Bacterial Cell Biology: Structures, Functions, and Diversity

1) Cell envelope: plasma membrane and cell wall

Plasma membrane (cytoplasmic membrane)

The plasma membrane is a thin lipid bilayer with embedded proteins. It acts as a selective barrier and a working platform for energy generation and transport.

• Selective permeability: small nonpolar molecules diffuse more easily; charged or large molecules require transport proteins.
• Transport work: membrane proteins import nutrients (e.g., sugars, amino acids) and export wastes; some pumps use ATP, others use ion gradients.
• Energy conversion: many bacteria build a proton motive force (H⁺ gradient) across the membrane to power ATP synthesis and transport.

Cell wall (peptidoglycan)

Most bacteria have a cell wall made of peptidoglycan, a mesh-like polymer of sugars (NAG and NAM) cross-linked by short peptides. The wall prevents osmotic lysis and helps maintain shape.

• Survival in hypotonic environments: without a rigid wall, water influx can burst the cell.
• Shape and growth: wall-building enzymes insert new material during elongation and division, coordinating with the cytoskeleton-like proteins.
• Drug target: because peptidoglycan is unique to bacteria, it is a major target for antibiotics that inhibit wall synthesis.

Gram-positive vs Gram-negative: what differs and why it matters

Permeability and treatment implications (practical reasoning): when a drug must reach an internal target (like ribosomes), it must cross the envelope. Gram-negative bacteria have an extra barrier (outer membrane), so entry often depends on porins and can be limited. Gram-positive bacteria lack this outer membrane, so many compounds reach the cell wall or membrane more readily. This is one reason why the same antibiotic can work well on one group and poorly on the other.

Step-by-step: predicting whether a molecule can enter a bacterium

1. Identify the envelope type: Gram-positive (no outer membrane) vs Gram-negative (outer membrane + periplasm).
2. Check the molecule’s properties: size, charge, polarity.
3. For Gram-negative: ask whether it can pass through porins (often small, hydrophilic molecules) or whether it needs a specific transporter.
4. For both types: consider whether the plasma membrane can be crossed (nonpolar diffusion vs transport proteins).
5. Predict outcome: limited entry often means reduced effectiveness for drugs targeting internal processes.

2) Internal organization: nucleoid, plasmids, ribosomes

Nucleoid (chromosomal DNA region)

Bacteria typically carry a single circular chromosome located in the nucleoid, a region not surrounded by a membrane. DNA is compacted by supercoiling and DNA-binding proteins, allowing rapid access for replication and transcription.

• Fast response: because transcription and translation can occur in the same compartment, bacteria can quickly produce proteins when conditions change.
• Replication coordination: chromosome replication begins at an origin and proceeds bidirectionally; timing is coordinated with cell division.

Plasmids

Plasmids are small, usually circular DNA molecules that replicate independently of the chromosome. They often carry genes that provide conditional advantages.

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• Trait examples: antibiotic resistance enzymes, toxin production, specialized metabolism, or adhesion factors.
• Copy number: some plasmids exist in many copies, increasing expression of their genes; others are low-copy and tightly regulated.

Ribosomes (70S)

Bacterial ribosomes (70S) translate mRNA into protein. They are abundant because growth depends on protein synthesis capacity.

• Growth rate link: rapidly growing cells often have more ribosomes.
• Drug relevance: many antibiotics target bacterial ribosomes by interfering with translation steps (initiation, elongation, or translocation).

3) External features: capsules, pili, flagella, biofilms

Capsules and slime layers (glycocalyx)

Many bacteria secrete a sticky outer coating of polysaccharide (sometimes protein). When well-organized and tightly attached, it is called a capsule; when loose, a slime layer.

• Attachment: helps cells adhere to surfaces (teeth, tissues, rocks, pipes).
• Protection: can reduce drying, limit penetration of harmful molecules, and hinder immune recognition in host-associated bacteria.
• Nutrient trapping: can retain water and dissolved nutrients near the cell.

Pili and fimbriae

Fimbriae are short, numerous protein fibers used mainly for attachment. Pili can be longer and may mediate DNA transfer or a crawling-like movement.

• Adhesion: specific binding to host receptors or environmental surfaces increases colonization success.
• Twitching motility: some pili extend, attach, and retract to pull the cell forward.
• Conjugation pilus: specialized pilus forms a connection for DNA transfer between cells.

Flagella

Flagella are rotating helical filaments powered by ion gradients across the membrane. Rotation can propel bacteria through liquids or across moist surfaces.

• Chemotaxis: bacteria bias movement toward attractants (nutrients) and away from repellents by adjusting run-and-tumble behavior.
• Energy cost: building and rotating flagella requires resources, so expression is often regulated.

Biofilms

A biofilm is a structured community of bacteria attached to a surface and embedded in a self-produced matrix (polysaccharides, proteins, DNA). Biofilms behave differently from free-swimming (planktonic) cells.

• Increased tolerance: the matrix can slow diffusion of antimicrobials; cells inside may grow slowly, making some treatments less effective.
• Division of labor: gradients of oxygen and nutrients create microenvironments where different metabolic strategies coexist.
• Persistence: biofilms can form on medical devices, teeth, and industrial surfaces.

Step-by-step: how a biofilm forms (conceptual workflow)

1. Initial attachment: cells contact a surface using fimbriae/pili and weak interactions.
2. Irreversible attachment: production of extracellular matrix increases “stickiness.”
3. Microcolony growth: cells divide and recruit others; channels begin to form.
4. Maturation: complex architecture develops with nutrient/oxygen gradients.
5. Dispersal: some cells detach to colonize new locations.

4) Metabolic diversity overview (energy flow)

Bacteria vary widely in how they obtain energy and carbon. A useful way to compare pathways is to track electron flow and the final electron acceptor, because this determines ATP yield and where bacteria can live.

Aerobic respiration

Uses oxygen (O₂) as the final electron acceptor. Typically yields the most ATP per unit of fuel because electron transport chains can generate a strong proton gradient.

Fuel (e.g., glucose) → electron carriers (NADH/FADH2) → ETC (membrane) → O2 → H2O + ATP

Anaerobic respiration

Uses a final electron acceptor other than oxygen (e.g., nitrate, sulfate, fumarate). ATP yield is often lower than aerobic respiration but higher than fermentation.

Fuel → electron carriers → ETC (membrane) → NO3− / SO4^2− / others → reduced products + ATP

Fermentation

Does not use an external electron acceptor and does not rely on an electron transport chain. ATP is generated mainly by substrate-level phosphorylation; organic molecules act as both electron donors and acceptors.

Fuel → glycolysis → small ATP gain + NADH → fermentation products (e.g., lactate, ethanol) + NAD+

Photosynthesis (in some bacteria)

Some bacteria capture light energy to drive electron flow and build a proton gradient. Depending on the group, electron donors can vary (not always water), and oxygen may or may not be produced.

Light → photosystems/pigments → electron flow (membrane) → H+ gradient → ATP (and reducing power) → biosynthesis

Practical comparison: choosing a metabolism for an environment

• Oxygen-rich surface waters/soils: aerobic respiration is favored for high ATP yield.
• Oxygen-poor sediments/gut: anaerobic respiration or fermentation dominates; different acceptors create different niches.
• Light-exposed environments: phototrophic bacteria can supplement or replace chemical energy sources.

5) Reproduction by binary fission and genetic variation mechanisms

Binary fission (how one cell becomes two)

Binary fission is bacterial asexual reproduction. It is efficient because it couples DNA replication, cell growth, and division.

Step-by-step: binary fission

1. Cell growth: the cell increases in size and synthesizes membrane and wall components.
2. Chromosome replication begins: DNA replication starts at the origin and proceeds as the cell elongates.
3. Chromosome segregation: replicated DNA regions move apart, helping ensure each future cell receives a copy.
4. Division machinery assembles: a protein ring forms at midcell and recruits enzymes to build a septum.
5. Septum formation and separation: membrane and wall pinch inward, producing two daughter cells.

Mutation: changing traits by DNA sequence change

Mutations are heritable changes in DNA sequence. They can arise from replication errors or DNA damage. Most are neutral or harmful, but some provide advantages (e.g., altered drug targets, new enzyme activity).

• Trait framing: mutation can change a protein’s function or expression level, which can alter growth rate, nutrient use, or drug susceptibility.

Horizontal gene transfer (HGT): acquiring traits from other sources

Horizontal gene transfer moves genes between cells (or via viruses), allowing rapid acquisition of new traits without waiting for slow accumulation of mutations.

Transformation

Cells take up free DNA from the environment and incorporate it into their genome or maintain it as a plasmid (if compatible).

1. DNA is released into the environment (e.g., from lysed cells).
2. A competent bacterium binds and imports DNA.
3. Imported DNA recombines with the chromosome or persists as a plasmid.
4. New trait may appear (e.g., new enzyme or surface protein).

Transduction

DNA is transferred by bacteriophages (viruses that infect bacteria). During phage replication, bacterial DNA can be mistakenly packaged and delivered to another cell.

1. Phage infects a donor bacterium and replicates.
2. Some phage particles package bacterial DNA fragments.
3. Phage injects this DNA into a recipient bacterium.
4. Recombination can integrate the DNA, changing traits.

Conjugation

DNA is transferred through direct cell-to-cell contact, often mediated by a conjugation pilus and plasmid-encoded machinery.

1. Donor cell carrying a conjugative plasmid attaches to a recipient.
2. A DNA strand is nicked and transferred through a mating bridge.
3. Both cells synthesize the complementary strand.
4. Recipient gains new genes (commonly resistance or metabolic functions).

Trait-centered view: how variation shows up in real outcomes

• Envelope genes change → altered permeability or surface antigens → different drug susceptibility or immune evasion.
• Metabolic genes gained → ability to use a new nutrient or electron acceptor → colonization of a new niche.
• Motility/adhesion genes changed → improved attachment or dispersal → altered colonization patterns.

Guided concept map: linking structure to function

Use the map below as a study tool: start at a structure, follow arrows to the function, then to the survival or growth advantage.

• Plasma membrane → selective transport + proton gradient → nutrient uptake + ATP generation → growth in changing environments
• Peptidoglycan cell wall → rigidity + osmotic protection → prevents lysis → survival in dilute environments
• Gram-negative outer membrane → permeability barrier + porins → controlled entry of molecules → increased tolerance to some antimicrobials
• Periplasm (Gram-negative) → enzymes + transport proteins → processing/inactivation of compounds → survival under chemical stress
• Nucleoid → compact DNA + rapid gene expression → fast response to conditions → competitive growth
• Plasmids → accessory genes → new traits (e.g., resistance, metabolism) → rapid adaptation
• Ribosomes → protein synthesis → enzyme production + cell building → growth rate control
• Capsule/slime layer → adhesion + protection → persistence on surfaces/hosts → colonization
• Fimbriae/pili → attachment (and sometimes twitching) → stable colonization + surface spread → niche establishment
• Conjugation pilus → DNA transfer → acquisition of new genes → rapid trait change
• Flagella → motility + chemotaxis → reach nutrients/escape stress → improved survival
• Biofilm matrix → community protection + gradients → tolerance + metabolic cooperation → long-term persistence
• Binary fission → rapid reproduction → population expansion → faster resource capture
• Mutation + HGT → genetic variation → altered traits → adaptation to drugs, hosts, and environments