Table of Contents
Basic Concepts: Are Viruses Alive?
Viruses, viroids, and prions are often called “subcellular” or “acellular” biological entities. They share some common features:
- They are much smaller than cells and lack the full cellular structure.
- They cannot reproduce on their own; they need a living host cell.
- They are built from only a few types of molecules (nucleic acids and/or proteins, sometimes lipids).
Because they do not have their own complete metabolism and cannot perform independent life processes, they are at the borderline between living and non-living. Biologists therefore often speak of them as “infectious agents” rather than fully living organisms.
In this chapter, the focus is on what these agents are made of, how they are organized, and in what ways they differ from cells and from each other.
Viruses
Structure of Viruses
All viruses share two basic components:
- Genetic material (genome)
- Either DNA or RNA, never both at the same time.
- Can be:
- Single-stranded (ss) or double-stranded (ds)
- Linear, circular, or segmented (in separate pieces)
- Contains the information for making viral proteins and for controlling the infection cycle.
- Protein coat (capsid)
- Built from repeating protein subunits called capsomeres.
- Protects the viral genome and helps it attach to and enter host cells.
- Has characteristic shapes, such as:
- Helical (rod-like, e.g., many plant viruses)
- Icosahedral (approx. spherical, made from 20 triangular faces, common in many animal viruses)
- Complex (e.g., bacteriophages with head-and-tail structure)
Some viruses also have:
- Envelope (viral envelope)
- A lipid membrane surrounding the capsid.
- Usually derived from the host cell membrane as the virus leaves the cell.
- Contains embedded viral glycoproteins that recognize and bind to host cell receptors.
- Typical of many animal viruses (e.g., influenza virus, HIV).
Because envelopes are made of lipids, they are sensitive to detergents, solvents, and drying. This affects how easily viruses are inactivated in the environment and is important for hygiene and infection control.
Diversity of Viral Genomes
Viruses are classified in part by the type and arrangement of their genetic material:
- DNA viruses
- dsDNA (e.g., many bacteriophages, herpesviruses)
- ssDNA (smaller, often infecting animals or plants)
- RNA viruses
- ssRNA with positive sense (+): genome can directly serve as mRNA.
- ssRNA with negative sense (−): genome must be copied into complementary RNA before translation.
- dsRNA: less common, typically in certain plant and animal viruses.
- Retroviruses
- ssRNA viruses that copy their RNA into DNA using a special enzyme (reverse transcriptase).
- The DNA can integrate into the host genome; HIV is the best-known example.
This diversity of genomes is one reason why viruses are so flexible and can adapt quickly to new hosts.
Host Specificity and Infection
Viruses are often highly host-specific and sometimes even tissue-specific:
- A plant virus typically cannot infect animals, and vice versa.
- Even within one animal, certain viruses only infect particular cell types (e.g., liver cells or immune cells).
This specificity is mainly determined by:
- Surface structures on the virus (capsid proteins or envelope glycoproteins).
- Receptors on the host cell membrane.
Only if these structures fit together (like a key in a lock) can the virus attach and enter the cell.
Basic Infection Strategies (Lifecycle Types)
Without going into full biochemical detail, viruses follow a few basic strategies during infection:
- Attachment and entry
Virus binds to host cell receptors and enters the cell (by fusion, endocytosis, or injection of genetic material). - Replication and synthesis
Viral genome is replicated; host cell’s machinery is used to produce viral proteins. - Assembly
New viral particles (virions) are constructed from genomes and capsid proteins (and envelopes, if present). - Release
- Lysis: the host cell bursts and dies (common in many bacteriophages).
- Budding: virus leaves the cell by pushing out through the membrane, often allowing the cell to survive for some time (common in enveloped animal viruses).
Some viruses also have latent phases, where the viral genome remains in the host cell with limited activity, sometimes integrated into the host DNA, and can reactivate later.
Bacteriophages: Viruses of Bacteria
Bacteriophages (or phages) are viruses that infect bacteria. They are important for basic research and biotechnology and show some special features:
- Often have a complex structure:
- Polyhedral head (containing DNA)
- Tail with contractile sheath and tail fibers
- Attach to bacterial cell walls or surface structures.
- Commonly show:
- Lytic cycles, where they rapidly multiply and lyse the bacterium.
- Lysogenic cycles, where phage DNA integrates into the bacterial chromosome and can be passed to daughter cells before reactivation.
Phages greatly influence bacterial populations in nature and are used experimentally to study genetic material and in some therapeutic approaches to combat resistant bacteria.
Viroids
What Makes Viroids Unique?
Viroids are even simpler than viruses:
- They consist solely of a short, circular, single-stranded RNA molecule.
- They do not have:
- a protein coat (no capsid)
- an envelope
- any genes for proteins (their RNA does not encode proteins)
So, viroids are “naked” RNA molecules.
Infection and Host Range
- Known viroids infect mainly plants.
- They can cause serious plant diseases that affect agriculture (e.g., dwarfing, deformations, reduced yield).
- They spread through:
- Plant-to-plant contact
- Contaminated tools (e.g., cutting instruments)
- Possibly through certain insects that feed on plants
How Can They Function Without Proteins?
Although they do not encode proteins, viroids can:
- Use the host cell’s RNA polymerases to replicate their RNA.
- Interfere with the host’s gene expression, for example by:
- Acting like regulatory RNAs
- Disrupting normal RNA processing and stability
Some viroid RNAs can form highly base-paired, stable structures, which helps protect them from degradation and may be involved in their replication.
Viroids illustrate how little molecular complexity is required to disturb the complex metabolism of a cell.
Prions
The Protein-Only Hypothesis
Prions are fundamentally different from both viruses and viroids:
- They appear to be composed only of protein, with:
- No nucleic acid (no DNA, no RNA).
- They are misfolded forms of a normal cellular protein, commonly called PrP (prion protein).
The key idea: A misfolded prion protein can cause normal PrP proteins to misfold as well, triggering a self-amplifying chain reaction.
Structure and Misfolding
The normal PrP protein is mainly alpha-helical in structure and is found in many vertebrate cells, especially in the nervous system.
The prion form:
- Has more beta-sheet structure.
- Is abnormally folded, very stable, and resistant to normal cellular degradation.
- Tends to aggregate into insoluble clumps.
These protein aggregates can accumulate in the brain, causing damage to nerve cells and leading to a group of diseases called transmissible spongiform encephalopathies (TSEs).
Prion Diseases (Concept Overview)
While the detailed medical aspects belong elsewhere, typical prion diseases share some features:
- Affects nervous tissue, especially the brain.
- Progresses slowly but is invariably fatal.
- Characterized by:
- Loss of neurons
- Spongy (porous) appearance of brain tissue under the microscope
- Often, severe neurological symptoms (movement disorders, changes in behavior, dementia)
Transmission can occur:
- Within a species (e.g., between animals of the same kind).
- Between species (with some barriers; not all prions cross species efficiently).
The striking feature of prions is that no nucleic acid is needed for infectivity. The information for propagation is thought to be stored in the three-dimensional shape of the protein.
Stability and Inactivation
Prions are notoriously difficult to inactivate:
- They withstand conditions that usually inactivate viruses and bacteria:
- Many disinfectants
- Moderate heat treatments
- Special protocols (e.g., very high temperatures and strong chemicals) are needed in medical or laboratory settings.
This stability and resistance are a direct consequence of the abnormal protein folding and aggregation.
Comparison: Viruses, Viroids, and Prions
To highlight the differences among these three types of infectious agents:
| Feature | Viruses | Viroids | Prions |
|---|---|---|---|
| Main component | Nucleic acid + protein coat | RNA only | Protein only |
| Nucleic acid type | DNA or RNA | Single-stranded circular RNA | None |
| Protein coat (capsid) | Yes (always) | No | No (but composed of protein) |
| Envelope | Sometimes (lipid membrane) | No | No |
| Encodes proteins | Yes | No | Host-encoded protein in misfolded form |
| Typical hosts | Bacteria, plants, animals, etc. | Mainly plants | Mainly animals (nervous system) |
| Genome function | Codes for viral proteins | Regulatory/replicative RNA roles | No genome; infectious shape |
| Replication | Via host machinery + viral genes | Via host RNA polymerases | By converting normal proteins to prion form |
| Status (living?) | Borderline, acellular | Borderline, acellular | Protein-based infectious agent |
Together, viruses, viroids, and prions demonstrate that:
- Infectious behavior does not require a full cell.
- Genetic information and biological effects can be carried by:
- Nucleic acid with proteins (viruses),
- Bare RNA (viroids),
- Or even protein conformation alone (prions).
This diversity helps define the limits of what we call “life” and clarifies the distinction between cells, which are the basic units of life, and simpler infectious agents that depend entirely on cells for their propagation.