Prokaryotes Bacteria and Archaea

Main notes

Bacteria and archaea are the oldest, most abundant, and most metabolically versatile organisms on Earth, and they shape every ecosystem and every human body. This chapter covers their cell structure, metabolic diversity, reproduction, gene sharing, ecological and medical roles, and the growing crisis of antibiotic resistance. Prokaryote biology also sets up later chapters on eukaryotic diversity, because the earliest eukaryotes evolved from prokaryotic ancestors, and on infectious disease, because a small fraction of prokaryotes are pathogens.

Cell Wall and Structure

Prokaryotes are single-celled organisms that lack a membrane-bound nucleus. Their DNA is a single circular chromosome packed into a region called the nucleoid, and many species also carry smaller circles of DNA called plasmids, which often hold extra genes such as resistance genes. Prokaryotic ribosomes are the smaller 70S type, a detail that matters later for how antibiotics work. The two prokaryotic domains are Bacteria and Archaea; they look similar under a microscope but differ deeply in chemistry.

The bacterial cell wall is built from peptidoglycan, a mesh of sugar chains cross-linked by short peptide bridges that gives the cell its shape and protects it from bursting in dilute water. The classic Gram stain separates bacteria by wall structure. Gram-positive bacteria have a thick peptidoglycan layer that traps the violet dye and stains purple. Gram-negative bacteria have a thin peptidoglycan layer plus an outer membrane studded with lipopolysaccharide (LPS), a molecule the human immune system detects as a danger signal; these cells lose the violet dye and take up a pink counterstain instead.

Common Mistake: A Gram-negative result does not mean the cell has no wall. Gram-negative bacteria keep a thin peptidoglycan layer; what changes the color is the extra outer membrane on top of it.

Archaea never make peptidoglycan. Their walls use pseudopeptidoglycan, protein S-layers, or polysaccharides, and their membrane lipids are ether-linked rather than the ester-linked lipids of bacteria. Many archaea are extremophiles: halophiles flourish in salt lakes, thermophiles grow near boiling-hot vents, and acidophiles tolerate strong acid. Other archaea, including the methanogens, live in cow rumens, wetlands, and sewage, and archaea turn out to be common in ordinary soils and oceans as well.

Beyond the wall, many prokaryotes carry a capsule, a slimy polysaccharide coat that helps them stick to surfaces and dodge immune cells. Flagella spin like propellers for swimming, while pili are thin protein fibers used for attachment and, in the case of conjugation pili, for DNA transfer. Facing starvation or heat, some bacteria form endospores, dormant cells wrapped in tough protein coats. An endospore can survive boiling water, drying, radiation, and disinfectants for years and even centuries, then germinate back into a growing cell when conditions improve; the genera Bacillus and Clostridium are famous endospore formers.

ELI-10

Picture a brick wall around a house. Some houses have a single thick brick wall, while others have a thin brick wall plus an extra outer door with warning labels. A purple dye reveals which kind of wall a house has. Archaea build their walls with a different material, like houses made of straw instead of bricks.

Metabolic Diversity

Prokaryotes run every metabolic strategy known on Earth, which is why they colonize every habitat. Metabolism is described along two axes: the energy source and the carbon source. Organisms that get energy from light are phototrophs, and those that get energy from chemical reactions are chemotrophs. Organisms that build their own organic compounds from carbon dioxide are autotrophs, while those that must take in organic compounds are heterotrophs. Combining the two axes gives four lifestyles.

Cyanobacteria run photosynthesis exactly as plants do, splitting water and releasing oxygen, and they are the reason Earth's atmosphere became breathable. Some bacteria perform anoxygenic photosynthesis, using hydrogen sulfide instead of water and producing no oxygen. For chemical energy, prokaryotes respire aerobically with oxygen, respire anaerobically with nitrate, sulfate, or iron as electron acceptors, or ferment sugars without any respiration at all. Nitrogen fixation is the conversion of atmospheric nitrogen gas into ammonia, a job only certain prokaryotes do, including free-living cyanobacteria and Rhizobium, which lives in nodules on legume roots and supplies crops with usable nitrogen. Methanogens are archaea that make methane gas in oxygen-free places such as cow rumens, rice paddies, and landfills, and the same microbes recycle nutrients as decomposers almost everywhere else.

ELI-10

Think of cells as tiny engines. Some engines run on sunlight, and others run on chemicals they eat. Some engines build their own fuel out of air, while others burn leftovers. Microbes run every one of these engine types, which is why they can live almost anywhere on Earth.

Binary Fission and Horizontal Gene Transfer

Prokaryotes reproduce by binary fission, a simple division that doubles the cell. First the circular chromosome duplicates, then the cell elongates, a wall-like septum grows across the middle, and the two cells pinch apart. There is no spindle, no chromosome sorting into nuclei, and no fusion of gametes, so binary fission is not a form of mitosis.

1. The circular chromosome replicates, starting at its origin.
2. The two chromosome copies anchor to opposite ends of the elongating cell.
3. The septum grows inward across the middle of the cell.
4. The septum closes, and two daughter cells separate.

Under ideal conditions Escherichia coli can divide about every 20 minutes, so a single cell becomes roughly one billion cells within ten hours; in the real world, nutrients and wastes limit growth. Because binary fission produces clones, new alleles arise mostly by mutation during DNA copying. The second engine of prokaryotic diversity is horizontal gene transfer (HGT), the movement of genes between living cells rather than from parent to offspring. The three modes are transformation, in which a cell takes up free DNA released by dead cells from its surroundings; transduction, in which a bacteriophage, the virus that infects bacteria, carries a piece of DNA from one bacterium to another; and conjugation, in which a donor cell extends a pilus to a recipient and transfers a plasmid copy directly across the bridge. Horizontal gene transfer explains how resistance genes, metabolic abilities, and toxin genes sweep through populations far faster than mutation alone could produce them.

Common Mistake: Binary fission is not a stripped-down mitosis. Mitosis is a eukaryotic process that sorts condensed chromosomes into daughter nuclei with the help of a spindle; bacteria have no nucleus and no spindle and simply split into two.

ELI-10

Binary fission is like a photocopier making a copy of one sheet of paper. One sheet becomes two, and each sheet is complete on its own. Horizontal gene transfer is different, like two kitchens swapping recipe cards. One kitchen can learn a trick invented in the other without starting from scratch.

Ecological and Medical Roles

Prokaryotes run the nutrient cycles that keep ecosystems alive. As decomposers they break down dead organic matter and release carbon, nitrogen, and other elements for reuse. Nitrogen fixers turn inert gas into ammonia, nitrifying bacteria oxidize that ammonia into nitrate for plants, and denitrifying bacteria return nitrogen to the air, closing the loop. Bioremediation uses bacteria to clean pollution: some species digest spilled oil, and others convert toxic metals into safer forms. Cyanobacteria are the main primary producers of the oceans, and the same photosynthesis that built the oxygen atmosphere still pumps out much of the oxygen we breathe.

Prokaryotes also live intimately with other organisms. The human gut microbiota is a community of hundreds of species, mostly bacteria, that digest fiber, make vitamins such as vitamin K and several B vitamins, and train the immune system. This relationship is mutualistic when both sides benefit, commensal when the microbe gains and the host is unharmed, and parasitic when the microbe causes harm. A small minority of prokaryotes are pathogens, organisms that cause disease: Vibrio cholerae causes cholera, Mycobacterium tuberculosis causes tuberculosis, Streptococcus pyogenes causes strep throat, and Clostridium tetani causes tetanus. Pathogens harm hosts through exotoxins, potent proteins they secrete, and endotoxins, components of the Gram-negative outer membrane released when cells die. The same fermentation that produces yogurt, cheese, sauerkraut, and sourdough bread is carried out by microbes we deliberately cultivate, and probiotics are live microbes marketed to restore gut health.

Common Mistake: The idea that almost all bacteria cause disease is wrong. Only a small fraction of prokaryotic species are pathogens; the rest are neutral, helpful, or essential to healthy ecosystems and bodies.

ELI-10

Imagine a city full of microscopic workers. Most workers recycle trash, make food, and keep the city running. A few workers cause trouble and make people sick. Medicine only needs to fight the troublemakers, not the whole city.

Antibiotic Resistance

Antibiotics are chemicals that kill bacteria or stop their growth by attacking prokaryote-specific targets. Penicillin and vancomycin block peptidoglycan synthesis, which is why they destroy growing bacteria but spare human cells, which have no peptidoglycan. Tetracyclines and macrolides jam the 70S ribosome, and sulfonamides block folic acid synthesis, which bacteria must perform themselves because they cannot import folate from food. Each of these drugs is a selective weapon, and resistance is the bacterial countermove.

Resistance arises by mutation, for example a change in a penicillin-binding protein that makes the drug's target unrecognizable, and it spreads by horizontal gene transfer on resistance plasmids, clusters of resistance genes that can move between species. Bacteria also resist drugs by pumping them out with efflux pumps, destroying them with enzymes such as beta-lactamase, or closing the porin channels that let drugs enter the cell. MRSA, methicillin-resistant Staphylococcus aureus, is the classic superbug: it carries an altered penicillin-binding protein, so the entire penicillin class fails against it, and it causes hard-to-treat skin, blood, and hospital infections. Resistance is amplified by misuse, because antibiotic use selects for survivors: every dose kills susceptible cells while resistant cells multiply, a process repeated when drugs are overprescribed, taken for too short a course, or fed to livestock on a large scale. Global estimates attribute about 2.5 million deaths each year to antimicrobial-resistant infections, and health agencies rank antimicrobial resistance among the top threats to modern medicine, since it can make routine surgery and chemotherapy dangerous again.

Common Mistake: A patient is not "resistant to antibiotics." Resistance is a property of the microbe, not the person, so a resistant infection fails to respond to a drug that would normally cure it.

High-Yield:

• Gram-negative bacteria pair a thin peptidoglycan layer with an outer membrane containing LPS; Gram-positive bacteria have only a thick peptidoglycan layer.
• Archaea have no peptidoglycan at all; their walls use pseudopeptidoglycan or protein S-layers.
• The three modes of horizontal gene transfer are transformation, transduction, and conjugation.
• Penicillin kills by blocking peptidoglycan synthesis, which is why it spares human cells.
• Antimicrobial resistance kills roughly 2.5 million people a year by global estimate.

ELI-10

Think of antibiotics as keys and bacteria as locked doors. Each key opens one kind of lock. A bacterium that gets a new lock survives when the key no longer fits. Its offspring inherit the new lock, so the whole population gradually becomes hard to open.

Quick Review

• Prokaryotes have no nucleus; their chromosome sits in the nucleoid, and plasmids carry extra genes.
• Bacterial walls contain peptidoglycan; archaeal walls use pseudopeptidoglycan or protein layers, and archaeal lipids are ether-linked.
• Gram-positive bacteria stain violet through a thick peptidoglycan layer; Gram-negative bacteria stain pink through a thin layer plus an outer membrane.
• Binary fission doubles a cell: one chromosome copy for each daughter, with no spindle and no mitosis.
• Transformation, transduction, and conjugation transfer genes between cells, spreading traits such as antibiotic resistance.
• Cyanobacteria oxygenate the planet, methanogens produce methane, and nitrogen fixers supply usable nitrogen to ecosystems.
• Only a minority of prokaryotes cause disease; most recycle nutrients, feed us, or live as symbionts in our gut.
• Antibiotic resistance, exemplified by MRSA, evolves by mutation and spreads by horizontal gene transfer, with an estimated 2.5 million global deaths a year.

Key terms

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Important formulas or processes

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Common mistakes

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