Viruses and Viral Reproduction

• Viruses are part of additional HL content, theme unity and diversity, level of organization cells for first exams in 2025.
• IB guiding questions: How can viruses exist with so few genes? In what ways do viruses vary?

HL Content: A2.3 Viruses

• A2.3.1: Structural features common to viruses.
• A2.3.2: Diversity of structure in viruses.
• A2.3.3: Lytic cycle of a virus.
• A2.3.4: Lysogenic cycle of a virus.
• A2.3.5: Evidence for several origins of viruses from other organisms.
• A2.3.6: Rapid evolution in viruses.

HL Key Terms

• Virus: A submicroscopic infectious agent that replicates only inside the living cells of an organism.
• Capsid: A protective protein coat surrounding the genetic material of a virus..
• Bacteriophage: A virus that infects bacteria.
• Lytic Cycle: One of the two cycles of bacterial infection caused by a virus.
• Lysogenic Cycle: One of the two cycles of bacterial infection caused by a virus.
• Prophage: The stage of a virus when it integrates into the host DNA.
• Lysogen: A bacterium containing a prophage.
• Lysis: The disintegration of a cell by rupture of the cell wall or membrane.
• Metabolism: All of the chemical reactions that occur within an organism.
• Parasite: An organism that lives in or on another organism (its host) and benefits by deriving nutrients at the host's expense.
• Obligate Parasite: A parasite that cannot complete its life cycle without exploiting a suitable host.
• Convergent Evolution: The independent evolution of similar features in different lineages.
• Evolution: Change in the heritable characteristics of biological populations over successive generations.
• Antibodies: Proteins produced by the immune system to neutralize pathogens.
• Antigens: Substances that trigger an immune response.
• Immunity: The ability of an organism to resist infection.
• Mutation: Change in the DNA sequence of an organism.
• Antigenic drift: A gradual change in the antigens on the surface of a virus.
• Antigenic shift: An abrupt change in the antigens on the surface of a virus.

A2.3.1: Common Structural Features of Viruses

• Relatively few features are shared by all viruses.
• These features include: small, fixed size; nucleic acid (DNA or RNA) as genetic material; a capsid made of protein; no cytoplasm; and few or no enzymes.
• Viruses infect all life forms, including animals, plants, and bacteria.
• Viruses are typically 20 to 200 nm in diameter, while bacteria are 2000 to 3000 nm.
• Viruses aren't cells; most scientists don't consider these to be alive.

A2.3.2: Virus Diversity

• Viruses are highly diverse in their shape and structure.
• Genetic material may be RNA or DNA, which can be either single- or double-stranded.
• Some viruses are enveloped in host cell membrane and others are not enveloped.
• Virus examples include bacteriophage lambda, coronaviruses and HIV.
• Most viruses can be classified as having an icosahedral shape (a 3D-shape with 20 faces) or a helical shape.
• Some viruses, such as bacteriophages, have a more complex shape.

A2.3.3: Lifecycle of Bacteriophage Lambda

• Students should appreciate that viruses rely on a host cell for energy supply, nutrition, protein synthesis and other life functions.
• Bacteriophage lambda is an example of the phases in a lytic cycle.
• Bacteriophage lambda is not alive and has no metabolism.
• It depends on its host cell for energy supply, nutrition, protein synthesis and all other life functions.
• Bacteriophage lambda infects Escherichia coli bacterial cells by means of two different cycles.
• The genetic material of bacteriophage lambda is a double stranded DNA molecule.

Stages of the Lytic Cycle

• Attachment: Bacteriophage lambda attaches to receptors on an E. coli cell, but the capsid remains outside.
• Penetration: Bacteriophage lambda injects its DNA into the E. coli cell.
• Phage DNA Replication: Endonuclease enzymes degrade E. coli chromosomes, allowing the bacteriophage to hijack the cells' transcription and translation metabolism.
• Host synthesizes many copies of the phage's DNA and capsid.
• Phage Assembly: The E coli cells metabolism is used to assemble phage DNA and capsids into many new bacteriophage lambdas.
• Host cell Lysis: Enzymes damage the E. coli cell wall, causing the cell to lyse (burst), releasing bacteriophage lambda to attach to and infect other E. coli cells.
• During the lytic cycle, the bacteriophage lambda DNA remains separate from the host's DNA and takes control of the cell's metabolism.

A2.3.4: Lysogenic Cycle of a Virus

• Bacteriophage lambda is used as an example.

Lysogenic Cycle of Lambda Bacteriophage

• Attachment: Bacteriophage lambda attaches to receptors on an E. coli cell.
• The capsid remains outside of the cell.
• Penetration: Bacteriophage lambda injects its DNA into the E. coli cell.
• Prophage Formation: The phage DNA is incorporated into the E. coli chromosome, to form a prophage.
• The infected bacterium is called a lysogen.
• E. coli reproduction: Infected E. coli lysogen reproduces; the lambda bacteriophage DNA is replicated along with the bacterial chromosome.
• All offspring of the infected bacteria contain the lambda bacteriophage DNA.
• Induction: An E. coli lysogen is triggered to enter the lytic cycle.
• The prophage (lambda bacteriophage DNA) is excised from the bacterial chromosome.
• Phage DNA Replication begins, leading to lysis and the is release of many copies of the lambda bacteriophage to infect other E. coli cells.

A2.3.5: Origins of Viruses from other organisms

• The diversity of viruses suggests several possible origins.
• Viruses share an extreme form of obligate parasitism, leading to shared structural features that could be regarded as convergent evolution.
• The genetic code is shared between viruses and living organisms.
• All viruses are obligate parasites that require host cells for replication.
• There are several competing hypotheses on the origin of viruses.
• It is possible that all viruses do not share a common ancestor, and that viruses could have developed in different ways.
• Similarities between viruses could result from convergent evolution, as similar adaptations are required for being obligate parasites.

Virus First Hypothesis

• Viruses existed before cells and ancestor viruses could have provided the raw material for the first cells because they are simpler.
• Strength: Virus genomes have genes that are not present in cells.
• Weakness: All modern viruses can only replicate via the use of cells, suggesting that viruses could not have existed before cells.

Escape Hypothesis

• Viruses evolved from sections of DNA or RNA that escaped from cells.
• Strengths: Modern bacterial cells exchange genetic material, suggesting a possible escape mechanism for genetic material.
• The hypothesis would explain the diversity of viruses if genetic material escaped many times.
• Weaknesses: Most of the genes and proteins found in viruses are not found in cells.

Regressive Hypothesis

• Viruses were once small cells that parasitized larger cells; the genes not required for parasitism have been lost over time.
• Strengths: Giant viruses have genetic material similar to parasitic bacteria.
• Weaknesses: The smallest cellular parasites do not resemble viruses.

A2.3.6: Rapid Evolution in Viruses

• Reasons for rapid evolution in some viruses.
• Examples of rapid evolution: evolution of influenza viruses and of HIV.
• Consequences for treating diseases caused by rapidly evolving viruses.
• Antigens are substances that trigger an immune response and the immune system produces antibodies to fight them.
• Parts of the capsid of viruses act as antigens, and stimulate the immune system to produce antibodies.
• If the genetic material of the virus mutates, this can cause the change of the shape of the protein coat, including the antigens.
• An example are the spike proteins on the Covid-19 virus .

Rapid Evolution of Viruses

• Some virus genomes are unstable and mutate rapidly.
• Viruses have a very high replication rate, increasing the chance of random mutation.
• Viruses do not have a proofreading mechanism during replication, making it more likely a mutation happens.
• RNA viruses such as the influenza virus and HIV are especially prone to mutation because of the lack of proofreading.
• Immune systems select against viruses that have failed to mutate and recognize the antigens on the capsid surface.
• The rate of evolution of viruses is also increased by the immune system; because immune systems select for mutated versions of the virus, and the immune system does not recognise the antigens on the capsid surface.
• The influenza virus (flu virus) is an RNA virus that mutates through antigenic drift and antigenic shift.
• Both processes involve mutations that cause a shape change to the HA and NA surface proteins of the influenza virus.
• Antigenic drift is a gradual process.
• The influenza's high replication rate results in mutations.
• Mutations accumulate in the genes coding for the HA and NA surface proteins (antigens).
• Mutations cause the shape of the HA and NA antigens to change over time, resulting in new strains of the influenza virus which the immune system no longer recognises.
• Immune individuals from the original virus will be vulnerable to the mutated virus.
• Antigenic shift involves a major change of the HA and NA surface proteins of the influenza virus.
• Antigenic shift happens when an organism, such as a pig, is infected with two different strains of the influenza virus.
• When viruses are synthesised by cells of the host, the genetic material from the two virus strains can recombine.
• Results are novel combinations of the HA and NA genes that the immune system does not recognise.
• Pandemics can result due to antigenic shift.
• HIV mutates rapidly.

Consequences of Rapid Evolution of Viruses

• Rapidly evolving viruses quickly develop resistance to existing drugs and treatment, requiring more research into new drugs.
• Mutations often produce novel subtypes of the virus that are no longer recognised by the immune system because current vaccines may become ineffective..
• Epidemics or pandemics can result if rapidly evolving viruses not contained.

IB Linking Questions

• What mechanisms contribute to convergent evolution?
• To what extent is the natural history of life characterized by increasing complexity or simplicity?

Explore the unique differences between viruses and bacteria, focusing on viral structure, replication cycles (lytic and lysogenic), and genetic diversity. Understand viral dependency on host cells, the role of bacteriophages, and the concept of prophages.