TS3 - Infectious Disease Flashcards
(88 cards)
1
Q
How do nucleoside analogues function as an antiviral drug? What type of inhibitor are they? What is their general structure?
A
A nucleoside is a unit of a nucleotide base with a pentose (RNA) or deoxypentose (DNA) sugar. 3 phosphates must then be added by a kinase for them to become active.
Analogues of these can incorporate into macromolecules and stop DNA or RNA synthesis via obligate chain termination. Hence, they’re competitive inhibitors.
Most nucleoside analogues are some spacer sugar that has a hydroxymethyl group and a nitrogenous base attached.
2
Q
What occurs in the dark zone of germinal centres?
A
B cell proliferation and somatic hypermutation.
3
Q
What molecules mediate T cell-dependent B cell activation?
A
TCR-MHC II and CD40L-CD40 interactions.
4
Q
What are the 6 strategies that viruses can use to make multiple proteins from one gene? Give an example of a virus that uses each of these.
A
- mRNA splicing (HIV)
- Read-through of stop codons (Rous sarcoma virus)
- Multiple start sites (HBV)
- Overlapping genes (HBV)
- Polyprotein cleavage (Zika virus)
- Ribosomal frameshifting (HCV)
5
Q
What is the main therapeutic antibody target in SARS-CoV-2?
A
The spike (S) protein, particularly the S1 RBD.
6
Q
What are two mechanisms of peripheral B cell tolerance?
A
Anergy and clonal deletion (clonal ignorance is also involved).
7
Q
What do all of the global viruses have in common? How can this be used in treatments against these viruses?
A
All viruses use common host-cell glycosylation machinery. The human host is known in advance so we can optimize drugs against this system before the next virus emerges.
e.g., inhibition of the glucosidases that impact viral glycoprotein folding in the ER
8
Q
Define: virion
A
An independent viral particle released from the cell
9
Q
Name two types of control measures currently used against malaria.
A
Existing control measures include mosquito nets, antimalarial drugs, and indoor residual spraying.
10
Q
What antibody class is typically produced in T cell-independent B cell activation?
A
IgM.
11
Q
Name two technologies for B cell enumeration.
A
Flow cytometry and CyTOF.
12
Q
Name two technologies listed for delivering antibody-inducing subunit vaccines against malaria.
A
Examples include pDNA, viral-vector, protein, VLP, and mRNA technologies.
13
Q
What are the genes encoded by the HIV genome? What are each of their roles?
A
HIV contains two pieces of single-stranded RNA.
- 5’ cap
- Gag (form the capsid of the virus)
- Pro (protease that processes polyprotein precursors)
- Pol (reverse transcriptase, RNase H and integrase)
- Env (envelope proteins)
14
Q
What type of immune response are antibody-inducing subunit blood-stage vaccines, like those targeting RH5, designed to elicit?
A
These vaccines aim to induce broadly neutralising polyclonal antibody responses, specifically high-level growth-inhibitory antibodies.
15
Q
What structural features define TI antigens?
A
Simple, repetitive epitopes.
16
Q
Compare the following for RNA to DNA viruses:
- Genome size
- Stability
- Polymerase fidelity
A
For all of these, RNA viruses are smaller/weaker compared to DNA viruses.
17
Q
How do neutralising antibodies protect against pathogens?
A
By binding to and inactivating viruses or toxins.
18
Q
What type of cells do HIV and HBV infect?
A
HIV: CD4+ T cells
HBV: hepatocytes
19
Q
How can the genome size of RNA viruses make them harder to target than DNA viruses?
A
RNA viruses tend to have much smaller genomes, and so the mutations have greater impact and each generation will likely be completely different to the ‘master strain’.
This makes them incredibly hard to target.
20
Q
What can result from deficient B cell activity?
A
Infection or cancer.
21
Q
Describe the structure of the hepatitis B virus.
A
A small, partially double-stranded genome within a protein capsid, surrounded by an outer envelope.
22
Q
What is a consequence of excessive B cell activity?
A
Autoimmunity.
23
Q
What are two mechanisms of central B cell tolerance?
A
Clonal deletion and receptor editing (anergy is also involved).
24
Q
What is RTS,S/AS01 made of?
A
RTS,S is a hepatitis B surface antigen virus-like particle with the CS malaria antigen fused to its surface, formulated with the AS01 adjuvant.
25
What makes a good antiviral drug?
- Active against WT and mutants without allowing for drug resistance emergence
- Minimal adverse effects
- Good pharmacokinetics
- Long elimination half life
- Easy to synthesize and formulate
26
What type of antigens typically trigger T cell-independent B cell activation?
Repetitive antigens like bacterial polysaccharides.
27
What nutrient, often limited in host tissues, is sequestered from bacterial pathogens?
Iron is an example of a nutrient that can be limiting in host tissues, and host systems sequester it from pathogens.
28
How does HIV enter host cells?
1. HIV binds the CD4 receptor via its gp120 glycoprotein trimer
2. gp120 conformational change
3. CCR5 binding site is now exposed
4. Binds CCR5 co-receptor
5. Triggers membrane fusion and insertion of the HIV capsid
29
What is the target of therapeutic antibodies against Ebola virus?
The viral glycoprotein.
30
Why might a reverse transcriptase drug not target HBV as well as HIV?
HIV is a retrovirus and so it relies on RT to integrates its genome into the host genome.
HBV is a hepadnavirus, and so by the time RT is used, it will have already infected the cell nucleus.
31
What are the three fundamental aspects of B cell biology?
Development (BCR/antibody diversity), Selection (central and peripheral tolerance), and Activation (response to infection).
32
What stage of the malaria parasite lifecycle is targeted by blood-stage vaccines?
Blood-stage vaccines target the merozoite stage that is released from the liver and infects red blood cells.
33
Name one stage of the Plasmodium parasite's complex life cycle that occurs in the human host.
The life cycle includes the liver stage where sporozoites infect hepatocytes, and the blood stage where merozoites infect erythrocytes.
34
Define: viral tropism
The ability of a virus to infect and replicate within specific types of cells or tissues in the body.
Different viruses have different preferences, and this is determined by the specific viral proteins that interact with receptors on the surface of host cells.
35
What's the difference between a vaccine and an antiviral drug?
Unlike a vaccine, which increases immunity, an antiviral drug treats someone who's already sick by attacking the virus itself.
36
Where does somatic hypermutation occur?
In germinal centres.
37
What happens when an interferon binds a neighbouring cell?
The receptors dimerize, autophosphorylate and recruit STAT proteins. These also become phosphorylated and dimerize before entering the nucleus to upregulate interferon-induced genes. These genes aim to make a hostile environment for incoming viruses, as well as genes to synthesize more MHC molecules for upregulation of antigen presentation.
38
How do retroviruses integrate their DNA into the host genome? What machinery is involved?
Integrase attacks the ends of the viral genes, creating 3'OH whilst the host DNA is simultaneously being attacked to form blunt ends, typically in hot spots. Cellular repair enzymes resolve this joining reaction and form the integrated provirus.
39
What is triggered when antibody-antigen complexes activate complement?
Classical pathway activation and antibacterial activity.
40
How is the mature virion (IMV) form of Mpox released?
By cell lysis.
41
Give a detailed explanation of the process of reverse transcription of HIV.
1. Primer tRNA anneals to the PBS sequence in the gRNA
2. tRNA is extended to form a DNA copy of the 5' end of the genomic RNA
3. RNase removes the RNA template
4. FIRST JUMP: DNA hybridizes to remaining RNA at the 3' end
5. DNA (-) strand is extended and completed. RNA is removed.
6. (+) strand DNA primes at the PPT and synthesizes to the 3' end.
7. RNase H degrades tRNA and PPT
8. SECOND JUMP: (+) strand DNA binds the PBS at the 3' end of the (-) strand.
9. Both strands extended and completed to give ds-DNA
42
Which domain of HA binds the host sialic acid receptor?
The globular head domain.
43
How do HIV protease inhibitors work?
They bind to the active site of the HIV protease enzyme, preventing it from cleaving the precursor polypeptide and producing the mature viral proteins that are necessary for the production of new viral particles.
44
What is the main antibody class produced after T cell-dependent B cell activation?
IgG and other class-switched antibodies.
45
How does HBV enter and replicate within the host cell?
1. Core particle is uncoated to release the partially ds-DNA genome
2. Within the nucleus, the genome is converted into cccDNA (covalently closed circular)
3. cccDNA remains in the nucleus and is transcribed by cellular machinery (RNA)
4. Viral transcripts are used as templates for the synthesis of new viral genomes by the viral polymerase (reverse transcription to DNA)
5. The DNA is used to form the genome of new viral core particles that bud off from the infected hepatocyte and are released into the bloodstream.
46
Why is RH5 considered an essential and highly conserved target for blood-stage malaria vaccines?
RH5 is considered essential and highly conserved because it is susceptible to broadly neutralising polyclonal antibodies and its interaction with basigin (CD147) is necessary for erythrocyte invasion.
47
What are the two large plasmids that carry virulence factors in Bacillus anthracis?
The virulence factors of B. anthracis are located on two large plasmids: pXO1 (encoding toxin genes) and pXO2 (encoding capsule genes).
48
What are two possible fates of B cells in the light zone of germinal centres?
Differentiation into memory B cells or plasma cells, or re-entry into the dark zone.
49
What characterises 3rd generation smallpox vaccines?
Non-replicating, attenuated VACV strains with improved safety.
50
What is the primary transmission route for Bacillus anthracis causing Anthrax in humans, according to the table?
The primary transmission route listed is ingestion, although respiratory and wound routes are also mentioned.
51
Define: zoonosis
Any disease or infection naturally transmissible from animals to humans
52
What are the potential problems with nucleoside analogues?
1. Delivery
2. Escape mutants
3. Toxicity
4. Metabolic instability
53
How are some people resistant to HIV? What is thought to have caused this?
A mutation in CCR5 prevents HIV from binding properly. This is a fairly new mutation, thought to be caused by positive selection from smallpox as this also uses CCR5 to enter cells.
54
Define: defective particles
An empty virus shell without the genetic material inside
55
What is cccDNA? Why is it important for HBV?
Covalently-closed circular DNA - a stable mini-chromosome that is present in the nucleus of infected hepatocytes.
It serves as a long-term reservoir for the viral genome, and is responsible for the persistence of chronic HBV infection.
56
What is pgRNA? What is its role in the HBV life cycle?
pregenomic RNA - intermediate molecule that links the transcription of the viral genome from the cccDNA to the synthesis of new viral DNA genomes and the assembly of new viral particles.
57
What variations are there of nucleoside analogue antivirals? Give an example and explain how it's specific to infected cells.
Modifications are usually only on the sugar, not the base as this can easily change the hydrogen bonding chemistry.
Acyclic nucleoside analogues have their rings removed. e.g., Acyclovir which is an analogue of deoxyguanosine.
In uninfected cells, the drug cannot be phosphorylated for activation. In infected cells, the virus encodes its own kinase.
58
What do obligate intracellular bacterial pathogens primarily exploit from their host cells?
Obligate intracellular pathogens exploit host cell metabolites.
59
What are the main Influenza antibody targets?
HA and NA proteins.
60
Where are many key virulence factors of Yersinia pestis located?
Many key Y. pestis virulence factors are located on plasmids, which were part of the accessory genome of its ancestors.
61
State the steps involved in developing a protease inhibitor.
1. Identify the protease cleavage site.
2. Build a peptide substrate
3. Build a peptidic inhibitor that modifies the cleavage site
4. Modify the inhibitor to reduce the peptidic nature
5. Solve the structure of the enzyme/inhibitor complex
6. Improve the fit of the inhibitor
62
How does the metabolic capacity of a bacterial pathogen generally compare to its ancestor?
The metabolic capacity of a pathogen is almost always much more limited than the ancestral organism from which it evolved.
63
Give a detailed explanation of reverse transcription in HBV.
1. RT-RNase H binds to the e sequence on the RNA (5' end). This signal is present at bond the 5' and 3' end, but only the 5' signal functions for encapsidation.
2. Core is recruited and the capsid assembles. In the absence of RNase H, core assembles into capsids that packages DNA randomly.
3. In the capsid, first-strand synthesis is initiated by using the -OH of a tyrosine in RNase H as the primer. 4 nucleotides are added using the RNA template before the first jump to the 3' end.
4. DNA synthesis of the first strand continues until the 5' end of the RNA is reached.
5. RNase H degrades the RNA, but leaves the 5' RNA cap. This cap is transferred to the 5' of the new DNA as a primer for second strand synthesis.
6. The new DNA begins to cyclize and the cap at the 5' end forms a 'bridge' that connects the 5' end of the cDNA to the 3' end.
64
How can B cell tolerance be assessed?
By testing B cell or antibody reactivity to self and non-self antigens.
65
Name two antibody-independent functions of B cells.
Cytokine production (e.g., IL-10) and antigen presentation to T cells.
66
How does opsonisation aid phagocytosis?
Antibodies label antigens for recognition and uptake by phagocytes.
67
What protein on the surface of the Plasmodium falciparum sporozoite is a target for anti-sporozoite vaccines like RTS,S?
The target is the Plasmodium falciparum Circumsporozoite protein (PfCSP) on the surface of the liver-invasive sporozoite.
68
What type of organism causes Malaria?
Malaria is caused by Plasmodium parasites.
69
Where do HBV virions bud from?
The ER
70
Name two technologies for assessing antibody specificity.
Antigen arrays and PhIP-Seq.
71
How does HIV replicate within host cells?
1. RTase converts its RNA genome into DNA
2. Rnase H degrades the RNA template
3. DNA is transcribed to form ds-DNA
4. Integration of the ds-DNA using integrase
5. ds-DNA is transcribed into mRNA
6. mRNA can be spliced, or left alone to encode Gag, RT and genomic RNAs
7. Genomic RNAs bud off from the host cell
8. Viral protease cleavage and maturation
72
What are interferons? Why are they tightly regulated? How are they used in antiviral immunity pathways?
Proteins released by cells in response to viral entry. They have short half-lives thanks to destabilization sequences as they can be damaging to the host.
When a viral infection is detected by host cells, they produce and release IFNs that bind to neighbouring cells and induce activation of antiviral pathways.
73
How do B cells and T cells differ in antigen recognition?
B cells recognise free antigens; T cells recognise MHC-bound antigens.
74
What disease is caused by the bacterial pathogen Yersinia pestis?
Yersinia pestis causes Plague.
75
What are the functions of each HIV accessory genes?
Vpr: (viral protein R) facilitates viral replication in non-dividing cells by transported subviral particles across the nuclear membrane.
Tat: (trans-activator of transcription) potent transcriptional activator that binds in the LTR promoter.
Rev: (regulator of expression of virion proteins) essential for nuclear export of unspliced and partially spliced mRNA.
Nef/Vif/Vpu: enhance production and release of infectious viral particles
76
Where does VDJ recombination occur?
In the bone marrow.
77
Why is Mpro a good target for all coronavirus drug treatments?
It's present in other coronaviruses and doesn't mutate easily so variants are less likely.
78
What's the difference between an RNA virus and a retrovirus?
RNA viruses are viruses that use RNA as their genetic material instead of DNA. RNA viruses can be further classified into different groups based on their genome structure, replication strategies, and mode of transmission.
Retroviruses, on the other hand, are a specific type of RNA virus that have a unique replication strategy that involves reverse transcription. Retroviruses use an RNA genome to produce a DNA intermediate that is then integrated into the host genome, where it can persist for the lifetime of the infected cell.
79
What erythrocyte surface protein does the P. falciparum RH5 protein interact with?
RH5 forms an essential interaction with basigin (CD147) on the erythrocyte surface.
80
What therapeutic uses do iminosugars have against viruses?
Iminosugars mimic the structures of carbohydrates. They can therefore interfere with the processing of viral glycoproteins that are vital for viral entry and release.
81
What is the typical clinical course of HIV infection? What are the symptoms at each stage?
Acute infection - virus replicates and the immune system responds, giving flu-like symptoms.
Clinical latency - can last several years or even decades where the virus replicates at low levels, gradually weakening the immune system. Many don't experience symptoms at this stage.
AIDS - severe immune deficiency and development of opportunistic infections and cancers. Symptoms include weight loss, persistent fever and frequent infections.
82
What public health observation indicates an urgent need for a malaria vaccine?
Progress in malaria control has stalled, highlighting the urgent need for a vaccine.
83
Give the steps of a generic viral replication cycle.
1. Attachment
2. Entry and uncoating
3. Synthesis of viral proteins and nucleic acids
4. Synthesis of viral structural proteins
5. Maturation/assembly
6. Release of new virions
84
What are the three main mechanisms generating B cell diversity?
VDJ recombination, somatic hypermutation, and class-switch recombination.
85
What two cost-effective interventions are cited as having achieved the greatest impact against infectious disease?
The two interventions are the provision of clean drinking water and vaccination against infectious disease.
86
Where does Mpox genome replication occur?
In the cytoplasm, in viral factories.
87
Name two considerations in designing therapeutic antibodies for infectious disease.
Target selection and resistance escape potential.
88
What is notable about the Mpox genome?
Large, linear, dsDNA with LTRs.
