Study Notes on Viruses, Viroids, and Prions

Okay, imagine there are super tiny things in the world, so small you can't see them without a super powerful microscope. Some of these tiny things can make us sick, but they aren't alive like animals or plants or even bacteria. They are called acellular, meaning 'not a cell'.

12.1 Viruses

• What they are: Viruses are like tiny little packages that carry a secret message inside them. They aren't 'alive' on their own, but they know how to sneak into a living cell (called a 'host' cell) and use that cell's tools to make lots and lots of copies of themselves.

• Viruses can infect all sorts of living things: tiny bacteria, plants, animals (like us!), and even fungi.

• Bacteriophage (Phage): This is a special type of virus that only infects bacteria. Think of them as 'bacteria eaters'!

• Virion: This is just a fancy word for one complete virus particle, like one tiny package.

What makes viruses special?

• Not real cells:

  • They don't have a 'skin' (plasma membrane) like cells do.

  • They can't split in half to make more of themselves (no binary fission).

  • They can't make their own 'energy food' (ATP).

  • They can't make their own building blocks (proteins) because they don't have the right machines (ribosomes).

• Obligate Intracellular Parasites: This is a big, important phrase! It means viruses must live inside another living cell. They are like guests who demand to use all of your house's stuff – your kitchen, your tools, your food – to make more copies of themselves. They basically take over the host cell and tell it to make virus parts. Because of this, if we want to study viruses in a lab, we need to grow them inside living cells.

12.2 Viral Structure

Think of a virus as a tiny, well-designed package.

Nucleocapsid: The main part of the package.

• What's inside?

  • Nucleic Acid (the viral secret message): This is the important blueprint! It's either DNA or RNA (like two different kinds of instruction manuals). This blueprint can be a long straight line, a circle, or even broken into several pieces. It can also be like a ladder that's full (double-stranded) or only half (single-stranded).

  • Capsid: This is the 'box' or 'shell' around the secret message. It's made of lots of small, repeating protein pieces called capsomeres. The way these pieces fit together usually gives the virus its shape.

How do we sort viruses?

• Viral Genome: The most important way we sort viruses is by looking at their 'secret message' (genome) and how they use it to make copies.

• Shape and Envelope: The shape of their 'box' and if they have an extra 'coat' also help us sort them.

Different types of viruses:

1. Naked Viruses (Non-enveloped):

   • These are just the 'box' (capsid) with the 'secret message' (genome) inside. They don't have an extra outer layer.

   • They are usually tougher and harder to get rid of with cleaners.

2. Enveloped Viruses:

   • These viruses have their 'box' (nucleocapsid) wrapped in an extra 'jacket' or 'coat' made of fatty stuff (a lipid bilayer).

   • This 'jacket' often has 'keys' or 'spikes' on its surface. These are called spike proteins (or tail fibers on some viruses that infect bacteria, or fiber proteins on naked viruses). These 'keys' help the virus unlock and get into the host cell. They are also what our body's 'police' (immune system) often recognize when they are trying to fight off a virus.

Common shapes of viruses:

1. Icosahedral Nucleocapsids:

   • Imagine a soccer ball or a 20-sided dice. These viruses look like that – very neat and symmetrical.

   • Example: The Herpesvirus looks like a tiny soccer ball under a special microscope.

2. Helical Nucleocapsids:

   • Think of a spring or a Slinky toy. The secret message is wound up inside a long, flexible tube, making the virus look like a long, flexible worm or filament. The outer 'jacket' (envelope) can sometimes hide this shape.

3. Complex/Amorphous Nucleocapsids:

   • These are the weird-shaped ones! They don't have a simple, easy-to-describe shape.

   • Some, like the complex-tailed bacteriophages (the ones that infect bacteria), look like a tiny spaceship with a round head (holding the secret message) and a long tail that injects the message into the host cell.

12.3 Viral Replication

This is how a virus makes more of itself inside a host cell, like following a recipe.

The general recipe (steps) for a virus to make copies:

1. Host Cell Recognition & Attachment: The virus's 'keys' on its surface find and stick to the 'locks' on the outside of a host cell.

2. Genome Entry: The virus (or just its secret message) gets inside the host cell, like sending a letter through a mail slot.

3. Biosynthesis: The virus takes over the host cell's 'factory' and makes it start building new copies of the virus's 'secret message' (genome) and new virus parts (proteins).

4. Assembly/Maturation: All the new virus parts come together and get built into brand new virus packages (virions). This usually happens before they leave the cell.

5. Release (Transmission): The new virus packages leave the host cell, ready to go infect new cells. Sometimes this step hurts and kills the host cell, and sometimes the new viruses just sneak out without destroying the cell.

How do bacteriophages (viruses that infect bacteria) make copies?

Two main ways:

1. Lytic (Virulent) Phage:

   • These are like 'wrecking crew' viruses. They get in, make lots of new viruses, and then burst the host cell open to get out.

   • Burst size: This is how many new virus packages come out when the cell busts open – often hundreds!

2. Temperate Phage:

   • These are the 'sneaky' viruses. They can hide their secret message inside the host cell's own secret message (this hidden virus message is called a prophage). When the host cell copies its own message, it copies the virus's message too! This is called lysogeny.

   • These hidden viruses can 'wake up' later and become a 'wrecking crew' (lytic phage) if conditions change.

Lytic Cycle (the 'wrecking crew' method):

1. Host Attachment: The phage's tail 'hands' grab onto special spots on the outside of a bacterium.

2. Genome Entry: The phage injects its secret message (genome) into the bacterium, sometimes using a special enzyme (lysozyme) to poke a hole in the bacterial cell wall.

3. Biosynthesis: The virus takes over! It might even chew up the bacterium's own secret message. Then it tells the bacterium's factory to make early virus parts, which then tell it to make late virus parts (the actual virus structures).

4. Assembly/Maturation: All the virus parts are carefully put together, step by step.    

5. Release: The bacterium's cell wall breaks open (lysis), and all the new virus packages burst out!

Lysogenic Cycle (the 'sneaky' method):

• Lysogenic Infection: The host bacterium continues to live and divide, carrying the hidden prophage (virus secret message) inside it. Sometimes, if the virus accidentally takes some of the bacterial DNA with it when it 'wakes up,' it can move that bacterial DNA to a new bacterium (this is called specialized transduction).

• Lysogenic Conversion: Sometimes, the hidden virus's genes can give the host bacterium new abilities or traits!

How do bacteria fight back against these phage infections?

1. Restriction-Modification Systems: Bacteria have special 'scissors' (restriction enzymes) that can cut up foreign secret messages (DNA) from phages. But they also have a 'marker' system (methylation) to make sure they don't cut up their own secret message.

2. CRISPR: This is like a 'mugshot book' for bacteria! If a phage has attacked a bacterium before, the bacterium can take a piece of the phage's secret message and put it into its own 'mugshot book.' If that phage, or a similar one, attacks again, the bacterium can quickly find and destroy the invading phage's secret message using special proteins.

12.4 Viroids & Prions

These are even weirder tiny things that can cause problems!

Viroids:

• What they are: Imagine a naked 'secret message' (RNA) without any protective 'box' (capsid) or outer 'jacket.' That's a viroid!

• What's special about them?:

  • They don't have any instructions for making proteins themselves. They are just the message.

  • They mostly infect plants and make them sick.

  • Scientists are still trying to fully understand how they make copies and cause disease, but they seem to mess with how the plant's own genes work.

Prions:

• What they are: These are the strangest! They are only made of protein, not even a secret message (no nucleic acid) at all! They are like a normal protein in your body that gets folded into the wrong shape.

• What's special about them?:

  • They are normal proteins found on nerve cells, but they get folded into a bad, abnormal shape.

  • These bad proteins are super tough! They can resist heat, UV light, and even things that usually break down proteins.

  • When a bad prion touches a good prion, it makes the good one turn bad too! This causes proteins to clump together in the brain, leading to serious brain diseases.

• Transmissible Prion Diseases: These are diseases that can be passed between living things.

  • Examples: Kuru, Creutzfeldt-Jakob disease (in humans), Mad cow disease (in cows), Scrapie (in sheep), and Chronic Wasting Disease (in deer). They all cause terrible damage to the brain.