic Positioning

• Nitrogenous bases (A, T, G, C) are tucked inside the helix, protected from water.

• Sugar-phosphate backbone interacts with the aqueous environment.

Explanation of the Double Helix

The arrangement of hydrophobic bases inside and hydrophilic backbone outside stabilizes the double helix and provides the classic double-helical shape of DNA.

• Spiral staircase analogy: visual model of the helix.

• Hydrophobic/hydrophilic distribution explains DNA stability and structure.

DNA Strand Orientation

• 5' end: phosphate on 5' carbon.

• 3' end: hydroxyl on 3' carbon.

• Strands are antiparallel (5'→3' vs 3'→5').

Genome Size

• Measured in base pairs (bp).

• Nasuia deltocephalinicola: ~112,091 bp, smallest known cellular genome.

• Human genome: ~6 billion bp, 46 nuclear DNA molecules + mitochondrial DNA copies.

Function of DNA's Structure

• Information storage: The linear sequence of bases encodes genetic instructions.

• Complementary base pairing enables exact copying for inheritance.

Genome Organization & Packaging

Nuclear Packaging

• Nucleus: ~5 μm diameter, DNA packed into nucleus.

• Organization allows easy access to specific genes.

• Protection from damage.

• Regulation of gene expression.

Prokaryotic vs. Eukaryotic Genomes

Prokaryotes

• Chromosome: Usually single, circular DNA molecule in nucleoid region.

• DNA folded into loops, stabilized by proteins and RNA.

• Haploid (single copy of genome).

• Exceptions: Epulopiscium (up to thousands of chromosomes), Agrobacterium tumefaciens (circular and linear chromosomes).

Plasmids

• Small, circular DNA molecules, not essential for survival but provide advantages.

Plasmid Type	Function	Example
Fertility (F) plasmids	Carry genes for conjugation (DNA transfer between cells)	F plasmid in E. coli
Resistance (R) plasmids	Encode resistance to antibiotics/heavy metals	R plasmid in Pseudomonas
Bacteriocin plasmids	Produce toxins to kill competing bacteria	Colicin plasmid in E. coli
Virulence plasmids	Encode factors (enzymes, toxins) making bacteria pathogenic	Plasmid in E. coli causing diarrhea

Eukaryotes

• Multiple chromosomes, often diploid (two copies).

• DNA wraps around histones to form nucleosomes (“beads on a string”).

• Chromosomes located inside the nucleus (double membrane).

• Linear chromosomes (some exceptions).

• Organelles (mitochondria, chloroplasts) have their own DNA.

Feature	Prokaryotes	Eukaryotes
Chromosome type	Usually circular (some linear)	Linear
Location	Nucleoid (no membrane)	Nucleus (double membrane)
DNA amount	Less DNA	Much more DNA
Histones	Absent in bacteria; present in Archaea	Present

DNA Packaging in Eukaryotes

• DNA wraps around histones → forms nucleosomes.

• Nucleosomes coil into chromatin fibers.

• Chromatin further folds into chromosomes.

• Heterochromatin: tightly packed, inactive DNA.

• Mitotic chromosomes: ~50,000x shorter than fully extended DNA.

Organelle Genomes

• Mitochondria: Circular DNA.

• Chloroplasts: Linear DNA (though once thought circular).

• Organelle DNA codes for ~5% of organelle proteins; most are encoded by nuclear DNA.

Example: Saccharomyces cerevisiae yeast

• ~70 copies of a small plasmid (6,300 bp).