Week 2 L2 - Viruses

Question 1

How big are virus particles?

Answer 1

They range from very small (polio virus, at 30nm) to large (vaccinia virus, at 400nm).

Question 2

List 3 features of viruses

Answer 2

• Contain a single type of nucleic acid – either DNA or RNA
• Parasites – cannot replicate without infecting another (host) organism
• Causes many infections of humans, animals, plants and bacteria.

Question 3

What is a capsid?

Answer 3

The protein coat surrounding the nucleic acid of a virus.

Question 4

What are the protein subunits that form a capsid called?

Answer 4

Capsomeres.

Question 5

What is the capsid with its enclosed genome referred to as?

Answer 5

Nucleocapsid.

Question 6

What is the envelope of a virus?

Answer 6

Lipids, proteins and carbohydrates cover the capsid of some viruses, known as the envelope.

Question 7

What is a virion?

Answer 7

A completely assembled and infectious virus.

Question 8

Viruses are classified into families based on what three things?

Answer 8

• Morphology
• Genetic material
• Host organism

Question 9

Morphology of viruses

Answer 9

• Very limited range of shapes that viruses can take - helical, polyhedral, complex.
• Have extremely small genomes – can’t code for a wide range of proteins
• Most simple virus encode only 4 proteins
• More complex virus encode 200 proteins

Question 10

Discuss the three shapes that viruses can take.

Answer 10

1) Helical:
- Resemble long rods that maybe rigid or flexible
- The viral nucleic acid is found within a hollow cylindrical capsid that has a helical structure
- Example – Tobacco Mosaic Virus (TMV)
2) Polyhedral or many-sided:
- The capsid of most polyhedral viruses is in the shape of an icosahedron
- A regular polyhedron with 20 triangular faces and 12 corners
- Example – Herpes simplex virus
3) Complex:
- A few viruses (bacterial viruses) have a combination of helical and icosahedral symmetry
- Example – Bacteriophages

Question 11

What’s the primary way scientists categorize and classify viruses?

Answer 11

The genetic material it contains.
• May be DNA or RNA, but never both
• May be linear and segmented or single and circular
• Much smaller than genomes of cells
• DNA viruses
– Contain either single stranded or double stranded DNA genomes (dsDNA, ssDNA)
• RNA viruses
– Contain either single stranded or double stranded RNA genomes (dsRNA, ssRNA)

Question 12

Which host group do viruses infect?

Answer 12

• Prokaryotes – Bacteria, Mycoplasma
• Eukaryotes – Algae, Plants, Protozoa, Invertebrates, Vertebrates
• Most viruses have a very narrow host range
• Examples: Smallpox virus only infects humans, Polio virus only infects humans and primates.

Question 13

What type of cells does a T4 bacteriophage infect?

Answer 13

E. Coli.

Question 14

Why do viruses need host cells in order to replicate?

Answer 14

• Viruses cannot reproduce by themselves - they do not contain enzymes for energy production or protein synthesis.
• For a virus to multiply, they must invade a host cell and hijack the host’s metabolic machinery to express their genes.

Question 15

The five steps of viral replication?

Answer 15

1. Attachment - some viruses (bacteriophages) attach to the outside of a host, and inject their genetic material into the host cell. Other viruses (animal viruses) use projections (viral spikes) on the viral surface to attach to specific receptors on the host cell, eg. adenovirus, HIV.
2. Penetration/Entry - The nucleic acid of the virus moves through the plasma membrane and into the host cell. The capsid of a phage remains on the outside – but many viruses that infect animal cells enter the host cell intact.
3. Biosynthesis - Once inside the cell, the virus instructs the host to make 3 kinds of proteins:
   * Early proteins: enzymes for viral DNA/RNA replication
   * Late proteins: capsid proteins
   * Lytic proteins: proteins to lyse the cell
4. Maturation/Assembly - the assembly of viral parts into complete virus particles. The enzymes encoded by the viral genes guide the assembly in step-by-step fashion.
   • Assembly and release of animal viruses:
   – Most DNA viruses assemble in nucleus
   – Most RNA viruses develop solely in cytoplasm
   – Number of viruses produced depends on type of virus and size and initial health of host cell
5. Release - The final stage – the assembled viruses are released from the cell.
   * For Bacteriophages it is called the lysis stage – because the cell ruptures (host cell is destroyed)
   * The enzyme involved in the bacterial cell breakdown - lysozymes
   * The newly released virus particles are free to infect neighbouring cells.
   * The process of budding in enveloped viruses:
   - The fully formed viral capsid reaches the cell membrane and pushes against it.
   - The glycoprotein surface of the cytoplasmic membrane form around the virus capsid as it pushes out.
   - The virus ‘buds off’ as an enveloped virion and can go on to infect other cells.

Question 16

What are the three mechanisms of entry for animal viruses?

Answer 16

1. Direct penetration, eg. polio virus - attaches to receptors on cytoplasmic membrane, viral genome enters, capsid remains outside.
2. Membrane fusion, eg. HIV - involves a capsid that is suppounded by an envelope made up of viral glycoproteins. They attach to receptors on cytoplasmic membrane, the viral glycoproteins remain in cytoplasmic membrane, the capsid containing the genome is engulfed, the now uncoated capsid is broken down, setting the viral genome loose inside the cell.
3. Endocytosis, eg. herpes virus. Also involves an enveloped capsid. The host cell engulfs the enveloped capsid as a whole, the envelope opens up inside the cell, the capsid is broken down, and the genome is released into the host cell.

Question 17

In the biosynthesis of proteins and genomes in animal RNA viruses, what’s the difference between the transcription of the complementary strand of +ssRNA (positive-sense) and the transcription of the complementary strand of -ssRNA (negative sense)?

Answer 17

The +ssRNA is transcribed by viral RNA polymerase to form the complementary -ssRNA strand (same for double stranded RNA), whereas the -ssRNA is transcribed by RNA-dependant RNA transcriptase to form the complementary +ssRNA strand.

Question 18

What is the pattern of virion abundance in persistent infections?

Answer 18

When the release of virions occurs due to cell lysis, there is a spike in the number of active virions in the medium that they’re in, whereas if the host cells shed the viruses slowly and relatively steadily, this leads to persistant infections.

Question 19

Animal viruses - Polio Virus Info

Answer 19

• They are among the smallest virions
• 27 nm in diameter
• naked icosahedron shaped capsid
• containing a single stranded (+ strand) RNA genome
• Enters the body via contaminated water and food
• They multiply first in the tonsils and then in the lymphoid tissues of the gastro intestinal tract
• Sometimes – enters into the blood stream and localise on the meninges – causing meningitis (paralysis of the arms, legs and body trunk may occur).

Question 20

Animal Viruses - Vaccinia Virus Info

Answer 20

• A large, complex, enveloped virus belonging to the pox virus family – related to smallpox virus (variola)
• Contains a linear double-stranded DNA genome
• The vaccinia virus is the “live virus” used in the smallpox vaccine

Question 21

Small Pox Info

Answer 21

• Smallpox last appeared in Australia – 1938
• Last case reported in the world – Somalia – 1977
• Samples of the small pox virus are currently held in secure labs - United States and Russia
• Most of the world’s population today has no immunity to the virus
• If exposed
– Vaccination within 3 days will prevent or significantly lessen the severity of the symptoms
– Vaccination 4 to 7 days may offer some protection from disease or may modify the severity of disease.

Question 22

Retroviruses, eg. HIV

Answer 22

• HIV is a member of the Retroviridae
• Contains 2 copies of single stranded (+) RNA
• Unique feature of RNA viruses – Reverse Transcriptase Enzyme
• Genome is surrounded by a cone shaped icosahedral capsid
• Envelope contains spikes for attachment and entry into cells.

Question 23

Basics of HIV viral replication

Answer 23

1. Attachment, entry and uncoating:
   - The spikes enable the virus to attach to the CD4 receptor and the CXCR4 co-receptor on host cells
   - HIV normally infects immune system cells of the blood and lymphatic system
   - CD4 receptors are found on helper T cells, macrophages and dendritic cells
   - Attachment of the virus is followed by entry into the cell
   - RNA genome and viral proteins are released into the cell
2. Reverse transcription and integration:
   - Reverse transcriptase makes a DNA copy of the RNA degrading the RNA at the same time
   - Then uses this DNA strand as a template to complete a DNA double helix
   - The DNA then enters the nucleus and integrates into the chromosomal DNA of the host – becoming a PROVIRUS
3. Biosynthesis:
   - The proviral DNA is transcribed into viral RNA fragments and translated into viral proteins
   - New capsids are assembled around viral RNA fragments and reverse transcriptase
4. Maturation and release:
   - The nucleocapsid “bud” from the plasma membrane as complete virus.

Question 24

The role of viruses in cancer

Answer 24

Viruses cause 15–20% of human cancers Some carry copies of oncogenes as part of their genomes Some influence the expression of proto-oncogenes or suppressor genes already present in host (e.g. insertional activation or deactivation).

Question 25

Specific viruses and cancer rates

Answer 25

Specific viruses are known to cause ~15% of human cancers
• Burkitt’s lymphoma - The endemic (African) type of Burkitt lymphoma is almost always linked to a previous infection with the Epstein–Barr virus (EBV). This is the virus that causes glandular fever.
• Hodgkin’s disease - infectious mononucleosis (sometimes called mono for short), an infection caused by the Epstein-Barr virus (EBV)
• Kaposi’s sarcoma – commonly found in people with AIDS caused by infection with a virus called the Kaposi sarcoma associated herpesvirus (KSHV) (same family as EBV)
• Cervical cancer - Human papillomavirus (HPV) sexually acquired – Ian Frazer (Brisbane): vaccine has halved cervical cancer rates.

Question 26

Distinguish between the structures common to all viruses and those that separate naked from enveloped viruses, use figures to illustrate your answer.

Answer 26

Common to all - genome surrounded by capsids composed of capsomeres, i.e. nucleocapsid.
No envelope = naked.
Enveloped - extra layer composed of lipids, proteins and carbohydrates, with spikes that allow attachment and fooling of receptors.

Question 27

Describe the different ways that viral nucleic acid can enter a host cell. Why is the synthesis of mRNA a central issue for all viruses? How do different types of viruses achieve this goal?

Answer 27

1. Direct penetration
2. Membrane fusion
3. Endocytosis
   * When the viruses make mRNA, the cell can’t tell that it is different and will continue to synthesise the proteins that the viral mRNA are encoding for.
   * Transcription can be done either by RNA polymerase, RNA-dependant RNA transcriptase, or reverse transcriptase enzyme (retroviruses).