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BIOL3017 - Molecular and structural basis for disease > Viruses > Flashcards

Viruses Flashcards

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1
Q

What is the most common drug hypersensitivity reaction? how does it occur

A

Morbilliform drug eruption:
amoxicillin treatment for sore throat and fever +
Epstein Barr Virus infection (EBV, mononucleosis)

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2
Q

What is Epstein Barr Virus?

A

EBV causes Infectious Mononucleosis (IM) also known as glandular fever (kissing disease)

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3
Q

Explain the herpes life cycle

A

See diagram

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4
Q

What are the three phases of gene expression in herpes

A
  1. tegument proteins regulate production of mRNAs and proteins of 
IE immediate early genes; they
    -protect the virus against innate host immunity
    -promote transcription of early genes
  2. production of E early 
mRNAs / proteins; they
    - are involved in 
viral replication
  3. production of L late
 mRNAs / proteins; they
    are involved in 
virus assembly
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5
Q

Explain how herpes ans EBV illustrate the virus principle

A
  1. specific ways to get into the
host cells: attachment and virus entry
  2. Distinguish the virus’ genetic material
    Host interactions to establish chronic infection
    Expression of viral genes is often in phases
  3. Virus replication, assembly and release
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6
Q

Explain features of Herpes and EBV

A

dsDNA - Linear in acute, circular in latent phase
120-140kb
120-200nm, envelope, capsid
down-regulate pro-inflammatory responses and MHC-II
can infect B and T cells
widespread infection

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7
Q

Explain points of intervention within the general virus life cycle

A
  1. receptor binding (COVID)
  2. entry (COVID)
  3. mRNA function- Interferon > RNA breakdown
  4. DNA/RNA synthesis
  5. assembly - Protease (COVID)
  6. release - Neuraminidase (Influenza)
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8
Q

How does INFy orchestrate viral defense?

A

Type 1 interferon (IFNa - dentrites and IFNb - fibroblasts) produced by infected cells (autocrine and paracrine)
production of >300 gene products and stimulates:
T cells and NK cells produce type II INFy
INFy kills virus infected cells/cancer cells
autocrine - virus replocation in hibition, apoptosis
paracrine - up-regulation of MHC-1 and NK activation

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9
Q

Virus epidemic examples

A

SARS outbreak 2002/3 - 8,000 cases, 800 deaths nearly 10% fatality

Middle east (MERS): 2012/3 - 1,300 cases, 400 deaths; nearly 40% fatality

COVID19 - 75,000,000 cases, 6,900,000 deaths, 0.9% fatality

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10
Q

what does R0/ the R number mean? give examples

A

of individuals one sick person will infect

2 = HepC, Ebola, Influenza
4 = SARS, HIV
6 = Pox
10 = Mumps
18 = Measles

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11
Q

Explain the use of Dexamethasone in COVID-19

A

Corticosteroid
in UK - tested on hospitalised patients with COVID-19
benefits for critically ill patients -reduction in mortality by 1/3 for people on ventilators, 1/5 for people on oxygen

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12
Q

Give examples of different types of approved drugs for virus treatment

A

Nirmatrelvir and Ritonavir (Paxlovid, protease inhibitor)
Remdesivir (Veklury, nucleotide interfering with viral RNA replication)
Molnupiravir(Lagevrio, same as above)
Sotrovimab (Xevudy) is a “biological” – monoclonal antibody or mAb

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13
Q

Explain features of the drug Paxlovid (CHECK WHAT IT TREATS)

A

Convenience: orally bioavailable (50% in rats) (95% absorbed from GI)
Efficacy: reduced hospitaliasation and mortality
Mechanism: inhibits the cystine protease Mpro that helps cleave and mature chains of the viral protein
prevents transmission

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14
Q

what are proteases required for in virus infection

A

virus entry
endosomal release
cleave polyproteins

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15
Q

Describe features of the drug Sotrovimab

A

Monoclonal antibody
Recognises spike protein of virus
used to treat symptomatic acute covid-19 infection in 12 and above
overcome infection and prevent serious illness

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16
Q

What is a mAB?

A

Monoclonal antibody:
- Mouse (or other animal) challenged with an antigen
- produces cells that produce specific antibodies
-Cross these cells with an immortal / cancerous cell
- Each cell colony then produces a specific antibody, a clone

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17
Q

Neutralising SARS mAB

A

Source animal is human
Make a monoclonal antibody, as before
Test effectivity against antigen, here SARS spike protein
Spike receptor binding domain (RBD) targeted mAb neutralise the virus (Graham 2021)

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18
Q

What is a virus factory?

A

A compartment within an infected cell, made by the virus to protect it from degradation/host defences

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19
Q

Example of a virus that creates a virus factory

A

Coronaviridae (COVID), Pox, Herpes

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20
Q

Examples of cytoplasmic virus factories

A

Coronaviridae use double membrane vesicles (DMVs) 
in the cytoplasm where the dsRNA is produced
Poxvididae form a viruplasm for viral replication and assembly

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21
Q

Examples of nuclear virus factories

A

Herpesviridae formnuclear replication compartments(RCs) 
for viral DNA replication and late gene transcription

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22
Q

Examples of RNA viruses

A

Paramyxovirus (mumps & measles):
RNA-negative strand (mRNA complement)
linear ssRNA– genome, 15.3 kb
enveloped, size 150 nm

Mumps: infection of the ductal epithelium lading to Parotitis; the mumps virus can cross the brain blood barrier and infect ependymal cells
Paramyxovirus down-regulates innate immunity by interfering with interferon responses

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23
Q

Explain virus classification

A

How they look: capsid, envelope

Their genome:
This can be either DNA or RNA

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24
Q

Do Viruses violate the central Dogma?

A

YES

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25
Virus classification by nuclear material (Baltimore classification)
double or single stranded DNA viruses I- dsDNA: all mechanisms like DNA genomic host cell II- ssDNA: convert to dsDNA first, then like host cell double or single stranded RNA viruses III - dsRNA: RNA used as template for mRNA IV - ssRNA: a positive strand has the same orientation as mRNA;
requires synthesis of complementary RNA first;
mRNA is then synthesized from the complementary RNA strand V - ssRNA: a negative strand is complementary to mRNA;
mRNA can be synthesized directly from the genome template VI: RNA genome but dsDNA intermediate VII: DNA genome but ssRNA intermediate
26
Examples of virus in the class 1 classification
dsDNA use normal cellular mechanisms Herpes, papilloma, pox
27
Examples of virus in the class 2 classification
ssDNA Convert to dsDNA first e.g. parvo
28
Examples of virus in the class 3 classification
dsRNA use normal cellular mechanisms e.g. reo, picobirna
29
Examples of virus in the class 4 classification
ssRNA+ must synthesise complementary strand 1st e.g corona
30
Examples of virus in class 5 classification
ssRNA- use the normal cellular mechanism e.g. paramyxo, filo, orthomyxo
31
Examples of virus in class 6 classification
ssRNA+, DNA intermediate (retrovirus) Convert their genome to DNA e.g. HIV
32
Examples of viruses in class 7 classification
dsDNA, RNA intermediate Use an RNA intermediate e.g. hepadna
33
estimate of how many viruses on earth
10^31 (2000 known species)
34
Which Baltimore class of virus is most common
4
35
Influenza life cycle
Attached to silica acids on the membrane surface and on proteins Internalised Sheds Cathrin coated vesicle Releases ribonucleoproteuin Makes mRNA that are spliced to make proteins RW
36
How does influenza enter cells
attachment endocytosis acidification of the endosome pH induced conformational change of hemagglutinin (surface protein) - exposure of hydrophobic residues Leads to loss of envelope and release of viral genome
37
Hemagglutinin features
active, virus form trimeric membrane protein bind glycosylated surface proteins on host membrane
38
Drugs targeting which proteins are being developed to target influenza
drugs against M1 and M2
39
Two external proteins of influenza
H=Hemagglutinin glycosylated protein binds to sialic-acid N=Neuraminidase hydrolyses sialic-acid glycosylation active against Hemagglutinin as well as surface proteins
40
How is targeting neuraminidase a point of therapeutic intervention
N Allows virus to leave the cell - this is a step of therapeutic intervention e.i inhibition of N enzyme
41
Examples of drugs that hinder virus release
Tamiflu (Oseltamivir) & Relenza (Zanamivir) 1. neuraminidase inhibitors 2. interfere with the release of the virus from the cell surface
42
Number of hemagglutinin and neuraminidase types
H = Hemagglutinin, 16 known N = Neuraminidase, 9 known Recombination of RNA segments generation of new virus types Segmental genome of 8 segments New virus variants are created by changing segments
43
Explain what classification of virus bacteria, plants and animals are primarily infected by
Bacteria infected by dsSNA viruses (primarily) Plants infected by SSRNA viruses (primarily) Animals are infected by all (but ssDNA) viruses
44
Ebola virus disease (EVD) features
ssRNA virus Large- not transmitted by air, need contact Glycoprotein on surface one of the worlds most virulent, fatal diseases
45
Explain the genome of ebola
NP = nuclear protein VP = viral protein GP = glycoprotein L = polymerase gene cleavage by host furin
46
What are natural hosts for ebola and why is it only found in particular countries?
Climate has to be right Pteropodidae fruit bats are the natural hosts of Ebola These bats are only present in the countries infected bat has a very advanced immune systems - they have the virus but it doesn’t matter
47
What 3 reactions does reverse transcriptase catalyse
RNA dependent DNA synthesis RNA degradation DNA dependent DNA synthesis
48
What does integration of the HIV genome into the host genome require
Integrase
49
Explain Integration and retrotransposition of viral DNA into the host genome
1. integrase cuts viral DNA 2. Attack of viral DNA on target DNA 3. Gap filling by DNA repair - Either side of integrated viral DNA there is short direct repeats of the target DNA sequence
50
Explain Retroviral-like retrotransposons, common in eukaryotic genomes
LTRs at each end (long terminal repeats)
51
Explain nonretroviral retrotransposons in eukaryotic genomes
Poly A at 3' end of RNA transcript; 5' end is often truncated a LINE: long interspersed nuclear element (~7000Bp) no tRNA binding site
52
What % of our genome are repeat sequences?
50%
53
Types of transposons
LINEs, SINEs, Retroviral-like element, DNA-only transposon 'fossils'
54
Explain DNA-only transposons, common in eukaryotic genomes
Short inverted repeats at each end Element moves as DNA cut-and-paste mechanism
55
Features of transposons
inverted repeats required (min 20 bp) transposase recognises 
the repeats transposase 
brings the 
ends together the 3´OH groups can attack the target chromosome
56
The HIV genome
9700 nt's long 5' LTR Gag – encodes capsid proteins Pol – encodes reverse transcriptase and integrase Env – encodes envelope proteins LTR 3'
57
Explain the processing of the HIV genome
primary transcript converted into polyprotein for Pol gene, further poteolytic processing of the polyprotein
58
Explain the pol gene
a gene encoding a poly-protein - protease: proteolytic processing of the polyprotein - integrase: retro-transposition - reverse transcriptase: RNA intermediate - ribonuclease H: degrade RNA
59
what is the gag gene of HIV required for
required to form virus like particles with transcripts
60
LTR features
repetitive sequences, several 100 bases in length tRNA binding sites in LTR help reverse transcription LTR recognised by integrase for retro-transposition
61
HIV regulatory protein
Gag (capsid), Pol (polymerase) and Env (envelope) Vif, Vpr, Vpu are regulatory proteins with various functions Rev regulates nuclear export of the RNA Nef interferes with protein trafficking Tat regulates transcription
62
HIV life cycle
see poster
63
Explain early HIV synthesis
Splicing of RNA - Rev, Tat and Nef are translated first happens inside nucleus then transported out into the cytosol
64
Explain late HIV synthesis
Mature RNA must not be spliced Rev enters the nucleus Rev binds to the RRE (rev response element) Rev protects RNA from splicing This ensures export of unspliced RNA (from nucleus to cytosol) Now all viral proteins have been synthesised and there is also unspliced RNA (all of which will be packaged into the virus
65
Structure of the GAG protein/gene
N-term - MA (pps) - CA(NTD) - CA (CTD) -(pps) SP1 (pps) - NC - (pps) SP2 (pps) - p6 - C-term
66
3D structure of assembled gag and EM structure
RW
67
Explain inhibitors that affect the hexamer-pentamer transition of Gag (HIV)
Small molecules that bind to the viral CA protein can be potent inhibitors of HIV infection Capsid-targeting drugs are predicted to exhibit high barriers to viral resistance, and ongoing work in this area is contributing to an understanding of the molecular biology of HIV uncoating and maturation
68
Name a caspid inhibitor that shows promise for clinical development
GS-CA1 (discovered in 2017)
69
Explain HIV cell entry
HIV Env protein receptor: CD4 secondary receptor for efficient attachment (CCR5) 1st phase of AIDS secondary receptor for efficient attachment (CXCR4) 2nd phase of AIDS
70
Examples of viruses that affect immune cells
HIV, EBV, Hep B
71
Why do so many viruses choose to invade immune cells
blood / immune cells are generally good vessels to travel the body cells of the immune system end up in lymphoid organs – more cells to infect here
72
define nucleocapsid
a capsid 
that encloses the nucleic acid
73
Icosahedral Capsid features
10-400nm advantage - can make the capsid from many copies of few proteins construction principle - 20 triangular faces Each triangle is made up from (at least) thee proteins The simplest virus capsid is made up from 60 proteins
74
What is the T number (in terms of Icosahedral viruses)
Triangulation number Larger viruses contain more than three proteins per triangle Multiplier is known as the T number Known: T = 1,3,4,,7,9,16,25
75
Explain capsid formation (T=3) and an example of a virus that undergoes this
RW (TBSV)
76
Jelly-roll motif
RW
77
Bacterial viruses/bacteriopage conastruction
head: icosahedral capsid tail: helical typically dsDNA genome
78
Example of plant virus and its construction
helical capsid, Ø 15-18 nm, 
length 300 nm single protein subunit associated with ssRNA+
79
Explain the structure of viruses that infect bacteria vs plants vs animals
Bacteria - usually head + tail, sometimes enveloped, rarely helical or icosahedral Plants - usually helical, sometimes icosahedral, sometimes enveloped (less), not head + tail Animals - usually icosahedral or enveloped, not helical/head + tail
80
What is Vaccinia vs cowpox vs Variola
Vaccinia: The vaccine virus Cowpox (CPXV) Variola: the disease virus (smallpox) - specific to humans
81
Features of Vaccinia (VACV), Cowpox (CPXV), Variola (VARV)
- enveloped, size 140-260 nm diameter - linear dsDNA genome, covalently closed, 130-375 kB - mRNA & protein synthesis in cytosol E early I immediate L late - replication & maturation in cytosol - “wrapping” in trans-Golgi membranes - Poxviridae, virus factories
82
Vaccinia envelope packaging
RW
83
Explain the two forms of smallpox
intracellular mature virus (IMV, fusion) and extracellular enveloped virus (EEV, endocytosis) Both forms are infectious (EEV is more virulent).
84
Explain poxvirus encoding approx 200 proteins
Early phase: essential viral proteins transcribed by viral RNA polymerase uncoating and release of of viral genome into cytoplasm Immediate phase: 2 hrs post infection triggers genomic DNA replication Late Phase: structural proteins viral assembly Virus release direct release: IMV passage through Golgi: EEV
85
Smallpox life cycle
RW
86
Pox: Viral factories
cytoplasmic or perinuclear recruit specific structures cell organelles, e.g. mitochondria, Golgi organise membrane structures: perinuclear replication complexes exclude host proteins interfere with signalling enable viral replication
87
When was smallpox declared eradicated
1980
88
Types of vaccines
Live attenuated Inactivated (killed antigen) Subunit (purified antigen) Toxoid (inactivated toxins)
89
Adenovirus – gene therapy and vaccination
DNA virus Popular vector for gene therapy in monogenic diseases Example: CF, cystic fibrosis Recombinant Adenovirus is being used as COVID19 vaccine
(AZ vaccine, Sputnik 5)
90
Explain RNA vaccines
delivered in fatty acids LNPs (lipid nanoparticle) for COVIS - candidates generated in weeks rather than months
91
Icosahedral virus example
Papovaviridae (italics) - HPV
92
HPV life cycle
RW
93
Human papillomavirus HPV features
more than 70 (120) strains icosahedral capsid 55 nm diameter dsDNA 8 kB circular genome encodes: L1 + L2 capsid proteins, E1 + E2 replication, E4 + E5 assembly / release, E6 + E7 oncogenic proteins
94
Explain how HPV influences cell cycle regulation
E6 dependent ubiquitination and degradation of p53 E7 deregulates the tumor suppressor pRb
95
Explain how HPV infections aren't usually persisrtant, but what happens when they are
- 70 % healed after one year, 90 % healed after two years - HPV6 and HPV11 cause 90% of all genital warts persistent infection - risk of cancer HPV16 and HPV18 cause 70% of all cervical cancers
96
Viral life cycles
Lytic EBV - acute - linear dsDNA Latent EBV - genome inactive - circular dsDNA form Chronic: Hepatitis B - long term - low levels of virus production Transforming: Pappilloma altering cell growth
97
Explain a vaccine against cancer
HPV Vaccination prevents against cancer HPV6/11 causes 90% of all genital warts - cervix, vulva, vagina, anus, penis - transmitted through sexual contact HPV16/18 cause 70% of all cervical cancers Cervarix protects against HPV16/18 Gardasil protects against HPV16/18 & HPV6/11 Nobel Prize 2008 to Harald zur Hausen
98
What protein protects against host immunity in herpes virus and when is it made
Tegument proteins, made in immediate early stage

BIOL3017 - Molecular and structural basis for disease (6 decks)

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