2.1 Cytoplasm #
2.1.1 Nucleoid, ribosomes, and inclusions #
There is no nucleus and no mitochondrion, endoplasmic reticulum, or Golgi. The chromosome sits in a nucleoid. In a typical bacterium it is one circular double-stranded DNA, compacted by supercoiling and by proteins that are not histone octamers. Many archaea use genuinely histone-like proteins. Replication and transcription are molecular biology. The fact used here is that translation can start on an mRNA that is still being made. Plasmids are smaller, usually circular, optional DNA molecules, often carrying resistance, a virulence factor, or a catabolic pathway. Conjugative transfer of their DNA is genetics.
Ribosomes are 70S: 30S with 16S rRNA, and 50S with 23S and 5S. Svedberg units do not add. Woese and Fox used 16S sequence in 1977 to show that archaea are not odd bacteria. Eukaryotic cytosolic ribosomes are 80S, which is why many antibiotics are selective (Chapter 7). The elongation step each drug blocks is molecular biology. Mitochondria keep 70S-type ribosomes, so some of those drugs have organelle side effects.
Inclusions are stores or enzyme packets, not eukaryotic organelles. Polyhydroxybutyrate and glycogen store carbon; polyphosphate stores phosphate; sulfur globules appear in sulfur organisms. Magnetosomes are the exception with a lipid membrane: magnetite or greigite crystals that orient the cell. Gas vesicles are hollow protein shells, permeable to gas, that give buoyancy; they are not bubbles of metabolic gas. Carboxysomes are protein shells around Rubisco. Lose the shell and the enzymes disperse. There is no organelle genome.
2.1.2 Endospores #
An endospore is a dormant, non-reproductive cell made inside a vegetative cell. One cell makes one spore; germination returns one cell. A fungal spore is reproductive and is made in large numbers (Chapter 6). The classical genera are Bacillus (aerobic or facultative) and Clostridium (obligate anaerobes). Clostridioides difficile, long placed in Clostridium, is the same structural type.
From inside out: core, inner membrane, cortex, outer membrane, protein coat, and sometimes an exosporium. The core holds the chromosome, ribosomes, small acid-soluble DNA-binding proteins, and a high concentration of calcium dipicolinate, and it is markedly dehydrated. The cortex is loosely cross-linked, modified peptidoglycan and helps pull water out of the core. The coat excludes many enzymes and chemicals. Heat denatures hydrated protein, so dehydration, calcium dipicolinate, the DNA-binding proteins, and the coat together explain survival of boiling, of desiccation, and of many chemicals. Metabolism is effectively absent. Boiling is therefore not sterilisation (Chapter 7).
Sporulation is a slow differentiation set off by starvation, not merely the start of stationary phase. Germination starts when inner-membrane receptors detect a nutrient signal: the cortex is hydrolysed, calcium dipicolinate leaves, water enters, and resistance collapses. Outgrowth rebuilds vegetative synthesis. C. tetani, C. botulinum, and C. perfringens persist as spores and harm largely by toxin. Bacillus anthracis persists as environmental spores. C. difficile spores survive alcohols, which are not sporicidal.
2.2 The bacterial envelope #
The study of The bacterial envelope provides fundamental principles governing cellular architecture, molecular interactions, and physiological regulation.
Bacterial Growth
2.2.1 The energy membrane, and peptidoglycan #
The plasma membrane is an ester-linked phospholipid bilayer. Because there is no mitochondrion, electron transport, the proton gradient, and ATP synthase sit here. It is the energy membrane. Mesosomes, once drawn as bacterial mitochondria, are fixation artefacts. Rapid freezing does not show them.
Almost all bacteria build peptidoglycan outside that membrane. Mycoplasmas do not: they stiffen the membrane with host sterols, ignore wall-active drugs, and lyse in dilute medium. In a walled cell the wall, not the membrane, resists turgor. A protoplast โ a Gram-positive cell stripped of its wall โ rounds up and bursts in dilute solution.
The glycan alternates N-acetylglucosamine and N-acetylmuramic acid in ฮฒ-1,4 linkage. The muramic acid carries a peptide. In E. coli it is L-alanine, D-glutamate, meso-diaminopimelic acid, D-alanine, D-alanine. Many Gram-positive stems use L-lysine and a bridge; in S. aureus the bridge is five glycines. D-amino acids are a bacterial signature, which is why a drug aimed at them can spare host protein. Precursor is built on a lipid carrier, flipped out, and polymerised by transglycosylases. Penicillin-binding proteins then cross-link: they cut the terminal D-alanine and join the remaining D-alanine to a neighbouring stem. Autolysins must open the wall for insertion of new material and for separation of daughters. FtsZ and binary fission are cell biology.
Lysozyme hydrolyses the ฮฒ-1,4 glycan bond. It is in tears and saliva. A beta-lactam resembles D-alanineโD-alanine. The transpeptidase attacks it and is covalently stuck, so cross-linking stops while autolysins continue. A growing cell lyses. A non-growing cell, whose wall is already cross-linked, often survives. Vancomycin instead binds the D-alanineโD-alanine terminus and hides it. It is too large to cross the outer membrane well, so it is mainly a Gram-positive drug. Resistance replaces that terminus with a depsipeptide (Chapter 7).
2.2.2 Two envelopes, LPS, and the acid-fast wall #
Thick peptidoglycan and teichoic acids, versus a thin wall, a periplasm, porins, and an outer membrane, and the reason the Gram stain keeps or loses crystal violet, are in the cell-biology notes. Teichoic acids are polyol-phosphate polymers. Wall teichoic acids anchor in peptidoglycan; lipoteichoic acids anchor in the membrane. They bind cations and help adhesion. Lipoteichoic acid can inflame. It is not endotoxin.
Gram Cell Wall
The Gram-negative outer membrane has phospholipid inside and lipopolysaccharide outside. Porins such as OmpF and OmpC pass hydrophilic solutes of a few hundred daltons, so many Gram-positive drugs never arrive. Braun’s lipoprotein ties the outer membrane to peptidoglycan. The periplasm often contains a beta-lactamase that destroys drug before it reaches the target. A spheroplast has a damaged wall but a remaining outer membrane.
Lipopolysaccharide has three parts. Lipid A, a phosphorylated, acylated glucosamine disaccharide, is the toxic moiety in the outer leaflet. The core polysaccharide is relatively conserved and includes Kdo. The O antigen is a variable repeating oligosaccharide and defines O serotypes. Strains without it are rough. Lipid A is heat-stable and is released in quantity when cells lyse. The receptor and the cytokines are immunology. Endotoxin is a piece of outer membrane, not a secreted protein.
The acid-fast wall is not a third Gram category. In Mycobacterium and Nocardia, peptidoglycan is linked to arabinogalactan esterified with mycolic acids, very long branched hydroxy fatty acids. The wax stains poorly by the Gram method, holds carbol fuchsin against acid-alcohol, and excludes many antibiotics, which is part of why growth is slow. Isoniazid blocks mycolic-acid synthesis, a target other bacteria lack. Cord factor, trehalose dimycolate, contributes to virulence of M. tuberculosis. There is no LPS outer membrane.
2.2.3 Glycocalyx, pili, and rotary flagella #
A capsule is organised polysaccharide, a halo where a negative stain cannot enter. A slime layer is loose. Either attaches a cell, resists drying, and can hide the surface from phagocytes. Pneumococcus, Klebsiella, Haemophilus influenzae type b, and meningococcus use capsules that way. Streptococcus mutans holds itself on a tooth with glucan. In a biofilm the deep cells grow slowly, so drugs that need growth, and agents that must diffuse, fail even when the same strain is susceptible once dispersed. That is tolerance, not a resistance gene. Persisters are a dormant minority that survive a cidal drug and then produce susceptible daughters.
Pili are thin protein filaments. Type 1 fimbriae of E. coli bind mannose. P fimbriae bind a digalactoside on urinary epithelium, which is why those strains ascend the tract. Type IV pili retract (twitching) and, in some species, take up DNA. A sex pilus holds conjugating cells together. The DNA processing is genetics.
Bacterial flagella are rigid flagellin helices turned by a rotary motor. Eukaryotic cilia are 9+2 axonemes that bend and burn ATP. The cell-biology notes record the contrast. Rings of the basal body span the envelope โ fewer of them in a Gram-positive cell, which has no outer membrane โ and a hook joins them to a hollow filament that grows at the tip. Proton or, in some species, sodium flow through the stator turns the rotor. The fuel is the proton-motive force.
E. coli runs when counterclockwise rotation bundles the filaments and tumbles when a motor reverses. Chemotaxis lengthens runs that happen to point up an attractant gradient. The cell compares the present with the recent past; it is too short for a useful difference between its ends. Receptors control CheA, which phosphorylates CheY, and phospho-CheY favours the tumble. Methylation of the receptor adapts the signal, so a constant concentration does not lock the motor. Flagella may be polar, tufted, or all over the cell. Spirochaete filaments lie in the periplasm and corkscrew Treponema and Borrelia through tissue. At high density an autoinducer, classically an acyl-homoserine lactone, switches on late products, often toxins (Chapter 8).
2.3 Archaea #
2.3.1 Ether lipids and walls without peptidoglycan #
Archaeal lipids use ether links to isoprenoid chains, and the glycerol stereochemistry is the opposite of the bacterial one. C20 phytanyl chains make a diether bilayer. C40 biphytanyl chains make a tetraether monolayer, often stiffened by rings. A monolayer does not peel apart in heat, and ethers resist hydrolysis in acid and alkali. Many hyperthermophiles are therefore archaea. Ordinary seawater and mud are also full of them: ammonia-oxidising archaea, and methanogens.
There is no peptidoglycan. Some methanogens make pseudomurein, N-acetylglucosamine and N-acetyltalosaminuronic acid in ฮฒ-1,3 linkage, without D-alanineโD-alanine. Lysozyme does not cut that bond, and beta-lactams and vancomycin have no substrate. Most archaea use an S-layer of protein or glycoprotein; a few, such as Thermoplasma, have no wall. Many divide with FtsZ. Sulfolobus uses ESCRT-related proteins; the eukaryotic membrane-scission machinery is the relative, and it is cell biology. Some haloarchaea add bacteriorhodopsin, a retinal protein that pumps protons in the light. That is a proton-motive force without chlorophyll. It is not the photosynthesis of Chapter 4.
2.4 Key terms, summary, and self-check #
Key terms. Nucleoid; plasmid; 70S ribosome; endospore; dipicolinic acid; SASP; peptidoglycan; penicillin-binding protein; lysozyme; lipid A; O antigen; mycolic acid; capsule; biofilm; persister; pilus; flagellin; CheY; ether lipid; pseudomurein; S-layer.
Summary. DNA is in a nucleoid and energy metabolism is in the plasma membrane. Peptidoglycan is a ฮฒ-1,4 glycan cross-linked through D-alanine peptides: lysozyme cuts the sugar, beta-lactams freeze the cross-linking enzyme, and growing cells then lyse. Gram-negative cells add porins and lipopolysaccharide, of which lipid A is endotoxin and the O antigen is the serotype. Mycolic acids make the acid-fast wall. Endospores of Bacillus and Clostridium survive heat because the core is dehydrated and armoured. Flagella rotate on proton flow and are biased by CheY. Archaea have ether lipids and no peptidoglycan, so murein-active drugs and lysozyme do not apply.
Self-check.
1. Which bond does lysozyme cut, and why does a beta-lactam often spare a non-growing cell?
2. Name two core features and one coat feature that let an endospore survive boiling.
3. Which part of lipopolysaccharide is toxic, and which defines an O serotype?
4. Why is a bacterial flagellar reversal not a eukaryotic ciliary stroke? What does phospho-CheY do?
5. Give two chemical reasons a beta-lactam does not act on pseudomurein.
