This unit is about the smallest players in biology, bacteria that are complete living cells and viruses that can only reproduce inside a host cell. After it, you should be able to describe how a prokaryote is built and grows, trace a viral infection step by step, and explain how microbes help and harm the ecosystems they live in, including your own body.
Read the overview first, then work through each topic note and answer its checkpoint before you look at the answer.
Microbiology studies microorganisms, most of which are too small to see without a microscope, as well as viruses. You'll compare prokaryotic cells with the eukaryotic cells from earlier units, then look at viruses, which don't fit neatly into the definition of life. The unit ends by showing how microbes interact with each other, with ecosystems, and with you.
Honors Biology Unit 13 covers prokaryotes and viruses. You learn the parts of a bacterial cell (cell wall, nucleoid, 70S ribosomes, plasmids, flagella, pili), how bacteria reproduce by binary fission, and how populations grow through lag, exponential, stationary and death phases. You then study viral structure (genome, capsid, sometimes an envelope) and the lytic and lysogenic replication cycles. The last topic covers microbial ecology, including symbiosis, biofilms, quorum sensing, opportunistic infections and the human microbiome. Some schools place this unit earlier or fold it into a unit on classification, so the order may differ in your class.
A bacterium has no nucleus or membrane-bound organelles, but it has ribosomes and can grow and divide. Some bacteria depend on host cells for growth. Under favorable conditions, a population of E. coli can double about every 20 minutes. That speed, plus gene sharing through plasmids, is why bacterial populations adapt so quickly.
A virus is genetic material in a protein coat, with no ribosomes and no metabolism of its own. It attaches to specific receptors, gets its genome inside, and uses the cell's machinery to build copies. Some bacteriophages follow a lytic cycle, which releases new viruses by bursting the cell. Others can enter a lysogenic cycle, in which viral DNA is maintained as the host cell divides.
Bacteria recycle nutrients, fix nitrogen and help you digest fiber and make vitamin K. Problems often start when the balance shifts, such as when antibiotics wipe out helpful gut bacteria or a weakened immune system lets harmless microbes overgrow.
Antibiotics can target bacterial peptidoglycan walls or 70S ribosomes, although they can still cause side effects in people. A virus's lack of those parts is why antibiotics do nothing to it. Receptors explain which cells a virus can infect, and a biofilm's slime explains why some infections refuse to clear. If you know the parts, you can usually predict the behavior.
Bacteria are prokaryotes, single cells with no nucleus and no membrane-bound organelles.
A virus is a set of genes, either DNA or RNA, packed inside a protein shell called a capsid.
Microbes live in relationships with other species.
Bacteria are prokaryotes, single cells with no nucleus and no membrane-bound organelles. Most have one circular chromosome in the nucleoid, a region of cytoplasm with no membrane around it. Some have multiple or linear chromosomes. Bacteria build proteins on 70S ribosomes, which are smaller than the 80S ribosomes in human cytoplasm. Many also carry plasmids, small DNA molecules that can hold antibiotic resistance genes.
Most bacteria have a peptidoglycan cell wall outside the membrane that keeps them from bursting when water rushes in. The Gram stain sorts bacteria by this wall. In some bacteria, flagella spin to move the cell, and pili help it stick to surfaces or pass DNA to a neighbor.
Bacteria reproduce asexually by binary fission. The cell copies its chromosome, grows longer, and pinches into two genetically similar daughter cells. Mutations can produce differences. New variation comes from mutation and horizontal gene transfer (conjugation, transformation and transduction), not from sexual reproduction. In a closed flask, a population moves through four phases: lag, exponential (log), stationary and death.
Worked example. E. coli can divide every 20 minutes. Starting with one cell, how many cells are there after 3 hours? The number of doublings is . The population is cells. If that doubling rate continues for 7 hours, , so million cells. Actual growth can slow as conditions change.
Check yourself: In a closed flask, why does a bacterial population stop growing and level off? (Answer: Nutrients run low and waste builds up, so the rate of new cells forming equals the rate of cells dying, which is the stationary phase.)
| Feature | Gram-positive | Gram-negative |
|---|---|---|
| Peptidoglycan layer | Thick | Thin |
| Outer membrane | No | Yes, outside the thin wall |
| Color after Gram stain | Purple (keeps crystal violet) | Pink (takes up the counterstain) |
| Response to penicillin | Usually more sensitive | Often less sensitive because the outer membrane blocks the drug |
A virus is a set of genes, either DNA or RNA, packed inside a protein shell called a capsid. Some viruses, like influenza and HIV, also have an envelope, a lipid layer taken from the host cell's membrane. Viruses have no ribosomes and no metabolism, so most biologists don't consider them alive. Many viruses are roughly 20-400 nm across, although some are larger. A typical bacterium like E. coli is about 2,000 nm long.
Every infection starts with attachment. Proteins on the virus bind to specific receptors on the host cell. Receptor binding helps determine which cells a virus can enter, but successful infection also depends on factors inside the cell. Then the viral genome gets inside.
In a lytic phage cycle, the cell copies viral genes, builds capsids, assembles new virions, and bursts (lyses) to release them. In lysogeny, phage DNA is maintained as a prophage and copied as the bacterium divides. A prophage often inserts into the bacterial chromosome, though some remain separate. Stress such as UV light can induce a prophage to enter the lytic cycle. An integrated viral genome in an animal cell is called a provirus.
Worked example. A phage has a burst size of 100, meaning each infected cell releases 100 new phages. One phage infects one bacterium. After round 1 there are 100 phages. If each infects a new cell, round 2 gives phages, and round 3 gives .
Check yourself: A bacterial culture looks healthy for many generations, then many cells suddenly burst after being exposed to UV light. What happened? (Answer: The bacteria carried a prophage from a lysogenic infection, and the UV stress induced it to leave the chromosome and enter the lytic cycle.)
| Feature | Lytic cycle | Lysogenic cycle |
|---|---|---|
| Viral DNA | Stays separate and takes over the cell | Is maintained in the host, often inserted into its chromosome |
| Host cell | Bursts and dies | Survives and keeps dividing |
| Speed | Fast, new virions within minutes to hours | Slow, can stay quiet for many generations |
| How the virus spreads | New virions infect nearby cells | Usually copied into daughter cells as the host divides |
| Classic example | T4 phage in E. coli | Lambda phage in E. coli |
Microbes live in relationships with other species. In mutualism both partners benefit. For example, some gut bacteria get nutrients from their host and produce compounds that the host can absorb and use. In commensalism one benefits and the other is unaffected, like many skin bacteria. In parasitism one benefits and the other is harmed, like Mycobacterium tuberculosis damaging lung tissue.
At the ecosystem level, bacteria act as decomposers that return nutrients to the soil, and some fix nitrogen gas into ammonia that plants can use.
Bacteria also act as groups. In quorum sensing, each cell releases signal molecules called autoinducers. When the signal reaches a threshold, the cells change gene expression, turning some genes on or off. Vibrio fischeri inside squid only glows once enough cells are present. Bacteria use the same trick to build biofilms, slimy communities on surfaces such as dental plaque, which can be far harder for antibiotics to reach.
Your microbiome is all the microbes living in and on you, with most in the gut. Roughly as many bacterial cells live in your body as human cells. Some break down fiber you can't digest and produce compounds your body can use. Gut microbes also interact with your immune system and can limit pathogen growth. Some make vitamins, but not all of those vitamins are available for your body to absorb. When antibiotics or a weak immune system disrupt that balance, normally harmless microbes can cause opportunistic infections, such as thrush from the fungus Candida albicans.
Check yourself: Why might someone get a gut infection right after a long course of antibiotics for strep throat? (Answer: The antibiotics also killed helpful gut bacteria, so a resistant or normally outcompeted microbe like C. difficile can overgrow without competition.)
| Term | Definition |
|---|---|
| Prokaryote | A single-celled organism with no nucleus or membrane-bound organelles, which includes bacteria and archaea. |
| Peptidoglycan | A mesh of sugars and amino acids that forms the bacterial cell wall and keeps the cell from bursting. |
| Gram stain | A lab stain that turns thick-walled Gram-positive bacteria purple and Gram-negative bacteria with an outer membrane pink. |
| Horizontal gene transfer | Movement of genes between bacteria by conjugation, transformation or transduction rather than from parent to offspring. |
| Conjugation | Direct transfer of DNA, usually a plasmid, from one bacterium to another through a pilus. |
| Envelope | A lipid membrane, taken from the host cell, that surrounds the capsid of some viruses such as influenza. |
| Lytic cycle | A viral cycle in which the virus takes over the host cell, makes new virions, and bursts the cell to release them. |
| Lysogenic cycle | A phage cycle in which viral DNA is maintained and copied as the bacterial host divides. It often joins the host chromosome and can later be induced to enter the lytic cycle. |
| Human microbiome | All the microorganisms and their genes living in and on the human body, mostly in the gut. |
Antibiotics target bacterial parts like peptidoglycan walls and 70S ribosomes. Viruses have neither, so antibiotics can't touch them. Your immune system responds to viral infections, and antiviral drugs can treat some of them. Vaccines help prevent certain infections or reduce the risk of severe disease.
The nucleoid is just the area where the bacterial chromosome clumps, and it has no membrane. If a diagram shows DNA inside a membrane-bound compartment, it's a eukaryotic cell. Also remember that prokaryotes include archaea, not only bacteria.
A prophage remains in a bacterium and is copied as the cell divides. It can express some genes, and stress can sometimes induce it to enter the lytic cycle. HIV is not a phage, but its integrated provirus can persist in human cells, which makes the infection hard to clear.
Individual bacteria don't adapt on purpose. Some bacteria may already have resistance from mutations or acquired genes. An antibiotic can kill susceptible bacteria or stop their growth, while resistant bacteria are more likely to survive and multiply. That's natural selection, and horizontal gene transfer spreads the resistance genes even faster.