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Virus Flashcards

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1
Q

What are the features of viruses?

A
  • simplest biological system
  • very small 20-30nm
  • non-cellular particles lacking cytoplasm or organelles
  • are obligate intracellular parasites that can affect both euk and prok
  • made up of nucleic acids and proteins
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2
Q

Why are viruses obligate intracellular parasites?

A

They lack the cellular machinery for self-reproduction
They can reproduce only by invading host cells and hijacking their cellular machinery

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3
Q

What are enveloped and naked viruses?

A

Enveloped viruses : have an additional membrane (lipid membrane) outside the protein coat
Naked viruses : does not have the additional membrane

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4
Q

What is the capsid / capsid coat?

A

Protein coat enclosing viral genome
Made up of protein subunits - capsomeres

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5
Q

What is the nucleocapsid?

A

Capsid coat + enclosed nucleic acid

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6
Q

What does the central core of nucleic acid of the virus contain?

A

Viral genes coding for the synthesis of different viral proteins
- viral enz involved in viral reproductive cycles
- components of protein capsid coat
- (for enveloped virus) glycoproteins inserted into viral lipid envelop
- other proteins that help stabilise the viral genome (some)

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7
Q

Features of nucleic acid

A

DNA or RNA
Linear or circular
Single or double stranded

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8
Q

What are the functions of capsid coat?

A
  • protect the nucleic acid from damage or digestion by enz
  • attach the virus to receptors on specific host cells via special sites or structures on capsid coat (nakes virus)
  • enable the virus to penetrate the cell membrane of the host cell or (in some cases) inject viral nucleic acid into the cytoplasm of the host cell cytoplasm
  • some contain viral enz molecules
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9
Q

What is the lipid/viral envelope composed of?
How is it formed (briefly)

A

Composed of phospholipids and cholesterols derived from the host cell membrane by budding when newly formed viruses leave the cell

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10
Q

What are glycoprotein spikes?

A

Incorporated viral proteins in the lipid envelope, by the virus

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11
Q

What is the function of glycoprotein spikes?

A

Attach the virus to receptors on specific host cells

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12
Q

What are the characteristics that define a living organism? (7)

A
  1. Display order - organised structures
  2. Exhibit homeostasis - maintaining constant internal environment
  3. Respond to stimuli from env
  4. Display heredity - controls growth and development
  5. Metabolism - ability to acquire, process and utilise energy
  6. Reproduce
  7. Evolve and adapt
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13
Q

Are viruses living or non-living?

A

They are on the borderline of being living and non-living
- do not appear alive until it affects host cell

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14
Q

What are the non-living characteristics of viruses ? (4)

A

Cannot reproduce on their own
- they lack the machinery to synthesis nucleic acids or proteins (strict intracellular parasites)

Do not carry out metabolism on their own
- unable to generate usable forms of energy like ATP

Do not have any sensory components or response mechanisms

Do not have internal mechanism to maintain homeostasis, lack cytoplasm = lack internal env to be maintained

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15
Q

What are the living characteristics of viruses?

A

Have organised structure and shape
- capsid coat

Are able to reproduce at a fast rate
- within host cells, can direct host cell machinery to synthesis its viral components

Contains genes and shows inheritance

Evolution occurs
- undergoes spontaneous mutation

Respond to certain external signals to trigger reproduction in host cell

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16
Q

What are the three principles of cell theory?

A
  1. all living organisms are composed of one or more cells
  2. The cell is the smallest and most basic unit of life
  3. Cells grow from pre-existing cells
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17
Q

How viruses challenge cell theory ?

A
  1. Viruses are non-cellular
    - all viruses have the basic structure made up of a core of nucleic acid surrounded by protein and this structure lacks cytoplasm and organelles
  2. Virus are smaller and more basic than a cell but are able to display some characteristics of life
  3. Viruses do not undergo cell division from pre-existing viruses
    - they infect their respective host cells and make use of host cell machinery and raw materials to synthesis new viral components for assembly into many new viruses
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18
Q

What are the 5 stages of the viral reproductive cycle?

A
  1. Attachment / Absorption
  2. Penetration / Entry
  3. Replication
  4. Assembly and maturation
  5. Exit / Release
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19
Q

What are bacteriophages (phages) ?

A

Viruses that infect bacteria
They multiply inside bacteria by making use of some or all of host cell machinery

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20
Q

What are the features of bacteriophages ?

A
  • 24-200nm in length
  • all contain a head structure made up of capsid coat
  • linear, double-stranded DNA
  • many have attached tail
  • may have base plate at the end of the tail with attached tail fibres
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21
Q

What is the function of tail in bacteriophage?

A

Tail consists of a hollow tube through which the viral DNA enters host bacterium
During infection, contractile sheath surrounding the tail contracts to inject viral DNA into host

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22
Q

What is the function of the base plate at the end of the tail of a bacteriophage with attached tail fibres?

A

Involved in the attachment of the phage to the bacteria cell

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23
Q

What are the two alternative mechanisms viruses reproduce by?
(What are the two cycles?)

A

Lytic cycle
Lysogenic cycle

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24
Q

What does the lytic cycle lead to ?

A

Death of the host cell

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25
Q

What is a virulent phage with a named example

A

A bacteriophage that only reproduces by the lytic cycle : T4 phage

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26
Q

What happens during attachment of t4 / lambda phage?

A

Tail fibres and base plate of t4 phage recognise and bind to specific receptions on the cell surface of the host bacterium

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27
Q

What happens during entry of t4 / lambda phage?

A
  • t4 phage penetrates the bacterium cell wall by contracting its contractile sheath of the tail which drives the hollow tube of the tail into the host bacterium
  • facilitate entry of viral DNA through hollow tube, leaving empty capsid outside
  • in some phages, a phage enz (lysozyme) drills a hole into the bacterial wall before injecting DNA
  • begins the eclipse period
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28
Q

What is the eclipse period ?
When does it end ?

A

Period of time between infection by a virus and the appearance of the new mature virus within host bacterium

During this period, no infectious phage particles can be found inside host bacterial cell

It ends when intracellular infectious mature viruses appear

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29
Q

What happens during replication of t4 / lambda (lytic cycle) phage?

A
  • one of the first phage genes (out of 100) expressed after viral DNA entry codes for a phage enzyme that degrades host cell DNA
  • shut down of host cell’s cellular activities : bacterium’s protein, RNA and DNA synthesis
  • the phage replicates its genome and uses teh bacterium’s protein synthesis machinery to synthesise phage enzymes and structural components
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30
Q

What happens during assemble and maturation of t4/lambda phage?

A

T4 phage enz and other structural components assemble around phage genome to form mature phage particles

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31
Q

What happens during exit of t4/lambda phage?

A
  • a phage-coded lysozyme breaks down the bacterial peptidoglycan cell wall causing lysis and release of intact bacteriophages
  • begins burst period
  • each newly produced phage can infect a healthy bacterium and successive lytic cycles can destroy an entire bacterium population in a few hours
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32
Q

What is the burst period?

A

Period where there is an abrupt rise in the number of infectious phage particles (due to release/exit)
(Start corresponds to death of host cell)

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33
Q

What is the latent period ?

A

Interval from infection until mature viruses are released from the host cell

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34
Q

What does the Lysogenic cycle do?

A

Replicates phage genome without destroying host bacterium

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35
Q

What is a temperate phage with a named example

A

A bacteriophage that reproduces by both the lytic and Lysogenic cycle : lambda phage

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36
Q

What is the difference between the structures of lambda and t4 phage

A

Lambda resembles t4 but only has one short tail fibre

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37
Q

What happens before lambda phage enters Lysogenic or lytic cycle in replication?

A

Within the host, the linear viral DNA molecule circularises

38
Q

What happens during replication of lambda phage (Lysogenic cycle) ?

A
  • lambda phage integrates itself into a specific site on host bacterial chromosome forming prophage
  • one prophage gene codes for a repressor protein that prevents transcription of most of other prophage genes (prophage gene is silenced) (no other viral proteins are made)
  • when bacterium divides, phage DNA is replicated along with its own thus quickly giving rise to a large population carrying the prophage
  • spontaneously or in response to external stimuli which may be adverse to the Lysogenic bacterium, the prophage can exit the host chromosome in a process called induction
  • certain proteases are produced due to adverse external conditions which hydrolysis the repressor protein and resulting in expression of prophage gene = start of lytic cycle
39
Q

What is a prophage (lambda) ?

A

The viral DNA integrated into a specific site on the host chromosome

40
Q

What is a Lysogen ?

A

The infected bacterium harbouring the prophage

41
Q

What are the two advantages of the Lysogenic pathway to the lambda phage virus?

A
  1. Prophage is replicated together with bacterial genome without killing host bacterium
    - allows viral DNA to be replicated many times and passed to many bacteria cells, resulting in large population of bacteria carrying the prophage
  2. Prophage can exit the bacterial genome and lytic cycle can be triggered
    - allows bacteriophage to escape from the host bacterium in unfavourable conditions
42
Q

What is the influenza virus ?

A

An animal virus that infects birds and mammals
- most virulent : influenza A virus

43
Q

What does influenza virus targets in mammals?

A

Epithelial cells of the respiratory track

44
Q

What is the structure of influenza ?

A
  • enveloped RNA virus
  • genome consists of 8 separate segments of single-stranded negative sense (-) RNA packed with several viral proteins : RNA-dependent RNA polymerase and nucleoproteins (both attached to RNA)
45
Q

What are the proteins the RNA segments of influenza code for?

A

Haemagglutinin (HA) : glycoprotein found on viral envelope

Neuraminidase (NA) : glycoprotein found on viral envelope

RNA-dependent RNA polymerase : enzyme involved in replication of viral genome

Capsomeres

46
Q

What is the function of haemagglutinin (HA)?

A

allows identification of target host cells by binding to specific receptors containing sialic acid on host cell membrane so that virus can enter host cell via endocytosis

47
Q

What is the function of neuraminidase (NA) ?

A

facilitates release of mature viruses form infected host cell by clearing the sialic acid from the host membrane

48
Q

Why does influenza have a rapid rate of viral evolution?

A

RNA-dependent RNA polymerase lacks proof reading mechanism which leads to high mutation rate in replication of viral genomes = rapid rates of viral evolution

49
Q

What happens during attachment of influenza virus?

A
  • it is spread to host animal through aerosolised viral particles
  • haemagglutinin (HA) on the viral envelope bind to sialic acid on specific receptors found on surfaces of epithelial cells of the respiratory tract
50
Q

What happens during entry of influenza virus?

A
  • virus enters host cell by endocytosis, placing the virus in an endosome (vesicle)
  • uncoating occurs :
    - the low pH of the endosome causes a conformation change in haemagglutinin (HA) which causes the viral envelope to fuse with the endosome membrane = release of nucleocapsid (capsid coat + RNA) into cytoplasm
    - the capsid coat is enzymatically removed, realising the viral RNA, accessory proteins and RNA-dependent RNA polymerase into the cytoplasm
51
Q

What is endocytosis?

A

The process in which influenza virus enters the cell :
The host cell surface membrane invaginates and pinches off, placing the virus in an endosome

52
Q

What happens during replication of influenza virus (of all 8 RNA strands) ?

A
  • accessory proteins and viral RNA form a complex that is transported into the nucleus
  • RNA-dependent RNA polymerase enters the nucleares and catalyses synthesis of singe-stranded positive sense (+) RNA using the viral (-) RNA as template
  • (+) RNA either stays in the nucleus as template to synthesis more copies of viral (-) RNA using RNA-dependent RNA polymerase or is exported into the cytoplasm as a template for translation of viral proteins using host cell ribosomes
  • viral proteins are synthesised by free ribosomes while glycoproteins like (HA, NA) are synthesised in the RER and glycosylated (+ carbohydrates) by Golgi apparatus
53
Q

How does RNA-dependent RNA polymerase work ?

A

It synthesises RNA strands using RNA as template

54
Q

What happens during assembly of influenza virus?

A
  • haemagglutinin (HA) and neuraminidase (NA) are transported (via golgi vesicles) to cell membrane where they are inserted at a site which serves as exit points for viral release
  • newly synthesised viral proteins (capsomeres and polymerase) are transported back into nucleus for assembly with viral (-) RNA to form nucleocapsid
  • newly formed nucleocapsids then leave the nucleus and are transported to the cell membrane (exit point)
55
Q

What happens during exit of influenza virus?

A

Budding occurs
- virus obtain their viral envelope from host cell membranes by budding at the exit points
- the new viruses bud off from the cell surface membrane of the host cell aided by neuraminidase (NA)

56
Q

What happens during budding?

A

Host cell membrane with incorporated viral glycoproteins evaginates (bulge/fold out) to surround the nucleocapsid and pinches off to form the viral envelope

57
Q

How does neuraminidase (NA) help new influenza viruses bud off?

A

As new viruses are produced by budding, they would immediately bind to sialic acid receptors on the cell surface and this will not be able to spread to other cells
Enz NA removes sialic acids form the surface of the host cells so that newly formed viruses can be released

58
Q

What is the human immunodeficiency virus (HIV)?

A

HIV causes acquired immunodeficiency syndrome (AIDS) - a human disease in which the progressive failure of the immune system allows life-threatening infections and cancers to thrive

59
Q

What does HIV target?

A

Lymphocytes (WBCs) such as the T helper cell involved in the immune system

60
Q

How is HIV transmitted?

A

Infection with HIV occurs by the transfer of body fluids like blood or semen

61
Q

What is the structure of HIV?

A
  • enveloped RNA virus
  • genome consists of 2 identical, single-stranded positive sense (+) RNA molecules packed with several viral proteins such as reverse transcriptase and integrase
62
Q

What proteins do the RNA molecules of HIV code for?

A

gp 120 and gp 41 : glycoproteins found on viral envelope

HIV reverse transcriptase : Enzyme which catalyses synthesis of viral double stranded DNA using the viral single stranded RNA as a template (replication)

HIV integrase : enz which inserts viral DNA into host DNA to form provirus (integration)

HIV protease : enz which cleaves synthesises viral polyproteins to release functional proteins

Capsomeres

63
Q

Why does HIV have a high mutation rate?

A

HIV reverse transcriptase lacks a proof-reading mechanism which leads to a high mutation rate during replication of the viral genome

64
Q

What happens during attachment of HIV ?

A
  • glycoprotein gp120 on HIV viral envelope binds to specific receptor : CD4 receptor and co-receptor (CCR5 or CXCR4)
65
Q

What happens during entry of HIV ?

A
  • binding of gp120 to CD4 receptor causes a conformation change to another viral glycoprotein gp41 that brings the viral envelope and host cell membrane close together for fusion to occur
  • fusion of viral envelop with cell surface membrane of host T helper cell releases the nucleocapsid into the cytoplasm
  • uncoating releases the viral DNA and enz into the cytoplasm (capsid coat hydrolysed)
66
Q

What happens during replication of HIV ?
(Genome)

A
  • reverse transcriptase then transcribes the single-stranded RNA into double stranded DNA to be integrated into the host cell DNA
  • viral DNA enters the nucleus and is inserted into host DNA by HIV integrase
  • the integrated viral DNA (provirus) is replicated along with the host DNA when host T helper cells undergo cell division
  • activation of T helper cell during an immune response results in transcription of the provirus (by host cell enz)
  • the viral (+) mRNA leaves the nucleus and serves as genome for new viruses and templates for translation of viral protein (by host ribosomes)
67
Q

What happens during replication of HIV ?
(Viral protein)

A
  • viral proteins (capsomeres, reverse transcriptase) are synthesised by free ribosomes while glycoproteins (gp120, gp41) are synthesised in RER and glycosylated in Golgi apparatus
  • some of the viral proteins are synthesised in the form of polyprotein (non-functional), HIV protease is important in clearing these polyproteins to release functional proteins
68
Q

What are retroviruses?

A

A type of virus that use a special enz called reverse transcriptase to translate its genetic information into DNA
- single stranded RNA > RNA-DNA hybrid > double stranded DNA (complementary DNA)

69
Q

What happens during assembly of HIV ?

A
  • gp120 and gp41 are transported (via golgi vesicles) to cell membrane where they are inserted at a site which serves as exit points for viral release
  • newly synthesised viral proteins assemble with viral RNA to form the nucleocapsid in the cytoplasm
70
Q

What happens during exit of HIV ?

A

-virus obtains their viral envelopes from host cell membrane by budding at exit points

71
Q

What are the four phases of HIV?

A
  1. Acute HIV infection phase : occurs a few weeks after infection
    - high HIV viral load, CD4 count (no. of T helper cells) drops
  2. Clinical latency - asymptomatic phase : occurs for the next few years (<10)
    - HIV still exists but does not multiply in large numbers, slow continuous destruction of immune cells
    - immune system is able to control both viral and opportunistic viral infections - presumed latency
  3. Symptomatic phase
    - recurrence of viral symptoms and further decrease of CD4 count
  4. AIDS : final phase of full blown HIV
    - CD4 cells become depleted totally
    - death ensues with opportunistic infections
    - patient to have very Low T-cell counts and compromised immune system makes them susceptible to infections and certain kinds of cancers
72
Q

How does variation arise in viral genomes?

A

Mutation
- RNA viruses usually tend to have a high rate of mutation because their replication enz are more error-prone due to the lack of proof-reading mechanism during replication of viral genome

73
Q

What are the 2 mechanisms in which genome of influenza virus may change?

A
  1. Antigenic drift : creates influenza viruses with slightly modified glycoproteins
  2. Antigenic shift : creates influenza viruses with entirely novel combinations of glycoproteins
74
Q

How does antigenic drift occurs?

A

When mutations to viral RNA coding for viral glycoproteins (HA, NA) leads to changes in the structural conformation of these glycoproteins

It occurs over a long period of time and is a gradual process

75
Q

What is the significance of antigenic drift?

A

Influenza viruses are able to infect the same person multiple times - antigenic drift is the reason behind seasonal epidemics that occur every year

  • after removing from infection by a particular influenza virus, immunity is acquired against the virus by development of antibodies specific to the glycoproteins
  • but due to mutations which alter the glycoprotein structures slightly, the antibodies may not be effective against the mutated virus (in recognising and binding to the mutated glycoproteins) and would thus be susceptible to infection
76
Q

What is antigenic shift?

A

A major change to the virus structure to create a new subtype of influenza virus

77
Q

How does antigenic shift occur?

A

Some species are able to be infected by different types of influenza virus :
- pigs get infected by avian influenza virus, human influenza virus and swine influenza virus

When different types of influenza viruses infect the same cell at the same time, newly-synthesised viruses may contain RNA segments (8 of them) from different virus types : genetic reassortment

78
Q

What is the significance of antigenic shift?

A
  • undesirable as a new subtype of human influenza virus may be produced which has surface glycoproteins like HA and NA that are from an avian influenza virus
  • the human immunity system has not encountered the avian glycoprotein before and may be unable to detect the new virus thus not able to combat the viral infection effectively
  • if human to human transmission becomes possible, a global pandemic may occur
79
Q

What is a disease ?

A

An abnormal condition of an organism in which bodily functions are impaired resulting in specific symptoms and signs

80
Q

How does viruses cause disease in humans?

A

Generally viral infections cause diseases due to damage and disruption of host tissue and functions :

  1. As virus makes use of the host cellular machinery for replication, it often involves the inhibition of normal host cell functions in DNA, RNA and protein synthesis
  2. Release of matured viruses from host cells by budding may result in cell death due to extensive loss of cell surface membrane
  3. Insertion of viral glycoproteins on the surface of infected host cells (exit point) may result in immune responses against infected cells
81
Q

How does insertion of viral glycoproteins into host cell membrane damage and disrupt host tissue and functions ?

A
  • infected host cells may be recognised as foreign by body’s immune system and are thus destroyed
  • the infected host cells may also release inflammatory cytokines, inducing an inflammatory reaction that damages adjacent healthy cells
  • beside damages caused by the virus, other symptoms involved with viral infection such as fever and aches are caused by the body’s immune respond to the virus
82
Q

What are cytokines?

A

Small proteins that function as signalling molecules between cells of the immune system, triggering inflammation and regulating the body’s immune system

83
Q

How does inhibition of host cell function lead to cell death?

A

inhibition of normal host cell functions in DNA, RNA and protein synthesis, together with depletion of raw materials in the host cells result in the host cells being unable to synthesis essential proteins leading to reduced cellular function and cell death

84
Q

How does influenza cause disease?

A

Influenza targets epithelial cells of the respiratory tract in mammals : death of these cells due to influenza infection results in impairment of functions
- reduced upward movement of mucus by ciliated epitelial cells that line the respiratory tract
- leading to reduced clearance of other infectious agents found in uncleared mucus resulting in immune response against them

85
Q

What are the symptoms of immune response against influenza?

A

Fever, sore throat, muscle pains, coughing and in serious cases pneumonia

86
Q

Why do some influenza subtypes have high lethality?

A

Due to the triggering of massive immune response further enhanced by high level of viral reproduction in these subtypes

Influenza can cause severe illness or death in people at high risk - children below 2 and adults > 65 and people with medical conditions like chronic lung disease or weakened immune system

87
Q

What are the challenges in treating influenza?

A

Influenza virus has a high rate of mutation due to antigenic shift and drift resulting in the occurrence of different subtypes making development of vaccination and antibodies difficult

88
Q

Why are antibiotics prescribed for common flu even though the disease is caused by viruses?

A
  • prevent secondary infection by bacteria
  • help reduce immune response against bacteria to reduce tissue damage
89
Q

What are T helper cells?

A

A sub-group of lymphocytes (WBCs) that are involved in activating and directing other immune cells and are thus particularly important in the immune system

90
Q

How does HIV lead to disease ?

A

Death of T helper cells due to HIV infections impairs the immune system leading to AIDS

HIV infected patients will not be able to defend against opportunist infections by other common viruses and bacteria

HIV infection may also induce fusion between adjacent T helper cells which result in the formation of giant multinucleated cells or syncytia (singular : syncytium)
- during HIV reproduction cycle, newly synthesised gp120 are inserted into the host cell membrane which may trigger fusion of membrane with neighbouring T cells causing death of many T helper cells from the infection of a single cell

Insertion of viral DNA into host genome may cause cancer due to the disruption of tumour suppressive genes or the conversion of proto-oncogene to oncogene
- the insertion of a more active viral promoter near a proto-oncogene may result in over-expression of the proto-oncogene thus converting it into an oncogene as there are more gene products that overstimulate the cell cycle

91
Q

What are the challenges in treating HIV?

A
  1. HIV has a high rate of mutation as HIV reverse transcriptase is error-prone, resulting in different strains of HIV with slightly altered gp120
    - antibodies effective against earlier strains may be ineffective against new strains making the development of effective antibodies and vaccinations difficult
  2. HIV may persist in latent state (virus does not assemble into infectious viral particles) for many years
    - AIDS patients typically only show symptoms after a latency period of 8-10 years following the initial HIV infection
    - ability of HIV to persist in infected host cell s is a major barrier in its eradication or cure
92
Q

Why are antibiotics ineffective against viruses ?

A

Viruses are obligate parasites and make use of host cellular machinery
Antibiotics interfere with metabolic processes like protein synthesis, enz action, cell wall function
But outside host cells, viruses do not have relevant metabolic processes

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