Exam 2 Study Guide

These three chapters carry the heaviest load of names in the book. Do not try to hold them as a list. Hold them on a frame instead: shape, stain, oxygen, and what the organism does. Read the "what to know" prose first. Then cover the right side of each table and rebuild it. Say the sequences out loud in order. Finish each chapter with its ten self-test items. The cram sheet at the end gathers every organism, test, drug and number in one place.

Chapter 4Bacterial Diversity and Classification

What to know

Almost every bacterium takes one of three shapes. A coccus is round, like a tiny ball. A bacillus is a rod, like a short stick or a grain of rice. A spirillum is curved or coiled, like a corkscrew. Two in-between forms matter too. A coccobacillus is a short plump rod, easy to mistake for a coccus. A vibrio is a short curve shaped like a comma, and that shape names Vibrio cholerae.

Shape is more than a label. It is built into the name of almost every germ. Staphylococcus and Streptococcus are spheres. Bacillus and Lactobacillus are rods. Spirochetes are coils. Reading the shape out of a genus name is a habit worth building early.

When a bacterium splits, the daughter cells may drift apart or stay stuck. The pattern is a second clue, and it helps most with cocci. Diplo- means pairs, so Neisseria forms diplococci. Strepto- means chains. Staphylo- means loose clumps shaped like a bunch of grapes. Cocci can also form flat squares of four, called tetrads, or cube-shaped packets of eight, called sarcinae. Rods more often line up end to end. They can also lie side by side like a fence, which is a palisade, and that is typical of Corynebacterium.

Now the stain. Gram-positive bacteria have a thick outer layer of peptidoglycan. The thick mesh traps crystal violet, so the cells look deep purple. That wall sits bare on the surface with nothing wrapped over it. So Gram-positive germs are the classic targets of the penicillin family.

Staphylococcus cells are Gram-positive cocci in clusters. The species that matters most is Staphylococcus aureus. Roughly a third of healthy people carry it in the nose and never know. Give it a break in the skin and the picture changes fast. It causes boils, abscesses, wound infections and cellulitis, which is a spreading infection of the skin and the tissue under it. It causes bloodstream infections. It causes endocarditis, an infection of the heart valves. Its toxins cause one kind of food poisoning and toxic shock syndrome. MRSA is methicillin-resistant S. aureus, the drug-resistant form, and it is why so many units use contact precautions. A related group is the coagulase-negative staphylococci, such as S. epidermidis. These live quietly on skin and are weak on their own. They still cause trouble by settling on catheters, artificial joints and heart valves.

Streptococcus cells are Gram-positive cocci in chains. The lab sorts them two ways: by how they break down blood on an agar plate, and by the marker proteins on their surface. Group A strep is S. pyogenes. It causes strep throat, impetigo, cellulitis and scarlet fever. It also causes necrotizing fasciitis, a fast infection that destroys tissue. Weeks later it can set off two immune problems: rheumatic fever, which can scar heart valves, and post-streptococcal glomerulonephritis, an injury to the filters of the kidney. Group B strep is S. agalactiae. It lives in the vagina of some pregnant people without symptoms, and it is a leading cause of newborn sepsis and meningitis. That is why screening is done at about 36 to 37 weeks. Streptococcus pneumoniae grows as a pair, not a chain. It is a top cause of pneumonia caught outside the hospital, plus middle ear infection and meningitis. It is the target of the pneumococcal vaccines.

Clostridium and its close relative Clostridioides are Gram-positive rods with two dangerous habits. They are obligate anaerobes, and they form endospores. The roll call is short. Clostridioides difficile causes colitis after antibiotics. Clostridium tetani causes tetanus. Clostridium botulinum causes botulism. Clostridium perfringens causes gas gangrene and a form of food poisoning. Because spores resist alcohol, an alcohol hand rub does not remove C. difficile. Hands must be washed with soap and water, and surfaces need a bleach cleaner.

Gram-negative bacteria carry only a thin layer of peptidoglycan. They lose the crystal violet during the wash and take up the pink counterstain instead. What really sets them apart is a second membrane wrapped outside the wall. Its outer face is studded with lipopolysaccharide, or LPS. One part of LPS, called lipid A, is a strong endotoxin. When Gram-negative cells die and break apart in the blood, lipid A spills out. Fever climbs, blood pressure drops, and at the far end septic shock follows.

Escherichia coli is a Gram-negative rod. It lives in the colon of every healthy person and does no harm there. Out of place, it is the single most common cause of urinary tract infections. It is also a frequent cause of Gram-negative sepsis and of meningitis in newborns. A few strains are true gut pathogens. Enterohemorrhagic E. coli, such as the strain O157:H7, makes Shiga toxin. It can cause bloody diarrhea and hemolytic uremic syndrome, which shreds red blood cells and is a cause of sudden kidney failure in children. E. coli is a facultative anaerobe, which is why it does well both in the low-oxygen gut and in the bladder.

Salmonella are Gram-negative rods. They spread through food and water, and through contact with reptiles and poultry. Most infections are a short, self-limited gastroenteritis, the classic food poisoning from undercooked eggs or chicken. One type behaves differently. Salmonella Typhi causes typhoid fever, an illness that spreads through the whole body with a long high fever. The lesson is worth keeping. In plain infectious diarrhea in an otherwise healthy adult, fluids and hand washing do the work. Routine antibiotics do not.

Pseudomonas aeruginosa is a Gram-negative rod and an obligate aerobe. It is one of the great opportunists of the hospital. It lives in wet spots: sink drains, breathing equipment, standing water, even flower vases. It causes pneumonia in people on ventilators. It infects burns and long-standing wounds. It causes urinary infections tied to catheters. It settles into the lungs for years in cystic fibrosis. It makes a blue-green pigment and smells like grapes or corn tortillas. It is also intrinsically resistant to many antibiotics, meaning the resistance is built in from the start.

A few important bacteria refuse to fit the Gram scheme at all. The mycobacteria matter most. Their cell wall is loaded with a waxy fat called mycolic acid, and the wax repels ordinary water-based dyes. To see these cells you need an acid-fast stain. Heat and a strong dye push color into the wall, and the color holds on even when acid-alcohol is used to wash it out. Mycobacterium tuberculosis causes tuberculosis. The waxy wall makes it slow to grow, so cultures take weeks. The same wax makes it tough out in the environment. TB travels through the air on tiny dried droplets called droplet nuclei. So it calls for airborne isolation: a negative-pressure room and a fitted N95 respirator, not a plain surgical mask. Its cousin Mycobacterium leprae causes leprosy, also called Hansen disease.

Spirochetes are long thin tightly coiled bacteria. They move with a corkscrew twist, driven by internal axial filaments, also called endoflagella. They are so slender that a routine Gram stain often misses them, and most will not grow on ordinary media. So they are usually found by blood tests rather than by culture. Three are worth knowing. Treponema pallidum causes syphilis. Borrelia burgdorferi causes Lyme disease and spreads by tick bite. Leptospira causes leptospirosis, picked up from water holding animal urine.

Mycoplasma are the smallest free-living bacteria, and they have no cell wall at all. With no rigid wall they have no set shape, which is called pleomorphic. No wall also means no peptidoglycan, so a penicillin has nothing to grab and beta-lactam drugs do not work. Mycoplasma pneumoniae causes walking pneumonia, a mild drawn-out lung infection common in younger people. It is treated with a macrolide or a tetracycline instead.

Oxygen is the last great sorting feature. An obligate aerobe must have oxygen. An obligate anaerobe is poisoned and killed by it. A facultative anaerobe prefers oxygen but can switch to fermentation without it, and most germs that grow easily in the lab sit here. A microaerophile needs oxygen but only a little. An aerotolerant anaerobe never uses oxygen, yet air does it no harm.

This is not a dry detail. Anaerobes thrive exactly where oxygen cannot reach: the depths of a puncture wound, the center of an abscess, crushed or dead tissue, the gut, and the pockets around the teeth. That is why deep, dirty and bite wounds are anaerobe problems, and so is gas gangrene. Air also kills obligate anaerobes on contact. A sample taken to look for them must be shielded from air and reach the lab fast in an oxygen-free container. Otherwise the germ dies first and the culture comes back falsely negative.

A few more dials finish the coordinate system. Most human pathogens are mesophiles, happiest near body temperature at 37°C. Bacteria are also grouped by how much acid and how much salt they tolerate. And they are grouped by whether they can live only inside host cells. Chlamydia and Rickettsia are obligate intracellular bacteria. Neither can copy itself outside a host cell, so neither grows on a standard plate.

Shapes and arrangements worth memorizing

The organisms worth memorizing

The bench tests worth memorizing

Oxygen classes, drawn

Sequences, in order

Naming an organism is a chain of narrowing questions. Run them in this order and almost any germ lands in a box.

1. Shape · coccus, bacillus or spirillum.
2. Arrangement · pairs, chains, clusters, tetrads or a palisade.
3. Gram reaction · purple or pink, or neither if it is acid-fast or wall-less.
4. Oxygen need · aerobe, anaerobe, facultative or microaerophile.
5. Growth needs · temperature, pH, salt, and whether it needs an enriched plate.
6. Lifestyle · free-living, or obligate intracellular like Chlamydia and Rickettsia.

How to reason through the question types

Chapter 5Viruses, Fungi and Parasites

What to know

A virus sits on the fence between living and non-living. It is acellular, so it is not a cell. It has no cytoplasm and no ribosomes. It cannot make its own energy and has no tools for copying itself. Left alone on a countertop, a virus just sits there.

A virus only comes to life inside a host cell, where it borrows the cell's machinery. Because it can never copy itself alone, a virus is an obligate intracellular parasite. This is also why antibiotics do nothing to a virus. Antibiotics attack parts only bacteria have, and a virus has none of them.

Strip a virus down and two parts are always there. At the center is the genome. A virus may carry DNA or RNA, never both, and that strand may be single or double. The choice matters. RNA viruses copy their genomes sloppily, so they change fast. Influenza, HIV, SARS-CoV-2 and hepatitis C are all RNA viruses, and their quick drift is why a new flu shot is needed each year.

Wrapped around the genome is the capsid, a shell built from repeating protein blocks called capsomeres. It guards the fragile genome and holds the surface proteins that grip a host cell. A helical capsid is a rod. An icosahedral capsid is a round cage with 20 flat faces. A complex capsid mixes parts, the way a bacteria-eating phage has a head and a tail. Genome plus capsid is the nucleocapsid.

Some viruses add a third layer. The envelope is a lipid membrane the virus steals from its host cell as it leaves. Stuck through it are viral spike proteins, also called glycoproteins. They are the keys for the next break-in. The SARS-CoV-2 spike and the influenza hemagglutinin are the famous ones.

Whether a virus has an envelope turns out to be very practical. An enveloped virus needs its lipid coat to infect, and lipids are easy to wreck. Soap, alcohol-based hand rub and plain drying pull the envelope apart. So flu, COVID, HIV and herpes are fairly easy to kill outside the body.

There is one exception not to smooth over. Hepatitis B has an envelope, yet it stays infectious in dried blood for a week or more. Spills of blood and body fluid are cleaned with an EPA-registered hospital disinfectant carrying a tuberculocidal or HBV claim, or with household bleach diluted 1:10. An alcohol wipe is not enough.

A non-enveloped virus, also called a naked virus, has only its tough protein capsid outside. It shrugs off alcohol and can last for days on a surface. Norovirus and poliovirus are the classic hardy naked viruses, and they call for bleach and careful scrubbing.

Replication is a story of hijacking, and the order of events is nearly always the same. First comes attachment, as a surface protein fits a matching receptor like a key in a lock. That fit is why one virus infects only certain cells. HIV binds CD4 on T cells. Rhinovirus binds cells lining the airway. Second comes entry, also called penetration, as the whole virus or just its genome slips inside.

Third, and this is the heart of it, comes biosynthesis. The viral genome takes over the cell's ribosomes, enzymes and raw material. The cell starts mass-producing viral proteins and genome copies. Fourth comes assembly, when those parts snap together into whole particles. Fifth comes release, when the new particles escape. One infected cell can turn out hundreds or thousands of particles.

Step three is where the three great kinds of virus part ways. Most DNA viruses send their genome into the nucleus and use your enzymes plus a few of their own. Herpesviruses bring along their own DNA polymerase, and that extra enzyme is what acyclovir is built to jam. Most RNA viruses set up shop in the cytoplasm instead. Your cells have no enzyme that copies RNA into RNA, so most RNA viruses carry their own RNA polymerase. Influenza is the odd one out, because it does copy its RNA inside the nucleus.

A retrovirus is stranger still. HIV carries reverse transcriptase, which writes a DNA copy of the viral RNA. A second enzyme, integrase, pastes that DNA into a host chromosome. From then on the cell copies the virus along with its own genes. Later a viral protease cuts long protein chains into finished pieces, and only then can the new particle infect anything.

The last step comes in two flavors, and the split lines up with the envelope. Naked viruses usually escape by lysis, filling the cell until it bursts. Enveloped viruses more often leave by budding, pushing out through the host membrane and wrapping themselves in a piece of it. Budding is slower and gentler, and that is part of how some enveloped viruses settle into long smoldering infections.

Some viruses do not replicate and leave. They hide. In latency a virus enters a cell, goes quiet, and parks its genome there. It makes few or no new particles and causes no symptoms, sometimes for decades. Later, often when the immune system is stressed, it reactivates.

The herpesvirus family are the masters of this. Varicella-zoster causes chickenpox, retreats into nerve roots, and can wake years later as shingles. Herpes simplex hides in nerves between cold-sore or genital outbreaks. These viruses keep their genome in the nucleus as a free-floating ring, so it rides along without joining the host DNA. HIV plays a harder version. It splices a DNA copy of itself, called a provirus, straight into the host chromosome. That is exactly why HIV can be held down but not yet cured.

Now the fungi. Fungi are eukaryotes. Like our cells, theirs keep DNA inside a nucleus. That family likeness is what makes a fungal infection hard to treat, because a drug that harms a fungal cell can easily harm a human cell.

Fungi grow with one of two body plans. A yeast is a single oval cell that reproduces by budding, pinching off a small copy of itself. Candida is the classic yeast. A mold grows as long branching threads called hyphae, which mat into a visible fuzzy colony called a mycelium. Molds spread by releasing tiny airborne spores. Some fungi are dimorphic: a mold out in the cool environment, a yeast at body temperature. Coccidioides is a near miss worth knowing, because in tissue it forms not a true yeast but a round sac called a spherule, packed with spores.

Two structural facts drive fungal drug choice. The fungal cell wall is made of chitin and glucan, not peptidoglycan. The fungal membrane is built on ergosterol, where ours uses cholesterol. Ergosterol is the chink in the armor that most antifungals aim for.

Fungal diseases are the mycoses, sorted mostly by how deep they reach. Superficial and cutaneous mycoses stay in skin, hair and nails. These are the dermatophyte infections, the ones named tinea: ringworm, athlete's foot, jock itch. Subcutaneous mycoses are pushed deeper by an injury such as a thorn prick. Systemic mycoses travel through the body and are the dangerous group, often landing in the lungs.

One theme runs through all of it. Many serious fungal infections are opportunistic, taking hold only when defenses are down. The greatest risk sits with people on chemotherapy, on long courses of antibiotics or steroids, living with poorly controlled diabetes, or living with HIV and AIDS.

A short list accounts for most of what turns up. Candida albicans causes oral thrush, the white plaques that scrape off a sore mouth, plus vaginal yeast infections and diaper rash. In the bloodstream of a very ill person it causes candidemia, which can be deadly. Dermatophytes cause the itchy ring-shaped tinea rashes. Aspergillus is a mold breathed in as spores, and it can carve out serious lung disease. Cryptococcus, picked up from dried bird droppings, causes a dangerous meningitis in advanced AIDS. Pneumocystis jirovecii causes the pneumonia shortened to PJP or PCP, a hallmark of advanced HIV. That last one is a true oddity. It is a fungus, but its membrane has no ergosterol, so the usual antifungals miss it and the treatment of choice is trimethoprim-sulfamethoxazole instead.

Next the protozoa. Protozoa are single-celled eukaryotes that behave like tiny animals. Many hunt, most move under their own power, and a great number live as parasites. Many lead a two-stage life. The trophozoite is the active form, which feeds, divides and causes the symptoms. The cyst is a tough walled-off resting form that survives outside the body, and it is usually the form that reaches the next person. The cyst is what clean water and hand hygiene are meant to block.

Malaria is caused by Plasmodium and spread by the bite of a female Anopheles mosquito, which makes it vector-borne. After the bite the parasite first multiplies quietly in the liver. Then it pours into the blood and invades red blood cells, multiplying inside them until they burst in waves roughly in step. Those bursts give malaria its signature: cycles of fever, chills and drenching sweats returning every two or three days. The most dangerous species is Plasmodium falciparum, which can clog the small vessels of the brain and cause fatal cerebral malaria. The habit of mind that matters most: a fever after recent travel to a malaria region is an emergency until proven otherwise.

Giardia is the protozoan you are most likely to meet close to home. Its hardy cysts contaminate lakes and streams, so it causes the diarrhea that campers and hikers bring back. The stools are foul-smelling, greasy and float, with gas and cramps alongside. It spreads fecal-oral. Because the cysts shrug off normal chlorine levels, prevention means boiling or filtering water rather than just treating it.

A few other protozoa come up again and again. Entamoeba histolytica invades the colon wall and causes bloody amebic dysentery, and it can seed an abscess in the liver. Trichomonas vaginalis is a common sexually transmitted infection. Toxoplasma gondii, picked up from cat feces or undercooked meat, is dangerous in pregnancy and in AIDS. Cryptosporidium causes waterborne diarrhea that turns severe and drags on when defenses are low.

Last come the worms. The helminths are parasitic worms, and strictly they are not microbes at all. An adult tapeworm can be meters long. They earn a place here because they are found the way microbes are found, by spotting their microscopic eggs and larvae in stool, blood or tissue.

Worms harm slowly. They steal nutrients, bring on anemia and malnutrition, block the bowel or the bile ducts, and set off allergy-like immune reactions. That last habit leaves a useful clue. Worm infections classically drive up the eosinophils, a white blood cell aimed at parasites. So an unexplained eosinophilia should raise the question of a worm. The clue is strongest for worms that push into tissue. A worm that stays in the gut lumen, such as pinworm, often leaves the count alone.

Nematodes are the roundworms. They are smooth, round in cross-section, unsegmented and tapered at both ends, and males and females are separate worms. The one you are sure to meet is the pinworm, Enterobius, the most common worm infection in the United States. The female crawls out at night to lay eggs on the skin around the anus. That causes fierce itching, and the eggs then travel easily on hands and bedding. Ascaris is a large intestinal worm that can reach about 35 centimeters, and a heavy load can block the bowel. Hookworms latch onto the gut wall and suck blood, which leads to iron-deficiency anemia. Trichinella comes from undercooked pork, and its larvae settle into muscle.

The platyhelminths, or flatworms, split into two clinical groups. The cestodes are the tapeworms: long flat ribbon-like worms made of repeating segments. The head, called a scolex, grips the gut wall with suckers, and the pork tapeworm adds a crown of hooks. Tapeworms have no gut of their own and soak up nutrients through their surface. People catch them from undercooked beef, pork or fish.

The trematodes are the flukes. Most are flat and leaf-shaped with two suckers, and nearly all pass through a snail on the way to a human host. Worldwide the most important fluke is Schistosoma, the blood fluke, and its eggs damage the bladder, liver and intestines over years. Blood flukes break the usual fluke pattern twice over. They are slender and round-bodied rather than leaf-shaped, and the sexes are separate, with the male carrying the female in a groove along his body.

Enveloped against naked, drawn

The organisms worth memorizing

The drug classes worth memorizing

Sequences, in order

Viral replication always runs in these five steps. Attach a drug class to each one and the whole antiviral shelf fits on one frame.

1. Attachment · a spike or surface protein fits a matching host receptor.
2. Entry · the virus or its genome crosses into the cell.
3. Biosynthesis · host machinery mass-produces viral parts. DNA viruses mostly work in the nucleus, RNA viruses mostly in the cytoplasm.
4. Assembly · the fresh parts snap together into whole particles.
5. Release · naked viruses burst the cell by lysis; enveloped viruses bud out through the membrane.

A retrovirus adds its own three enzymes inside step three and step four.

1. Reverse transcriptase writes a DNA copy of the viral RNA.
2. Integrase pastes that DNA into a host chromosome, where it becomes a provirus.
3. Protease cuts long protein chains into finished pieces, and only then can the particle infect.

Malaria runs a fixed route through two hosts.

1. A female Anopheles mosquito bites and injects the parasite.
2. The parasite multiplies quietly in the liver.
3. It pours into the blood and invades red blood cells.
4. It multiplies inside them until they burst in waves roughly in step.
5. Those bursts give the fever, chill and sweat cycles every two or three days.

How to reason through the question types

Chapter 6Microbial Growth and Metabolism

What to know

To grow, a microbe has to build more of itself, and building takes raw material. Most of any cell is made from six elements: carbon, hydrogen, oxygen, nitrogen, phosphorus and sulfur. These are the macronutrients, needed in bulk. Cells also need tiny amounts of micronutrients, also called trace elements, and iron, zinc and copper are the common ones.

Some microbes can build every complex molecule they need. Others cannot, and must be handed finished vitamins or amino acids. A ready-made extra like that is a growth factor. A microbe that cannot make one or more of its own growth factors is fastidious. The word means fussy, and it is the right word. It is the reason some pathogens need special enriched plates to grow at all. It is also the reason a lab using the wrong medium can report no growth on someone who really is infected.

Carbon is the backbone of every molecule in a cell, so the first question is where the carbon comes from. An autotroph builds its own organic molecules out of carbon dioxide, which is inorganic. A heterotroph cannot do that. It has to take in carbon another living thing already put together, such as sugars, proteins and fats. Every microbe that infects a person is a heterotroph.

The second question is where the energy comes from. A phototroph catches energy from light. A chemotroph pulls energy out of chemical bonds. Put the two answers together and you have the microbe's nutritional type. The names come apart cleanly: read the front half for energy and the back half for carbon. A chemoheterotroph gets both carbon and energy from organic compounds. The bacteria, fungi, protozoa and helminths that cause disease are all chemoheterotrophs, and so are you.

Now oxygen. For a microbe it cuts both ways. Burning fuel with oxygen releases far more energy than any other route, so organisms that can use it grow fast. But oxygen chemistry also throws off reactive oxygen species, mainly superoxide and hydrogen peroxide. They tear up proteins, membranes and DNA. To live with oxygen safely a microbe needs enzymes that clean them up. Superoxide dismutase neutralizes superoxide. Catalase splits hydrogen peroxide into water and oxygen. A microbe without these enzymes is killed by ordinary air.

Microbes fall into five groups by how they handle oxygen, and the classic way to see it is a thioglycolate tube. The broth is rich in oxygen at the top and free of it at the bottom, and each organism grows only in the band where it can survive. An obligate aerobe grows only at the top. An obligate anaerobe grows only at the bottom. A facultative anaerobe grows all through the tube, thickest near the top. A microaerophile forms a thin band just under the surface. An aerotolerant anaerobe grows evenly from top to bottom.

One more group is worth knowing. Capnophiles grow best in air holding extra carbon dioxide. Neisseria and Haemophilus are the usual examples, and the lab grows them in a jar enriched with carbon dioxide.

Every microbe has three cardinal temperatures. A minimum, below which it stops growing. An optimum, where it grows fastest. And a maximum, above which its proteins cook and the cell dies. Microbes are grouped by where that optimum falls. Psychrophiles love the cold. Mesophiles prefer middling warmth. Thermophiles thrive in hot springs and compost. Hyperthermophiles flourish in water close to boiling.

One fact here matters more than the rest. Human pathogens are mesophiles, with an optimum right around 37°C. That is exactly why the body is such a welcoming home, and why lab incubators are set to 35 to 37°C.

Microbes also have a preferred acidity. Most human pathogens are neutrophiles, growing best near neutral at about pH 6.5 to 7.5, which matches blood and most tissue. Acidophiles prefer acid, and the lactobacilli that hold the vagina at a low protective pH are acidophiles. Alkaliphiles grow best in basic surroundings. The stomach sits near pH 2, which is a chemical wall that kills most microbes you swallow. That makes Helicobacter pylori all the more striking, because it neutralizes the acid around itself and settles into the stomach lining.

Microbes also need liquid water they can actually use. Heavy salt or heavy sugar pulls water straight out of a cell by osmosis. That is exactly how salting meat and sugaring jam keep food. Halophiles actually require high salt. Osmotolerant organisms do not need it but put up with it, which is why Staphylococcus aureus grows on skin and in salty food that stops other bacteria cold. The lab uses that trait on purpose with high-salt selective media. One more warning sits here. Listeria grows in the fridge, so chilling something is not the same as sterilizing it.

Most bacteria reproduce by binary fission. One cell copies its DNA, grows, then splits into two identical daughter cells. The time it takes one cell to become two is the generation time, also called the doubling time. It can be startlingly short. Escherichia coli can double every 20 minutes when conditions are ideal. Each generation doubles the population, so the counts run 1, 2, 4, 8, 16 and on. Growth shaped like that is exponential.

One cell dividing every 20 minutes becomes more than a million in about seven hours. Check it yourself. Seven hours is 420 minutes, and 420 divided by 20 gives 21 doublings. Two multiplied by itself 21 times is 2,097,152. The formula is short. Write the starting count as N₀ and the count now as N. Then N = N₀ × 2ⁿ, where n is the number of doublings. Rearrange it and you get the generation time: divide the growing time by n.

Generation time is not a fixed fact about a species. It is what that species manages under the conditions it is in. Twenty minutes is what E. coli does in rich broth at 37°C with plenty of air. Cool the flask, sour it, starve it or take the oxygen away and the same cell takes far longer.

Drop a few bacteria into fresh broth and the population moves through four phases, in the same order every time. In the lag phase the cells are not dividing yet. They are gearing up, making enzymes and building blocks. In the log phase, also called the exponential phase, they divide at full speed and the numbers explode. These are the healthiest, busiest cells of the whole run. Then nutrients run short and waste piles up, and the population moves into the stationary phase, where new cells appear about as fast as old ones die. Last comes the death phase, also called the decline phase, when cells die faster than they can be replaced.

The phase a population is in changes how it answers treatment. Many antibiotics can only kill bacteria that are actively building and dividing, and the cell wall drugs are the clearest case. So those drugs work best against log-phase cells and far less well against the slow, nearly dormant cells of the stationary phase. That is one reason deep, walled-off and biofilm infections are so stubborn. It is also why steady drug levels and a full course matter.

To study a microbe or to name it, we usually have to grow it on a culture medium. Solid media are set with agar, a jelly pulled from seaweed. Microbes cannot digest agar, and it stays firm at body temperature, which is exactly what is needed.

Media come in types for different jobs. A general-purpose medium supports a wide range of organisms. An enriched medium adds extra nutrients such as blood or serum so fastidious pathogens can grow. A selective medium holds back the organisms you do not want. A differential medium holds a dye or a sugar that makes different organisms look different. Plenty of real plates do both jobs at once, and MacConkey agar is selective and differential together. One more type never tries to grow anything. A transport medium only keeps a sample alive and unchanged on the trip to the lab, so the mix that left the body is the mix that arrives.

Put a single bacterial cell on solid agar and leave it alone. It divides again and again on the same spot until millions of its descendants pile into a visible mound. That mound is a colony, and every cell in it came from one original cell. Pick one and you have a pure culture. Getting there is the whole point of the streak plate. An inoculating loop drags the sample across the plate in a shrinking pattern, until the last cells land far enough apart to form separate colonies.

Colonies are also how we count microbes. We assume each colony started from one cell, or from one clump stuck together. So lab counts are reported as colony-forming units, written CFU, rather than as exact cell numbers. That is more than bookkeeping. A urine culture growing a high CFU count of a single organism points to a real urinary tract infection. A low count, or a mix of many different organisms, often means the sample picked up contaminants during collection. A culture report has three parts worth reading together: the organism, the CFU count and the sensitivities.

The growth curve, drawn

The groupings worth memorizing

The media worth memorizing

Sequences, in order

The four phases always run in this order. Attach a consequence to each one.

1. Lag · no division yet. This is the delay before symptoms, or before a culture turns positive.
2. Log · full-speed doubling. Antibiotics land hardest here, and cultures should be drawn before drugs start.
3. Stationary · new cells match dying cells. Slow cells resist drugs, and toxins or spores may form.
4. Death · deaths outpace divisions, and the population collapses.

Turning a swab into a named organism runs through a fixed chain too.

1. Collect the specimen properly and carry it in the right medium.
2. Streak plate the sample so the last cells land far apart.
3. Incubate, and each isolated cell grows into a visible colony.
4. Pick one well separated colony. That gives a pure culture.
5. Identify the species, count the growth in CFU, and test sensitivities.

How to reason through the question types

One pageCram sheet