Genetics of viruses

Describe group V viruses.

(-) sense single-stranded RNA viruses Genome must be converted to (+) sense RNA by a RNA-dependent RNA polymerase before translation

Describe the general steps in reproduction of an enveloped virus.

(1) Adsorption The virus attaches to its host cell by specific binding of its glycoproteins to host cell receptors. (2) Penetration The virus is engulfed into a vesicle and its envelope is uncoated, thereby freeing the viral nucleic acid into the cell cytoplasm. (3) Synthesis & Replication: Synthesis of viral proteins and replication of viral nucleic acid Under the control of viral genes, the cell synthesises the basic components of new viruses: nucleic acid, capsomeres and glycoproteins. (4) Assembly Viral glycoproteins are inserted into the host cell membrane for the viral envelope. Nucleocapsid / capsid is formed from nucleic acid and capsomeres. (5) Release Enveloped viruses bud off of the membrane, carrying away an envelope with the glycoproteins. This complete virus or virion is ready to infect another cell.

Describe the common viral structural features of the influenza virus. (Genome)

(1) Genome - Nucleic acid - Eight different segments of negative (-) sense single-strand RNA - (-) sense strand RNA must be converted into the complementary (+) sense RNA before it can be used for translation of viral proteins.

Describe the common viral structural features.

(1) Genome - nucleic acid linear double-stranded DNA. DNA is transcribed by host cell machinery into mRNA for translation of viral proteins. (2) Capsid capsomeres surrounds the nucleic acid, contained in the head of the phage

Describe the specific lambda bacteriophage structural features.

(1) Head contains the DNA of the virus - The 5'-terminus of each DNA strand is a single-stranded tail of 12 nucleotides long which is important in prophage formation. (2) A single tail fibre (non-contractile) which allows the phage to adsorb onto the surface of the bacterial cell by binding to the specific receptor site found on the cell surface.

Describe the common viral structural features of the influenza virus. (Capsid)

(2) Capsid - nucleoprotein (NP) associate with the viral nucleic acid to form nucleocapsid

Describe the specific influenza structural features. (Enzymes)

- PB1, PB2, PA - to form RNA-dependent RNA Polymerase (replicase) responsible for replication and transcription - NS 1 - regulates viral replication mechanisms and cellular signaling pathways

Describe step 4 of the lytic cycle.

- Viral proteins are assembled to form phage heads, tails and tail fibres each. - The different components are assembled into the complete bacteriophage.

What are the arguments for viruses being non-living organisms?

1. Viruses are not cells Viruses are not cells and do not have protoplasm or organelles. The basic structure of a virus consists of a protein capsid surrounding a nucleic acid core which is composed of DNA or RNA. In some viruses, the capsid is surrounded by a membranous envelope. 2. Viruses lack some of the characteristics of living organisms Viruses are able to reproduce and respond to stimuli while in the intracellular state (i.e. within their host cells). However, in their extracellular state, they are - unable to carry out metabolic processes, such as nuclei acid and protein synthesis, - do not require nutrition, such as amino acids and nucleotides, - unable to synthesise their own ATP as an energy source - unable to respond to stimuli - neither grow nor excrete.

Describe the inheritance of the T4/lambda viral genome.

A generalised model of replication of DNA viruses, such as the bacteriophages, requires that the host cell transcribe genes from the DNA genome of the bacteriophage to produce mRNA. The mRNA is then translated into viral proteins necessary for the replication process. The viral DNA genome is also replicated by the host cell machinery to form multiple copies for use in the assembly of the new bacteriophage

Describe how reassortment results in variation in the genomes of viruses.

A host cell may be infected with 2 viral strains which introduce two sets of genetic material into the host cell. During formation of the viral progeny, different segments of the viral genome may be packaged into the progeny virus. This would result in a sudden and drastic change in the viral genome and leading to an antigenic shift

What is the lytic cycle?

A phage reproductive cycle that finally results in death of the host cell

Describe the specific T4 bacteriophage structural features. (Tail)

A tail - consisting of a tail sheath, multiple tail fibres and base plate Tail fibres - allow the phage to adsorb onto the surface of the bacterial cell by binding to the specific receptors site found on the cell surface (e.g. lipopolysaccharide receptor of the E. coli host). - This enables the base plate to come into contact with the surface of the cell. This triggers a conformational change in both the base plate and the tail sheath such that the central tube is pushed through the bacterial wall Tail sheath - tail sheath surrounds a central tube. - tail sheath contracts during penetration to thrust the central tube through the host cell wall and membrane.

What is the definition of an antibody?

A type of glycoprotein molecule, also called immunoglobulin (Ig), produced by B lymphocytes, that binds antigens, often with a high degree of specificity and high affinity.

Describe the CAPSID.

All viruses have a protein coat, CAPSID, which either encloses or surrounds the viral genome. Each capsid is constructed from identical protein subunits called capsomeres.

What is the definition of an antigen.

An antigen is any substance that can be recognized by the immune system. It is a molecule that binds to an antibody or a T- cell receptor (TCR) which elicits a B cell or T cell response respectively.

Describe antigenic shift in influenza virus.

An antigenic shift arises when different influenza A strains infect a host and subsequently form progeny viruses whose genome is a new combination of RNA from the different strains. The influenza virus, which contains 8 single- stranded RNA, is susceptible to such reassortment since it can easily reshuffle it's genome during packaging of the new virion Different viruses of different origins may infect a pig, which provides the opportunity for the viruses to reassort, resulting in formation of a new virus which contains different surfaces antigens from both the avian and human influenza strains. This would result in the formation of viruses with new combinations of hemagglutinin and neuraminidase. This assembly of RNA segments from the two different influenza viruses would result in the introduction of a novel influenza A strain with a new combination of hemagglutinin and/or neuraminidase into a population. As the new strain would not have been circulating in the population, there would not likely be any immunity against this novel strain and resulting in the virus being easily transmissible

How does antigenic drift arise?

Antigenic drift arises when viruses undergo continuous, subtle antigenic changes due to accumulation of mutations to the hemagglutinin and/or neuraminidase genes

What is the definition of antigenic drift.

Antigenic drift is the gradual accumulation of minor mutations in the genes of influenza viruses that results in altered antigenicity. It happens continually over time in the genes of viruses like the influenza virus as the virus replicates. These result in small changes which produce viruses that are closely related to each other and usually share the same antigenic properties.

What is the definition of antigenic shift?

Antigenic shift is a sudden change in the antigenicity of a virus owing to reassortment of the segmented virus genome with another genome of a different antigenic type. In the influenza virus, antigenic shift results in new hemagglutinin and/or new hemagglutinin and neuraminidase proteins in the viruses that infect humans. Antigenic shift results in a new influenza A subtype or a virus that has emerged from an animal population that is so different from the same subtype in humans that most people do not have immunity to the new virus.

What is the result of the processes of antigenic shift and antigenic drift.

As a result of these processes, viruses' (notably influenza) genomes undergo changes, resulting in the formation of new surface proteins (antigens). In influenza, the surface proteins which are changed are hemagglutinin and neuraminidase respectively. These changes affect the antigenicity of the virus and are essential in mediating their ability to evade host defence mechanisms.

What are the factors which influence the rate of mutation of viral genomes?

As the genome of influenza consists of 8 single-strand RNA strands which lack a complementary strand, polymerases cannot perform proofreading during replication. Viral polymerases are also prone to errors and will introduce mutations during the course of DNA replications. Retroviruses, such as HIV, encode on average of one point mutation for every replication cycle as a result of viral reverse transcriptase being unable to correct nucleotide misincorporation errors. these mutations result in the production of surface proteins with different 3D conformations, resulting antibodies no longer being complementary to them and thus will not recognise and bind to them

Describe bacteriophages.

Bacteriophages are DNA viruses that infect bacteria. The bacteriophages may undergo two distinct cycles, the lytic and lysogenic cycles, during the course of the course of their replication. Bacteriophages can also be involved in the transfer of genetic material between bacteria by transduction

Describe what is included in the basic structure of a virus.

Basic structures of viruses include: - Genome comprising DNA or RNA (present in all viruses) - Capsid (a protein coat) comprising protein subunits, capsomeres (present in all viruses) - Envelope comprising phospholipids from host cell (not present in all viruses) - Enzymes

Describe the common viral structural features of HIV. (Capsid)

Capsid surrounds the nucleic acid

Describe the specific T4 bacteriophage structural features. (Head)

Contains the DNA of the virus

What are the enzymes involved in nucleic acid replication and/or transcription in viruses?

DNA-dependent RNA polymerase RNA-dependent RNA polymerase / viral replicase DNA-dependent DNA polymerase RNA-dependent DNA polymerase / reverse transcriptase

Describe group I viruses.

Double-stranded DNA viruses

Describe the effect of antigenic shift and drift.

Due to antigenic shift or antigenic drift, viruses are able to mutate and change the antigens presented on their surfaces. This prevents antibodies, which are proteins generated by the host immune system to help identify and remove foreign antigens on viruses, from recognising them and allowing the viruses to evade detection by the host immune system. Vaccines would become ineffective since the antibodies generated would not be able to bind specifically to the new surface antigen due its new and different 3D conformation. This would allow the virus to evade the host's immune system and continue its reproductive cycle. The magnitude of impact on the human population would however be different due to the different mechanisms for change in surface proteins.

Describe HIV.

HIV (Human Immunodeficiency Virus) is a retrovirus that causes AIDS (Acquired Immunodeficiency Syndrome). Retroviruses are enveloped RNA viruses which replicate by means of a DNA intermediate synthesised by the enzyme reverse transcriptase

Describe the inheritance of HIV genome.

HIV, like influenza, is an RNA virus, hence it too has a different mode of inheritance from that of typical DNA viruses. Due to its ability to integrate into host DNA, HIV will undergo reverse transcription, a process of making a double-stranded DNA molecule from a single-stranded RNA template. The DNA then integrates into the host genome and remains in a latent phase until the correct environmental cue is received. At that point, HIV subsequently produces mRNA which acts as templates for translation, and act as its genome. The RNA and viral proteins are then packaged into a new virion and released.

Describe the specific influenza structural features. (Surface glycoproteins)

Haemagglutinin (HA) - HA binds to sialic acid containing receptors - Attach virus to the receptor on the host cell membrane Neuraminidase (NA) - hydrolyses mucus allowing virus to enter cells of the respiratory tract - facilitate budding by cleaving sialic acid containing receptors

What are the essential proteins that all viral genomes would contain genes for?

I. Regulatory proteins which are necessary for regulating the action of the host genes. Host cell machinery is thus used by the virus to replicate the viral genome and synthesise the various components necessary for formation of the virus. II. Structural proteins, such as the viral capsid protein, which are essential for assembly of the complete virus.

Describe the inheritance of influenza viral genome.

Influenza is a negative (-) sense single-stranded RNA virus, hence its mode of inheritance differs from that of DNA viruses that transcribe mRNA from the DNA genome. Influenza virus must first convert the negative (-) sense single-stranded RNA to a positive (+) sense single-stranded RNA for use in synthesis of viral proteins. Negative (-) sense single-stranded RNA is also subsequently synthesised from the positive (+) sense single-stranded RNA for use as genomic material and packaged together with the viral proteins to form new virions

Describe the specific influenza structural features. (Protein envelope)

Matrix protein forms second layer of envelope, enclosing the nucleocapsid. - M1 - monomers of matrix protein - M2 - acts as an ion channel to lower or maintain the pH of the endosome in the host cell

Describe the specific HIV structural features. (Protein coat)

Matrix protein forms second layer of protein envelope, enclosing the capsid

What are the three molecular mechanisms which result in variation in the genomes of viruses?

Mutation Recombination Reassortment

Define each of the words Obligate, Intracellular and Parasites.

Obligate: by necessity Intracellular: within the cell Parasite: an organism living and feeding on a host

What are temperate phages?

Phages capable of using both the lytic and lysogenic modes of reproduction within a bacterium Once an environmental trigger (such as the presence of UV light or certain chemicals) activates the virus, it switches from the lysogenic cycle to the lytic cycle.

Describe the specific HIV structural features. (Viral envelope)

Phospholipid bilayer obtained from host upon budding

Describe the specific influenza structural features. (Membrane/viral envelope)

Phospholipid bilayer obtained from host upon budding

Describe the specific HIV structural features. (Enzymes)

Reverse transcriptase - 2 molecules, each associated with 1 RNA molecule - to reverse transcribe viral RNA into DNA Integrase - facilitates incorporation of double-stranded DNA into host cell's genome Protease - cleaves viral polypeptide into functional proteins during viral maturation

Describe the differences between antigenic shift and antigenic drift. (Nature of change)

Shift Abrupt and major change in genome virus Drift Gradual accumulation of minor point-mutations in genome of virus

Describe the differences between antigenic shift and antigenic drift. (Cross species transmission)

Shift May result in a progeny virus which can infect a new species Drift Virus only infects individuals of the same species

Describe the differences between antigenic shift and antigenic drift. (Effect of host immunity)

Shift Population has no immunity to novel combination of surface proteins No drugs or vaccines present to treat virus Drift A proportion of the population may still have pre-existing immunity to the modified surface proteins Anti-viral drugs and seasonal vaccines available to treat virus

Describe the differences between antigenic shift and antigenic drift. (Number of viruses)

Shift Two or more viral strains are involved Drift Only one viral strain is involved

Describe the differences between antigenic shift and antigenic drift. (Rate of occurrence)

Shift Occasionally occurs to give rise to pandemics Drift Regularly occurring to give rise to seasonal epidemics

Describe the differences between antigenic shift and antigenic drift. (Mechanism for change)

Shift Reshuffling of genome between different strains Results in dramatic alternation of type of hemagglutinin or neuraminidase on progeny virus Drift Accumulation of point mutations in the gene of the surface antigen Results in minor alteration of 3D conformation of hemagglutinin or neuraminidase on progeny virus

Describe group VI viruses.

Single-stranded RNA-reverse transcriptase (RT) viruses Makes use of reverse transcriptase which is RNA-dependent DNA polymerase, to produce DNA from the initial chiral RNA genome

Describe step 1 of the reproductive cycle of the influenza virus.

Step 1: Adsorption - Haemagglutinin (HA) molecules on the viral membrane bind to sialic acid containing receptors on the membrane of the host cell.

Describe step 1 of the lytic cycle.

Step 1: Adsorption - The multiple tail fibres of the T4 phage attach to specific receptor sites on the surface of a bacterial host cell such as E. coli. - The base plate settles down on the host cell surface.

Describe step 1 of the lysogenic cycle.

Step 1: Adsorption - The single tail fibres of lambda (λ) phages attach to specific receptor sites on the surface of a bacterial host cell. - The base plate settles down on the host's cell surface.

Describe step 1 of the replication cycle of HIV.

Step 1: Adsorption / Attachment - Glycoprotein gp120 on the surface of the HIV binds to the CD4 receptor, a cell-surface receptor found on T helper cells and macrophages of the host immune system.

Describe step 2 of the lytic cycle.

Step 2: Penetration - Conformational changes occur in the tail sheath causing it to contract and its core/ tube pierces through the bacterial cell wall and cell membrane - T4 uses lysozyme to hydrolyse peptidoglycan, degrading a portion of the bacterial cell wall for insertion of the tail core - DNA is extruded from the head, through the tail tube into the host cell. - The capsid is left on the outside of the bacterial cell wall.

Describe step 2 of the lysogenic cycle.

Step 2: Penetration - The lambda (λ) phages have tails that are not contractile and serve to deliver the viral DNA to the cell membrane. - DNA is extruded (movement of DNA through the tube) from the head, through the tail tube and injected into the host cell passing through both the bacterial cell wall and cell membrane. - The capsid is left on the outside of the bacterial cell wall.

Describe step 2 of the reproductive cycle of the influenza virus.

Step 2: Penetration - The virus is then taken in by receptor-mediated endocytosis, forming an endocytic vesicle within the host cell called an endosome, with the influenza virus attached to its inner surface. - Fusion of this vesicle with an acidic lysosome lowers the pH of the vesicle. This triggers conformational changes in the HA protein, which causes the viral envelope and endosome membranes to fuse, releasing the eight viral segments of the influenza genome directly into the host cell cytoplasm. - The viral RNAs are then transported into the nucleus.

Describe step 2 of the replication cycle of HIV.

Step 2: Penetration - upon binding to CD4, gp120 undergoes a conformational change, allowing it to bind to a co- receptor known as CXCR4 on the surface of T helper cells and CCR5 on macrophages. - gp41 pulls the virus closer to the host cell. The co-receptor (CXCR4 / CCR5) facilitates the entry of the gp120-CD4 complex through the host cell membrane. - The HIV envelope fuses with the host cell membrane, releasing the viral contents consisting of viral nucleic acid and enzymes into the host cell.

Describe step 2A: prophage formation of the lysogenic cycle.

Step 2A: *Prophage formation* - The lambda (λ) phage genome circularises and inserts itself into a specific site on the bacterial chromosome, known as the prophage insertion site, by genetic recombination. Note that this does not cause any loss of the host DNA. This integrated lambda (λ) phage is known as a prophage. - In this integrated state, the viral DNA is replicated along with the chromosome each time the host cell divides, and is passed on to generations of host daughter cells. A single infected cell can soon give rise to a large population of bacteria carrying the viral DNA in prophage form.

Describe step 2B of the lysogenic cycle.

Step 2B: Spontaneous Induction - When there is an environmental trigger, such as UV radiation or the presence of certain chemicals, the viruses switches from the lysogenic cycle to the lytic cycle. - Lysis genes which were repressed during lysogeny are activated, allowing the lambda (λ) phage genome to be excised from the bacterial chromosome to give rise to new active phages.

Describe step 3 of the lytic cycle.

Step 3: Synthesis and replication: Synthesis of phage proteins, replication of phage nucleic acid - Soon after the phage DNA is injected into the host cell, the synthesis of host DNA, RNA and proteins is halted. The host cell machinery is taken over by the virus for: (A) Viral Nucleic Acid Synthesis - T4 Phage DNA is replicated by host DNA polymerase. o The host DNA is degraded into nucleotides, providing raw materials for phage DNA replication. (B) Viral Protein Synthesis - T4 Phage mRNAs are synthesised by the host RNA polymerase via transcription. o The phage mRNAs are translated by host cell ribosomes, tRNAs and translation factors into viral proteins and enzymes required to take over the host cell and replicate phage nucleic acids. o These include enzymes for viral replication and inhibitory factors that stop host cell RNA and protein synthesis.

Describe step 3 of the replication cycle of HIV.

Step 3: Synthesis of viral components, replication of viral genome HIV virus entering the latent phase will need to integrate into the host's genome - Reverse transcriptase first reverse transcribes the viral RNA into a complementary DNA strand. The RNA strand of the DNA-RNA is broken down by the ribonuclease H component of the reverse transcriptase and the newly synthesised DNA strand is used as a template for synthesis of the other complementary DNA strand, forming a double-stranded DNA molecule. - This DNA molecule then passes through the nuclear pore and enters into the host nucleus. - The enzyme integrase catalyses the integration of the viral DNA into the genetic material of the host. - This newly integrated viral DNA is called a provirus, which may remain in a latent (inactive) state for several years, producing few or no copies of HIV. The latent phase ends when the host cell is stimulated in an immune response.

Describe step 3 of the reproductive cycle of the influenza virus.

Step 3: Synthesis of viral components, replication of virus genome Viral replicase (RNA-dependent RNA polymerase), already included as part of the virion, copies the (-) sense RNA template into complementary (+) sense RNAs. The (+) sense RNA can be used for the following purposes. (A) Viral Nucleic Acid Synthesis - (+) sense RNAs are used as templates for synthesis of full-length (-) sense strand viral RNAs by viral replicase. - These (-) sense viral RNAs can be packaged into new viral particles as their nucleic acid. (B) Viral Protein Synthesis - The (+) sense RNAs are used as mRNA which are translated in the cytoplasm by host protein synthesis machinery. - Three sets of proteins are synthesised, namely enzymes, matrix and capsomeres proteins as well as glycoproteins. - Free ribosomes are used to synthesise enzymes, matrix and capsomeres as they are ultimately folded into final conformation in the cytoplasm and packaged into the new virion. - Viral transmembrane surface glycoproteins are synthesised by rER-bound ribosomes and transported to Golgi apparatus for glycosylation and then incorporated into the host cell membrane via vesicle which fuses with host cell membrane.

Describe step 4 of the reproductive cycle of the influenza virus.

Step 4: Assembly of new virion - Assembly of the viral particle is complete when the viral components of eight (-) sense viral RNAs associated with NP and enzymes like viral replicase (ie: PB1, PB2 and PA) are packaged. - Acquisition of the glycoprotein studded membrane envelope occurs during the release of the virus.

Describe step 4 of the replication cycle of HIV.

Step 4: Assembly of new virions - Copies of HIV proteins and HIV's RNA genome assemble near the host cell membrane to form a new virus particle. - Assembly of the viral components occur when the viral components of 2 single-stranded RNA molecules associated with reverse transcriptase and enzymes like integrase and protease are surrounded by assembled capsid.

Describe step 5 of the replication cycle of HIV.

Step 5: Release - Acquisition of the glycoprotein studded membrane envelope occurs during the release of the virus. - The newly assembled immature HIV buds off from the host cell, surrounded by host membrane. - Viral maturation occurs when the HIV protease cleaves the single long chains of HIV proteins into smaller functional proteins, forming a mature HIV particle.

Describe step 5 of the lytic cycle.

Step 5: Release - The T4 phages lyse the host cell by the action of the enzyme lysozyme, which digests the bacterial cell wall. - Water enters the cell by osmosis causing the cell to swell and burst.

Describe step 5 of the reproductive cycle of the influenza virus.

Step 5: Release - The virus is finally released from the host cell by budding, acquiring with it the host cell's lipid bilayer as the virus's envelope. - The host membrane containing HA, NA and a third protein, M2, buds off from the host cell with the virion components. - With the presence of HA on the viral envelope and sialic-acid containing cellular receptors on the host cell's membrane, budding invariably bring both together and results in the new viral particle remaining attached to the host cell. - Neuraminidase (NA) then aids to release the virus by cleaving sialic acid residues on the cellular receptor that bind the newly formed virions to the cell. - This releases the virions, allowing infection to continue

What is the definition of antigenicity.

The capacity of an antigen to induce an immune response in a host.

Describe the envelope of enveloped viruses.

The envelope of a virus is derived from host cells. When they are released from the host cell by budding, they take with them the host's cell surface membrane, i.e. the phospholipid bilayer and insert proteins of viral origins into the membrane. These proteins include viral glycoproteins which are exposed on the outside of the envelope. Such glycoproteins are essential for the attachment of viruses to the next host cell. The envelope protects the virion's nucleic acid from the effects of various enzymes and chemicals. Viruses which are not surrounded by the lipid membrane envelope are referred to as naked or non-enveloped viruses.

Describe the human influenza virus.

The human influenza virus is an enveloped virus in which the viral negative (-) sense single-stranded RNA is present in the virion in eight separate pieces. The (-) sense viral RNAs must first be converted to positive (+) sense single-stranded RNA which serves as mRNA for translation.

Describe step 3 of the replication cycle of HIV. (B) viral protein synthesis

The proviral DNA is also transcribed into viral mRNA, which is then translated to produce a single long chain of HIV proteins which is later cleaved. Viral proteins synthesised include enzymes, matrix and capsomeres proteins as well as glycoproteins. Viral surface glycoproteins are synthesised by rER-bound ribosomes and transported to Golgi apparatus for glycosylation and then incorporated into the host cell membrane via vesicles which fuses with host cell membrane.

What are virions?

The virion is metabolically inert and does not carry out respiratory or biosynthetic functions. The virion is the structure by which the virus genome is carried from the cell in which it has been produced to another cell where the viral nucleic acid can be introduced.

Describe the function of lysozyme in viruses.

This enzyme makes a small hole in the bacterial cell wall that allows the viral nucleic acid to enter. The same enzyme is produced in large amounts in the later stages of infection, causing lysis of the host cell and release of the virus.

Describe the function of neuramindase in viruses.

This group of enzymes breaks down glycosidic bonds of glycoproteins and glycolipids of the connective tissue of animal cells, thus aiding in the liberation of the virus. Neuraminidase is associated with the viral envelope instead of being located within the capsid like most other viral enzymes.

Describe the common viral structural features of HIV. (Genome-nucleic acid)

Two identical single-stranded RNA. The single-stranded RNA is converted to DNA for integration into the host genome. The DNA is then used for transcription of viral mRNA which is translated into viral proteins and for use as the viral genome in the progeny virions.

What happens when viruses are in their intracellular states?

Viral replication occurs. The viral genome and proteins that make up the virus coat are synthesised and assembled to form new viruses. A cell that a virus can infect and reproduce in is called a host cell.

What are viruses called in their extracellular states?

Virions

How do viruses challenge the cell theory that cells are the smallest unit of life?

Viruses also they lack the necessary molecular machinery to conduct many of the biochemical reactions a normal cell would need. However, like cells, they contain the genetic material necessary to form the next generation and are able to evolve in response to the environment.

How do viruses challenge the cell theory that all living organisms are composed of cells?

Viruses are acellular and do not have protoplasm or organelles. They thus are not considered cells since they need a host cell to carry out many functions necessary to reproduce. Additionally, while in the extracellular virion state, it is also metabolically inert and does not carry out respiration or biosynthesis.

How do viruses challenge the cell theory that all cells come from pre-existing cells?

Viruses are capable of replicating but rely on host cells to provide the energy and materials needed for replicating their genomes and synthesising their proteins. Consequently, they cannot replicate unless they have entered a suitable host cell.

What are the arguments for viruses being living organisms?

Viruses can reproduce Although viruses can reproduce, unlike cells, viruses are only able to reproduce in the intracellular state. In fact, the way a virus multiplies is very different from that of cells. In cells, reproduction always forms a new cell directly from a pre-existing cell, but a new virion is never formed directly from pre-existing virion. Replication in viruses involves the synthesis of large number of viral components in host cells, followed by their assembly into virions. Viruses are able to direct metabolic processes Even though as a virion, a virus does not exhibit most of the metabolic life processes of cells, they can however direct them when existing in a virus state (intracellular). They are thus, more than inert and lifeless molecules. These life processes include processes like protein synthesis and genome replication. Viral genomes can evolve Different types of viruses vary greatly in their structural and genetic complexity and no single gene is shared by all viruses/viral lineages. Furthermore, viral genomes can consist of single- or double- stranded DNA/RNA molecules. This indicates that viruses descended from more than one ancestral lines and do not share a common ancestor. Viruses evolve with their host and acquire their metabolic and translational genes from the host cells. In addition, genetic recombination can result in different / changing viral genomes.

How do viruses identify their host cells?

Viruses identify their host cells by a complementary fit between proteins on the outside of the virus and specific receptor molecules on the surface of the host cells

Why are viruses call obligate Intracellular parasites?

Viruses lack enzymes for most metabolic processes, as well as the machinery for protein synthesis, and thus are dependent on their living host cells

Describe how recombination results in variation in the genomes of viruses.

Viruses may also undergo recombination with the genome of another strain, resulting in these genomes exchanging genetic information and resulting in genomes with new combinations of alleles. Thus, viral progeny formed from such a process contain some genes from both the original viral strains.

Describe step 3 of the replication cycle of HIV. (A) viral nucleic acid synthesis

When the host cell receives a signal, the proviral DNA is transcribed by the host RNA polymerase into RNA which serves as nucleic acid for new virions.

Describe how mutation results in variation in the genomes of viruses.

While the genomes in eukaryotes undergo rigorous proofreading resulting in very low error rates of 1 error for every million or even billion bases copied, this is not so in viruses. As RNA is typically only a messenger molecule in eukaryotic cells, there are no proofreading mechanisms in the host cell. As a result, RNA viruses will experience much higher rates of mutations since errors are not corrected. In addition to this, certain viral enzymes such as reverse transcriptase in HIV have very low fidelity and regularly introduce errors into the genome. This results in errors in every replication cycle and is responsible for antigenic drift

What are viruses dependent on their living host cells for?

building-blocks such as amino acids and nucleotides protein-synthesising machinery (e.g. ribosomes) energy, in the form of adenosine triphosphate (ATP) In other words, viruses can only reproduce within a living host cell

Describe the specific T4 bacteriophage structural features. (Base plate)

comes into contact with the host cell surface and undergoes a conformational change to allow DNA to be extruded from the head, through the central tube and into the host cell.

Describe the specific HIV structural features. (Surface glycoproteins)

gp120 - binds to CD4 receptors on white blood cells like macrophages and T helper cells gp41 - aids in the fusion of the HIV envelope and the host cell membrane

What are the 3 groups for classification by host range of viruses?

i. bacterial viruses or bacteriophages (eg: T4 and lambda phage), ii. animal viruses (eg: influenza and HIV) and iii. plant viruses

What happens to the virus upon exiting the lysogenic cycle?

steps 3 - 5 of the lytic cycle resumes

What is the lysogenic cycle?

the lysogenic cycle involves replication of the phage genome without destroying the host in the initial steps.