6. Infectious particle (virus) Flashcards
what are viruses? (2 ish)
- ____A____ cells of viruses include which groups of cellular organisms?
- outside of ____A_____, viruses exist as ______ _________ _________ called ______B_______
- each type of virus is essentially WHAT enclosed in WHAT
- how many types of nucleic acid is found in the ____B_____ of a give virus? examples
- Viruses are obligate intracellular parasites (ie piece of code that highjack organisms) –> they can replicate only inside host cells (ie not independent: typically not metabolically active when outside host)
- Host cells of viruses include all groups of cellular organisms (bacteria, archaea, eukarya)
- Outside of the host, viruses exist as inert infectious particles called VIRIONS
- Each type of virus is essentially a piece of nucleic acid enclosed within a protein coat (capsid)
- Only one type of nucleic acid is found in the virion of a given virus.
– DNA virus
– RNA virus
*Both can have either single stranded or double stranded genomes
- how many proteins in a simple virus? vs in a complex virus?
- in all cases, who supplied the building block, the machinery and the energy required to produce new virus particles?
- simple: 3, complex: >100 proteins
- HOST cells supply building blocks (nucleic acids, aa), machinery (at least ribosomes) and energy required to produce new virus particles
*some viruses have DNA polymerases though
*No virus code for their own ribosome
*no correlation between host of virus (animals, bacteria, plants) and size of virus)
STRUCTURE OF VIRIONS:
describe:
- capsid
- nucleocapsid
- capsomeres
- envelope
- what in the envelope are virus specific and are encoded on what? usually involved in what?
- shape of virus is determined by what? (2)
CAPSID: protein coat around nucleic acid
NUCLEOCAPSID: nucleic acid + protein coat
CAPSOMERE: protein subunit that makes up the capsid
ENVELOPE: lipid containing layer with embedded proteins; in animal viruses, this envelope originates from cytoplasmic membrane of host cells
- proteins! –> encoded on viral genome –> usually involved in attachment of virus to the next host cell –> ie spikes made of glycoproteins
- by nature of capsomere and length of genome
what are 2 different types of virus?
a) __________ virus
- example
- # identical capsomeres/virion
- typical of many _______ viruses
b) __________ virus:
- most common shape is what? describe
- # of capsomeres?
- example
a) HELICAL VIRUS
- tobacco mosaic virus (model organism)
- 2130 identical capsomeres
- typical of many plant viruses
b) POLYHEDRAL VIRUS
- several shapes are possible but most common is icosahedron –> regular polyhedron with 20 triangular faces (a and b) made of 3 capsomeres
*kinda like a sphere –> easiest way to encapsulate genome
- bc of geometry, only some capsomere numbers are possible
- other viruses may have more faces –> human papilloma virus contains 72 clusters of 5 capsomeres
what is the most complicated virus in terms of structure (and not necessarily in terms of what)? describe
bacteriophages!
*not necessarily complicated genome organization
- capsid + viral genome = nucleocapsid
AND 2° structure: use it to inject DNA in bacteria
- what are viroids?
- is it a virus?
- replication is dependent on what?
- cause of which 2 diseases ish
- pathogen of which organisms?
- how do they move ish?
- are closed circles of single stranded RNA containing 240-380 nucleotides (just a circular piece of RNA hybridized on itself)
- no capsoid, so technically not really a virus
- replication is dependent on host machinery: disease is caused by overtaking of this machinery by the viroid
- cause of: cadang-cadang disease of coconuts + potato spindle tuber
- of plants!
- move through pores/plasmodesma –> can more from cell to cell inside plants (can also move from plant to plant through like insects and animals)
what are prions?
- cause _________ ________ disorders –> 5 examples
- prions consist solely of 1 protein (just 1 protein, not a genome)
- Scrapie (sheep) –> scratch all its wool off
- Bovine spongiform encephalopathy (cattle) – BSE – mad cow disease.
- Creutzfeldt-Jakob disease – CJD (human)
- vCJD: transmitted by ingestion of BSE-contaminated product (human) (variant of CJD)
- Kuru (human) –> tribe, older women had neurodegenerative disease –> when they died, ppl eat their brain..
explain prions: misfolded proteins
- 2 types of proteins
- how to accumulate bad type ish
- what happens when you have the bad type?
1) endogenous PrP^C (folded correctly) –> everyone produces it in neurons, we don’t really know why
2) PrP^SC –> misfolded protein
- if there’s a stressor, OR spontaneous generation of PrP^SC OR conversion of mutant PrP into PrP^SC OR inoculation of PrP^SC OR if you eat brain of someone who had prions (but can only reach brain after a long time + have to eat a lot = low probability)
- once you have misfolded prion proteins (PrP^SC) –> they induce misfolding of PrP^C protein
*the prion protein does NOT replicate –> it induces accumulation of misfolded PrP^SC proteins (so brain produces more PrP^C proteins but they all converted to PrP^SC –> which kills the cells
*PrP^C protein is primarily found in neurons
how can you visually see misfolded protein in brains of patients with CHD?
sponge-like lesions in brain tissue!
- filled with holes = dead neurons
TAXONOMY OF VIRUSES:
- viruses are grouped into ________ (ending in WHAT)
- viruses are given a ________ name (end in WHAT)
- viruses are given a _________ name (usually in what language?)
classification based on 5 characteristics
- families –> end in -viridae (ie retroviridae)
- genus name: end in -virus (ie lentivirus)
- species name: usually in english (ie human immunodeficiency virus
- Nature of the host (animal, plant, bacteria, etc.), ie infect who Ex.: bacteriophages infect bacteria.
- Type of disease caused (enteric, leukemia, pneumonia). Ex. Murine leukemia virus (MLV).
- Life cycle (pathways of nucleic acid replication and transcription).
- Naked or enveloped
- Type of nucleic acids and strandedness (+ strand: same as mRNA)
baltimore classification scheme –> classification based on WHAT?
- why useful?
- what does the virus metabolism consists of? (2)
2 types of RNA genomes. describe
- based on type of genome! useful bc the kind of genome will dictate the replication mechanism
- make capsid (proteins) + replicate DNA
RNA GENOMES:
- plus configuration (+ssRNA): same stand than mRNA –> can be translated directly
- minus configuration (-ssRNA): complementary to mRNA –> needs to be transcribed into plus strand before it can be translated
describe the relationship between -ssRNA and +ssRNA and viral proteins
- what is needed for each conversion?
*schéma!
- positive single strand RNA can be transcribed into negative ss RNA using viral RNA-dependent RNA polymerase(RdRP) (needs to be supplied by virus! doesn’t exist in cells (animals plants, bacteria))
- -ssRNA can also be transcribed into +ssRNA by RdRP
- only +ssRNA can be read by HOST ribosomes and translated into viral proteins using host’s ribosomes
- to make more +ssRNA, convert/copy +ssRNA to -ssRNA –> then make more +strand using -strand
explain the 5 step life cycle of viruses
- ATTACHMENT (adsorption): phage attaches to surface of the host –> spike proteins attaches to specific receptors!
*ie bacteriophage attaches to bacteria cell
*plat viruses are usually introduced into host by insect vectors or following mechanical damage - PENETRATION: viral DNA enters the host cell (sometimes whole virus also enters)
- BIOSYNTHESIS: phage GNA/genome replicates (transcription) and phage proteins are synthesized (ie proteins that the virus genome codes for)
- MATURATION: new phage particles are assembled (ie virus components, nucleic acid, nucleocapsid and accessory proteins to form new virions!) and mature –> done spontaneously OR helped by proteins
- RELEASE/LYSIS: mature virions exit the host cell by means of budding OR by causing lysis of the cell: releasing newly made phages/virions
*plant viruses exit and are transmitted by means of vectors
what are 3 ways viruses can enter the host cell?
*which one is the most used ish?
- naked virus (no envelope) –> nucleic acid injected in the cell (capsid left at surface)
- enveloped viruses: membrane fusion (virus + host) –> nucleocapsid goes inside cell (and envelope left at cell surface) –> capsid degraded inside cell + genome released
- most enveloped viruses of eukaryotes use endocytosis (viropexis: complete virion enters the cell) –> membrane fusion but membrane reformed inside the cell (ie the entire virus gets phagocytosed) –> such viruses MIGHT be delivered to lysosomes which degrade the capsid (uncoating) –> nucleic acid is then released into the cytoplasm
what are the 4 important steps ish of virus replication
*schéma of number of infectious virions (y) vs hours (x)
- INOCULATION: inoculum of virus binds to cells (decrease in number of virions)
- ECLIPSE/latent periods: time necessary for host cells to replicate the viral genome and to synthesize the viral components (proteins, nucleic acid…)
*flat line - BURST: virions are detected OUTSIDE of cells
- lysis: virus-encoded proteins damage the cytoplasmic membrane. In bacteria, a virus- encoded protein destroys the peptidoglycan layer.
- budding (enveloped virus) –> usually slower
- line increases rapidly! - BURST SIZE: number of virions released (varies according to virus, host cell)
- line is flat, but high
how long for virus replication:
- bacterial
- animal
bacterial: 20-60min
animal virus: 8-40 hours
*explain delay between getting infected and symptoms
explain steps of budding (how a virion is expelled from host)
*3 steps ish
- viral capsid moves to where the membrane proteins are
- viral capsid pushes against membrane (where viral glycoproteins are) and forms a ball ish
- budding of envelopped virus: has an enveloppe with viral glycoproteins on it! + completely detaches from host cell
best studied bacteriophages infect WHAT
- most phages contain what type of nucleic acid?
- are they naked or with envelope?
- infect E.coli (gram neg)
- most contain linear double stranded DNA genomes (but can also have RNA or single stranded DNA)
- most are naked but some possess lipid envelopes
what are the 2 types of bacteriophages + describe + examples
VIRULENT phages:
- infection of host cells always leads to replication resulting in host cell lysis (lytic pathway).
Ex.: T4.
TEMPERATE phages
- have two options:
1) lytic pathway or
2) lysogenic pathway: genome becomes incorporated into the bacterial host genome (stays dormant in the cell
Ex.: Lambda (Discovered by Ester Lederberg, 1922- 2006).
explain the life cycle of bacteriophage T4 (4 steps)
- difference between virulent and temperate phages
1) Adsorption: T4 attaches to the core region of LPS by the tail fibers.
2) Following attachment, the tail sheath contracts, forcing the central core through the outer membrane. 3) Tail lysozymes digest the peptidoglycan layer, forming a small pore.
4) The phage DNA is then injected into the cytoplasm of the host cell.
- Virulent phages: replication and release of new virions.
- Temperate phages: the phage genome may integrate the chromosome, resulting in a prolonged, latent state of infection (lysogeny).
most double stranded phage genomes are linear/circular with ____A______
- upon entry into cells, ____A______ form what?
- most dsDNA phage genomes are linear with cohesive ends, a region of single stranded complimentary DNA
- upon entry into cells, cohesive ends join, forming a circular molecules of dsDNA
explain the life cycle of bacteriophage: lambda
(temperate phage replication)
- phage attaches to host cell and injects DNA
- phage DNA circularizes and enters lytic or lysogenic cycle:
LYSOGENIC CYCLE:
3a. if good conditions and not much stress: phage DNA integrates within bacterial chromosome –> forms a prophage –> lysogen: bacteria that contains a prophage
4a. lysogenic bacterium reproduces normally: happily replicates: every daughter cell also has a prophage with the virus DNA
5a. occasionally (ie if conditions turn bad), prophage excise from the bacterial chromosome and enters the lytic cycle
LYTIC CYCLE:
3b. new phage DNA and proteins are synthesized and assembled into virions
4b. cell lyses, releasing phage virions
bacteriophage lambda replication (temperate phage)
- after circularization, lambda genome is integrated where? using which enzyme? this enzyme is encoded where?
- what is a prophage?
- what is a lysogen?
- what is excision?
- what (3 examples) typically activate the lytic pathway?
- integrated at a specific site in bacterial chromosome: the attλ site –> the att region in the phage genome is homologous to the attλ site
*enzyme lambda integrase catalyzes integration of phage genome at this site –> lambda integrase is encoded on phage genome - PROPHAGE: phage genome within host cell chromosome
- LYSOGEN: bacterium that contains a prophage
- EXCISION: prophage exits the chromosome and continue along the lytic pathway, resulting in production of new virus particles and host cell lysis
- in stressful conditions like starvation, antibiotics, non-optimal temp
- in eukaryotic cells, DNA replication occurs where?
- genome of DNA viruses usually replicated where?
- genome of RNA viruses usually replicated where?
- DNA replication (and transcription of mRNA) –> in nucleus!
- genome of DNA virus –> nucleus of cell (virus DNA needs to enter nucleus!)
- genome of RNA virus: replicated in cytoplasm of cell
ANIMAL VIRUSES: DNA genome
- example?
- where is DNA replication?
- what is penetration?
- host transcription/translation apparatus synthesizes which proteins at which stage ish
- assembly (of proteins) occurs where? is there an envelope?
- ssDNA genome first converted to WHAT?
- Herpesvirus
- in nucleus of animal cell!
- PENETRATION: fusion of cell cytoplasmic membrane with virus envelope –> Nucleocapsid is transported to nucleus where viral DNA is uncoated.
Host transcription/translation apparatus synthetizes:
a) Immediate early proteins (transcription factors and, in some cases, virus-specific RNA polymerase).
b) Delayed early proteins (viral-specific DNA polymerase, and other viral proteins necessary for replication.
c) Late proteins: nucleocapsid
- Assembly occurs in the nucleus –> envelope is added via a budding process through inner membrane of the nucleus.
*The complete virions are then secreted out of the cell by the ER-Golgi pathway.
- ssDNA genome: first converted to a dsDNA replicative form.
what are examples of + strand RNA viruses? (3)
- can genome be translated directly?
- translated into what?
- what else can be done to the + strand RNA?
- poliovirus, hepatitis A virus, Sars-Cov 2
- genome can be translated directly!
- in poliovirus: + strand RNA serves as a template for synthesis of a large polyprotein that is cleaved into proteins (structural components like structural coat proteins, proteases and RNA replicase)
- +strand DNA can also be used to synthesize a minus strand (using RNA dependent RNA polymerases) + convert minus strand back to positive strand using the same enzyme
does SARS-CoV-2 act in the same way as poliovirus where the DNA/RNA produces a big protein that is cleaved?
no!
DNA produces +gRNA –> replicated/transcripted to smaller pieces of RNA that are then translated
what are examples of - strand RNA viruses? (3)
- can genome be translated directly?
- what can cell do with only nssRNA? vs needs what? to function?
- Measles, rabies (rhabdovirus), influenza (orthomyxovirus)
- genome CANNOT be translated directly. The RNA genome (minus- strand) is first transcribed into a plus- strand RNA by an RNA-dependent RNA polymerase carried inside the virions.
- nothing! needs to inject DNA AND RNA-dependent RNA polymerase inside host cell
what are examples of double stranded strand RNA viruses? (1)
- can genome be translated directly? explain
Rotavirus (Reovirus).
- The dsRNA genome CAN NOT be translated. First, a plus-strand RNA must be synthetized by a viral-encoded RNA-dependent RNA polymerase using the minus strand as the template.
- The plus-strand is then translated into proteins and is used as a template to synthesize a minus strand to yield dsRNA genomes.
(double strand = bit more protected)
Retrovirus
- what type of virus?
- example?
- virion carries what? enveloped?
- what are LTRs?
- what is a provirus?
- ds RNA genome
- HIV.
- virion carries two identical copies of the genome (plus-strand ssRNA), reverse transcriptase, integrase and proteases.
*the reverse transcriptase is an RNA- dependent DNA polymerase that reverse transcribes the RNA genome into DNA.
*The DNA genome travels to the nucleus and is integrated into the host DNA. - LTR: long terminal repeats (at end of ssRNA). Contain promoters for transcription and participate in the integration process.
- PROVIRUS: integrated viral DNA. Contrary to the lambda prophage, the provirus cannot excise from the host genome.
SUMMARY SLIDE:
- mode of replication of virus depends on WHAT?
6 different classes!
(2 big categories + 2 sub in first one and 3 + 1 sub in second one) describe!
depends on what the genome is!
DNA:
*has to enter nucleus! transcribed in nucleus!
1) dsDNA (+) –> transcription of minus strand into mRNA –> makes protein of virus
2) ssDNA (+) –> synthesis of double strand (dsDNA intermediate) –> transcription of minus strand into mRNA –> makes protein of virus
RNA:
3) dsRNA (+) –> transcription of minus strand into mRNA –> makes protein of virus
4) ssRNA (+) –> used directly as mRNA! (translated right away by host)
5) ssRNA (-) –> transcription of minus strand into positive strand mRNA
6) ssRNA (+) retrovirus! –> reverse transcription into dsDNA intermediate –> integrates in DNA of eukaryote OR transcription of minus strand into mRNA
- what is the consequence of viral infection in bacterial cells?
- what are 4 consequences of viral infection in animal cells?
BACTERIA:
- bacteria lyses/exploses and dies
ANIMAL cells (multicellular orgs)
1) death of cell and release of virus –> lysis
2) transformation into tumor cell –> tumor cell division –> transformation
3) attachment and penetration –> cell fusion
4) slow release of virus without cell death/virus present but not replicating –> latent/persistent infection
consequences of viral infection in animal cells
what are the consequences of/explain:
1) LYSIS
2) TRANSFORMATION
3) CELL FUSION
4) LATENT/PERSISTENT INFECTION
1) LYSIS
- destruction of tissues and organs –> can make your organ non-functional and you die
- can also leave scars –> changes structure of organ
2) TRANSFORMATION
- forms tumor cell –> cell acquires immortality, characterized by uncontrolled replication
3) CELL FUSION
- enveloped viruses that fuse with host cell cytoplasmic membrane carries viral proteins that fuse biological membranes –> cell fusion results in hybrid cells (2 cells fused together with a fused nucleus) that have chromosomal aberrations (ie sometimes twice # of chromosomes) and are usually weird/affect performance of cells/ short-lived
4) LATENT/PERSISTENT INFECTION
- cell doesnt carry out function very well
- may revert to lytic infection
- are both DNA and RNA viruses known to cause tumors in animals and humans? which ones? (5)
- estimated that ___-___% of all human cancers are associated with one of 5 virueses
- what are the 4 mechanisms through which viruses are oncogenic?
- yes!
DNA: Epstein-Barr virus (mononucleose) and Human Papillomavirus (cause cervix cancer)
RNA: Hepatitis C virus, Hepatitis C virus (cause liver cancer) and human T-lymphotrophic virus type 1 (retrovirus) - 15-20%
1) transduction
2) insertion of a strong promoter
3) inactivation of a tumor suppressor gene
4) expression of a viral protein that induces transformation (DNA virus! Epstein Barr or Human papillovirus) IMPORTANT ONE FOR THE CLASS
ONCOGENIC VIRUSES: expression of a viral protein
- DNA or RNA virus?
- does the viral protein have a cell counterpart?
- does the viral genome always integrated host genome?
- explain what happens ie with human papilloma virus
- DNA virus!
- does NOT have a cell counterpart
- integration of viral genome into host genome may occur (ie adenovirus) OR viral genome may persist in cell as an extrachromosomal episome
1) where 2 sheets of epithelium meet, there’s a “hole” where the virus can come in and reach base layer (cells that are actively replicating)
2) virus infects base layer cells –> episome in host cell –> normal replication of virus = spread of virus + get greedy and make E6 and E7 (?) –> create virus protein + actively replicate, but then die (purple cells)
3) 1 in a million chance –> DNA of virus recombines into nucleus –> then replication of virus stops BUT E6 and E7 are still expressed –> so red cells divide like crazy and cause cancer!!!
*slide: Some DNA viruses that cause tumors do so because they have infected a nonpermissive host, in which they cannot complete their infection cycle. The cell is infected and undergoes uncontrolled replication. Because the virus cannot complete its replication, the cells will never die.
can there be a vaccine against human papillome virus? useful? for both males and females?
yes! HPV vaccine
- very useful! decreased infection rate to <1% in 2018
- for both! females get the cervix cancer but males can give it to females
- are antivirals worth it?
- do antibiotics work on virus infections?
- what are the most commonly used antivirals? (3)
- Most antiviral drugs also target host structures, resulting in toxicity (viruses use host cell machinery). Risk to the host may NOT justify the use of antiviral. –> ie not worth it for flu bc antiviral might kill you (and the flu won’t)
- Antibiotics are ineffective.
1) nucleoside analogs
- most successful and commonly used antivirals
- (e.g., AZT, Acyclovir, Malnupiravir): block reverse transcriptase and production of viral DNA (RNA viruses) (ie block RNA dependent RNA polymerase)
2) Protease inhibitors inhibit the processing of large viral proteins into individual components (e.g. Paxlovid).
3) Fusion inhibitors prevent viruses from successfully fusing with the host cell.
