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A level H2 Biology > B4-1 Genetics of Viruses > Flashcards

B4-1 Genetics of Viruses Flashcards

1
Q

Viruses are

A

Obligate Intracellular Parasites

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2
Q

Viruses should be considered living organisms because

A
  1. Viruses can reproduce.
  2. Viruses are able to direct metabolic processes.
  3. Viral genomes can evolve.
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3
Q

Viruses should not be considered living organisms because

A
  1. Viruses are not cells and do not have protoplasm or organelles.
  2. Viruses lack some of the characteristics of living organisms. (Elaborate - 5)
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4
Q

Cell Theory

A
  1. Cells are the smallest unit of life.
  2. All cells come from pre-existing cells.
  3. All living organisms are composed of cells.
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5
Q

How viruses challenge the cell theory

A
  1. Lack the necessary molecular machinery, but contain genetic material necessary to form next generation & can evolve in response to the environment.
  2. Cannot replicate (do not have energy and materials ) their genomes unless they have entered a suitable host cell.
  3. Acellular, do not have protoplasm or organelles. Metabolically inert, does not carry out respiration or biosynthesis.
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6
Q

Infectious particles

Intracellular vs Extracellular

A

Active - Intracellular virus state

Inactive - Extracellular virus state

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7
Q

(+) sense ssRNA

A

Genome serves as viral mRNA and thus can be immediately translated by the host cell

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8
Q

(-) sense ssRNA viruses

A

Complementary to mRNA

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

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9
Q

SS RNA-Reverse transcriptase (RT) viruses

A

Make use of RT (RNA-dependent DNA polymerase) to produce DNA from the initial viral RNA genome
Purpose is for ds DNA to be integrated into host genome

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10
Q

DS DNA-RT viruses

A

DNA is transcribed by RNA polymerase into viral mRNA. With the use of RT, the mRNA produced will be used as a template to form viral DNA

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11
Q

All viral genomes contain genes coding for essential (lacking in host) proteins such as (2)

A
  1. Regulatory proteins to regulate action of host genome (replicate viral genome and synthesise components necessary for formation of virus)
  2. Structural proteins such as viral capsid proteins (essential for assembly of complete virus)
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12
Q

Basic structures of Viruses

A
  • Genome (DNA/RNA - at least genes coding for regulatory proteins (regulate action of host genes), structural proteins for assembly of virus e.g. viral capsid protein)
  • Capsid (protein coat) comprising protein subunits capsomeres

Some viruses

  • Envelope (containing phospholipids from host cells)
  • Enzymes
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13
Q

How enveloped viruses derive envelopes

A

When viruses are released from 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
Proteins include viral glycoproteins on outside of envelope - essential for attachment of viruses to next host cell

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14
Q

Purpose of viral envelopes

A

Protects the virion’s nucleic acid from effects of various enzymes and chemicals

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15
Q

Roles of viral enzymes

A

Aid in entering cells in initial stages or release of virus from host cells in final stages of infection process

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16
Q

Lysosyme

A

Makes a small hole in bacterial cell wall

Allows viral nucleic acid to enter (initial) and causes lysis of host cell and release of virus

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17
Q

Neuraminidase

A

Group of enzymes breaks down glycosidic bonds of glycoproteins and glycolipids of connective tissue of animal cells - Liberation of virus
Associated with viral envelope, not located within capsid like most other viral enzymes

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18
Q

Polymerases (4 types)

Viruses (2 types)

A

DNA-dependent RNA polymerase
RNA-dependent RNA polymerase / viral replicase
DNA-dependent DNA polymerase
RNA-dependent DNA polymerase / reverse transcriptase

Bacteriophages - DNA viruses, infect bacteria, transfer of genetic material between bacteria by transduction

  • Virulent - Only lytic - T4
  • Temperate - Only lysogenic - Lambda

Enveloped Animal Viruses - Membranous envelope (derived from host cell membranes, contain viral membrane proteins and glycoproteins) surrounding nucleocapsids
Influenza and HIV

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19
Q

Viruses identify host cells by

A

Complementary fit between proteins on outside of virus and specific receptor molecules on surface of host cells

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20
Q

General steps of enveloped virus reproduction

A
  1. Adsorption
  2. Penetration
  3. Synthesis of viral proteins & Replication of viral nucleic acid
  4. Assembly
  5. Release
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21
Q

T4 phage - Genome & Capsid

A

Nucleic acid - Linear double-stranded DNA (transcribed by host cell machinery into mRNA for translation of viral proteins)
Capsid - Capsomeres surround nucleic acid contained in head of phage

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22
Q

T4 phage - 3 structural features (elaborate on 2 out of 3 features)

A

Head - Contains viral DNA
Tail
Base Plate - Comes into contact with host cell surface and undergoes conformational change to allow DNA to be extruded/released from the head, through the central tube and into the host cell

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23
Q

T4 phage - Tail

A

Tail sheath - Surrounds central tube, Contracts during penetration to thrust the central tube through the host cell wall and membrane

Multiple tail fibres - Allow the phage to adsorb/attach onto the surface of the bacterial cell by binding to specific receptors site found on cell surface
Enables base plate to come into contact with surface of cell. Triggers conformational change in both base plate and tail sheath such that central tube is pushed through the bacterial wall.

24
Q

T4 phage - Reproductive cycle

A

Lytic cycle

25
Q

Lytic cycle (General)

A

Finally results in death of host cell
“Lytic” refers to last stage of infection
Phage that reproduces only by a lytic cycle - virulent phage

26
Q

Lytic cycle (Stages)

A
  1. Adsorption
  2. Penetration
  3. Synthesis and replication
  4. Assembly
  5. Release
27
Q

Lytic cycle - Stage 1: Adsorption (T4, Lambda, Influenza, HIV)

A

Multiple tail fibres (T4)/ Single tail fibre (lambda) of phage attach to specific receptor sites on surface of a bacterial host cell.
[Influenza] HA molecules on viral membrane bind to sialic acid containing receptors on the membrane of the host cell.
[HIV] Glycoprotein gp120 on the surface of the HIV binds to the CD4 receptor, a cell-surface receptor found on T helper cells and CCR5 on macrophages.

Base plate settles down on host cell surface.

28
Q

Lytic cycle - Stage 2: Penetration (T4) - 4 steps

A

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 peptidoglycan, degrading a portion of the bacterial cell wall for insertion of 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.

29
Q

Lytic cycle - Stage 3: Synthesis and replication

A

Soon after phage DNA is injected into host cell, synthesis of host DNA, RNA and proteins is halted. Host cell machinery is taken over (damage to host cell) by the virus for:

Viral Nucleic Acid Synthesis

  • T4 DNA replicated by host DNA polymerase
  • Host DNA degraded into nucleotides, providing raw materials for phage DNA replication

Viral Protein Synthesis

  • T4 mRNAs are synthesised by host RNA polymerase via transcription
  • Phage mRNAs translated by host cell ribosomes, tRNA and translation factors into viral proteins and enzymes required to take over host cells and replicate phage nucleic acids
  • E.g. Enzymes for viral replication, Inhibitory factors stopping host cell RNA and protein synthesis
30
Q

Lytic cycle - Stage 4: Assembly

A

Viral proteins assembled to form phage heads, tails, tail fibres
Different components assembled into complete bacteriophage

31
Q

Lytic cycle - Stage 5: Release

A

Phages lyse host cell by action of enzyme lysozyme, which digests the bacterial cell wall
Water enters the cell by osmosis, causing the cell to swell and burst

32
Q

Lambda phage (Temperate phage) - Genome & Capsid

A

Genome - Linear ds DNA, later transcribed by host cell machinery into mRNA for translation of viral proteins
Capsid - Capsomeres surround nucleic acid, contained in head of phage

33
Q

Specific lambda Bacteriophage structural features

A

Head contains DNA of virus

  • 5’ terminus of each DNA strand is a ss-tail of 12 nucleotides long which is important in prophage formation
  • A single tail fibre allows the phage to adsorb onto the surface of the bacterial cell by binding to specific receptor site found on cell surface
34
Q

Lysogenic cycle (3)

A

Lysogenic cycle involved in replication of the phage genome without destroying host in initial steps
Environmental trigger need to switch from lysogenic to lytic cycle
Both cycles share step 1

35
Q

Lysogenic cycle - Stage 2: Penetration

A

Lambda phages have tails that are not contractile (unlike for influenza) and serve to deliver the viral DNA to the cell membrane

36
Q

Lysogenic cycle - Stage 2A: Prophage formation

A
  • Phage genome circularises and inserts itself into a specific site on the bacterial chromosome, known as prophage insertion site (No loss of host DNA). Integrated phage is known as prophage
  • In the integrated state, 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 large population of bacteria carrying viral DNA in prophage form.
37
Q

Lysogenic cycle - Stage 2B: Environmental triggers

A

When there is an environmental trigger (e.g. UV radiation, presence of certain chemicals), virus switches from lysogenic to lytic cycle.
Lysis genes which were repressed during lysogeny are activated, allowing phage genome to be excised from the bacterial chromosome to give rise to new active phages
Upon exiting lysogenic cycle, steps 3-5 of lytic cycle resumes.

38
Q

Influenza - Genome & Capsid

A

Genome - 8 different segments of (-) sense ssRNA
(-) sense ssRNA must be converted into complementary (+) sense RNA before it can be used for translation viral proteins
Capsid - Nucleoprotein (NP) associate with viral nucleic acid to form nucleocapsid (8 separate nucleocapsid)

39
Q

Influenza - Structural features (Membrane, Protein envelope, Enzymes)

A

Membrane/Viral Envelope - Phospholipid bilayer obtained from host upon budding

Protein envelope - Matrix protein forms a second layer of envelope, which encloses the nucleocapsid

  • M1 Monomers of matrix protein
  • M2 Ion channel to lower or maintain pH of endosome

Enzymes

  • PB1, PB2, PA - Form RNA-dependent RNA polymerase (replicase) responsible for replication and transcription
  • NS1 - Regulates viral replication mechanisms and cellular signalling pathways
40
Q

Influenza - Structural features (Surface Glycoproteins)

A

Surface Glycoproteins -
Haemagglutinin (HA) - Role in adsorption, Binds to sialic acid containing receptors on host cell membrane, Attach virus to receptor on host cell membranes
Neuraminidase (NA) - Role in release, Hydrolyses mucus allowing viruses to enter cells of the respiratory tract, Facilitate budding by cleaving sialic acid containing receptors

41
Q

Rep Cycle - Stage 2: Penetration (Influenza)

A
  • Viruses taken in by receptor-mediated endocytosis, forming endocytic vesicle within host cell called endosome, with virus attached to inner surface
  • Fusion of this vesicle with acidic lysozyme lowers pH of vesicle. Triggers conformational changes in HA protein, which causes viral envelope and endosome membranes to fuse, releasing the 8 viral segments of influenza genome into host cell cytoplasm
  • Viral RNAs transported into nucleus
42
Q

Rep Cycle - Stage 3: Synthesis & Replication (Influenza)

A

Viral replicase (virion) copies (-) sense RNA template into complementary (+) sense RNAs. (+) then used for:

Viral Nucleic Acid Synthesis

  • (+) used as template for synthesis of full-length (-) by viral replicase
  • (-) packaged into new viral particles as their nucleic acid

Viral Protein Synthesis

  • (+) used as mRNA which are translated in the cytoplasm by host protein synthesis machinery
  • 3 sets of proteins synthesised (enzymes, matrix & capsomeres proteins, glycoproteins)
  • Free ribosomes used to synthesis EMC as they are ultimately folded into final conformation in cytoplasm and packaged into new virion
  • Viral transmembrane surface glycoprotein synthesised by rER-bound ribosomes and transported to GA for glycosylation and then incorporated into host cell membrane via vesicle which fuses with host cell membrane
43
Q

Rep Cycle - Stage 4: Assembly of new virion (Influenza, HIV)

A

Copies of HIV proteins and HIV’s RNA genome assemble near host cell membrane to form a new virus particle

Complete when 8 (-) sense viral RNAs associated with NP and enzymes like viral replicase / viral components of 2 ssRNA molecules associated with RT and enzymes like protease and integrase are packaged
Acquisition of glycoprotein studded membrane envelope occurs during release of virus

44
Q

Rep Cycle - Stage 5: Release (Influenza)

A
  • Virus is finally released by budding, acquiring it with host cell’s lipid bilayer as the viral envelope
  • Host membranes containing HA, NA, M2
  • With presence of HA on viral acid and sialic-acid containing cellular receptors on host cell membrane, budding invariably bring them together, resulting in new particle remaining attached to host cell
  • NA cleaves sialic acid residues on cellular receptor that bind newly formed virions to the cell
  • Virus released
45
Q

HIV (General)

A

Retrovirus, Causes AIDS

Retroviruses are enveloped RNA viruses which replicate by means of a DNA intermediate synthesised by the enzyme RT.

46
Q

HIV - Genome & Capsid

A

Genome - 2 identical (+) ssRNA
ssRNA is converted to DNA for integration into the host genome. DNA is then used for transcription of viral mRNA which is translated into viral proteins and for use as the viral genome in the progeny virus.

47
Q

HIV - Viral Envelope, Surface Glycoprotein, Protein coat

A

Viral Envelope - Phospholipid bilayer obtained from host upon budding
Surface glycoproteins
gp120 - binds to CD4 receptors on wbc like macrophages and T helper cells
gp41 - aids in fusion of HIV envelope ad host cell membrane
Protein Coat - Matrix protein forms second layer of protein envelope, enclosing the capsid

48
Q

HIV - Enzymes (3)

A

RT - 2 molecules, each associated with 1 RNA molecule, reverse transcribe viral RNA into DNA
Integrase - Facilitate incorporation of dsDNA into host cell’s genome
Protease - Cleaves viral polypeptide into functional proteins during viral maturation

49
Q

Rep Cycle - Stage 2: Penetration (HIV)

A
  • Upon binding to CD4, gp120 undergoes a conformational change, allowing it to bind to a co-receptor known as CXCR4 on the surface of 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
  • HIV envelope fuses with the host cell membrane, releasing viral contents consisting of viral nucleic acid and enzymes into the host cell
50
Q

Rep Cycle - Stage 3: Synthesis and Replication (HIV)

A

RT first RTs the viral RNA into a complementary DNA strand. The RNA strand of the DNA-RNA is broken down by RT and newly synthesised DNA strand is used as a template for synthesis of the other complementary DNA strand, forming a dsDNA.
DNA molecules then passes through the nuclear pore and enter host nucleus
Enzyme integrase catalyses integration of viral DNA into genetic material of the host
Newly integrated viral DNA is called provirus, which may remain in latent (inactive) cell for several years producing few or no copies of HIV, until the host cell is stimulated in an immune response.

Viral Nucleic Acid Synthesis
- When host cell receives a signal, proviral DNA is transcribed by host RNA polymerase into RNA which serves as nucleic acid for new virions.

Viral Protein Synthesis

  • Proviral DNA also transcribed into viral mRNA, which is then translated to produce a single long chain of HIV proteins which is later cleaved.
  • Viral surface glycoproteins are synthesised by rER-bound ribosomes, transported to GA for glycosylation, incorporated into host cell membrane via vesicles that fuse with it
51
Q

Rep Cycle - Stage 5: Release (HIV)

A

Newly assembled immature HIV buds of from host cell, surrounded by host membrane
Viral maturation occurs when HIV protease cleaves single long chains of HIV proteins into smaller functional proteins, forming a mature HIV particle

52
Q

Antigen

A

Any substance that can be recognised by the immune system

Molecule that binds to an antibody or a TCR which elicits a B cell or T cell response respectively

53
Q

Antigenic Shift

A

Sudden and drastic change in antigenicity of a virus owing to reshuffling of the segmented virus genome between different strains

Influenza - New HA and/or HA & NA proteins in the viruses that infect humans
Population has no immunity to novel combination of surface proteins
May result in a progeny virus which can infect a new species

54
Q

Ways antigenic shift occur (3)

A
  1. Different viruses of different origins may infect the same animal, providing the opportunity for the viruses to reassort to form a new combination of RNA (genome)
  2. Without undergoing genetic change, one strain can jump directly from one species to another
  3. Without undergoing genetic change, one strain can jump directly from one species to an intermediate animal host and then to humans
55
Q

Antigenic Drift

A

Gradual accumulation of minor point mutations in the genes of surface antigens of influenza viruses that results in altered antigenicity.
Happens continually over time in the genes of viruses as the virus replicates. These result in minor alteration of 3D conformation of HA or NA on progeny viruses
A proportion of population may still have pre-existing immunity to the modified surface proteins, and viruses can only infect individuals of the same species

56
Q

Factors which influence rate of mutation of viral genomes (3)

A
  1. As the genome of influenza consists of 8 ssRNA strands which lack a complementary strand, polymerases cannot perform proofreading during replication
  2. Viral polymerases are also prone to errors and will introduce mutations during the course of DNA replications
  3. Retroviruses encode on average of 1 point mutation for every replication cycle as a result of viral RT being unable to correct nucleotide misincorporation errors

Together, these mutations result in production of surface proteins with different 3D conformations, resulting in antibodies no longer being complementary to them and thus will not recognise and bind to them

57
Q

Mechanism for Variation in Viral Genomes

A

A. Mutation (AD)

  • No proofreading mechanisms for RNA in host cells, RNA viruses experience much higher rates of mutations
  • Certain viral enzymes such as reverse transcriptase in HIV have very low fidelity and regularly introduce errors into genome
  • Errors every replication cycle

B. Recombination (AS) with genome of another strain
Exchange info, resulting in genomes with new combinations of alleles

C. Reassortment (AS)
Host cell infected with 2 viral strains, introduce 2 sets of genetic material into host cell
Formation of viral progeny - different segments of viral genome may be packaged into progeny virus
Sudden and drastic change in viral genome

A level H2 Biology (7 decks)

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