Genome Structure and Organization
Every cell carries a complete set of genetic instructions in its DNA, but how that DNA is organized, packaged, and accessed varies dramatically between different types of cells. This section covers how genomes are structured in prokaryotes and eukaryotes, how DNA is physically packaged inside cells, and why extrachromosomal DNA matters for microbiology.
Genes, Genotypes, and Phenotypes
A gene is a specific sequence of DNA that codes for a functional product, usually a protein or an RNA molecule. Genes are the fundamental units of heredity.
- Genotype refers to the specific set of alleles (gene versions) an organism carries in its DNA. Two bacteria can look identical but have different genotypes if they carry different alleles of a particular gene.
- Phenotype is the observable trait that results from gene expression interacting with the environment. Examples include eye color in humans, colony morphology in bacteria, or antibiotic resistance.
The key relationship: genotype + environment = phenotype. A bacterium might carry a gene for antibiotic resistance (genotype), but that resistance only shows up as a phenotype when the gene is actually expressed.
DNA Packaging in Cells
Cells face a real physical problem: their DNA is far longer than the cell itself. An E. coli chromosome, for instance, is about 1.6 mm long but must fit inside a cell roughly 2 µm in length. Tight packaging solves this.
Prokaryotic DNA packaging:
- A single circular chromosome is concentrated in the nucleoid region, which is not membrane-bound
- The chromosome is attached to the cell membrane and organized into supercoiled loops
- Histone-like proteins (such as HU and IHF) help condense and organize the DNA, though these are structurally distinct from eukaryotic histones
Eukaryotic DNA packaging:
- Multiple linear chromosomes are housed within a membrane-bound nucleus
- DNA wraps around octamers of histone proteins to form units called nucleosomes, which coil further into chromatin
- Chromatin exists in two functional states:
- Euchromatin: loosely packed, transcriptionally active (genes here can be expressed)
- Heterochromatin: tightly packed, transcriptionally inactive (genes here are silenced)
- During cell division (mitosis and meiosis), chromatin condenses further into the compact chromosomes visible under a microscope
Genetic Organization: Prokaryotes vs. Eukaryotes
These two cell types organize their genetic information in fundamentally different ways.
Prokaryotic genomes:
- Typically a single circular chromosome
- Genes are closely spaced with minimal non-coding DNA
- Related genes are often organized into operons, where a cluster of genes is transcribed together under the control of a single promoter (e.g., the lac operon in E. coli)
- No membrane-bound nucleus; transcription and translation can occur simultaneously
Eukaryotic genomes:
- Multiple linear chromosomes enclosed in a nucleus
- Genes are widely spaced, with large amounts of non-coding DNA between them
- Individual genes contain introns (non-coding sequences spliced out during RNA processing) and exons (coding sequences that remain in the mature mRNA)
- Gene expression is regulated by complex elements including promoters, enhancers, and silencers
- Transcription occurs in the nucleus; translation occurs in the cytoplasm, so the two processes are separated in time and space
Significance of Extrachromosomal DNA
Not all genetic information lives on the main chromosome(s). Extrachromosomal DNA elements are especially important in microbiology.
Plasmids:
- Small, circular DNA molecules that replicate independently of the main chromosome
- Most common in prokaryotes, though some eukaryotes carry them
- Often carry genes for specialized functions like antibiotic resistance, toxin production, or metabolic capabilities
- Can be transferred between cells through horizontal gene transfer (conjugation, transformation, transduction), which is a major way antibiotic resistance spreads through bacterial populations
- Widely used as vectors in molecular biology and genetic engineering
Mitochondrial DNA (mtDNA):
- Circular DNA found in the mitochondria of eukaryotic cells
- Encodes proteins essential for cellular respiration and energy production (though most mitochondrial proteins are actually encoded by nuclear DNA)
- Maternally inherited in most species, since mitochondria are passed through the egg cell
Chloroplast DNA (cpDNA):
- Circular DNA found in chloroplasts of photosynthetic eukaryotes
- Encodes proteins involved in photosynthesis
- Also maternally inherited in most species
Both mtDNA and cpDNA support the endosymbiotic theory, which proposes that mitochondria and chloroplasts originated as free-living prokaryotes that were engulfed by ancestral eukaryotic cells. Their circular DNA and bacterial-like ribosomes are key pieces of evidence for this.
DNA Structure and Function
A few core concepts tie genome structure to function:
- DNA is built from nucleotides, each consisting of a sugar (deoxyribose), a phosphate group, and a nitrogenous base (A, T, G, or C)
- The double helix is held together by complementary base pairing: adenine pairs with thymine (, two hydrogen bonds) and guanine pairs with cytosine (, three hydrogen bonds). The pair is stronger, which affects DNA stability.
- DNA replication copies the entire genome before cell division, ensuring each daughter cell receives a complete set of genetic instructions
- Gene expression is a two-step process: transcription converts a DNA sequence into mRNA, and translation uses that mRNA to build a protein
- Mutations are changes in the DNA sequence. They can be harmful, neutral, or occasionally beneficial, and they are the raw material for evolution and genetic diversity