chapter 11: genetics of viruses

Question 1

what is the cell theory?

Answer 1

• cells are the smallest unit of life
• all cells come from pre-exosting cells
• all living organisms are composed of cells

Question 2

why are viruses considered living organisms?

Answer 2

• all viruses have a common heriditary molecule (DNA or RNA) that can result in the production of polypeptides
• viruses are able to replicate to pass on genes from one viral generation to the next
• some viruses contain viral enzymes which may be used in their reproductive cycles
• viruses are also able to evolve

Question 3

why are viruses considered non-living organisms?

Answer 3

• viruses are unable to replicate indepedently outside the host cell
• it is metabolically inactive when outside its host cell
• viruses are acellular and challenge the cell theory

Question 4

obligate parasites

what is a feature that account for viruses being obligate parasites?
(nucleic acid)

Answer 4

they only contain one type of nucleic acid as genome
- either DNA or RNA but not both
- However, most viruses need bothe RNA and DNA like prokaryotes and eukaryotes
- DNA is needed for the replication of genome
- and RNA is needed for translation for protein synthesis
- hence, viruses use their host’s cell machinery to synthesise both types of nucleic acids

Question 5

obligate parasites

what is another feature that account for viruses being obligate parasites?
(no enzymes)

Answer 5

• viruses are unable to synthesise essentaial molecules like ATP
• so they use host cell’s raw materials or metabolic machinery to synthesise them:
• ATP
• amino acids, nucleotides
• enzymes involved in protein synthesis ( aminoacyl tRNA synthesase, DNA polymeras, RNA polymerase and ribosomes

Question 6

why are viruses parasitic

Answer 6

1. they take over the host cell’s metabolic machinery to synthesise and assemble new viral componenet to produce progeny viruses
   - this disrupts the host cell aciticities upon infecting host cell
   - may cause death of host cell upon release of progeny virus after infection
   - therefore some viruses cause diseases
2. exhibit specific host range
   - each type of virus infects only a limited variety of hosts, though they can increase host range via antigenic drift and shift
   - antigenic drift: small mutations in a virus’s surface proteins can help it evade immune responses, potentially allowing virus to infect new hosts, expanding its host range
   - antigenic shift: when two different strains of a virus combine, the resulting new subtype may have the ability to infet a broader range of hosts, significantly increasing the virus’s host range
3. exhibit viral specificity
   - each type of virus infects a limited variety of cells within the multicellular host as a consequence of virus binding to specific cell surface receptors molecules found on only certain type of cells

Question 7

comparing viruses and living microorganisms

compare the nucleic acid type.

Answer 7

viruses: DNA or RNA
living organisms: both DNA and RNA

Question 8

comparing viruses and living microorganisms

compare the outer covering

Answer 8

viruses:
- a protein coat called capsid
- some with envelope

living microorganisms:
- membrane
- cell wall

Question 9

basic structures of viruses

what is the nucleic acid genome?

Answer 9

• it is either DNA or RNA
• determines whether viruses are divided into RNA or DNA viruses

nucleic acid can be:
1. linear, circular or segmented

2. single stranded or double stranded
3. for ss RNA genomes, they can be positive sense or negative sense
   - positive sense ss RNA can act directly as mRNA for protein translation
   - negative sense ssRNA is complemetary to positive sense RNA
   - negative sense cannot be translated directly, it needs to be transcribed into a positive sense

Question 10

basic structures of viruses

what are capsid proteins?
(what is it composed of?)
( the arrangement)
(the function)

Answer 10

• they are composed of individual protien subunits called capsomeres
• it is arranged in a precise and repetive pattern around the nucleic acid genome

function:
- the capsid protein determines the specific shape of the virus, together with the envelope in enveloped viruses
- provides the only protection for the nucleic acid genome in non-enveloped viruses
- for some viruses, the capsid has glycoprotein for attachment to host cell’s receptors for entry

Question 11

basic structures of viruses

what does the envelope consist of?

Answer 11

• a typical phospholipid bilayer membrane outside capsids in enveloped viruses
• the envelope is connected to the capsid by a layer of matrix proteins

Question 12

how is the envelope formed?

Answer 12

• as the virus buds, the host cell surface membrane surrounds the nucleocapsid and other proteins encoded by the virus forming the envelope
• as the envelope is acquired from the cell surface membrane of the infected host cell, the envelope consists of the phospholipids, glycoproteins and cholesterol from the host cell
• for some viruses, the envelope also contains glycoproteins encoded by virus genome which are synthesised and then embedded on host cell surface membrane
• these glycoproteins are important for the attachment of the virus to specific host cells

Question 13

what does lysozyme found in bacteriophage do?

Answer 13

1. lysozyme in bacteriophage:
   - found in the base plate of bacteriophages to degrade a portion of the bacterial cell wall and membrane to allow the bacteriophage genome to enter the bacterial cell
   - produced in large amounts in the later stages of lytic cycle, causing lysis of the host cell and release of bacteriophages

Question 14

what does nucleic acid polymerases do?

Answer 14

• RNA viruses like HIV and influenza viruses must either carry the enzyme or have the genes coding for these enzymes as part of their genome
• because eukaryotic host cells do not have the enzymes to copy viral RNA genomes
• (RNA-dependent) RNA polymerase in -ve sense RNA viruses to act as a template during transcription to replicate viral RNA and to make a complementary +ve snese mRNA for translation by host ribosomes to make viral proteins
• reverse transcriptase in RNA viruses to synthesise complementary DNA from RNA genome template for isnertion into the human host by DNA integrase

Question 15

what are the three shapes that the capsid can have?

Answer 15

• helical
• multifaceted
• complex

Question 16

what are the two mechanisms that bacteriophages can reproduce by? and what are the phages that are reproduced by these cycles?

Answer 16

1. the lytic cycle
2. they lysogenic cycle

• the phage that reproduces only by a lytic cycle is known as a virulent phage, eg. T4 bacteriophage
• a phage that reproduces by the lytic cycle and lysogenic cycle is known as a temperate phage

Question 17

what is the structure of a T4 bacteriophage and what kind of cycle does it undergo?

Answer 17

the T4 phage has 2 distinct regions: head and tail
- head: the head is a complex icosahedral capsid enclosing a linear double-stranded DNA genome
- tail: the tails is attached to the head and it consists of a tail core surrounded by a tail sheath
- the tail core protein has a hollow core for the passage of nucleic acid during infection
- at the end is the base plate with long tail fibres and baseplate pins

host: Escheria coli bacteria

the T4 bacteriophage is a virulent phage that only undergoes the lytic cycle

Question 18

what are the five basic steps to produce more viruses?

Answer 18

1. adsorption/ attachment
2. entry/ penetration
3. synthesis
4. assembly and packing
5. release

Question 19

stages of the lytic cycle:

what happens during adsorption/ attachment?

Answer 19

• attachment sites on the tail fibre of T4 phage bind to complementary surface receptor sites on host bacterium cell membrane

Question 20

stages of the lytic cycle:

what happens during entre/ penetration?

Answer 20

• the tail fibres bend to anchor baseplate pins which attach irreversibly to the bacterial cell surface for infection to proceed
• lysozyme in base plate released to degrade a portion of the bacterial peptidoglycan cell wall and membrane
• the tail sheath that surround the core contracts
• the tail core protein is driven through the wall to the membrane, puncturing it as the phage dsDNA is injected through the core towards bacterial inner membrane
• pilot protein helps phage DNA to cross inner membrane and phage DNA enters bacteria cytosol
• the empty capsid is left outside

Question 21

stages of the lytic cycle:

what happens during synthesis?

Answer 21

• the T4 phage DNA codes for an enzyme endonuclease, that hydrolyses the bacterial DNA
• the host’s metabolic machinery (ribosomes, DNA polymerase, RNA polymerase and raw materials like amino acids, ATP, DNA and nucelotides) are then directed towards:
• transcription of genes on phage DNA followed by translation of mRNA to synthesise phage proteins like
  > enzymes, structural components
• replication of phage DNA t usign original phage DNA molecules as template

Question 22

stages of the lytic cycle:

what happens during assembly and packing?

Answer 22

• new phages are assembled to form new phage heads, tails and tail fibres
• the phage dsDNA is packaged inside the capsid as the head forms

Question 23

stages of the lytic cycle:

what happens during release?

Answer 23

• lysozyme breaks down the bacterial peptidoglycan cell wall
• with the cell wall damaged, entry of water into the cell by osmosis causes the cell to swell and burst
• 100-200 phage particles are relased upon host cell lysis

Question 24

what is the structure of the lambda (λ) bacteriophage and what type of cycle does it undergo?

Answer 24

head: similar to T4 phage, the head is a complex icosahedral capsid enclosing a linear dsDNA genome
tail: the tail core protein is surrounded by a (non-contractile) tail sheath
> there is only one tail fibre at the end of the tail

host: escheria coli bacteria

• the lambda λ bacteriophage is a temperate phage which undergoes the lysogenic cycle and ends in the lytic cycle
• upon entering the bacteria cell, the lambda DNA integrates into the bacterial chromosomes as a prophage

Question 25

what are the five stages of the lambda lysogenic cycle?

Answer 25

1. adsorption/ attachment
2. entry/ penetration
3. integration
4. prophage replication
5. prophage spontaneous induction

Question 25

stages of the lambda λ lysogenic cycle:
1. what happens during adsorption?

Answer 25

• attachment site on the tail fibre of lambda phage binds to complementary surface receptor sites

Question 26

stages of the lambda λ lysogenic cycle:
3. what happens during integration?

Answer 26

• lambda ds linear DNA circularises ( to prevent it from being degraded by the host exonuclease) and is integrated into a specific site on the bacterial chromosome
• at this stage the phage genome is known as a prophage

Question 26

stages of the lambda λ lysogenic cycle:
2. what happens during penetration?

Answer 26

• the phage dsDNA enters bacterial cytosol and the empty capsid is left outside
• no injection of bacterial genome> because tail sheath is non-contractile

Question 27

stages of the lambda λ lysogenic cycle:
4. what happens during prophage replication?

Answer 27

• a prophage gene codes for a repressor protein (lambda repressor) that blocks transcription of most other prophage genes, ensuring that the rest of the prophage remains transcriptionally silent in the bacterium
• each time the host cell divides via binary fission, it replicates the λ DNA along with its own bacteria DNA and passes copies of the λ DNA to daughter cells
• thus, a single infected cell can give rise to large population of bacteria carrying the virus in prophage form.
• this enables the viruses to propagate/ reproduce/ replicate without killing the host cells on which they depend on

Question 30

stages of the λ cycle:

5. prophage spontaneous induction?

Answer 30

• upon detection of host cell damage or stress
  ( due to factors like starvation, radiation, and presence of poisons such as antibiotics)
• the prophage is induced to exit the lysogenic cycle
• the lambda repressor protein may be broken down resulting in expression of the repressed phage genes
• the prophage is excised from the bacterial chromosome and enters the lytic cycle
• the viral DNA directs the host cell metabolic machinery to generate active phases that eventually lyse their host cell metabolic

Question 31

what is the structure of an influenza virus?

Answer 31

• it is an enveloped virus that is usually spherical or ovoid in shape
• with a lipid membrane derived from the host cell’s plasma membrane

the two varieties of glycoproteins that are embedded in the envelope:
- haemagglutinin (HA or H)-80%: a glycoprotein that facilitates attachment of virus to host cell’s plasma membrane membrane by binding to specific receptors containing salic acid
- neuraminidse: (NA or N)-20%: an enzyme that facilitates the release of newly formed virus from the infected host cell’s plasma membrane by cleaving the receptors containing sialic acid

Question 32

what is the structure of an influenza virus?

Answer 32

• it is an enveloped virus that is usually spherical or ovoid in shape
• with a lipid membrane derived from the host cell’s plasma membrane

the two varieties of glycoproteins that are embedded in the envelope:
- haemagglutinin (HA or H)-80%: a glycoprotein that facilitates attachment of virus to host cell’s plasma membrane membrane by binding to specific receptors containing salic acid
- neuraminidse: (NA or N)-20%: an enzyme that facilitates the release of newly formed virus from the infected host cell’s plasma membrane by cleaving the receptors containing sialic acid

Question 33

what is the genome of an influenza virus?

Answer 33

the influenza genome comprises 8 distinct linear segments of negative sense ssRNA, each wrapped in a helical capsid

Question 34

what is an enzyme in the influenza virus and what is it used for?

Answer 34

• an RNA dependent RNA polymerase is also carried by the virus because it is not present in the host cell
• the enzyme is needed to make a positive sense RNA that is used to replicate negative sense viral RNA and also acts as mRNA to make viral proteins during translation

Question 35

what are the stages of the influenza reproductive cycle?

Answer 35

1. adsorption/ attachment
2. penetration and uncoating
3. synthesis
4. assembly
5. release

Question 36

stages of the influenza reproductive cycle:
stage 1: adsorption/ attachment

Answer 36

haemagglutinin on the viral envelope binds to specific receptors containing sialic acid on the surface of a suitable host cell

Question 37

stages of the influenza reproductive cycle:
stage 2: penetration and uncoating

Answer 37

• the virus is engulfed by receptor-mediated endocytosis as the host cell membrane invaginates, fuses and pinches off
• virus is enclosed in an endocytic vesicle
• the viral envelope fuses with the membrane of the endocytic vesicle, releasing the nucleocapsid into the cytoplasm

uncoating:
- the capsid is then degraded by cellular enzymes, releasing the following into the cytoplasm:
- 8 -ve sense ssRNA genome segments
- viral RNA dependent RNA polymerase

the viral RNA polymerase and -ve sense ssRNA are then transported into the cell nucleus