A2.3 Viruses (HL Only)
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Basic Viral Structure
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Today we are exploring the basic structure of viruses. To start with, can anyone tell me what genetic materials viruses might contain?
I think viruses can have either DNA or RNA.
Correct! Viruses can have single-stranded or double-stranded DNA, and single-stranded or double-stranded RNA. Now, what protects this genetic material?
The capsid, right? It's made of proteins!
Exactly! The capsid is made from protein subunits called capsomeres. Viruses can have different shapes, like helical or icosahedral. How many can name one type of virus shape?
The Tobacco mosaic virus has a helical shape!
Great job! Some viruses also have envelopes. Does anyone remember what an envelope is and why itβs important?
It's a lipid layer that comes from the host cell, and it helps the virus infect the host!
Exactly! The envelope can contain glycoproteins that help attach to host cells. Remember, 'Glycoproteins Grab'. This can help us remember their function. Let's summarize todayβs session: viruses store genetic material inside a protective capsid, and many have an envelope for host interaction.
Viral Classification
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Now that we understand the basic structure of viruses, let's move on to how they are classified. Who can tell me how we initially categorize viruses?
By the type of nucleic acid they have?
Correct! Viruses can be classified as DNA or RNA viruses. What else do we look at when classifying them?
Their capsid shape?
Yes! The geometric arrangement, such as helical or icosahedral, is important too. Classification also includes determining if the virus has an envelope. What's another aspect that some viruses have that can vary?
Segmentation of their genome!
That's right! Some viruses have segmented genomes, which can lead to reassortment during replication. Letβs remember 'DNA, Shape, Envelope, Segmentation' as our classification basics. Great job today!
Viral Replication Cycles
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Next, we're diving into the viral life cycle. Can anyone outline the main steps of how a virus replicates?
First, the virus attaches to the host cell.
Exactly! That's the attachment. What comes next?
Then the virus enters the cell.
Yes! After entry, what important process follows?
Uncoating, where the genetic material is released.
Correct! And after uncoating, what's the next step?
The virus replicates its genome and makes proteins.
Right! This includes protein translation, followed by assembly of new viruses. Finally, how do they exit the host?
They can bud off from the cell or cause it to lyse.
Exactly! Let's summarize: the viral life cycle components are attachment, entry, uncoating, replication, assembly, and release. Remember 'A-ER-U-R-A-R: Attach, Enter, Uncoat, Replicate, Assemble, Release'.
Lytic vs. Lysogenic Cycles
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Now let's discuss the different cycles bacteriophages go through β the lytic and lysogenic cycles. Who can tell me about the lytic cycle?
In the lytic cycle, the virus infects the cell and eventually causes it to burst!
Correct! The lytic cycle leads to the destruction of the host cell. And what about the lysogenic cycle?
In the lysogenic cycle, the virus integrates into the host genome and can remain dormant for a while.
Exactly! This integration creates a 'prophage' that, under certain conditions, can switch back to the lytic cycle. Can anyone give me an example of that switch?
Stress conditions might trigger it to enter the lytic cycle!
Well done! Letβs summarize: the lytic cycle results in cell lysis while the lysogenic cycle is about integration and dormancy. Remember 'Lysis is lytic, Latency is lysogenic'.
Viral Pathogenesis and Host-Virus Interactions
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Finally, let's talk about viral pathogenesis and how viruses interact with their hosts. What determines the host range of a virus?
The presence of specific receptors on the host cell!
Exactly! This receptor compatibility is crucial for a virus to infect its host. What about the immune response? What happens when a virus enters a host?
The immune system tries to fight it off with different responses!
Great! We have innate immunity that acts as the first line of defense and adaptive immunity that develops specific responses. Can anyone think of a viral evasion strategy?
Some viruses change their surface proteins to avoid being recognized!
Exactly! Thatβs antigenic variation. To sum up, viruses can evade immune detection and interact with host cells through specific receptor recognition. Remember 'Receptor Recognition and Evasive Responses'. Well done today!
Introduction & Overview
Read summaries of the section's main ideas at different levels of detail.
Quick Overview
Standard
This section details the structure, classification, replication cycles, pathogenesis, and ecological significance of viruses. It discusses their genetic makeup, various forms, and the unique mechanisms through which they interact with host organisms, illustrating their complexities and roles in both health and disease.
Detailed
A2.3 Viruses (HL Only)
Viruses present an intriguing boundary between living and non-living entities, as they lack cellular structures and cannot replicate independently, remaining inactive outside of a host. Despite their simple structures, they possess genetic material, undergo mutations, and evolve rapidly, posing significant implications for biology and medicine. This section dives deep into essential aspects of viruses:
1. Basic Viral Structure
- Genetic Material: Viruses can contain either DNA (single-stranded or double-stranded) or RNA (positive-sense, negative-sense, or double-stranded), with some classified specifically as retroviruses that convert their RNA into DNA within the host.
- Capsid: The protein shell of the virus, composed of subunits known as capsomeres, displays varying symmetry: helical (like Tobacco mosaic virus), icosahedral (like Adenovirus), or complex (like Bacteriophage T4).
- Envelope: Some viruses possess an external lipid bilayer acquired from the host cell membrane during replication, making them more sensitive to environmental factors compared to non-enveloped viruses. Their surface includes viral glycoproteins crucial for host cell attachment.
2. Classification of Viruses
Viruses are classified based on multiple factors:
- Type of nucleic acid (DNA vs. RNA)
- Capsid symmetry
- Presence of an envelope
- Genome segmentation
- Replication strategies, as illustrated in the Baltimore Classification system.
3. Viral Replication Cycles
The typical viral life cycle includes:
- Attachment: Specific binding of viral proteins to host receptors.
- Entry: Mechanisms differ for enveloped and non-enveloped viruses, with some entering via fusion or endocytosis.
- Uncoating: Release of the viral genome inside the host.
- Genome replication and transcription: Varies depending on the virus type, utilizing host machinery to reproduce.
- Protein synthesis: Involves early and late proteins for replication and structural integrity.
- Assembly: Creation of new virions from assembled genomes and proteins.
- Release: Newly formed viruses exit the host, either through lysis or budding.
4. Lytic vs. Lysogenic Cycles in Bacteriophages
- Lytic Cycle: Involves the destruction of the host cell and the release of new phages.
- Lysogenic Cycle: Phage DNA integrates into the host chromosome (producing a prophage), which can be activated under stress to enter the lytic cycle.
5. Viral Pathogenesis and Host-Virus Interactions
Viruses demonstrate a range of host interactions, influenced by their receptor compatibility and viral strategies for evasion of host immune systems. This includes:
- Host Range: Specificity to host cells based on receptor presence.
- Host Immune Responses: Innate and adaptive immune mechanisms activated against viral infections.
- Viral Evasion Strategies: Techniques employed by viruses to avoid immune detection, such as antigenic variation.
6. Oncogenic Viruses
Certain viruses can induce cancer by altering host genomic integrity and cellular regulation (e.g., HPV leading to cervical cancer).
7. Viruses in Evolution and Ecology
Viruses significantly influence ecosystem dynamics and evolutionary processes, including:
- Horizontal Gene Transfer (HGT): Facilitation of genetic material transfer between species, impacting evolution.
- Viral Ecology: Regulation of microbial populations and nutrient cycling through gene transfer between organisms.
- Co-evolution: Continuous adaptation among hosts and viruses driven by evolutionary pressures.
Understanding viruses' structure, classification, and the mechanisms they utilize for replication and interaction with hosts is imperative in microbiology and medicine, providing insights into their role in both diseases and ecosystem dynamics.
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Basic Viral Structure
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Chapter Content
- Basic Viral Structure
- Genetic Material
- DNA Viruses: Single-stranded (ssDNA) or double-stranded (dsDNA).
- RNA Viruses: ssRNA (positive-sense [+] or negative-sense [β]) or dsRNA.
- Retroviruses: Enveloped ssRNA positive-sense viruses that reverse transcribe RNA into DNA (e.g., HIV).
- Capsid
- Protein coat protecting nucleic acid; composed of repeating protein subunits called capsomeres.
- Capsid Symmetry:
- Helical: Rod-shaped capsomeres form a helical tube (e.g., Tobacco mosaic virus).
- Icosahedral: Spherical shape approximated by 20 equilateral triangular faces (e.g., Adenovirus).
- Complex/Asymmetric: Combined icosahedral head and helical tail (e.g., bacteriophage T4). Some poxviruses have complex brick-shaped capsids.
- Envelope (in some viruses)
- Lipid bilayer derived from host cell plasma or organelle membranes during budding.
- Contains viral glycoproteins (spikes) that mediate host cell recognition and membrane fusion.
- Enveloped viruses (e.g., influenza, HIV, herpesviruses) are generally more sensitive to detergents and desiccation than naked viruses.
- Non-Enveloped (Naked) Viruses
- Lack an envelope; more resistant to environmental conditions (pH, detergents).
- Entry typically via receptor-mediated endocytosis or direct penetration.
Detailed Explanation
This chunk covers the fundamental structure of viruses, which includes their genetic material, capsid, and sometimes an envelope. Viruses can either have DNA or RNA as their genetic material, and this can be single-stranded or double-stranded. The capsid is a protein coat surrounding the genetic material and can have different shapes, such as helical, icosahedral, or complex. Some viruses also possess an envelope made from lipids taken from the host cell membrane, which helps them enter host cells. Non-enveloped viruses, on the other hand, are generally more robust.
Examples & Analogies
Think of a virus like a package being delivered. The genetic material is the contents of the packageβthis could be a DNA or RNA message. The capsid is like the cardboard box protecting whatβs inside, while the envelope is like plastic wrap that some packages have for additional protection. Some packages might be sensitive to the elements (enveloped viruses), while others can survive being dropped or getting wet (non-enveloped viruses).
Classification of Viruses
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Chapter Content
- Classification of Viruses
Viruses are classified based on:
- Type of Nucleic Acid
- DNA vs. RNA; single-stranded vs. double-stranded; positive vs. negative sense for ssRNA.
- Capsid Symmetry
- Helical, icosahedral, or complex.
- Envelope Presence
- Enveloped vs. non-enveloped.
- Genome Segmentation
- Some viruses have segmented genomes (e.g., Influenza A has eight RNA segments), enabling reassortment.
- Replication Strategy (Baltimore Classification)
- Group I: dsDNA β mRNA (e.g., Herpesviridae).
- Group II: ssDNA β dsDNA intermediate β mRNA (e.g., Parvoviridae).
- Group III: dsRNA β mRNA (e.g., Reoviridae).
- Group IV: (+) ssRNA β mRNA (directly serves as mRNA; e.g., Togaviridae).
- Group V: (β) ssRNA β (+) mRNA (requires RNA-dependent RNA polymerase; e.g., Orthomyxoviridae).
- Group VI: (+) ssRNA with reverse transcriptase β DNA intermediate β mRNA (Retroviridae).
- Group VII: dsDNA viruses with reverse transcriptase (e.g., Hepadnaviridae).
Detailed Explanation
This chunk explains how viruses are classified. Classification is important for understanding their biology and medical implications. Classification criteria include the type of nucleic acid (DNA or RNA), the shape of the capsid, whether they have an envelope, and whether their genome is segmented or not. The Baltimore classification organizes viruses based on their replication strategies, including how they convert their genome to mRNA, which is essential for protein production.
Examples & Analogies
Imagine a library where books (viruses) are organized not just by title, but by the type of content (nucleic acid), the cover design (capsid symmetry), and whether they are hardcovers (enveloped) or paperbacks (non-enveloped). Just as different genres or styles help us find what we're looking for in a library, these classification systems help scientists understand and manage various viruses.
Viral Replication Cycles
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Chapter Content
- Viral Replication Cycles
Although specifics vary, most viral life cycles involve:
- Attachment
- Binding of viral surface proteins (capsid or envelope glycoproteins) to specific host cell receptors (proteins, glycoproteins, carbohydrates).
- Tropism: Virus can infect only cells expressing the appropriate receptor(s).
- Entry (Penetration)
- Naked viruses: Often enter via receptor-mediated endocytosis, then uncoat in endosomes.
- Enveloped viruses:
- Fusion with plasma membrane (e.g., HIV gp41βgp120 complex) releases nucleocapsid into cytoplasm.
- Endocytic entry: After endocytosis, low pH in endosome triggers envelope fusion.
- Uncoating
- Release of viral genome (and some viral proteins) into host cytoplasm or nucleus.
- Genome Replication and Transcription
- DNA Viruses: Most replicate in host nucleus using host DNA polymerases (except poxviruses, which replicate in cytoplasm using viral polymerases).
- RNA Viruses:
- (+) ssRNA: Viral RNA acts directly as mRNA; ribosomes translate viral proteins, including RNA-dependent RNA polymerase (RdRP) to replicate genome.
- (β) ssRNA: Viral RdRP packaged in virion synthesizes complementary (+) mRNA and replicates genome.
- Protein Translation and Processing
- Early (Immediate) Proteins: Regulatory proteins that modulate host environment, counteract host defenses, and prepare for genome replication.
- Late Proteins: Structural proteins forming capsid, envelope glycoproteins.
- Post-translational modifications (glycosylation, cleavage by host/viral proteases).
- Assembly (Maturation)
- New viral genomes and capsid proteins assemble into nucleocapsids.
- Envelope glycoproteins are inserted into host cell membranes (plasma or organelle membranes).
- Release
- Budding: Enveloped viruses bud through host membrane (plasma, endoplasmic reticulum, or Golgi), acquiring envelope and glycoproteins. Budding may or may not kill the cell.
- Lysis: Non-enveloped viruses often cause cell lysis to release progeny; host cell membrane ruptures.
Detailed Explanation
In this section, the viral replication cycle is outlined, detailing the steps viruses take to reproduce inside host cells. After attachment to the host cell, viruses penetrate and release their genetic material into the host's cytoplasm. Depending on whether they have DNA or RNA, viruses will replicate their genomes using specific host mechanisms or their enzymes. After proteins are synthesized and assembled, new viral particles are either released by budding (for enveloped viruses) or by lysis (for non-enveloped viruses), continuing the cycle.
Examples & Analogies
Think of the viral replication cycle as a home invasion. The virus (intruder) first knocks on the door (attachment) and finds a way to get in (entry). Once inside, it takes over the house (the host cell) to make copies of itself (replication). Eventually, it produces many copies (assembly) and leaves the house either quietly (budding) or by blowing the door off (lysis), spreading to other homes to find new victims.
Lytic vs. Lysogenic Cycles (Bacteriophages)
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Chapter Content
- Lytic vs. Lysogenic Cycles (Bacteriophages)
- Lytic Cycle:
- Attachment to host cell surface.
- Injection of phage DNA into cytoplasm.
- Phage DNA directs host machinery to replicate viral components.
- Assembly of phage particles.
- Release of new phages by lysis of host cell.
- Lysogenic (Temperate) Cycle:
- Phage attaches and injects DNA.
- Phage DNA integrates into host chromosome (prophage).
- Host replicates normally, copying prophage DNA to daughter cells.
- Under induction (stress), prophage excises and enters lytic cycle.
Detailed Explanation
This chunk compares two types of bacteriophage life cycles: the lytic cycle and the lysogenic cycle. In the lytic cycle, the virus quickly takes over the host cell, replicates itself rapidly, and eventually causes the cell to burst (lyse), releasing new phage particles. In contrast, the lysogenic cycle allows the virus to integrate its DNA into the host's genome, remaining dormant. When conditions are favorable or the host is under stress, the virus can switch to the lytic cycle to reproduce rapidly.
Examples & Analogies
Consider the lytic cycle as a hostile takeover of a business, where the takeover agent quickly shuts down the current operations and replaces them with their own. The lysogenic cycle is like a business partnership where the new partner is integrated into the existing structure but may choose to stay quiet for a while, only taking control when the current management is under stress or problems arise.
Viral Pathogenesis and HostβVirus Interactions
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Chapter Content
- Viral Pathogenesis and HostβVirus Interactions
- Host Range and Tissue Tropism
- Determined by receptor compatibility, intracellular factors, and immune evasion strategies.
- Example: HIV infects CD4βΊ T lymphocytes, macrophages (requires CD4 receptor and CCR5/CXCR4 coreceptors).
- Host Immune Responses
- Innate Immunity: First line of defenseβinterferons (IFN-Ξ±, IFN-Ξ²) produced by infected cells, activating antiviral states in neighboring cells; natural killer (NK) cells lyse infected cells.
- Adaptive Immunity:
- Humoral (B cell) Response: Production of neutralizing antibodies targeting viral capsid or envelope proteins; preventing viral entry.
-
Cell-Mediated (T cell) Response:
- CD8βΊ cytotoxic T lymphocytes recognize peptideβMHC class I complexes on infected cells, inducing apoptosis.
- CD4βΊ helper T cells coordinate immune responses.
- Viral Evasion Strategies
- Antigenic Variation: Frequent mutations in viral surface proteins (antigenic drift in influenza) or genome segment reassortment (antigenic shift), evading antibody recognition.
- Latency: Some viruses (e.g., herpesviruses) remain dormant within host cells (e.g., neurons), periodically reactivating under stress.
- Downregulation of MHC: Viruses interfere with antigen presentation (e.g., cytomegalovirus reduces MHC I expression).
- Inhibition of Apoptosis: Viral proteins (e.g., baculovirus p35) block host cell apoptosis to prolong replication period.
Detailed Explanation
This section focuses on how viruses interact with their hosts. The range of cells a virus can infect (host range) is determined by the specific receptors on the host cell surface that the virus can bind to, while tissue tropism refers to the specific tissues within the host that the virus prefers to infect. The host's immune system mounts defenses through both innate and adaptive mechanisms. Additionally, viruses have evolved several strategies to evade the immune response, including changing their surface proteins and hiding from immune detection.
Examples & Analogies
Imagine a thief sneaking into a secure building. The virus is like the thief, using specific ways to get inside (host range and receptor compatibility). The building's security system represents the immune response, which tries to detect and eliminate the intruder. Some thieves might be skilled at disguising themselves or altering their appearance (viral evasion strategies), making it harder for the security personnel to catch them.
Viral Evolution and Ecology
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Chapter Content
- Viruses in Evolution and Ecology
- Horizontal Gene Transfer (HGT)
- Viruses can facilitate gene transfer between unrelated species (transduction in bacteria; viral vectors in eukaryotes).
- Genetic material from viruses (endogenous retroviruses) comprises significant proportions of eukaryotic genomes (e.g., ~8% of human genome), influencing genome architecture and regulation.
- Viral Ecology
- Viruses regulate population dynamics of microbial communities (phages controlling bacterial abundance in aquatic ecosystems).
- Viral shunt: Viral lysis releases organic matter, fueling microbial loop in marine environments.
- Co-evolution
- Arms race between host immune defenses and viral countermeasures drives rapid evolution in both.
- Red Queen hypothesis: Continual adaptation required by both host and virus to maintain status quo.
Detailed Explanation
In this section, we explore how viruses impact evolution and ecology. Viruses are not only infectious agents but can also act as vehicles for horizontal gene transfer, allowing genes to move between different species. This capability influences evolutionary processes and can shape the genetic structure of populations. In the ecological context, viruses play significant roles in regulating microbial populations and nutrient cycling. The co-evolution seen between viruses and their hosts drives much of the genetic diversity in both groups.
Examples & Analogies
Think of viruses as both a delivery service and regulators in a marketplace. They can send genetic 'packages' between different vendors (unrelated species), influencing how they function and compete. At the same time, they control the flow of goods (microbes) in the market, ensuring that no single type overwhelms the others due to their presence. This constant interaction leads to an evolutionary dance, where both vendors and delivery services continually adapt to changing environments.
Key Concepts
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Viruses are non-living entities that require host cells for replication.
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They can have DNA or RNA genomes and may be enveloped or non-enveloped.
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The viral life cycle involves attachment, entry, uncoating, replication, assembly, and release.
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Bacteriophages can follow lytic or lysogenic cycles.
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Viral pathogenesis involves host interactions and immune evasion strategies.
Examples & Applications
HIV is a retrovirus that integrates into the host's DNA.
Influenza virus is an example of an enveloped virus with RNA genetic material.
Memory Aids
Interactive tools to help you remember key concepts
Rhymes
Viruses are sneaky, they enter our cells, but with the right clues, we can warn our shells.
Stories
Imagine a tiny burglar (virus) that sneaks into a house (host cell) at night. Once inside, it steals the 'identity' (genetic material) of the house and makes copies of itself. Eventually, the house is so full of copies that it bursts open!
Memory Tools
Remember 'A-ER-U-R-A-R' for the viral life cycle: Attach, Enter, Uncoat, Replicate, Assemble, Release.
Acronyms
G.E.C. for Viruses
Genetic material
Envelope
Capsid.
Flash Cards
Glossary
- Virus
A microscopic infectious agent that requires a living host cell to replicate.
- Capsid
Protein shell that encases the viral genome, composed of capsomeres.
- Envelope
A lipid layer surrounding some viruses, derived from the host cell membrane.
- Bacteriophage
A type of virus that infects bacteria.
- Lytic Cycle
The viral replication cycle that leads to the destruction of the host cell.
- Lysogenic Cycle
A viral replication cycle where the viral DNA integrates into the host genome and can remain dormant.
- Pathogenesis
The process by which an organism causes disease in another organism.
- Receptor
A protein molecule on the host cell surface that a virus binds to for entry.
- Retrovirus
A type of RNA virus that reverse transcribes its RNA into DNA within a host.
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