viruses

Question 1

what are bacteriophages?

Answer 1

bacteriophages are non-enveloped viruses that infect bacteria

Question 2

what are the 2 ways that bacteriophages can reproduce by? and name the type of bacteriophages for each way

Answer 2

bacteriophages can reproduce by
1. lytic cycle only - lytic phage (eg. T4 phage)
2. lytic and lysogenic cycle - lysogenic phage (eg. lambda phage)

Question 3

describe an example of a lytic phage.

Answer 3

an example of a lytic phage is T4 phage, which infects bacterium E.coli
T4 phage consists of a double-stranded DNA genome packed in a icosahedral capsid head attached to a tail sheath, which is connected to tail fibers and a base plate.

Question 4

what are the stages in a lytic cycle?

Answer 4

APSAR

1. adsorption
2. penetration
3. synthesis of viral proteins and genome
4. assembly
5. release and reinfection

Question 5

describe what happens during adsorption in lytic cycle.

Answer 5

the attachment sites on tail fibers of T4 phage
recognise and bind to
specific receptor sites on cell wall of bacterium E.coli
by complementary shapes

Question 6

describe what happens during penetration in lytic cycle.

Answer 6

the base plate is in contact with the cell wall of the bacterium
lysozyme (viral enzyme) located at the base plate then degrades a small partition of the host bacterium cell wall and cell surface membrane
the tail sheath contracts, driving a hollow tube through the cell wall and plasma membrane into the bacterium cell
this injects DNA in the capsid head into the cytoplasm of the bacterium
the phage genome enters the bacterium, while the capsid protein remains outside the bacterium

Question 7

describe how the synthesis of viral genome and proteins occur during lytic cycle.

Answer 7

viral proteins:
- the viral DNA is then transcribed to form viral mRNA using host RNA polymerase
- viral mRNA is then translated to form viral proteins and enzymes using host ribosomes

viral genome:
- viral DNA also used as template to make new viral DNA genome by using
phage-encoded DNA polymerase or host DNA polymerase

Question 8

state 3 uses of the viral proteins and enzymes.

Answer 8

1. shut down host macromolecular synthesis
2. hydrolyse host DNA to reuse nucleotides to form new copies of phage DNA
3. direct host transcription and translation machinery to synthesise phage enzymes and phage structural components for assembly of new T4 phages

Question 9

describe what happens during assembly of lytic cycle.

Answer 9

the viral proteins self-assemble to form capsid head, tail sheath and tail fibers of new bacteriophages
phage genome is packaged into the capsid head
lysozyme is packaged into the base plate

Question 10

describe what happens during release and reinfection in lytic cycle.

Answer 10

phage-encoded lysozyme lyses the bacterium cell wall from the inside,
breaking down the bacterium peptidoglycan cell wall
water enters the bacterium by osmosis, causing it to burst, thus releasing mature viruses
new phages are then released and spread to nearby cells, infecting them and the lytic cycle repeats

Question 11

relate the structure of T4 phage to its function in the lytic cycle.

Answer 11

1. icosahedral capsid head - protect the viral DNA genome
2. DNA genome - template for DNA replication to form new copies of viral DNA genome + code for viral structural proteins and enzymes for assembly of new T4 phages
3. tail fibres - attachment sites that recognise and bind to specific receptors on bacterium cell wall
4. base plate - contain lysozyme that degrades a small portion of host bacterium cell surface membrane and cell wall to facilitate viral entry and subsequent release
5. tail sheath - can contract to allow piercing of cell wall and cell surface membrane by hollow tube and subsequent injection of viral genome into host cell

Question 12

describe an example of lysogenic phage.

Answer 12

an example of a lysogenic phage is a lambda phage, which infects bacterium E.coli
the lambda phage has a double-stranded DNA genome packed in a icosahedral capsid head attached to a tail sheath which is connected to only 1 tail fibre

Question 13

state the stages of lysogenic cycle.

Answer 13

APL
1. adsorption
2. penetration
3. latency

Question 14

describe adsorption during lysogenic cycle.

Answer 14

attachment sites on the tail fiber of lambda phage
recognises and binds to
specific receptor sites on the cell wall of host bacterium
via complementary shape

Question 15

describe penetration during lysogenic cycle.

Answer 15

lambda phage injects its double-stranded DNA genome into the cytoplasm of bacteria
(note that there is no contraction of tail sheath)

Question 16

describe latency during the lysogenic cycle.

Answer 16

within the host bacterium, DNA molecule is incorporated into a specific attachment site on the bacterial chromosome to form a prophage
one prophage gene codes for a repressor protein is expressed
the repressor protein prevents the transcription of the other prophage genes
the prophage is replicated together with the host DNA so that every daughter cell contains a prophage

Question 17

describe how the induction of the lytic cycle occurs from the lysogenic cycle.

Answer 17

when the host bacterium exhibits signs of stress, induction occurs
the viral repressor protein is destroyed by an activated bacterial enzyme
the prophage genes are then able to be expressed to form viral proteins, which excise the prophage from the bacterial genome and enter the lytic cycle

Question 18

describe what happens during the lytic cycle which occurs after the lysogenic cycle.

Answer 18

the synthesis of viral genome and proteins occurs
1. viral genome:
- the viral prophage is used as a template to make new viral DNA genome with the phage-encoded DNA polymerase or with the host DNA polymerase

2. viral proteins:
   - viral DNA is transcribed to form viral mRNA using host RNA polymerase
   - viral mRNA is translated to form viral proteins and enzymes using the host ribosomes

uses of viral proteins and enzymes same as in lytic cycle

Question 19

describe assembly, release and reinfection for lysogenic phage.

Answer 19

viral proteins self-assemble to form capsid head, tail and tail fibers of new bacteriophages
phage genome is packaged into the capsid head
when environmental conditions are unfavourable, the host bacterium is lysed and new phages are released, and can infect other nearby cells

Question 20

what happens when the lysogenic phage is
1. in favourable environmental conditions
2. in unfavourable environmental conditions

Answer 20

in favourable environmental conditions (eg. enriched nutrients, optimal temperature):
1. the lysogenic phage does not result in immediate host cell lysis
2. viral DNA incorporated into bacterium DNA at specific attachment site to form prophage
3. prophage undergoes passive replication with host genome during latency

in unfavourable environmental conditions:
1. lysogenic phage enters lytic cycle to reproduce large numbers of progeny viruses
2. lysis of bacterium

Question 21

how do bacteria defend themselves from bacteriophages?

Answer 21

1. natural selection favours bacterial mutants with receptors that are no longer recognised by a particular type of phage
2. when phage DNA successfully enters bacterium, it is identified as foreign and broken up by bacterial restriction enzymes (cellular enzymes). however, the bacterium’s DNA is methylated in a way that prevents attack by its own restriction enzymes

(note that natural selection also favours phage mutants that can bind to altered receptors or resistant to specific restriction enzymes)

conclusion: host bacteria- bacteriophage constantly evolving

Question 22

describe the structural components of influenza virus.

Answer 22

1. viral envelope
   - made of phospholipid bilayer from the host cell surface membrane
   - includes inserted viral proteins: glycoproteins (haemagglutinin HA, neuraminidase NA), membrane protein M2 proton channel)
2. helical viral nucleocapsid
   - contains viral RNA genome which is 8 single-stranded negative sense RNA segments
   - segments: different nucleotide sequence
   - negative sense RNA: template to make positive sense RNA + then translation to form viral proteins
   - each of 8 segments of viral RNA genome wrapped around capsid proteins to form helical nucleocapsid
3. viral RNA-dependent-RNA polymerases
   - heterotrimeric: each polymerase made of 3 different subunits: PB1, PB2, PA
4. M1 matrix protein
   - forms layer under viral envelope

Question 23

state the stages of reproductive cycle of influenza virus.

Answer 23

1. adsorption
2. entry
3. uncoating
4. replication
5. maturation
6. release

Question 24

describe adsorption in reproductive cycle of influenza virus.

Answer 24

influenza virus infects epithelial cells of respiratory tract (host cells)
haemagglutinin on viral envelope recognises and binds to sialic acid receptors on host cell surface membrane by complementary 3D conformation

Question 25

describe the process of entry during reproductive cycle of influenza virus.

Answer 25

the virus enters the host cell by receptor-mediated endocytosis, where the host plasma membrane invaginates and pinches off, placing the virus in a endosome (endocytic vesicle)

Question 26

describe uncoating in the reproductive cycle of influenza virus.

Answer 26

fusion of endosome with acidic lysosome lowers the pH of the endosome
the acidic condition in the endosome activates the M2 proton channel to allow protons into the virus, causing the inside of the influenza virus to be acidic
this causes the viral envelope (phospholipid bilayer with embedded proteins) to fuse with the membrane of the endosome (phospholipid bilayer of epithelial cells)
this causes the viral nucleocapsid to be released into the host cell cytoplasm
the viral capsid is then enzymatically removed, releasing the viral genome and transported to the nucleus of epithelial cell

Question 27

describe replication that occurs during the reproductive cycle of the influenza virus.

Answer 27

replication occurs in the nucleus of the epithelial cell
the viral RNA-dependent RNA polymerase uses the negative sense RNA as a template
1. to synthesise complementary positive sense RNA strand - which acts as a template to replicate more negative sense RNA viral genome
2. to synthesise complementary positive sense RNA strand - which migrates to cytoplasm and act as template for host cell ribosomes to synthesise viral proteins and enzymes during translation

Question 28

describe the maturation stage during the reproductive cycle of influenza virus.

Answer 28

newly synthesised viral envelope proteins (haemagglutinin, neuraminidase, M2 proton channel) transported through the rough endoplasmic reticulum and Golgi body and then inserted into the host cell surface membrane

newly synthesised viral enzymes (RNA-dependent-RNA polymerase) and viral nucleocapsid are assembled

newly formed viral nucleocapsid and viral enzymes migrate through cytoplasm to region near host cell surface membrane where glycoproteins and M2 proton channel have been inserted

Question 29

describe the release during reproductive cycle of influenza virus.

Answer 29

the host cell surface membrane where the glycoproteins and M2 proton channel are pinches off to form viral envelope by budding, enclosing the viral nucleocapsid and enzymes
the sialic acid is cleaved and removed from the envelope of the new viral particle by neuraminidase
this aids the release of new viral particles from each other, preventing agglutination of viruses, which can be caused by haemagglutinin molecules on a viral particle attaching to sialic acid on another viral particle if the sialic acid is not removed by neuraminidase
the new viral particles are then released and able to travel to infect other cells

Question 30

relate the structure of influenza virus to its function in the reproductive cycle.

Answer 30

1. viral envelope
   - haemagglutinin: recognise and bind to sialic acid receptors on host plasma membrane to facilitate adsorption to epithelial cells of respiratory tracts
   - neuraminidase: aid in cleavage and removal of sialic acid from viral particles, to prevent agglutination and allow release of viruses to infect other cells
2. RNA genome (negative sense RNA)
   - serves as a template to synthesise positive sense RNA (mRNA) which can be used to synthesise
   - more negative sense RNA for viral genome (RNA replication)
   - translation for more viral structural proteins and enzymes (translation)
3. RNA-dependent-RNA polymerase
   - uses positive sense RNA as template to make more negative sense RNA as viral genome (RNA replication)
   - uses negative sense RNA as template to make positive sense RNA (translation)

Question 31

state the 2 ways that genetic variability of influenza virus is possible.

Answer 31

1. antigenic drift
2. antigenic shift

Question 32

describe what antigenic drift is.

Answer 32

antigenic drift is the accumulation of mutations (eg. point mutation, insertion, deletion) which leads to step-by-step modification of virus proteins
mutations are caused by lack of proof-reading of viral RNA-dependent-RNA polymerase
this results in spontaneous mutations in the viral genome, especially in the mutation of genes coding for antigens haemagglutinin and neuraminidase, causing minor changes in 3D conformation of haemagglutinin and neuraminidase

haemagglutinin function: recognise and bind to sialic acid receptors on plasma membrane of epithelial cells of respiratory tract to facilitate adsorption of virus on cells
neuraminidase function: cleavage of sialic acid from viral envelope to prevent agglutination of influenza viruses

Question 33

describe what antigenic shift is.

Answer 33

antigenic shift is the exchange of whole genome segments during simultaneous infection of host cells by 2 different influenza viruses (parent virus), which results in variety of different hybrid viruses (progeny virus) with different characteristics from the parent viruses

1. two or more different strains of influenza virus infects the same host cell at the same time
2. reassortment of viral RNA segments = new combinations of RNA segments in new viral particles = new combinations of surface antigens haemagglutinin and neuraminidase
3. new virus strain

Question 34

describe the effects of antigenic shift and antigenic drift in influenza virus

Answer 34

1. unable to be detected by existing antibodies present in the immune system, and thus antibodies does not bind to viruses to stop viral replication/ unable to recruit macrophages to destroy virus
   - antigenic shift can cause pandemics
   - antigenic drift effects less severe than antigenic shift as viral strain remains the same after antigenic drift
2. difficult to provide a singular influenza vaccination that protects one for life because of genetic variability due to antigenic shift and antigenic drift thus need for annual vaccines
3. influenza strain can acquire the ability to infect other organisms (previously only infect animals now can infect humans - avian H1N1 can recognise and bind to human cells)

Question 35

describe the structure of human immunodeficiency virus (HIV).

Answer 35

1. viral envelope
   - made of phospholipid bilayer from host plasma membrane
   - inserted viral proteins (glycoproteins: Gp120, Gp41)
2. nucleocapsid
   - viral genome: 2 genetically identical single-stranded positive sense RNA strands
   - capsid protein: encloses viral genome + viral enzymes (viral reverse transcriptase [RNA-dependent DNA polymerase], viral integrase, viral protease) - RIP enzymes BAHAHHAH
3. matrix protein
   - forms layer under the viral envelope

Question 36

state the stages during the reproductive cycle of HIV.

Answer 36

1. adsorption
2. penetration
3. reverse transcription
4. integration
5. latency
6. activation and gene expression
7. maturation
8. assembly
9. budding and release

Question 37

describe what happens during adsorption in reproductive cycle of HIV.

Answer 37

Gp120 on HIV envelope recognises and binds to
1. CD4 receptor on T-helper cells and macrophages (host cells)
2. co-receptors
by complementary shapes

Question 38

describe what happens during penetration in reproductive cycle of HIV.

Answer 38

binding triggers a conformational change in Gp41 protein on HIV envelope
Gp41 pierces through the host cell membrane, causing fusion of HIV envelope (phospholipid bilayer with embedded proteins) and host (CD4 T cells) plasma membrane (phospholipid bilayer)
the viral nucleocapsid enters the host cell
the viral capsid is enzymatically removed and the viral genome and proteins are released

Question 39

describe what happens during reverse transcription in reproductive cycle of HIV.

Answer 39

HIV virus uses viral reverse transcriptase (RNA-dependent DNA polymerase), to catalyse synthesis of single-stranded complementary DNA strand using viral positive sense RNA as template
the reverse transcriptase then degrades the RNA, and catalyses the synthesis of the second DNA strand complementary to the first DNA strand, forming a double-stranded DNA which is formed by complementary base pairing through hydrogen bonding

Question 40

describe what happens during integration in reproductive cycle of HIV.

Answer 40

double-stranded viral DNA enters host cell nucleus
viral integrase catalyses the integration of the double-stranded viral DNA into the chromosomal DNA of host cell, forming a integrated viral DNA is then called a provirus

Question 41

describe what happens during latency in reproductive cycle of HIV.

Answer 41

the provirus may persist in latent state, replicating passively with the host cell DNA, resulting in production of more daughter cells with viral DNA without destroying host cell

Question 42

describe what happens during activation and gene expression during reproductive cycle of HIV.

Answer 42

when a appropriate signal is received, the provirus is then used as a template
the host RNA polymerase is used to transcribe the provirus DNA into viral RNA/ viral positive sense RNA which are:
1. new viral positive sense RNA genomes for new viral particles
2. alternately spliced to give mRNAs for translation into viral polyproteins using host ribosomes

Question 43

describe what happens during maturation of reproductive cycle of HIV.

Answer 43

long chains of viral polyproteins are transported through rough endoplasmic reticulum and Golgi body
viral polyproteins are then cleaved by HIV proteases and host proteases into smaller, individual functional proteins (eg. Gp41 and Gp 120) through proteolysis

Question 44

describe what happens to assembly during reproductive cycle of HIV.

Answer 44

synthesised viral envelope glycoproteins (Gp 120, Gp 41) translocates to and incorporated into the host plasma membrane
the viral genome and viral proteins then move towards the host plasma membrane where Gp 120 and Gp 41 are incorporated
the plasma membrane with the glycoproteins Gp120 and Gp41 then surround the newly synthesised viral RNA and viral proteins to form the viral envelope
the nucleocapsid is self-assembled within the viral envelope

Question 45

describe what happens during the budding and release of reproductive cycle of HIV.

Answer 45

the host plasma membrane pinches off to form viral envelope by budding, enclosing the viral nucleocapsid and enzymes, forming a new viral particle, which is then released to infect other cells

Question 46

relate the structure of HIV to its function in the reproductive cycle.

Answer 46

1. viral envelope
   - glycoproteins on viral envelope:
   Gp120 - recognise and bind to CD4 receptors and co-receptors on host plasma membrane of T-helper cells and macrophages to facilitate adsorption onto cells
   Gp41- undergo conformational change and pierce through host cell membrane to bring fusion of HIV envelope and host plasma membrane
2. nucleocapsid
   - RNA genome: serve as template for synthesis of single stranded complementary DNA strand

• viral reverse transcriptase: uses positive sense RNA as template for synthesis of single-stranded complementary DNA which is then used as a template for synthesis for second DNA strand complementary to first DNA strand to form double-stranded DNA
• viral integrase: catalyse integration of double-stranded viral DNA into chromosomal DNA of host cell
• viral protease: with host protease, catalyse proteolytic cleavage of long viral polyproteins into smaller functional polypeptides

Question 47

state 2 ways in which genetic variability of HIV is achieved.

Answer 47

1. rapid reproduction and spontaneous mutation
2. genetic recombination

Question 48

explain how rapid reproduction and spontaneous mutation (antigenic drift) can contribute to genetic variability of HIV.

Answer 48

lack of proof-reading of reverse transcriptase results in the inability to remove mismatched deoxyribonucleotides and insert the correct ones, leading to spontaneous mutations during reverse transcription of viral RNA template to form complementary DNA synthesis, resulting in minor changes in 3D conformation of Gp120 and Gp41 proteins if mutation occurs in segment of viral RNA that encodes for glycoprotein Gp120 and Gp41

Question 49

explain how genetic recombination contributes to genetic variability in HIV.

Answer 49

when 2 or more different strains of HIV infect the same host cell, RNA strands from different parent strains can be packed together into the same viral particle.
when this same viral particle subsequently infects another cell, the reverse transcriptase may switch between the 2 different RNA templates (normal HIV has 2 identical single-stranded positive sense RNA strands), forming recombinant complementary DNA
transcription of recombinant complementary DNA after activation leads to formation of recombinant RNA genome, forming new viral strains

Question 50

state the effects of antigenic drift and genetic recombination in HIV.

Answer 50

1. existing antibodies produced in immune system from exposure to previous strains/ infectious may not be able to recognise the altered 3D shape of viral antigens Gp120 and Gp41, thus antibodies do not bind to viruses and stop replication or recruit macrophages to destroy viruses
2. difficult to develop effective vaccine for HIV due to fast recombination rate for virus

Question 51

explain how viruses challenge the cell theory.

Answer 51

1. all living organisms composed of cells
   - but virus not made of cells eh it made of nucleic acid and capsomere proteins (capsid head)
2. cell is smallest unit of life and basic unit of structure and organisation in organisms and each cell is capable of maintaining their own metabolic activity
   - virus cannot grow, reproduce, maintain homeostasis or metabolise on their own
3. all cells come from pre-existing cells and each cell contains its own hereditary materials passed from parent to daughter cell
   - virus contain own hereditary material in form of DNA or RNA, but they cannot reproduce or grow on its own but only when they utilise the host cell mechanisms

Question 52

state the living characteristics of viruses.

Answer 52

1. reproduce/ carry out metabolism activities because some viruses contain enzymes
2. contains genetic material that can be replicated and passed down to progeny (DNA replication)
3. contains genetic material which carries coded information that can result in production of polypeptides (transcription and translation)
4. can mutate as mutation of genetic material result in phenotypes which are best suited to adapt and survive in particular environment

Question 53

state the non-living characteristics of viruses.

Answer 53

1. unable to carry out any metabolic activity outside the host cell due to lack of cellular structures
2. unable to reproduce unless inside the living cells as viral enzymes involved in reproduction only function in the cytoplasm of living host cell

Question 54

explain why viruses are considered obligate parasites.

Answer 54

obligate parasites cannot function without the host cell.
1. virus contains either DNA or RNA and never both
2. virus lack certain enzymes (eg. DNA-dependent DNA polymerase & DNA polymerase) and thus rely on host cell enzymes for replication or transcription
3. virus cannot synthesise ATP on its own, and ATP is the energy source to allow metabolic activities
4. virus lack transcription and translation machineries such as enzymes and ribosomes, and thus rely on host cell’s enzymes and ribosomes to make viral proteins
5. virus lack raw materials for reproduction, and thus rely on host cell’s nucleotides, amino acids, ATP for synthesis of viral nucleic acids and proteins

Question 55

state the structural components of viruses.

Answer 55

ECG
1. envelope
2. capsid
3. genome

Question 56

describe the genome in viruses.

Answer 56

genome is the genetic material of the virus, which varies among different viruses.
1. DNA or RNA = DNA/ RNA virus
2. segmented or non-segmented molecules of nucleic acid
- segmented viral genomes: 2 or more different molecules of nucleic acid with different nucleotide sequences
- non-segmented viral genomes: identical nucleotide sequences
3. linear or circular molecules of nucleic acid
4. single-stranded or double-stranded nucleic acid
5. positive or negative sense of ambisense nucleic acid
- positive sense RNA genome: used as mRNA directly as template for translation
- negative sense RNA genome: transcribed into complementary positive-sense RNA before protein synthesis
- ambisense genome: single-stranded genome containing both positive and negative sense sections in nucleic acid

Question 57

explain the function of genome in viruses.

Answer 57

the DNA in DNA viruses/ formed from reverse transcription using viral RNA as template in RNA virus codes for
1. new viral genome
2. proteins that make viral structural components
3. viral enzymes involved in viral replication
for assembly of new viral particles

Question 58

describe what a capsid is and the 3 shapes.

Answer 58

protein coat made of protein subunits known as capsomeres
encasing the viral genome

1. helical capsid
   - genome is coiled up in a helical pattern
   - capsomeres are arranged orderly manner enclosing the genome to form helical capsid
2. icosahedral capsid
   - genome enclosed within capsid
   - capsomeres arranged to form icosahedral capsid
3. complex shape capsid
   - elongated icosahedral capsid
   - tail sheath
   - tail fibers
   - base plate

Question 59

explain the 3 functions of a capsid in virus.

Answer 59

PAP
1. protection
- protect viral genome from inactivation by adverse environmental conditions
- physical: shearing by mechanical forces causes viral genome to breakup into smaller fragments
- chemical: free radicals cause chemical modification of nucleotides in viral nucleic acid
- enzymatic: nucleases derived from dead cells or deliberately secreted by host cells, leading to hydrolysis of viral nucleic acid

2. attachment and specificity
   - viral glycoproteins on capsid surface/ viral envelope allow viron to recognise and bind to specific receptor sites on cell surface membrane/ cell wall of host cell by complementary shapes
3. penetration
   - proteins on the viral surface that enable the virus to penetrate the host cell surface membrane (eg. Gp41 on HIV)
   - in some cases, can inject viral nucleic acid into cell cytoplasm (not Gp41)

Question 60

describe what a envelope of virus is.

Answer 60

virus envelope consists of phospholipid bilayer surrounding nucleocapsid, derived from host plasma membrane through budding
viral envelope may have viral glycoproteins incorporated in it

Question 61

state function of viral envelope.

Answer 61

viral glycoproteins on viral envelope contribute to attachment and specificity of virons to specific host cells due to complementary shape recognition between viral glycoproteins and specific receptors on host cells