Viruses
Viruses and Other Non-Living Infectious Agents
Justify viruses being considered non-living.
Basic Tenets of Life (organisms possess these; viruses generally do not):
Organization: Made up of one or more cells.
Metabolism: Has its own way of producing energy.
Homeostasis: Can maintain its internal environment.
Growth: Capable of growing in size or building more complex molecules.
Reproduction: Can reproduce on their own.
Response: Can respond to stimuli.
Evolution: Can adapt to their environment over time.
Why viruses are NOT living:
They cannot exist independently from the host cell.
They are not made of cells.
Cannot produce their own energy.
Referred to as infectious particles that can be either active or inactive.
Obligate intracellular parasites: Viruses cannot multiply unless they invade a specific host cell and instruct the host's genetic and metabolic machinery to make and release new viruses.
Explain how scientists have had to redefine the “central dogma” because of viruses.
The conventional Central Dogma states: DNA > RNA > Protein.
Viruses, particularly RNA viruses and retroviruses, challenge this by:
RNA Viruses: Some replicate their RNA directly without a DNA intermediate (e.g., using RNA-dependent RNA polymerase).
Retroviruses: These are RNA viruses that replicate through a DNA intermediate. They use reverse transcriptase to synthesize DNA from an RNA template (RNA > DNA > RNA > Protein), fundamentally reversing the flow of genetic information from RNA to DNA, thereby necessitating a redefinition of the strict one-way flow of the central dogma.
Explain the naming system for viruses and how this differs from other microorganisms.
Viruses are classified by the International Committee on the Taxonomy of Viruses.
Classification includes: 3 orders, 73 families (denoted by “-viridae”), 287 genera (denoted by “-virus”), and species with unique names, with strains typically designated by numbers or series of letters.
Examples:
Herpesviridae > Simplexvirus > Human herpesvirus (HHV) > HHV-1
Coronaviridae > Betacoronavirus > Severe Acute Respiratory Syndrome (SARS) > SARS-CoV-2
This hierarchical system involving orders, families, genera, and species (with specific suffixes) is a unique and standardized way for naming viruses.
Label and describe the function of the key parts of a virus.
Viruses contain only essential parts to invade a host cell:
Core: Contains the genetic material (DNA or RNA).
Capsid: A protein shell that holds the core.
Capsomere: The individual protein subunits that make up the capsid.
Spikes: Surface proteins that extend from the capsid or envelope and aid in attachment to host cells.
Some viruses also have:
Enzymes (proteins): Inherent in or outside the core, such as RNA-dependent polymerases or reverse transcriptase, and enzymes on the envelope/capsid (spikes) for attachment, release, or immune evasion.
Envelope: A lipid layer that surrounds the capsid, sourced from the host cell membrane.
Naked virus: Includes core and capsid but lacks an envelope.
Complex Structures (e.g., Bacteriophage):
Components include: head (containing genetic material), collar, endplate, tail, tail fibers (for attachment), and tail pins.
Compare bacteriophages and animal/plant viruses.
Hosts infected:
Bacteriophages: Infect bacterial host cells.
Animal/Plant viruses: Infect animal or plant host cells, respectively.
Genome:
Bacteriophages: Most contain double-stranded DNA (dsDNA); rarely single-stranded RNA/DNA (ssRNA/dsRNA).
Animal/Plant viruses: Can have a wider variety of genome types (dsDNA, ssDNA, dsRNA, ssRNA).
Penetration/Entry:
Bacteriophages: Typically inject their nucleic acid into the host cell; the capsid does not enter the bacterial cell.
Animal viruses: The whole virus or its nucleic acid penetrates the host's flexible cell membrane (e.g., via endocytosis or membrane fusion).
Structure:
Bacteriophages: Often have complex structures with a head, tail, and tail fibers.
Animal/Plant viruses: Can be helical, icosahedral, or complex, and may or may not possess an envelope.
Describe the replication cycles of viruses as determined by their unique structures and genomes.
The replication cycle generally involves five phases:
Attachment (adsorption): The virus specifically binds to receptors on a susceptible host cell (proteins, carbohydrates, glycoproteins, lipids, or complexes).
Entry (penetration/injection): The virion or its nucleic acid enters the host cell. Animal viruses or their nucleic acids penetrate the cell membrane, while bacteriophages typically inject only their nucleic acid.
Synthesis: Free viral nucleic acid takes control of the host cell’s synthetic and metabolic machinery to produce virus nucleic acid and proteins.
Animal DNA Viruses: Enter the host nucleus for replication and assembly; may bring their own polymerases.
Animal RNA Viruses: Replicate and assemble in the nucleus/cytoplasm; must possess their own RNA-dependent polymerases or Reverse Transcriptase.
Bacteriophages: Access host RNA polymerase immediately.
Assembly (maturation): Capsids are assembled, and viral genomes are packaged into new virions.
Release: Mature virions are released from the host cell (e.g., by lysis, budding).
Retroviruses: RNA viruses that use reverse transcriptase to synthesize a DNA intermediate, which then integrates into the host genome. This DNA is then transcribed back into RNA for new virions.
Arrange the steps of a viral infection by bacteriophage in correct order, specifically, either a temperate or lytic phage.
General Steps of Viral Replication (as detailed in question 6):
Attachment (adsorption) of the virus to a susceptible host cell.
Entry (injection) of the viral nucleic acid into the cell.
Synthesis of virus nucleic acid and protein by cell metabolism as redirected by the virus.
Assembly of capsids and packaging of viral genomes into new virions (maturation).
Release of mature virions from the host cell.
Specific Modes for Bacteriophages:
Virulent (Lytic) Mode: Follows the general steps, culminating in the lysis and death of the host cell to release progeny virions.
Lysogenic/Temperate Mode: After attachment and entry, the viral genome (prophage) integrates into the host chromosome. Virus genes are not expressed, and the prophage is replicated along with the host chromosome without killing the cell. Under certain conditions (e.g., stress), the lysogenic virus may revert to the lytic pathway, excise its genome, and proceed with synthesis, assembly, and lysis.
Compare the viral enzymes needed by RNA, DNA, and retroviruses.
RNA Viruses:
Need RNA-dependent RNA polymerases to replicate their RNA genomes or transcribe mRNA from an RNA template.
DNA Viruses:
May bring their own DNA polymerases or utilize host DNA polymerases for replication.
Retroviruses:
Require reverse transcriptase to synthesize DNA from their RNA genome.
Also require integrase to integrate the newly synthesized viral DNA into the host genome.
General Viral Enzymes (may be found in nucleocapsid, on envelope/capsid spikes):
May cleave host proteins for attachment or release of the virus.
Involved in immune evasion mechanisms (e.g., hemagglutinin and neuraminidase).
List the host enzymes/processes needed by viruses.
Viruses are obligate intracellular parasites and extensively rely on the host cell's machinery.
They redirect the host's genetic and metabolic machinery.
Specific host components and processes utilized by viruses include:
Host RNA polymerase: Bacteriophages access this immediately for transcription.
Host ribosomes: For translation of viral mRNA into viral proteins.
Host amino acids, nucleotides, ATP: Building blocks and energy for viral synthesis.
Host protein synthesis machinery: For synthesizing viral capsids and enzymes.
Host cell membranes/lipids: For forming viral envelopes (e.g., through budding).
Host DNA polymerase: Some DNA viruses may use these, while others bring their own.
Host transcription factors and other regulatory proteins: For controlling viral gene expression.
Describe how a temperate/lysogenic phage can contribute to disease, and give one example.
A temperate or lysogenic phage can contribute to disease through a process called lysogenic conversion.
Lysogenic conversion: When a bacterium acquires new traits or virulence factors due to the incorporation of phage DNA (prophage) into its genome.
These new traits can make the bacterium more pathogenic.
Example: The diphtheria toxin produced by Corynebacterium diphtheriae is encoded by a gene within a temperate phage’s DNA. Without the lysogenic phage, the bacterium is non-toxic and cannot cause diphtheria.
Define the terms CRISPR and restriction and modification with regard to a bacteriophage infection.
CRISPR-Cas System (Clustered Regularly Interspaced Short Palindromic Repeats):
A prokaryotic immune system that enables bacteria and archaea to evade viral destruction and maintain genome stability.
Mechanism: Foreign DNA segments (spacers) from previous infections are incorporated into the CRISPR locus. These are transcribed into a long RNA molecule, cleaved by Cas proteins into crRNA (CRISPR RNA). When a subsequent infection by the same phage occurs, the crRNA guides Cas proteins to bind to incoming foreign nucleic acids (viral DNA/RNA) and cut them, tagging them for destruction. It acts as a form of “prokaryotic immune memory.”
Restriction Modification Systems:
A DNA destruction system found in prokaryotes that is effective against double-stranded DNA viruses.
Mechanism: Consists of two components:
Restriction enzymes: Recognize and cleave foreign DNA at specific nucleotide sequences, effectively chopping up the invading phage genome.
Modification enzymes: Chemically modify (e.g., methylate) the host cell's own DNA at these same recognition sequences, protecting it from cleavage by its own restriction enzymes.
Distinguish between persistent, transforming, and latent infections.
These are different outcomes of animal viral infections:
Persistent infections: The virus remains in the host cell or organism for a long period, continuously producing and releasing new virions, often without immediate cell lysis. Examples include chronic hepatitis B or C infections.
Transforming infections: Occur with oncogenic viruses, leading to the alteration of host cells, potentially turning them cancerous. The virus integrates its genetic material into the host genome, leading to uncontrolled cell growth and division. Examples include Human Papillomavirus (HPV) causing cervical cancer.
Latent infections: The virus remains dormant in the host cell, and its genes are not expressed (or only minimally expressed); the virus does not actively replicate or produce new virions. The virus can reactivate later, often under specific conditions (e.g., stress, immunosuppression), leading to acute disease symptoms. Example: Herpes simplex virus (HSV) causing cold sores, which can reactivate during stress.
Describe methods for growing viruses.
Information on methods for growing viruses is not explicitly provided in the current note.
List useful ways viruses are utilized.
Information on useful ways viruses are utilized is not explicitly provided in the current note.
Describe viroids and prions and the diseases they cause.
Viroids:
Small, circular, single-stranded RNA molecules that lack a protein coat (capsid).
They are among the smallest known infectious agents, approximately nm, and are considered non-living.
The note does not specify the diseases they cause, but they are known to cause diseases primarily in plants.
Prions:
Infectious proteinaceous particles that contain no nucleic acid.
They are abnormal, misfolded forms of normal cellular proteins (PrP^C^ converted to PrP^Sc^).
They are approximately nm and are considered non-living.
The note does not specify the diseases they cause, but they are known to cause transmissible spongiform encephalopathies (TSEs), which are neurodegenerative diseases (e.g., mad cow disease, Creutzfeldt-Jakob disease).