Virus

Question 1

Describe the basic structure of a virus

Answer 1

• Genome comprising of DNA or RNA
• Capsid (protein coat) comprising protein subunits,capsomeres
• Envelope comprising phospholipids from host cells
• Enzymes

1 and 2 are found in all viruses but 3 is not

Question 2

What are 1 group viruses

Answer 2

Double-stranded DNA viruses

Examples include T4 and lambda phages

Question 3

What are V viruses

Answer 3

(-) Sense single-stranded RNA viruses

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

Examoples include influenza virus

Question 4

What is a VI viruse

Answer 4

Single-stranded RNA-reverse transcriptase (RT) viruses

Make use of reverse transcriptase which is an RNA-dependent DNA polymerase, to produce DNA from the initial viral genome

Examples include HIV

Question 5

Arguments for Viruses being living organsims

Answer 5

• Viruses can reproduce

Unlike cells, viruses can only reproduce in the intracellular state.

• Viruses are able to direct metabolic processes

Although as a virion, a virus does not exhibit most of the metabolic life processes of cells, they can however direst them when existing in a virus state (intracellular)

• Viral genome 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.

Question 6

Arguments for viruses being non-living organisms

Answer 6

1. Viruses are not cells (they do not have a protoplasm or organelles)
2. Viruses lack some of the characteristics of living orgasnism
   
   • In their extracellular state they are
     
     • unable to carry out metabolic processes
     • do no require nutrition
     • unable to synthesise their own ATP as an energy source
     • unable to respond to stimuli
     • niether grow nor excrete

Question 7

How do viruses challenge the cell theory

Answer 7

Ways in which viruses deviate from this theory

1. Cells are the smallest unit of life
2. All cells come from pre-existing cells
3. All living organisms are composed of cells

Question 8

Name 2 common enzymes found in viruses

Answer 8

1. Lysozyme
   
   • This enzyme makes a small hole in the bacteria cell wall that allows the viral nucleic acid to enter. The enzyme is prouced in large amounts in the later stages of infection, causing lysis of the host cell and release of the virus.
2. Neuraminidase
   
   • Breaks down the glycosidic bonds of glycoproteins and glycolipids of the connective tissue of animal cells, thus aiding in the liberation of the virus.
   • It is associated with the viral enveloipe instead of being located within the capsid like most other viral enzymes

Question 9

The general steps in reproduction of an enveloped virus

Answer 9

1. Adsorption
2. Penetration
3. Synthesis and Replication
4. Assembly
5. Release

Question 10

What are bacteriophages

Answer 10

DNA viruses that infect bacteria.

• May undergo 2 distinct cycles, the lytic and lysogenic cycles, the lytic and lysogenic cycles
• Bacteriophages can also be involved in the transfer of genetic material between bacteria by transduction
  *

Question 11

Lytic cycle overview

Question 12

Specific T4 bacteriophage structural features

Answer 12

1) Head containing DNA of the virus
2) A tail (consisting of tail sheath, multiple tail fibres and base plate)
3) A 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 celll.

Question 13

What is the function of tail fibres

Answer 13

• To allow the phage to adsorb into the surface of the bacterial cell by binding to the specific receptors site found on the cell surface
• This anbles 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

Question 14

What is the function of a tail sheath

Answer 14

• Tail sheath surrounds a central tube
• Tail sheath contracts during penetration to thrust the central tube through the host cell wall and membrane

Question 15

Describe the step 1 of the lytic cyles (adsorption)`

Answer 15

• 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

Question 16

Describe step 2 of the lytic cycle (penetration)

Answer 16

• 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 petidoglycan, 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 capsids is left on the outside of the bacterial cell wal

Question 17

Describe step 3 of the lytic cycle

(Synthesis and replication: synthesis of phage proteins, replication of phage nucleic acid)

Answer 17

• 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:
  1) Viral Nucleic Acid synthesis
• T4 phage DNA is replicated by host DNA polymerase,
  • The host DNA is degraded into nucleotides, providing raw materials for phage DNA replication

2) Viral protein synthesis

• T4 phage mRNAs are synthesised by the host RNA polymerase via transcription.
  
  • 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
  • These include enzymes for viral replication and inhibitory factors that stop host cell RNA and protein synthesis

Question 18

Describe step 4 and 5 of the lytic cycle

(Assembly and Release)

Answer 18

Step 4

• Viral proteins are assembled to form phage head, tails and tail fibres each
• The different components are assembled into complete bacteriophage

Step 5

• 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

Question 19

Specific lambda Bacteriophage structural features

Answer 19

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 bacteria cell by binding to the specific receptor site found on the cell surface

Question 20

What is the lysogenic cycle

Answer 20

In contrast to the lytic cycle, which kills the host cell, the lysogenic cycle involved replication of the phage genome without destroying the host in the initial steps.

Phages capable of using both the lytic and lysogenic cycle are called temperate phages. ONce an envrion

Question 21

List the steps of the lysogenic cycle

1 and 2

Answer 21

1. Adsorption
   * Same as lytic cycle
2. Penetration

• The lambda phages have tails that are not contractile and serve to deliver the viral DNA to the cell membrane
• DNA is extruded 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 bacteril cell wall

2a. Prophage formation

• The lambda phage genome circularises and inserts itself into a specific site on the bacterial chromosome, known as the prophage insertion site by genetic recombination. This does not cause any losss of the host DNA. The integrated lambda phage is known as a prophage
• 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 lrage population of bacteria carrying the viral DNA in prophage form.

Question 22

Describe 2a of the lysogenic cycle

Answer 22

2a. Prophage formation

The lambda phage genome circularises and inserts itself into a specific site on the bacterial chromosome, known as the prophage insertion site by genetic recombination. This does not cause any losss of the host DNA. The integrated lambda phage is known as a prophage

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 lrage population of bacteria carrying the viral DNA in prophage form.

Question 23

Describe 2b of the lysogenic cycle

Answer 23

2b.

• When there is an environmental trigger, such as UV radiation or the presence of certain chemicalsm the viruses switches form the lysogenic cycle to the lytic cylcle.
• Lysis genes which were repressed during lysogeny are activated, allowing the lambda phage genome to be excised from the bacterial chromosome to give rise to active phages.

Upon exiting the lysogenic cycle, step 3-5 of the lytic cycle resumes.

Question 24

What about enveloped animal viruses

Answer 24

They can infect humans

• Many groups have membranous envelope surrounding their nucleocapsids
  
  • envelopes are derived from host cell membranes but contain viral membrane proteins and glycoproteins as well
    
    • These viral proteins that are involved in virion binding to hot cell receoptors are often formed on the surface of the envelope.

Question 25

Specific

Question 26

How is the influenza viral genome inherited

Answer 26

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 the synthesis of viral protein.
• 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.

Question 27

Describe steps 1 and 2 of the reproductive cycle of the influenza virus

Answer 27

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

Question 28

Describe step 3 of the reproductive cycle of the influenza virus

Answer 28

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 via vesivles which fuses with host cell membrane

Question 29

Describe step 4 of the reproductive cycle of the influenza virus

Answer 29

• 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

Question 30

Describe step 5 of the reproductive cycle of the influenza virus

Answer 30

• The virus is finally released from the host cell by budding (NOT exocytosis), 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 the host cell with the viriopn 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
• Neuramidase (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 the infection to continue

Question 31

Describe the specific HIV structural features

Question 32

Describe Steps 1 and 2 of the reproductive cycle of HIV

Answer 32

Step 1: Adsorption/ / Attachment

• Glycoprotein gp120 on the surface of the HV binds to the CD4 receptor, a cell-surface receptor found on T helper cells and macrophages of the host immune system

Step 2 : Penetration

• Upon binding to CD4, gp120 undergoes a conformational change, allowing it to bind to a co-receprot known as CXCR4 on the surface of the 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

Question 33

Describe Step 3’s latent phase of the reproductive cycle of HIV

Answer 33

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 molecules 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

Question 34

Describe the steps after the latent phase

Answer 34

(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

(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 capsomere protens as well as glycoproteins
• Viral surface glycoproteins are synthesised by rER-bound ribosomes and transported to Glogi apparatus for glycosylation and then incorporated into the host cell membrane via vesicles which fuses with the host cell membrane

Question 35

Describe Step 4 of the reproductive cycle of HIV

Answer 35

• 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 moleucles associated with reverse transcriptase and enzymes like integrase and protease are surrounded by assembled capsid

Question 36

Describe Step 5 of the reproductive cycle of HIV

Answer 36

• 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.