Unit 2 Exam Recall Q's Flashcards
What do you know about viruses? Start generally and go into more applied observations.
Do not define.
Generally:
- eat and breathe billions of them regularly
- infect our pets, domestic food animals, wildlife, plants, insects (crossing species barriers constantly - zoonotic infections)
- most abundant entities in global ecosystems
- different viruses face radically diff. challenges in host & extracellular environments
Applied:
- can co-evolve with hosts
- we carry viral genomes as part of our own genetic material
- exchange genetic info between virus & host
- viruses capture human genes (can encode things needed in our genes to use to adv. or not at all)
- too big to diffuse across PM (must create mechanisms to bypass these layers)
Do marine viruses affect the global carbon cycle? If yes, how/why? Explain generally & with ex of whales.
- Microbes represent large majority
of biomass in the ocean - Every milliliter of seawater has at least 10 million virus particles
Why/how?
- pathogens steal energy from ocean bacteria, preventing them from sucking up the greenhouse gas carbon dioxide
- impact material cycles and energy flows in the food web
Whales
- massive shedding events
- infected by virus from calicivirus family
How infected are we really with viruses? Define VZV, HCMW and EBV as examples.
- majority of viruses are innocuous (not harmful)
- persistent, life long infections (for ex: herpes virus(es) don’t jump species, attended to our biology, reactivation possible)
Defining
- VZV: human herpesvirus 3, chicken pox & shingles
- HCMV: Cytomegalovirus, leads to prenatal effects
- EBV: Human gammaherpesvirus 4, Mono (triggered by multiple Sacroiliitis)
What is the evidence that viruses have been with us since ‘the beginning’? What percent of our genome has retro-virus sequences?
- presence is evident in genomes of
vertebrates - retroviruses integrate into host genomes, meaning they have shaped evolution & gene expression
- 10% of the human genome consists of retrovirus-like sequences
- Similar findings in other genomes (mouse, rat, etc.)
How are these viral sequences ‘fixed’ in the human genome?
- fixed as they infect cells that are apart of humans germ line cells
- integrated and passed to progeny
Explain how retroviruses are in the process of being ‘fixed’ in the Koala host genome? What is the virus called?
- Koala retrovirus (KoRV)
- Infectious cause of Koala Immune Deficiency Syndrome (KIDS) which is like AIDS
- KoRV is being ‘endogenized’ or integrated in Koala genome
- spreads ‘horizontally’ and ‘vertically
Do integrated ancient viruses have an effect on us? Syncytin?
Syncytin
- viral gene (endogenous retrovirus)
- Ancient cell attachment protein
- Located in human chromosome 7
Overall:
- retroviral envelope protein involved in human placental development
- protects the fetus from the mother’s immune system until delivery
- creates fused synctiotrophoblast layer
Explain the process of Syncytin creating a synctiotrophoblast layer. Why important?
Process:
- takes cells and makes them fuse together
- fuses into 1 cell, many nuclei created
Why?
- needed to maintain semipermeable barrier between mother and fetus
during pregnancy
Define what a virus is and what it lacks. Explain what you know about virus particles?
Definition:
- toxic/poision
- submicroscopic (smaller than diffraction limit on most microscopes) , obligate intracellular parasites
- smaller than bacteria
Lacks:
- genetic info to generate metabolic energy and synthesize proteins (very dependant on overtaking host machinery, use this to learn about host/virus)
Virus Particles:
- physical structures
- molecular structures that package virus genomes in infected cells and transmit them to new host cells (virus makes components in host cells, assemble into package and release from cell)
- do not divide or grow
Why do viruses overtake cellular process? Would we consider them living/alive?
- certainly viruses multiply, but they do not ‘grow’
- viruses harness cellular processes to direct genome replication and assembly of progeny virions
Alive?
- inside the host cell: viruses are alive
- outside of the host cell: complex assemblages of metabolically inert
chemicals
How do we visualize viruses? Give two examples and explain.
- Plaque assays (indirect)
- serial dilute inoculum
- add to layer of susceptible cells
- overlay with agar
- wait for cytopathic effect (cell destruction)
- plaques are holes in the single layer of cells.
Notes:
- virus destroys host cell on replication, so infects cells w/ viruses from sample
- overlay cells are in immobilizing agar, infectious cells grow laterally
- cytopathic effect allows visualization of cell death (intact = like intact cobblestone, infected = scattered)
- plaques show initial infection event via holes present
- Electron Microscopy (direct)
- powerful method to visualize viruses
- electrons pass through a stained, ultrathin sample
What are physical properties of viruses?
- capsids (protein shells)
- genomes (dsDNA, ssDNA, dsRNA, +ssRNA, -ssRNA)
- optional components: tegument and envelopes
Key:
ds = double stranded
ss = single stranded
+ = ready to be translated
- = must decode into + to translate
Explain what you know about virions. Give steps in order of reaching host cell.
Virion:
- a complete, infectious, virus particle
Steps:
1. Assembled correctly
2. Escape the cell (where made)
3. Survive extracellular environment
4. Attach to and enter another host cell
5. Uncoat and release the viral genome
Explain all you know about virus capsids. What do they protect from? What’s a capsomer?
Capsids:
- a rigid, symmetrical container for viral genomes
Protect fragile nucleic acid genome from:
1. Physical damage - shearing by mechanical forces
2. Chemical damage - UV irradiation (from sunlight) leading to chemical
modification
3. Enzymatic damage - nucleases derived from dead/leaky cells or
deliberately secreted by vertebrates as defence against infection
Capsomers:
- subunit of the capsid, an outer covering of protein that protects the genetic material of a virus.
- self-assemble to form the capsid.
Why do virus capsids need to be metastable?
- strong enough to withstand environment and protect genome
- able to be ’unlocked’ and disassemble during virus entry (uncoating)
capsid (box) –> cell cytoplasm –> nucleus (turn on virus genes)
What are the four virus morphologies? Explain each.
- Helical
- simplest capsid
- composed of single type of capsomer stacked around a central axis
- forms a helical structure
- hollow center of helix contains the viral genome (usually ssRNA) - Icosahedral
- animal viruses have icosahedral symmetry (e.g. poliovirus, adenovirus, and hepatitis A virus)
- Icosahedron - a polyhedron with 20 faces, 30 edges and 12 vertices
- 5 fold symmetry (differing proteins create variability of structure)
- Many viruses with ‘naked’ icosahedral capsids are enteric viruses (affecting gastro. tract)
- get rid of w/ bleach - Enveloped
- cover themselves in outer layer of host cell lipid membrane (plasma membrane, or internal membranes ie: NM, ER)
- have membrane-spanning viral glycoproteins (important roles in infection)
- Matrix proteins found just beneath the lipid envelope and provide link between the envelope and the nucleocapsid
- a lot of examples (Rabies, SARS-CoV-2, Ebola, HIV, influenza, herpes)
- sensitive to cleaning agents like detergents - Complex
- ex: Bacteriophage T4 (explain later)
- have a capsid which is neither purely helical, nor purely icosahedral,
- may have extra structures such as protein tails or a complex outer wall.
How do these capsomers bind to the viral genome? Is it likely to be sequence specific?
They bind to viral genome due to electrostatic interactions
- RNA (-)
- Amino acids (+)
- electrostatic int. aid in assembly as they guide RNA into protein subunits, each subunit needs amino acid inside
No, not sequence specific
<—- right to left assembly
What governs the length and diameter of the helix?
- length of helix is determined by the length of the genome
- diameter determined by turns in helix or width of the coil
Explain Fraenkel-Conrat & Williams experiment of TMV and what they found out about (helical) capsids/viral particles?
Experiment:
- when mixtures of purified tobacco mosaic virus (TMV) RNA and coat protein were incubated together, virus particles formed.
Discovery/conclusion:
- virus particles could form spontaneously from purified
subunits w/o any extraneous information
- particle in the free energy minimum state
- some viruses are fragile and unable to survive outside the protected host cell environment, but many persist for long periods, in some cases for years (capsids aid in stability)
Why do so many viruses adopt the icosahedral capsid shape? Give four reasons.
- Strength of the icosahedral structure
- Resistance to shear forces (& fluid)
- Tight packaging of the genome – maximal volume:surface area ratio
- Genetic Economy – can be built from a few repeating subunits (can do a lot w/ small genome)
How is the cosahedral structure advantageous for these enteric viruses? How should we decontaminate surfaces covered with these viruses? Give two examples.
Advantageous
- strong and resistance enzymes
- low hostile pH environment
Decontamination:
1. bleach
- oxidizes proteins
- lose ability to attach to host cell or replicate genome
- takes time
- detergent (possibly)
- denatures proteins to an extent
- disrupts lipid envelope
- honestly better for enveloped viruses (don’t like -OH, more susceptible to agents)
What do you know about glycoproteins? Why sugar proteins important for protein function?
What are the two types of glycosylation?
Glycoprotiens
- Viral glycoproteins are modified with host sugars added in the ER and Golgi apparatus
- normal host process, many host integral membrane proteins are glycosylated (virus reworked normal system for benefit)
Types of glycosylation
1. N-glycosylation: addition of sugar chains on amide nitrogen of asparagine
2. O-glycosylation: addition of sugar chains on serine/threonine
These sugar decorations are often CRITICAL for protein function:
- won’t work if not properly glycosylated
- can’t hide from immune response
- fight to keep away antigens
Compare structural and non- structural proteins.
Structural Protein
- found in the virion
- even if it does not play a structural role its called structural protein
- ie: polymerase in ebola virus, only plays role once INSIDE host
Non-structural Protein
- made in the infected cell but not
found in the virion.
- can still be essential to the life cycle of the virus even if it is not part of the virion.
- ie: can help in making progeny but not passed on
Go into detail about the involved virus; Herpes Simplex Virus.
- Herpesviruses have envelopes AND tegument proteins
- Tegument proteins are delivered into cytoplasm upon virus entry (allows them to act early in infection, to prevent antiviral responses)
Tegument
- space for enzymes to be delivered and do work (virus may dump these enzymes out to antagonize host immune system)
Briefly explain structure of bacteriophage T4
Hint: Complex virus morphology
- Icosahedral head: containing viral dsDNA genome
- Helical tail
- Hexagonal base plate
- Protruding protein tail fibres
Give an overview of the form and functions of different virus parts. There should be seven named.
- Spike protein (receptor binding)
- Envelope (entry and exit)
- Matrix protein (assembly & stability)
- Capsid (stability)
- Nucleocapsid (genome packaging)
- Genome - RNA or DNA
- Polymerase (genome replication)
What are the steps viruses follow in a single replication cycle? Acronym?
APUTTGAR
Attachment
Penetration
Uncoating
Transcription
Translation
Genome Replication
Assembly
Release
Note:
- first three apart of entry
- last three apart of maturation
What are the two biggest concepts relating to viral entry?
- Where the virus infects with in the body, where the virus can enter, is
dictated by the location in the body of the virus receptor - Where the virus is infecting within the body dictates the disease
How does bacteriophage T4 attach to E. coli?
- initial reversible binding via long tail fibres
- browses cell surface to find right spot - irreversible binding via short tail fibres
- bottom of tail
- interacts w/ cell receptors
- attempt to infect cell
Note:
- Attachment, penetration and uncoating at occur at bacterial cell surface
Explain the steps in bacteriophage entry, more specially, how Phage T4 binds to specific receptors on E. coli cell surface.
- Long tail fibres recognize outer membrane protein C (OmpC) or lipo-
polysaccharide (LPS) of E. coli (REVERSIBLE) - After at least 3 long tail fibers have bound, there is a conformational change in the baseplate, and short tail fibers extend and bind irreversibly to the core region of the host cell LPS. (IRREVERSIBLE)
- Contraction of tail sheath and penetration of outer membrane
- T4 lysozyme (virus structural enzyme) degrades (pokes holes in) protective peptidoglycan layer
- Inner membrane is degraded
- Phage DNA is delivered into cytoplasm
Briefly describe viral infection of EUKARYOTIC cells. Attachments? Penetration types? Locations?
- Initial attachment
- reversible electrostatic interactions - Stable attachment
- irreversible tight interactions with receptor(s) - Viruses penetrate host cells by
- Membrane fusion at the cell surface
- or receptor-mediated endocytosis
Where beginning stages occur:
Attachment - cell surface
Penetration - cell surface or internal membrane(s)
Uncoating - cytoplasm
What is Virus–Receptor Promiscuity and specificity? (VAP)?
- VAP = Virus attachment protein
- Different viruses can bind the same receptor (ie: Adenovirus and Coxsackievirus bind to same
cellular receptor) - Related viruses in the same family can bind different receptors
- Virus entry sometimes requires more than one receptor (there is an order to receptor engagement; receptors first, co-receptors second)
- Receptor-coreceptor system
Ultimately just:
- Complex interactions with the different cell surface receptors
- Some require a combo of receptors to confer entry
Describe Influenza Virus’s cell receptor; Sialic Acid.
Note:
- viral entry into human cells
- a generic term for the N- or O substituted derivatives of neuraminic acid, a monosaccharide with a nine-carbon backbone
- Sialic acids are found widely distributed in animal tissues mostly in glycoproteins
- occur @ end of sugar chains connected to the surfaces of cells and soluble proteins
Sialic acid is ubiquitous on cell surfaces. What does this mean for influenza virus tropism?
- able to infect many cell types.
- diff. strains bind more strongly to diff. types of sialic acid chains
Describe the steps the influenza virus does to achieve viral entry by endocytosis. There are six.
- Initial attachment of HA envelope glycoprotein to cell surface sialic acid
- Receptor-mediated endocytosis
- pH drops in endosomes (pH 7 to pH 5)
- Low pH induces conformational change in HA, exposing hydrophobic fusion peptide.
- Fusion..viral and cell membranes mix.
- Influenza virus genome delivered into host cell
