Biology | Viruses (HL)

Hello, Future Biologists! Diving into the World of Viruses (HL)

Welcome to the chapter on viruses! This is a fascinating area of biology because viruses sit right on the edge of what we consider "life." They are the ultimate biological paradox, forcing us to redefine the boundaries of living systems.

Since this is an HL topic, we will dive deep into their intricate structures, their complex life cycles, and specifically look at how retroviruses, like HIV, manage to hijack host cells. Understanding viruses is crucial for understanding disease, immunology, and the evolution of life itself (Unity and Diversity!).

Don't worry if these tiny structures seem complicated at first; we'll break down the major processes step-by-step. Let's get started!

Section 1: The Structure of a Virus (The Biological Paradox)

1.1 Defining the Virus (The Non-Living Agent)

A virus is an obligate intracellular parasite. This means it absolutely *must* enter a living host cell to reproduce. Outside a host cell, a virus is essentially inert—a chemical package awaiting a ride.

Viruses are generally much smaller than prokaryotic cells (bacteria) and eukaryotic cells.

1.2 Fundamental Components of the Virion

The complete, infectious viral particle, known as a virion, is made up of just a few core components:

1. Nucleic Acid Core (The Genetic Blueprint):
- This is the viral genome, which can be DNA or RNA.
- It can be single-stranded (ss) or double-stranded (ds). This diversity in genetic material is a key factor in viral classification and diversity.

2. Capsid (The Protein Coat):
- A protective layer of protein subunits called capsomeres.
- The shape of the capsid determines the basic morphology of the virus (e.g., helical, polyhedral, or complex).

3. Envelope (The Optional Outer Layer):
- Some viruses, like the flu virus or HIV, are enveloped viruses.
- The envelope is a lipid membrane derived from the host cell's plasma membrane when the virus "buds" out.
- This envelope contains viral-encoded glycoproteins (spikes) that help the virus attach to new host cells.
- Viruses lacking this membrane are called naked viruses.

Analogy Alert!

Think of a virus as a tiny, highly specialized USB stick. The nucleic acid core is the data (the malicious program), the capsid is the protective casing, and the envelope (if present) is the special packaging that allows it to sneak past security (the host immune system).

Quick Takeaway: Viruses are simple packages of genetic material wrapped in protein, requiring a host cell's machinery to perform their only "life function"—reproduction.

Section 2: Viral Life Cycles (Lytic vs. Lysogenic)

Once a virus successfully attaches to a host cell, it begins one of two major replication pathways: the lytic cycle or the lysogenic cycle.

2.1 The Lytic Cycle: Destruction Mode

The lytic cycle is characterized by rapid replication and immediate destruction (lysis) of the host cell.

Step-by-step Lytic Cycle:
1. Attachment (Adsorption): Viral surface proteins bind specifically to receptors on the host cell surface (Host Specificity).
2. Entry (Penetration): The viral genome is injected into the host cell (common for bacteriophages) or the entire virus is engulfed (endocytosis).
3. Synthesis (Replication): The viral genome hijacks the host cell's metabolic machinery (ribosomes, enzymes, nucleotides) to synthesize many copies of the viral nucleic acid and viral proteins (capsomeres and enzymes).
4. Assembly (Maturation): New viral nucleic acids are packaged into newly synthesized capsids, forming hundreds of new virions.
5. Release (Lysis): The virions produce an enzyme (like lysozyme) that causes the host cell wall/membrane to break open (lysis), releasing the new viruses to infect surrounding cells.

This cycle is quick and destructive, like a home intruder who breaks in, makes copies of himself using the homeowner's materials, and then blows up the house on the way out.

2.2 The Lysogenic Cycle: The Silent Spy

The lysogenic cycle is a period of dormancy where the virus integrates its genome into the host's DNA.

Step-by-step Lysogenic Cycle:
1. Attachment and Entry: Similar to the lytic cycle.
2. Integration: The viral nucleic acid integrates into a specific region of the host cell's chromosome. When integrated, the viral genome is called a prophage (in bacteria) or a provirus (in eukaryotes).
3. Replication of Host Cell: The host cell divides normally. Because the viral DNA is integrated, every daughter cell receives a copy of the viral genome. The virus is passively replicated along with the host.
4. Induction: Under certain environmental stresses (e.g., UV light, chemicals, starvation), the prophage/provirus excises itself from the host genome.
5. Switch to Lytic Cycle: Once excised, the viral genome immediately enters the synthesis and assembly stages of the lytic cycle, leading to host cell lysis and release of new virions.

Key Takeaway: The lytic cycle is rapid replication and cell death. The lysogenic cycle is integration, dormancy, and passive replication, waiting for the right moment to switch to lytic.

Section 3: Retroviruses and Reverse Transcription (HL Deep Dive)

3.1 What is a Retrovirus?

A retrovirus is a specific type of RNA virus that requires a unique enzyme to replicate. The most well-known example is the Human Immunodeficiency Virus (HIV).

In the standard central dogma of biology, information flows from DNA → RNA → Protein. Retroviruses reverse the first step.

3.2 The Role of Reverse Transcriptase

Retroviruses carry the enzyme reverse transcriptase within their capsid. This enzyme is essential for them to convert their RNA genome into DNA once they enter the host cell.

The Process (Reverse Transcription):
1. The retrovirus releases its single-stranded RNA (ssRNA) genome and reverse transcriptase into the host cytoplasm.
2. Reverse Transcriptase uses the viral RNA as a template to synthesize a complementary strand of DNA (RNA → DNA).
3. The enzyme then degrades the original RNA strand and synthesizes a second complementary DNA strand, resulting in a stable, double-stranded DNA (dsDNA) molecule.
4. This new dsDNA is then transported to the host nucleus and integrated into the host's chromosome, forming a provirus.

Memory Aid: Reverse Transcriptase

The enzyme is named because it performs the "reverse" of standard transcription (which is DNA → RNA). It’s RNA → DNA.

3.3 The HIV Life Cycle (A Chronic Provirus)

HIV is highly significant because it targets T-helper lymphocytes (T-cells), which are critical components of the adaptive immune system.

1. Attachment: HIV's envelope glycoproteins specifically bind to CD4 receptors (and a co-receptor) found on T-helper cells.
2. Integration: The double-stranded DNA (created by reverse transcriptase) integrates into the T-cell genome, becoming a provirus.
3. Persistence: The provirus can remain dormant for years (like the lysogenic cycle), replicating every time the T-cell divides, slowly depleting the T-helper cell population.
4. Replication and Release: When activated, the provirus is transcribed by the host machinery, leading to the production of new viral RNA and proteins. New virions are released by budding (a form of release that often does not immediately lyse the cell, allowing the cell to produce more virus for a time).

The progressive destruction of T-helper cells leads to Acquired Immunodeficiency Syndrome (AIDS), leaving the host vulnerable to opportunistic infections.

Key Takeaway: Retroviruses use reverse transcriptase to turn their RNA into DNA, allowing them to integrate into the host genome as a provirus, enabling long-term infection (e.g., HIV in T-cells).

Section 4: Host Specificity, Classification, and Intervention

4.1 Understanding Host Specificity

Viruses are incredibly selective about which organisms and even which cell types they can infect. This is called host specificity.

- Mechanism: The specific glycoproteins on the viral surface must precisely match the unique receptor proteins found on the surface of the target host cell. This is often described as a "lock-and-key" mechanism.
- Example: Bacteriophages (viruses that infect bacteria) cannot infect human cells because they lack the proper surface receptors.
- Example: A rhinovirus (common cold) targets respiratory epithelial cells, not liver cells, due to specific receptor availability.

4.2 Viral Classification and Diversity (Unity and Diversity)

Viruses demonstrate massive diversity despite their simple structure. They are classified based primarily on:

1. Nucleic Acid Type: DNA or RNA? Single-stranded (ss) or double-stranded (ds)?
2. Capsid Symmetry: Helical, icosahedral (polyhedral), or complex.
3. Presence of Envelope: Enveloped or naked.
4. Replication Strategy: Lytic, lysogenic, or reverse transcriptase required.

4.3 Viral Disease and Antiviral Drugs

Treating viral infections is challenging because viruses use the host cell's machinery. Drugs that kill the virus often kill the host cell too.

Antiviral drugs target specific steps of the viral life cycle that are unique to the virus, rather than to the host cell. Common targets include:
- Preventing attachment or entry into the host cell.
- Inhibiting reverse transcriptase (crucial for HIV treatment).
- Blocking the assembly or release of new virions (e.g., neuraminidase inhibitors for influenza).

Did You Know?

Bacteriophages (viruses that attack bacteria) are being researched as a potential alternative to antibiotics to combat antibiotic-resistant infections. This approach is called phage therapy.

Key Takeaway: Host specificity is determined by the precise fit between viral surface proteins and host cell receptors. Antivirals exploit unique viral processes (like reverse transcription) to stop replication without harming the host cell.

Quick Review Box for Challenging Concepts (HL)

Difference Check:
- Lytic Cycle: Immediate takeover and destruction (Lysis).
- Lysogenic Cycle: Integration and dormancy (Provirus/Prophage).

Retrovirus Requirements:
- Start with RNA.
- Must have Reverse Transcriptase.
- Goal: Create dsDNA Provirus for integration.

Common Mistake to Avoid: Confusing a virus with a bacterium. Bacteria are single-celled organisms that can reproduce independently and are treated with antibiotics. Viruses are non-living parasites that require a host cell and are treated with antivirals.