2.3 Viruses

Question 1

Animal viruses: Influenza: Genome

Answer 1

8 segments of single-stranded RNA
The RNA genome is a negative-strand
RNA is packaged with protein into a helical nucleoprotein form with 3 segments coding for 3 different polymerases that form the RNA dependent RNA polymerase which functions in both replication and transcription
the other 5 segments code for haemagglutinin [HA], neuraminidase [NA], nucleoprotein [NP], matrix protein M1 [M] and non-structural proteins [NS]

Question 2

Animal viruses: Influenza: Capsid

Answer 2

protein lining the inner side of the envelope

Question 3

Animal viruses: Influenza: Envelope

Answer 3

The influenza virion is an enveloped virus that derived its lipid bilayer from the plasma membrane of a host cell
HA and NA are embedded in the envelope
different types of HA and NA glycoproteins give rise to different strains of influenza virus

Question 4

Animal viruses: Influenza: Attachment

Answer 4

HA on influenza virus binds to sialic acid receptor on host cell membrane

Question 5

Animal viruses: Influenza: Penetration and uncoating

Answer 5

Influenza virus enters by endocytosis; the host plasma membrane invaginates and pinches off, placing the virus in an endocytic vesicle/ endosome
The vesicle fuses with a lysosome causing its pH to drop
low pH environment stimulates the viral envelope to fuse with lipid bilayer of the vesicle membrane and nucleocapsid is released into the cytoplasm
The capsid is degraded by cellular enzymes leaving behind the helical nucleoprotein which enters the nucleus of the cell

Question 6

Animal viruses: Influenza: replication

Answer 6

The viral genome (-) is used as a template to synthesise the viral mRNA/ (+) strand RNA catalysed by RNA dependent RNA polymerase
mRNA produced acts as template to synthesise new viral RNA genome
the mRNA strands then exit the nucleus into the cytosol and RER where they are translated into structural components such as glycoproteins to be incorporated into the viral envelope (at RER) and capsid proteins (in cytosol)

Question 7

Animal viruses: Influenza: Maturation

Answer 7

Viral glycoproteins are transported by the vesicles from the ER and are incorporated into the plasma membrane
Capsid proteins associate with these glycoproteins at the plasma membrane
The viral genome associates with proteins to form the helical nucleoprotein which interacts with the capsid proteins at the plasma membrane of the host cell
Interaction of the capsid with the nucleoprotein initiates the budding process

Question 8

Animal viruses: Influenza: Release by budding

Answer 8

Each new virus buds from the cell (evagination)
It acquires the host membrane with viral glycoproteins embedded
With enveloped viruses, host cell may or may not be lysed
The release is facilitated by neuraminidase which cleaves sialic acid from the cell surface and progeny virions, facilitating release from infected cells

Question 9

Animal viruses: HIV: Genome

Answer 9

2 copies of single-stranded RNA
(+) strands i.e. the viral genome
RNA is tightly bound to proteins; nucleocapsid proteins
HIV genome contains three major genes: 5’-gag-pol-env-3’ encoding major structural proteins as well as essential enzymes
gag: structural proteins (capsid, matrix, nucleocapsid protein)
pol: viral enzymes (reverse transcriptase, integrase, HIV protease)
env: glycoproteins gp120 and gp41

Question 10

Animal viruses: HIV: Capsid

Answer 10

The capsid is usually conical shaped and made of another type of proteins different from the nucleocapsid proteins
Within the capsid are 2 molecules of enzyme reverse transcriptase which transcribes RNA into DNA, integrase and protease
capsid + viral genome = virus core

Question 11

Animal viruses: HIV: Envelope

Answer 11

Glycoproteins gp120 and gp41 protrude through the envelope and have a specific conformation that allows the virus to bind to certain receptors on T4 helper cells

Question 12

Animal viruses: HIV: Attachment

Answer 12

gp120 on the surface of the viral particle interacts with the CD4 receptor on the target cell (T-lymphocytes and macrophages) with the help of a co-receptor

Question 13

Animal viruses: HIV: Penetration and uncoating

Answer 13

With the help of gp41, the viral envelope will fuse with the host cell membrane and the capsid is then released into the cell, leaving the envelope behind
The capsid and nucleocapsid protein are degraded, releasing viral enzymes and RNA into the cytoplasm

Question 14

Animal viruses: HIV: replication

Answer 14

Viral reverse transcriptase enzyme catalyses the conversion of viral RNA to DNA [Reverse transcriptase will first catalyse synthesis of a DNA strand complementary to the viral RNA strand to form a RNA-DNA hybrid]
RNA strand is degraded and second DNA strand complementary to the first is synthesised to form a double-stranded DNA molecule
Viral DNA enters the host cell nucleus where it is integrated into the genetic material of the host. It is now known as a provirus. The enzyme integrase catalyses this process. Once the viral DNA is integrated into the host genetic material, it may persist in its latent state for many years.
Activation of the host cell results in transcription of viral DNA into viral RNA which serves as the mRNA
mRNA exits the nucleus into the cytoplasm where it is translated into viral polyproteins
Envelope glycoproteins gp120 and gp41 are made in the ER and vesicles will transport them to the cell membrane
Viral RNA also forms the genetic material for the next geenration of viruses

Question 15

Animal viruses: HIV: Maturation

Answer 15

Polyproteins and HIV genomic RNA assemble at the inner surface of the plasma membrane of the host cell

Question 16

Animal viruses: HIV: Release

Answer 16

After assembly at the plasma membrane, the virus bus off/evaginates from the cell
The viral envelope is derived from the host cell membrane containing gp120 and gp41
Polyproteins will be cleaved into functional proteins by HIV protease
The functional proteins include structural proteins (matrix, capsid, nucleocapsid proteins) and viral enzymes (reverse transcriptase, integrase, HIV protease)
The virion is now considered matured and ready to infect another cell

Question 17

Define antigenic drift

Answer 17

A mechanism of variation by viruses that involves the accumulation of mutations in the genes encoding the surface glycoproteins of the virus. The resulting viruses have surface antigens or glycoproteins that have a different conformation from the previous virus strain

Question 18

How does antigenic drift lead to the increase in spread of viruses?

Answer 18

The new virus strain cannot be recognised by antibodies against previous strains making it easier for them to infect the host and spread throughout a partially immune population

Question 19

What leads to antigenic drift?

Answer 19

1. Lack of proof reading ability of RNA-dependent RNA. polymerase
2. Fast/ High rate of replication of the virus

Question 20

What virus does antigenic drift generally occur on? Briefly explain.

Answer 20

Influenza (A&B)
Sites recognised on haemagglutinin and neuraminidase proteins by host immune systems are under constant selective pressure
Antigenic drift allows for evasion of these host immune systems by small mutations in the haemagglutinin and neuraminidase genes that make the protein unrecognisable to pre-exisiting host immunity

Question 21

Define antigenic shift

Answer 21

A process whereby there is a sudden and major change in the surface antigens of a virus. The genetic change that enables a flue strain to jump from one animal species to another

Question 22

When does antigenic shift occur?

Answer 22

It occurs when two or more different strains of a virus, or strains of two or more different viruses, combine to form a new subtype having a mixture of the surface antigens of the two or more original strains

Question 23

Why does antigenic shift occur?

Answer 23

Antigenic shift occurs because the genome of the virus is segmented, allowing for major genetic changes of type by re-assortment of its segmented RNA genome

Question 24

How does antigenic shift lead to the increase in spread of viruses?

Answer 24

The human immune system has difficulty recognising the new influenza strain, most people do not have pre-existing antibody protection to these novel viruses
The new strain may further evolve to spread from person to person and this could cause the formation of a highly virulent virus and a flu pandemic may arise

Question 25

Compare Antigenic DRIFT and Antigenic SHIFT

Answer 25

minor antigenic change / major antigenic change
Formation of new strain of virus / formation of new sub-type
Only one virus involved / One or two viruses involved
Infect animals of the same species / May jump from one species to another
small mutation of RNA / large change in nucleotides of RNA
occurs as a result of accmulation of point mutation in the gene / occurs as a result of genome reassortment between different subtypes
usually responsible for epidemics / usually. responsible for pandemics

Question 26

Structure of viruses: Genome

Answer 26

Single/segmented, circular/linear molecules of nucleic acid that functions as the genetic material of the virus
Either DNA OR RNA, NEVER BOTH
nucleic acid can be single stranded or double stranded
The genome codes for the synthesis of viral components and viral enzymes for replication and assembly of a virion

Question 27

Structure of viruses: Capsid

Answer 27

Composed of protein subunits called capsomeres
The capsid serves to protect, attach and introduce the genome into host cells
Capsid +. viral nucleic acid = nucleocapsid

Question 28

Structure of viruses: Envelope

Answer 28

Composed of phsopholipids and glycoproteins that are arranged to form a lipid bilayer
For most viruses, it is derived from the host cell membranes by a process called budding; the envelope may come from the host cell’s nuclear, vacuolar or plasma membranes
Although the envelope is usually of host cell origin, the virus does incorporate proteins of its own, often appearing as glycoprotein spikes, into the envelope
Viruses that are composed of just the nucleocapsid are called naked viruses/ non-enveloped viruses

Question 29

Viral replication: Bacteriophages
What are bacteriophages?
What are the two main types of bacteriophages and what type of life cycle does each undergo?

Answer 29

Bacteriophages are viruses that only infect bacteria
The two primary types of bacteriophages are lytic and temperate phages
Lytic bacteriophages undergo the lytic life cycle; they lyse the host bacterium as a normal part of their life cycle
Temperate phages undergo the lysogenic life cycle; either replicate via the lytic life cycle or it can incorporate its DNA into the bacterium’s DNA and become a prophage

Question 30

Lytic cycle: T4 bacteriophage:

1. Attachment

Answer 30

Attachment sites on the tail fibres recognise and attach or adsorb to complementary receptor sites on the bacterial surface (The attachment is a chemical interaction in which weak bonds are formed between the attachment and receptor sites)

Question 31

What is viral specificity?

Answer 31

Specific strains of bacteriophages can only adsorb to specific strains of host bacteria

Question 32

Lytic cycle: T4 bacteriophage:

2. Penetration

Answer 32

The bacteriophage tail releases an enzyme, phage lysozyme that digests the bacterial cell wall, allowing molecules to be released. When these molecules reach the virus, they trigger a change in the shape of the base plate that initiates a contraction of the bacteriophage tail sheath , thrusting the hollow core tube through the cell wall
When the tip of the core reaches the plasma membrane, DNA from the bacteriophage is injected into the bactrial cell
The empty capsid remains outside the cell

Question 33

Lytic cycle: T4 bacteriophage:

3. Replication

Answer 33

bacteriophage DNA is transcribed to synthesise RNA using host RNA polymerase
Highly virulent phages produce early proteins that completely take control from the host cell
Enzymes coded by the phage genome takes over the host cell macromolecular synthesising machinery for its own use
The phage uses the host cell’s nucleotides and several of its own enzymes to synthesise many copies of phage DNA
Soon after, biosynthesis of viral proteins begin; it uses the bacterium’s metabolic machinery to synthesise phage enzymes and phage structural components

Question 34

Lytic cycle: T4 bacteriophage:

4. Maturation

Answer 34

bacteriophage DNA and capsid are assembled into a DNA-filled head
The head, tail and tail fibres are then assembled independently and joined with each other: Tail fibres join with tail followed by DNA-filled head attaching to the tail

Question 35

Lytic cycle: T4 bacteriophage:

5. Release

Answer 35

Lysozyme, coded for by a phage gene, is synthesised within the cell and causes the bacterial cell wall to break down and the newly produced bacteriophjages are released from the host cell

Question 36

Lytic/ Lysogenic cycle: Lambda bacteriophage
[Lytic attachment and penetration, Maturation and Release]
3. Replication

Answer 36

The originally linear phage DNA forms a circle;
the circular DNA can multiply and be transcribed leading to the production of new phage and to cell lysis [Lytic]
OR
Circular DNA can intergate into and become part of the circular bacterial DNA [Lysogenic]
Inserted phage is called a prophage
Most of prophage genes are repressed by repressor proteins produced by phage genes, stopping transcription of all other phage genes
prophage DNA remains latent in host cell chromosomes

Question 37

Lysogenic cycle:

Spontaneous induction

Answer 37

Induction occurs spontaneously but its frequency is enhanced by irradiation with UV light/ agents that damage DNA;
It activates the cellular proteases
Repressor protein is destroyed by increased protease activity
Prophage is no longer repressed but is excised and enters the LYTIC cycle