Prokaryotes: Structure, Diversity, and Global Roles

Prokaryotes: Structure, Diversity, and Global Roles

Aims and Learning Outcomes

This study guide outlines the key properties of prokaryotic cells, including their structural organization, specific cellular structures, and their relationship to the external environment. It also covers the classification of life, differences between prokaryotes and eukaryotes, bacterial diversity, and the role of prokaryotes in global nutrient cycles.

• Describe the three-kingdom classification of life

• Understand basic and specialized structures of prokaryotic cells

• Compare cell walls of gram-positive and gram-negative bacteria

• Explain the structure and function of the bacterial flagellum

• Describe DNA organization in prokaryotes

• Recognize the diverse environments inhabited by prokaryotes

• Appreciate the contribution of prokaryotes to global nutrient cycling

The Three-Kingdom Theory (Carl Woese)

Classification of Life

The three-kingdom theory divides life into Bacteria, Archaea, and Eukarya, based on molecular data, especially small subunit ribosomal RNA (SSU rRNA) sequences.

• SSU rRNA: Universally present, slow evolution, used for phylogenetic analysis

• Phylogenetic trees: Show evolutionary relationships and branching order

• Metagenomics: Environmental sequencing without isolating organisms

Prokaryotic and Eukaryotic Cells

Key Differences

Feature	Prokaryotes (Eubacteria + Archaea)	Eukaryotes
Size	0.1–5 μm	10–100 μm
Cell Division	Binary fission	Mitosis and meiosis
Genetic Material	Not enclosed in nucleus	Enclosed in nucleus
Ribosomes	70S	80S
Organelles	Absent	Present
Flagella	Bacterial type	9+2 type

Microbial Taxonomy

Classification and Naming

Taxonomy is the science of categorizing and classifying organisms. Names often reflect discoverers, characteristics, or environments.

Name	Derivation
Escherichia coli	Named after Theodor Escherich
Deinococcus radiodurans	Radiation-resistant
Thermus aquaticus	Heat-loving, found in water
Helicobacter pylori	Helical shape, found in pylorus
Klebsiella pneumoniae	Named after Edwin Klebs, causes pneumonia

Bacterial Diversity

Phylogenetic Relationships

• Based on SSU rRNA sequences

• Phylogenetic trees show evolutionary relationships and distances

• Branch lengths indicate evolutionary time

• Major groups: Gram-positive and Gram-negative bacteria

Prokaryotic Cell Structure

Typical Prokaryotic Cell: Escherichia coli

• Cell wall: Peptidoglycan

• Plasma membrane

• Nucleoid: Circular DNA

• Flagellum: Motility

• Pili/Fimbriae: Attachment and conjugation

• Capsule/Slime layer: Protection

The Bacterial Cell Wall

Components

• Peptidoglycan: Main structural component

• Lipopolysaccharides (Gram-negative)

• Teichoic acids (Gram-positive)

• Flagellum, pili, capsule/slime layer

Gram-Positive vs. Gram-Negative Cell Walls

Feature	Gram-Positive	Gram-Negative
Peptidoglycan Layer	Thick (20–80 nm)	Thin (1–3 nm)
Teichoic/Lipoteichoic Acids	Present	Absent
Outer Membrane	Absent	Present (with LPS)
Periplasmic Space	Small	Large

Capsules and S-Layers

Functions and Composition

• Capsule/Slime Layer: Polysaccharides, protection, attachment, motility

• S-Layer: Glyco-proteins, found in bacteria and archaea, protection and virulence

Bacterial Flagellum

Structure and Types

• Filament: Long, helical structure

• Hook: Connects filament to basal body

• Basal Body: Anchors flagellum in cell wall/membrane

• Types: Monotrichous (single), Amphitrichous (both ends), Lophotrichous (tuft), Peritrichous (all over)

Pili and Fimbriae

Structure and Function

• Sex Pili: Long, few per cell, conjugation

• Fimbriae: Short, numerous, surface attachment

Inside the Prokaryotic Cell: Cytoplasmic Matrix

Components

• Cytoplasmic proteins

• Bacterial cytoskeleton

• Metabolic enzymes

• Inclusion bodies

• Free 70S ribosomes

The Bacterial Cytoskeleton

Comparison Table

Eukaryotic Protein/Filament	Prokaryotic Homologue	Function
Tubulin	FtsZ	Cell division
Actin	MreB, Mbl, ParM, MamK	Cell growth and shape
Intermediate filaments	CresS	Curved shape
Molecular motors	Not found yet	-

Inclusion Bodies

Types and Functions

• Storage: Glycogen, poly-beta-hydroxybutyrate (PHB), polyphosphate

• Floating: Gas vacuoles

• Photosynthesis: Carboxysomes (cyanobacteria)

• Magnetic navigation: Magnetosomes

• Endospores: Survival under harsh conditions, dormant, resistant to extremes

Bacterial Ribosomes

Structure

• 70S ribosomes: Svedberg unit (S) measures sedimentation rate

• Composed of 50S (large) and 30S (small) subunits

• Each subunit contains rRNA and protein subunits

The Nucleoid

Genetic Material

• Circular DNA: Main chromosome

• DNA/RNA polymerases

• Scaffolding proteins: RecA, RecBCD, condensins

• Circular plasmids: Extra-chromosomal DNA

The Archaea

Characteristics

• Often found in extreme environments

• Utilize diverse energy sources

• Closer evolutionary relationship to eukaryotes

• Size: 0.1–1.5 μm

Structural Differences Between Archaea and Bacteria

Structure	Bacteria	Archaea
Cell wall	Peptidoglycan	Pseudomurein
Cell membrane	Ester-linked side chains	Ether-linked branched side chains
DNA structure	No histones	DNA bound by histones
RNA polymerase	Bacterial type	Similar to eukaryotes

DNA Sequencing and Metagenomics

Techniques

• DNA sequencing: Determines nucleotide sequence

• Methods: Sanger, NGS, Nanopore

• PCR: Amplifies DNA fragments

• Metagenomics: Sequencing DNA from environmental samples

Archaea-Eukaryote Relationship

Asgard Archaea and TACK

• Share eukaryotic signature proteins (e.g., actin, tubulin, histones)

• Meta-genomes reveal evolutionary links

Useful Terminology

Term	Definition
Aerobic	Requires oxygen
Anaerobic	Does not require oxygen
Autotroph	Produces its own food
Heterotroph	Obtains energy from other organisms
Chemotroph	Obtains energy by oxidizing chemicals
Phototroph	Uses light as energy source
Methanotroph	Uses methane as energy source
Methylotroph	Uses C1 compounds as energy source

Microorganisms and Global Nutrient Cycles

Role in Biogeochemical Cycles

• Carbon cycle: Conversion of CO2, CH4, organic matter

• Nitrogen cycle: Nitrogen fixation, nitrification, denitrification (many steps only performed by prokaryotes)

• Sulphur cycle: Sulfate reduction, oxidation, assimilation

Summary of Key Points

• Prokaryotes evolved before and alongside eukaryotes

• Bacteria and archaea are prokaryotes

• Prokaryotes are highly diverse and found everywhere

• Bacterial cell wall contains peptidoglycan

• Gram-positive and gram-negative bacteria have different wall structures

• Bacterial flagellum is a molecular motor

• Bacteria have a cytoskeleton, nucleoid, and 70S ribosomes

• Inclusion bodies serve different functions

• Archaea are closer to eukaryotes than bacteria

• Archaea have unique membrane lipids, cell wall components, and histones

• Prokaryotes drive global nutrient cycles