viruses

Question 1

how do viruses challenge the cell theory?

Answer 1

1 - cells are the smallest unit of life

• viruses lack the necessary molecular machinery to conduct many of the biochemical reactions a normal cell would need
• but viruses contain the genetic material necessary to form the next generation and can evolve in response to the environment

2 - all cells come from pre-existing cells

• viruses can replicate but rely on host cells to provide the energy and materials needed for replicating their genomes and synthesising their proteins
• viruses cannot replicate without entering a suitable host cell

3 - all living organisms are composed of cells

• viruses are acellular and do not have protoplasm or organelles so they are not considered cells
• when in the extracellular virion state, viruses are metabolically inert and don’t carry out respiration or biosynthesis

Question 2

what structures are present in all viruses?

Answer 2

• genome (comprising DNA/RNA)
• capsid (protein coat) comprising protein subunits, capsomeres

the following structures are NOT present in all viruses
- envelope comprising phospholipids from host cell
- enzymes

Question 3

describe the viral genome

Answer 3

• viral genomes contain either DNA or RNA, but not both
• viral genomes may be single-stranded, double-stranded, linear or circular
• viral genomes are small, typically encoding functions that the virus cannot adapt from the host
• all viral genomes contain genes coding for essential proteins like respiratory proteins (regulate the action of host genes) and structural proteins (like viral capsid proteins)

Question 4

describe the capsid (protein coat)

Answer 4

• the capsid encloses the viral genome
• each capsid is constructed from identical protein subunit called capsomeres
• capsomeres are made up of capsid proteins

Question 5

describe the viral envelope (present in enveloped viruses only)

Answer 5

• the envelope is derived from host cells: when viruses are released from the host cell by budding, they take with them the host’s cell surface membrane (phospholipid bilayer) and insert proteins of viral origins into the membrane
• the proteins include viral glycoproteins that 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 that are not surrounded by the lipid membrane envelope are referred to as naked or non-enveloped viruses

Question 6

what are bacteriophages?

Answer 6

bacteriophages are DNA viruses that infect bacteria

Question 7

what are 2 examples of bacteriophages?

Answer 7

1. T4 phage
2. lambda phage

Question 8

what are structural features of the T4 phage?

Answer 8

genome - linear double-stranded DNA
capsid - capsomeres surrounds the nucleic acid, contained in the phage’s head
tail - consisting of tail sheath, tail fibres and base plate.
tail fibres - allows phage to adsorb onto surface of bacterial cell
tail sheath - surrounds a central tube and enables central tube to pass through host cell wall and membrane
base plate - comes into contact with host cell surface, allowing DNA to enter host cell

Question 9

what are structural features of the lambda phage?

Answer 9

genome - linear double-stranded DNA
capsid - capsomeres surrounds the nucleic acid, contained in the head of the phage
head - the 5’ terminus of each DNA strand is a single-stranded tail that is 12 nucleotides long, which is important in prophage formation
single tail fibre - allows phage to adsorb onto the surface of the bacterial cell by binding to the specific receptor found on the cell surface

lambda phages’ tails are NOT CONTRACTILE and serves to deliver the viral DNA to the cell membrane

Question 10

define lytic cycle and lysogenic cycle

Answer 10

lytic cycle: a phage reproductive cycle that finally results in the death of the host cell

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

VIRULENT phages (eg T4 phage) reproduce through the lytic cycle
TEMPERATE phages (eg lambda phage) reproduce through the lysogenic cycle)

Question 11

true or false: the T4 phage reproduces through the lytic cycle

Answer 11

TRUE

T4 phage, a virulent phage, reproduces using the LYTIC CYCLE

Question 12

lytic or lysogenic?

which reproductive cycle does the lambda phage use to reproduce?

Answer 12

lysogenic.

lambda phage, a temperate phage, reproduces through the lysogenic cycle.

Question 13

APSAR

what are the 5 step of the lytic cycle?

Answer 13

1. adsorption
2. penetration
3. synthesis (of phage proteins) & replication (of phage nucleic acid)
4. assembly
5. release

Question 14

using the T4 phage as an example, describe, in detail, the lytic cycle.

Answer 14

step 1: adsorption

• T4 phage’s multiple tail fibres attach to specific receptor sites on the surface of a bacterial host cell
• the base plate settles down on the host cell surface

step 2: penetration

• conformational changes occur in the tail sheath, causing it to contract and its 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

step 3: synthesis & replication

• after phage DNA is injected into the host cell, synthesis of host DNA, RNA and proteins is halted. the host cell machinery is taken over by the virus for synthesis of viral nucleic acids and viral proteins
• host DNA is degraded into nucleotides, providing raw materials for T4 phage DNA replication by host DNA polymerase
• T4 phage mRNAs are synthesised by host RNA polymerases through transcription
• T4 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.

step 4: assembly

• viral proteins are assembled to form phage heads, tails and tail fibres
• these components are assembled into the complete bacteriophage

step 5: release

• the T4 phages LYSE the host cell using the lysozyme, which digests the bacterial cell wall
• water enters the cell by osmosis, causing it to swell and burst

1. lysozyme (an enzyme) makes a small hole in the bacterial cell wall, allowing the viral nucleic acid to enter
2. proteins translated from T4 phage mRNAs include enzymes for viral replication and inhibitory factors that stop host cell RNA and protein synthesis

Question 15

APPS

what are the 4 steps of the lysogenic cycle?

Answer 15

1. adsorption
2. penetration
3. prophage formation
4. switch to lytic cycle

Question 16

using the lambda phage as an example, describe, in detail, the lysogenic cycle.

Answer 16

step 1: adsorption

• the single tail fibre of the lambda phage attaches to a specific receptor site on the surface of a bacterial host cell
• the base plate settles down on the host’s cell surface

step 2: penetration

• DNA is extruded from the head, through the tail tube and injected into the host cell, passing through the bacterial cell wall and cell membrane
• the capsid is left on the outside of the bacterial cell wall

step 3: prophage formation

• the lambda phage genome circularises & inserts itself into a specific site on the bacterial chromosome (prophage insertion site) by genetic recombination. there is NO LOSS of host DNA.
• the integrated lambda phage is known as a prophage
• in the integrated state, the viral DNA is replicated along with the chromosome each time the host cell divides, and is passed on to generations of the host daughter cells
• a single infected cell can soon give rise to a large population of bacteria carrying the viral DNA in prophage form

step 4: switch to lytic cycle

• when there is an environmental trigger (eg UV radiation) the virus switches from the lysogenic cycle to the lytic cycle
• lysis genes which were repressed during lysogeny are activated, allowing the lambda phage genome to be excised from the bacterial chromosome, giving rise to new active phages
• steps 3-5 (synthesis and replication, assembly, release) of the lytic cycle resumes

lambda phages’ tails are NOT CONTRACTILE and serves todeliver the viral DNA to the cell membrane

Question 17

what are enveloped animal viruses and state two examples of it.

Answer 17

enveloped animal viruses are viruses with a membranous envelope surrounding their nucleocapsids.
examples of enveloped animal viruses include the influenza virus and human immunodeficiency virus (HIV)

Question 18

what is the influenza virus?

Answer 18

• the influenza virus is an enveloped virus in which the viral negative (-) sense single-stranded RNA is present in the virion in 8 separate pieces.
• the negative (-) sense viral RNAs must first be transcribed to positive (+) sense single-stranded RNA which serves as mRNA for translation
• (-) sense single-stranded RNA is subsequently synthesised from (+) sense single-stranded RNA for use as genomic material and packaged with the viral proteins to form new virions

Question 19

what are structural features of the influenza virus?

Answer 19

genome - 8 different segments of negative (-) sense single-strand RNA. (-) sense RNA must be transcribed to complementary (+) sense RNA before it can be used for translation of viral proteins
capsid - nucleoprotein (NP) associate with the viral nucleic acid to form nucleocapsid
membrane/viral envelope - phospholipid bilayer obtained from host cell surface membrane upon budding
surface glycoproteins - haemagglutinin (HA) and neuraminidase (NA)
protein envelope - matrix protein (M1 & M2) forms second layer of envelope, enclosing the nucleocapsid
enzymes - PB1, PB2 & PA forms RNA-dependent RNA polymerase (replicase), NS1 regulates viral replication mechanisms

details of protein envelope & enzymes dn memo

haemagglutinin - binds to sialic acid containing receptors, attaching virus to receptor on host cell membrane
neuraminidase - hydrolyses mucus, allowing virus to entercells of the respiratory tract & facilitates budding by cleaving sialic acid containing receptors

Question 20

APSAR

what are the 5 steps of the reproductive cycle of influenza virus?

Answer 20

1. adsorption
2. penetration
3. synthesis (of viral components) and replication (of viral genome)
4. assembly of new virion
5. release

Question 21

describe, in detail, the reproductive cycle of influenza virus

Answer 21

step 1: adsorption

• haemagglutinin (HA) molecules on the viral membrane binds to sialic acid containing receptors on the membrane of the host cell (epithelial cells of the respiratory tract)
• (HA molecules have a complementary 3D shape with the receptor)

step 2: penetration

• the virus is taken in by receptor-mediated endocytosis, forming an endocytic vesicle within the host cell, aka endosome, with the influenza virus attached to its inner surface
• fusion of the endosome with an acidic lysosome lowers the pH of the vesicle, triggering conformational changes in the HA protein, causing the viral envelope and endosome membranes to fuse, releasing the 8 viral segments of the influenza genome directly into the host cell cytoplasm.
• viral RNAs are transported into the nucleus

step 3: synthesis & replication

• viral replicase (incuded as part of the virion) copies the (-) sense RNA template into complementary (+) sense RNAs for synthesis of viral nucleic acids and viral proteins.
• (+) sense RNAs are used as templates for synthesis of full length (-) sense strand viral RNAs by viral replicase. the (-) sense viral RNAs can be packaged into new viral particles as their nucleic acid
• (+) sense RNAs are used as mRNA which are translated in the cytoplasms by host ribosomes, synthesising enzymes, matrix proteins capsomere proteins and glycoproteins.
• free ribosomes synthesise enyzmes, matrix and capsomeres as they are ultimately folded into final conformation in the cytoplasm and packaged into the new virion. rER-bound ribosomes synthesise viral transmembrane surface glycoproteins, which are transported to the golgi apparatus for glycosylation before being incorporated into the host cell membrane via a vesicle which fuses with the host cell membrane

step 4: assembly

• 8 (-) sense viral RNAs associate with nucleoprotein (NP), and enzymes (eg viral replicase) are packaged, completely assembling viral particle.
• the glycoprotein studded membran envelope is acquired during the release of the virus

step 5: release

• the virus is released from the host cell by budding, acquiring the host cell’s lipid bilayer as the virus’ envelope
• the viral membrane containing HA, NA and M2 (matrix protein) buds off from the host cell with the virion components
• because HA is present on the viral envelope and sialic-containing cellular receptors are on the host cell’s membrane, budding brings the virus and host cell together, resulting in the new viral particle remaining attached to the host cell
• neuraminidase (NA), helps release the virus by cleaving sialic acid residues on the cellular receptor that binded the newly formed virions to the cell
• this releases the virions, allowing infection to continue

virion: new virus that is synthesised

Question 22

what is human immunodeficiency virus (HIV)?

Answer 22

HIV (human immunodeficiency virus) is a retrovirus that causes AIDS (acquired immunodeficiency syndrome)

a retrovirus is an enveloped RNA virus which replicates by means of a DNA intermediate synthesised by the enzyme reverse transcriptase

Question 23

what are structural features of HIV?

Answer 23

genome - 2 identical single-stranded RNA. the single-stranded RNA is reverse transcribed to produce DNA for integration into the host genome. the DNA is then used for the transcription of viral mRNA which is translated into viral proteins and for use as the viral genome in the progeny virus
capsid - surrounds the nucleic acid
viral envelope - is the phospholipid bilayer obtained from the host cell upon budding
surface glycoproteins - gp120 (binds to CD4 receptors on WBCs like macrophages & T helper cells) and gp41 (helps HIV envelope & host cell membrane fuse)
protein coat - made of matrix protein, forming the 2nd layer of the protein envelope and enclosing the capsid
enzymes - reverse transcriptase (reverse transcribes RNA into DNA), integrase (facilitates incorporation of double-stranded DNA into host cell’s genome) and protease (cleaves viral polypeptide into functional proteins)

Question 24

APSAR

what are the 5 steps of the reproductive cycle of HIV?

Answer 24

1. adsorption/attachment
2. penetration
3. synthesis (of viral components) & replication (of viral genome)
4. assembly of new virions
5. release

Question 25

describe, in detail, the reproductive cycle of HIV

Answer 25

***step 1: adsorption/attachment*** - glycoprotein **gp120** on the surface of HIV binds to the **CD4 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-receptor**, CXCR4 on T helper cells and CCR5 on macrophages - **gp41** pulls the virus **closer to the host cell**. the co-receptor 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 ***step 3: synthesis & replication*** - **reverse transcriptase** 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 syntesised 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**, entering the host nucleus - **integrase** catalyses the **integration** of the **viral DNA** into the genetic material of the **host** - the newly integrated viral DNA is called a **provirus**, which remains latent (inactive) until the host cell is stimulated in an immune response - when the host cell receives a signal, the **proviral DNA** is **transcribed** by **host RNA polymerase** into **RNA** - 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 include enzymes, matrix & capsomeres proteins, glycoproteins - viral surface glycoproteins are synthesised by rER-bound ribosomes and transported to the golgi apparatus for glycosylation and then **incorporated into the host cell membrane** via vesicles which fuses with the host cell membrane ***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** associate with **reverse transcriptase**, and enzymes like **integrase** and **protease** are surrounded by assembled capsid. ***step 5: release*** - the **glycoprotein studded membrane envelope** is acquired during the **release of the virus** - the newly assembled immature HIV **buds off** from the host cell, surrounded by the **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

Question 26

what are the 3 mechanisms for variation in viral genomes?

Answer 26

1 - mutation - **no proofreading mechanisms** in host cell → RNA viruses have **higher rates of mutation** as errors are not corrected. - enzymes like reverse transcriptase (HIV) also has **very low fidelity** → **regularly introduce errors** into the genome - responsible for **antigenic drift** 2 - recombination - viruses may undergo **recombination** with the genome of another strain → **exchange of genetic information** → **new combinations of alleles** 3 - reassortment - a host cell may be infected with 2 viral strains, introducing **two sets of genetic material** into the host cell → **different segments of the viral genome** may be packaged into the **progeny virus** when it is being formed → **sudden and drastic change** in the viral genome → **antigenic shift**

Question 27

what is an antigen?

Answer 27

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 antigenicity is the capacity of an antigen to induce an immune response in a host ## Footnote antigenic shift & antigenic drift results in the formation of new antigens, changing the antigenicity of the virus and are essential in mediating their ability to evade host defence mechanisms

Question 28

define antigenic shift

Answer 28

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 haemagglutinin** (and sometimes **new neuraminidase**) proteins in the viruses that infect humans. antigenic shift results in **new influenza A subtype** or a virus that has emerged from an **animal population** that is so differen from the same subtype in humans that most people **do not have immunity** to the new virus.

Question 29

using influenza as an example, describe the mechanism of antigenic shift

Answer 29

- antigenic shift arises when **different influenza A strains** infect a host and subsequently forms progeny viruses whose **genome is a new combination of RNA** from the different strains - the influenza virus, containing **8 single-stranded RNA** is susceptible to such **reassortment** as it can easily reshuffle its genome during the packaging of the **new virion** - different viruses of different origins may infect a pig, providing the opportunity for the viruses to **reassort**, forming a **new virus** which contains **different surfaces antigens** from both the avian and human influenza strain - forms viruses with **new combinations of haemagglutinin and neuraminidase** → new strain of influenza would not have been circulating in the population → **not likely be any immunity** against this novel strain, and the new virus is easily transmissible

Question 30

define antigenic drift

Answer 30

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

Question 31

describe the mechanism of antigenic drift.

Answer 31

antigenic drift arises when viruses undergo **continuous, subtle antigenic changes** due to **accumulation of mutations** to the haemagglutinin and/or neuraminidase genes factors that influence the rate of mutation of viral genomes: - as the influenza genome consists of 8 single-stranded RNA strands which **lack a complementary strand**, **mismatch repair cannot be carried out** - viral polymerases are **prone to errors** and will introduce mutations during DNA replications (as RNA polymerase **does not have proofreading ability**) - HIV encodes an average of 1 point mutation for every replication cycle as viral reverse transcriptase is **unable to correct nucleotide misincorporation errors** these mutations result in the production of surface proteins with **different 3D conformations**, resulting in antibodies no longer being complementary to them and **will not recognise and bind to them**

Question 32

compare the differences between antigenic shift and antigenic drift

Answer 32

***no. of viruses*** - antigenic shift: **2 or more** viral strains involved - antigenic drift: **only 1** viral strain involved ***mechanism for change*** - antigenic shift: **reshuffling of genome between different strains**, resulting in **dramatic alteration** of type of haemagglutinin or neuraminidase on progeny virus - antigenic drift: **accumulation of point mutations** in the gene of the surface antigen, resulting in **minor alteration** of 3D conformation of haemagglutinin or neuraminidase on progeny virus ***nature of change*** - antigenic shift: **abrupt & major** change in genome of virus - antigenic drift: **gradual accumulation of minor** point mutations in genome of virus ***rate of occurrence*** - antigenic shift: **occasionally** occurs, giving rise to **pandemics** - antigenic drift: **regularly** occurring, giving rise to **seasonal epidemics** ***effect of host immunity*** - antigenic shift: population has **no immunity** to novel combination of surface proteins, and **no drugs or vaccines** are present to treat the virus - antigenic drift: a proportion of the population may have **pre-existing immunity** to the modified surface proteins, and **anti-viral drugs and seasonal vaccines are available** to treat the virus ***cross-species transmission*** - antigenic shift: may result in a progeny virus which can **infect a new species** - antigenic drift: only infects individuals of the **same species**

Question 33

what are the effects of antigenic shift and antigenic drift?

Answer 33

1. **ANTIGENIC SHIFT & DRIFT.** viruses mutate & **change the antigens** on their surfaces → prevents **antibodies** from recognising them → allows viruses to **evade detection** by the host immune system. 2. **ANTIGENIC SHIFT & DRIFT.** vaccines would become ineffective as antibodies generated would be **unable to bind specifically** to the new surface antigen which has a new and different 3D conformation → virus can **evade the host's immune system** and continue its reproductive cycle. 3. **ANTIGENIC SHIFT.** major change in surface proteins causes a **large number of people** being susceptible to the new virus, causing a pandemic. **ANTIGENIC DRIFT.** gradual & minor change in surface proteins allows **some people to be unaffected** due to pre-existing immunity, causing a seasonal epidemic.