Prokaryotic cells and viruses

Prokaryotic cell structure

Prokaryotic cells are the bacteria and the archaea, and they are small, typically 0.5 to 5 µm across, against 10 to 100 µm for a eukaryotic cell. A whole bacterium is about the size of a mitochondrion, a similarity the endosymbiotic theory accounts for.

Describe the drawing

A prokaryotic cell drawn as a rod with rounded ends. From the outside in there is a slime capsule, a murein cell wall drawn as a thick band, and the plasma membrane. Inside the cytoplasm lie a single circular chromosome drawn as a closed loop with no envelope round it, two smaller circles of plasmid DNA, and scattered ribosomes. Short pili project from the top surface and a long flagellum trails from one end. Nothing inside the cell is wrapped in its own membrane.

Start at the outside. The cell wall is made of murein, also called peptidoglycan, a mesh of polysaccharide chains cross-linked by short peptides. It is not cellulose and it is not chitin, and the difference is exactly what penicillin exploits: the drug blocks the cross-linking, so a growing bacterium builds a wall too weak to resist osmotic entry of water and bursts. Human cells have no cell wall, so the drug has no equivalent target in them.

Bacteria fall into two groups by the structure of that wall, and the Gram stain tells them apart. A Gram-positive wall is a thick layer of murein, which holds the purple crystal violet stain. A Gram-negative wall has only a thin layer of murein, covered by an outer membrane containing lipopolysaccharide; the purple washes out, and the cells take up the red counterstain instead. The outer membrane also keeps many antibiotics away from the murein, so penicillin, and the enzyme lysozyme, act far more strongly on Gram-positive bacteria than on Gram-negative ones.

Outside the wall, many species secrete a capsule of slime. It holds water, helps the cell stick to surfaces and to other bacteria, and makes phagocytosis harder for a white blood cell. The capsule is one reason some strains are dangerous and closely related ones are not.

Inside the wall is the plasma membrane, and inside that the cytoplasm, where the main differences from a eukaryotic cell lie. There is no nucleus. In the bacteria this course describes, the DNA is a single circular molecule, lying free in the cytoplasm in a region called the nucleoid, with no envelope and no histone proteins wound into it (the other prokaryote domain, the archaea, breaks that tidy rule: many species carry histone proteins, and chromosome arrangements vary). There is no endoplasmic reticulum, no Golgi apparatus, no mitochondrion and no lysosome. The electron transport chain and ATP synthase sit in the plasma membrane itself, so the one membrane holding the cell together is also the membrane it respires on. Older textbooks drew the chain on infoldings called mesosomes; the infoldings were made by the fixing chemicals and are not there in a living bacterium. The only structure in there that a eukaryotic cell also has is the ribosome, and even that is smaller, at 70S against the eukaryote's 80S.

Three extras appear in many species. Pili are short protein projections that attach the cell to surfaces or, as a sex pilus, to another bacterium so that a plasmid can pass across. Plasmids are small circles of DNA, separate from the main chromosome, carrying a handful of genes that are useful rather than essential, such as resistance to an antibiotic. They replicate independently and can be passed from one bacterium to another, which is how resistance spreads through a population far faster than mutation alone could manage. A flagellum is a long protein filament, anchored in the membrane and rotated by a molecular motor, which drives the cell forward. It is not the same structure as a eukaryotic flagellum and does not move the same way: this one spins, like a propeller.

Prokaryotic cell

A cell with no nucleus and no membrane-bound organelles, whose DNA is a single circular molecule free in the cytoplasm.

Plasmid

A small circular molecule of DNA, separate from the main chromosome, which replicates independently and often carries genes such as antibiotic resistance.

Capsule

A layer of slime outside the cell wall which retains water, aids attachment and gives some protection from phagocytosis.

Nucleoid

The region of a prokaryotic cell occupied by its circular DNA, with no surrounding membrane.

Comparing prokaryotic and eukaryotic cells

Answer a comparison in matched pairs: a statement about the prokaryote beside the corresponding statement about the eukaryote. "Prokaryotes have no nucleus" states only one side of the comparison.

Two rows need care. The DNA row is not simply 'circular against linear'. The absence of histone association is a separate point, as is the presence of one main chromosome rather than several.

The organelle row does not mean a bacterium has nothing inside it: it has ribosomes, enzymes, food stores and often internal membranes. What it lacks is any compartment sealed off by its own membrane.

One overlap is worth stating. Mitochondria and chloroplasts contain circular DNA not associated with histones, and 70S ribosomes: prokaryotic features within a eukaryotic cell. A complete answer to where 70S ribosomes occur in a leaf therefore includes the chloroplasts and mitochondria as well as any bacteria on the surface.

Binary fission and population growth

A prokaryote does not use mitosis. It has no nucleus to break down, no spindle and no set of chromosomes to line up. Instead it divides by binary fission, and the sequence is short: the circular DNA replicates, any plasmids replicate separately and in variable numbers, the cell grows and the two DNA circles move apart, then the cytoplasm divides and new wall material is laid down between the daughter cells.

Each daughter cell receives one copy of the chromosome. Plasmids are not distributed equally, so two daughters of the same cell can differ in the number of plasmid copies, and therefore in the number of resistance genes they carry.

Fission is rapid. Escherichia coli in warm conditions with ample nutrients divides about every 20 minutes, so the population doubles three times an hour.

Virus structure

A virus particle is between about 20 and 300 nm across, mostly smaller than the resolving limit of a light microscope, so viruses were not observed until the electron microscope was developed. Size is not the reason a virus is excluded from the definition of living; its structure is.

A virus consists of genetic material, either DNA or RNA, enclosed in a protein coat called a capsid, with attachment proteins on the outside. Some viruses also have a lipid envelope, derived from the membrane of the host cell the particle left. There is no cytoplasm, no ribosome, no mitochondrion and no enzyme system for respiration. A virus cannot make a protein, cannot release energy from food and cannot reproduce by itself. It is acellular, meaning not made of cells, and it is an obligate intracellular parasite, meaning it can only be copied by hijacking a host cell's ribosomes and enzymes.

The attachment proteins determine host specificity. Each type binds to a particular receptor molecule on a particular host cell, by the same complementary-shape interaction as a substrate binding an enzyme. Influenza therefore infects airway epithelium rather than liver tissue, and a virus of tobacco plants cannot attach to human cells.

Describe the drawing

A human immunodeficiency virus particle drawn in section as a sphere. Glycoprotein attachment spikes stand out all round the outside. Below them is the lipid envelope taken from a host cell membrane, and inside that a matrix layer. A cone-shaped protein capsid sits in the centre holding two single strands of RNA and two molecules of reverse transcriptase. There is no cytoplasm, no ribosome and no membrane-bound organelle anywhere in the particle.

HIV is built in layers. On the outside are glycoprotein attachment proteins, which bind to the CD4 receptor found on helper T cells. Beneath them is the lipid envelope taken from the host membrane, and inside that a layer of matrix protein. At the centre a cone-shaped capsid holds two single strands of RNA and several molecules of the enzyme reverse transcriptase. That enzyme catalyses the synthesis of DNA from the viral RNA template, the reverse of the usual direction of information flow, and the DNA copy is then inserted into the host chromosome. A virus that replicates in this way is a retrovirus.

Virus

An acellular infectious particle consisting of nucleic acid within a protein capsid, sometimes with a lipid envelope, which can only replicate inside a host cell.

Capsid

The protein coat surrounding a virus's genetic material.

Attachment protein

A protein on a virus's surface with a shape complementary to a receptor on its host cell, which determines which cells it can infect.

Reverse transcriptase

An enzyme carried by retroviruses such as HIV which catalyses the synthesis of DNA from an RNA template.

The lytic cycle and latency

Pearson Edexcel Biology B asks for the lytic cycle of a virus and for latency. The standard example is lambda (λ) phage, a double-stranded DNA virus whose host is the bacterium Escherichia coli. A phage, short for bacteriophage, is any virus that infects bacteria.

In the lytic cycle the virus replicates at once and the host cell is destroyed at the end of it. It runs in five stages.

Describe the drawing

Five panels across the top show the lytic cycle of lambda phage in a bacterium. In the first a phage, an angular head on a tail, attaches to the cell surface. In the second it has injected its DNA, drawn as wavy lines inside the cell, while the empty head stays outside. In the third the viral DNA has been copied several times and separate capsid heads have been made. In the fourth complete phages are assembled inside the cell, and in the fifth the cell wall, drawn dashed, has broken open and new phages are escaping. Below, an arrow from the injection stage leads to the latent route: a cell whose circular chromosome carries the phage DNA as a prophage, then two daughter cells each inheriting it after division. A coloured arrow labelled DNA damage, such as ultraviolet light, leads from the latent cells back up to the replication stage of the lytic cycle.

Viruses of animals follow the same sequence with two differences. The whole particle usually enters the cell, by endocytosis or by its envelope fusing with the cell-surface membrane, and the capsid is then removed to free the nucleic acid. And an enveloped virus often leaves by budding, wrapping itself in a piece of host membrane as it goes, so the cell may survive for a time while it releases virus.

In latency the viral genome stays in the host cell without new particles being made, and the cell lives on. Lambda can take this route instead. After injection its DNA can be inserted into the E. coli chromosome at a particular site, where it is called a prophage. A repressor protein, coded for by one of the phage's own genes, keeps the genes needed for the lytic cycle switched off. Every time the bacterium divides by binary fission the prophage is replicated with the chromosome, so every daughter cell inherits it. This latent route in a phage is called the lysogenic cycle.

Latency ends when the repressor is lost. Damage to the bacterium's DNA, for example by ultraviolet light, leads to the repressor being destroyed. The prophage is then cut out of the chromosome and enters the lytic cycle, and the cell bursts.

Latency is common in viruses of humans. Herpes simplex virus stays latent in the nuclei of sensory neurones, as a separate circle of DNA rather than inserted into a chromosome, and stress, fever or strong sunlight can reactivate it, so a cold sore returns in the same place. The chickenpox virus can reactivate decades after the original infection as shingles. HIV inserts a DNA copy of its genome into the chromosome of a helper T cell, and in some cells that copy stays silent for years.

Lytic cycle

Viral replication in which the virus attaches, injects or releases its nucleic acid, replicates it, assembles new particles and then bursts the host cell to release them.

Latency

A state in which a viral genome remains in a host cell without new virus particles being made, until a trigger reactivates it.

Prophage

The DNA of a phage such as lambda inserted into the chromosome of its host bacterium and copied with it at each division.

Bacteriophage

A virus that infects bacteria, often called a phage.

Why antivirals target replication

A virus is not a living cell, so it has no metabolism of its own to block. An antibiotic works by stopping something a bacterium does for itself: building a murein wall, translating on its 70S ribosomes, running its own enzymes. A virus does none of these. It follows that an antiviral drug must work by inhibiting virus replication, which means blocking one of the stages of the cycle above.

Selectivity is the difficulty. A virus replicates with the host cell's own ribosomes and enzymes, and a drug that stopped those would harm the patient as much as the virus. The useful targets are therefore the molecules a virus codes for itself, which differ from anything the host cell needs to stay alive.

Aciclovir shows how selective a drug can be. It is inactive until an enzyme coded by the herpes virus adds a phosphate group to it, so it is switched on almost only in infected cells.

Two limits follow from the same reasoning. A drug that blocks replication cannot touch a latent virus, because nothing is being replicated, so aciclovir shortens an outbreak of cold sores without removing the virus, and treatment for HIV is taken for life. And because many viral genomes mutate quickly, a single drug selects for resistant variants. HIV is treated with a combination of drugs acting at different stages, so that a variant would need several mutations at once to escape all of them.

Antiviral

A drug that inhibits a stage of virus replication, such as entry, copying of the genome, assembly or release, ideally by targeting a molecule coded for by the virus.