Virus Structure and Replication Flashcards
What is a Virus?
- Obligate intracellular parasite
- Small
- submicroscopic “filterable” infectious agent
- Possesses genetic material
- DNA or RNA
- ds or ss
- Infectious to a variety of living organisms:
- Humans, animals, plants, bacteria, invertebrates, fungus
What is the size of viruses?
- 100 nm
- vs bacteria at >300nm
What is special about Viral DNA/RNA?
- Have DS DNA & RNA
- Have SS DNA & RNA
- vs Animals, plants, etc DS = DNA SS = RNA
How are viruses classified?
- Originally classified by size
- Then classified by pathogenic properties, transmission ecology, or organ tropism
- Yellow fever, Hep A, B, &C, Rift valley fever would all be hepatitis viruses
- NOW:
- Order -virales
- Family -viridae
- Sub-family -virinae
- Genus -virus
- Species (Common Name) - viruses “share common features” (molecular/structural)
- Isolate, strain, etc.
What are the types of viral genomes?
- Composition: DNA or RNA
- Form: SS or DS
- Polarity of SS RNA:
- Positive
- Negative
- Ambisense
- Polarity of SS RNA:
How do viruses replicate?
- Viral genomes MUST make mRNA that can be read by the host ribosomes
- mRNA is (+)sense RNA
- mRNA can be translated into a protein
What is Reverse Transcriptase?
- Unique to retroviruses
- Cells do NOT have a polymerase to turn RNA to DNA - A virus MUST bring its own
What are the Coding Regions of the Viral Genome?
- Genes that produce proteins
- Open Reading Frame (ORF):
- has start codon
- stop codon
- intervening sequence that codes for a polypeptide of at least 100 amino acids
- Non-structural proteins
- Structural Proteins
What are the Non-coding regions of the Viral genome?
- Normally referred to as “untranslated regions” (UTRs)
- Contain:
- Regulatory elements
- Scaffolding
- Terminal repeats
What are Non-structural Viral Proteins?
- Participate in processes important to the virus
- Viral replication
- Regulating gene expression
- Replication of the genome
- Facilitating the assembly of the virus particle
What are viral structural proteins?
- Components of the virion
- envelope proteins
- matrix proteins
- capsid proteins
- additional virion-associated proteins
- provide receptor-binding sites
What information is contained in the viral genome?
- Replication
- Assembly and packaging
- Regulation of the replication cycle
- Modulation of host defense
- Spread
What information is NOT contained in the Viral Genome?
- Complete protein synthesis
- Membrane synthesis
- Energy production
What is a capsid?
- The protein shell surrounding the nucleic acid genome
- Self-assembled into a “minimum structure, maximal space” to stably package the genome
- 2 Main types of capsid structures
- Symmetrical
- icosahedral and helical
- Complex
- Symmetrical
What do Symmetrical Capsids look like?
-
Icosahedral
- EX: Parvoviruses
- 20 equilateral triangles
- Made up of 60 identical copies of the capsid protein
- EX: Parvoviruses
-
Helical:
- Cylindrical structure
- Capsomeres arranged in a spiral staircase with a central pole as the axis
- EX: Rhabovirus (Rabies)
- Coiled helical nucleocapsid with a bullet shaped virion morphology
What does a complex capsid look like?
- Not helical or icosahedral
- Possess no symmetry
- EX:
- Filoviridae
- Poxviridae
What is the function of the Capsid?
- Genome Packaging
- Host cell attachment and entry- (non-enveloped viruses)
- Un-packaging of the genome and release into cells
What is a Nucleocapsid?
- The complete protein-nucleic acid complex that is the packaged from of the genome in a virus particle
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What is the structure of Nucleocapsids?
- Helical capsids
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What Families of Viruses have Helical capsids and (-)ssRNA genomes
- Paramyxoviridae (bovine parainfluenza virus 3)
- Rhabdoviridae (rabies)
- Orthomyxoviridae (Influenze A)
- Filoviridae (Marburg and Ebola)
What are the contents of Enveloped Viruses?
- Lipid Envelope
- Capsid
- Genome
What are the contents of Non-enveloped Viruses?
- Capsid
- Genome
How is a viral envelope created?
- Lipid bilayer is derived or “stolen” from the host cell membrane because the viral genome does not have the machinery to encode a lipid bilayer
- Stolen from:
- Nuclear membrane
- Endoplasmic reticulum (ER)
- Golgi
- Plasma membrane
What are the functions of the Viral envelope?
- Membrane glycoproteins - Antigenic sites, attachment, fusion
- Protects the nucleocapsid - the capsid with the viral nucleotides
- Facilitates direct transmission of virions to adjacent cells (cell-to-cell spread)
- Camouflage- (surrounded by host cell material)
Are Enveloped viruses stable?
- Enveloped viruses are often more unstable than non-enveloped viruses
What is E protein?
- Major structural protein on the surface of mature flavivirus virion
- Each E monomer consists of:
- Domain 1 (red)
- Domain II (yellow)
- Domain III (blue)
Are viruses alive?
- Viruses are NOT alive
- Do Not reproduce
- Do Not evolve
- Do Not metabolize…..
- Without first infecting a cell
What is a Virion?
The entire virus particle
What is a virus particle?
A structure that has evolved to transfer nucleic acid from one cell to another
How are Viruses classified?
- Viral genome characteristics and nucleotide sequence
- Capsid symmetry
- Enveloped and non-enveloped
What are the types of viral genomes?
- Composition: RNA, DNA
- From: single or double stranded
- Polarity: for ssRNA - Positive or Negative
- Presence of Reverse transcriptase (RT)
What is the Viral envelope made of?
- Lipid bilayer from the host cell
- Has Viral envelope Glycoproteins
- “spikes”
- Specific to the virus
How many different viral genomes are there?
- Double stranded (dsDNA)
- Single stranded (ssDNA)
- Double stranded (dsRNA)
- single stranded positive (ss+RNA)
- single stranded negative RNA (ss-RNA)
- single stranded positive RNA with a DNA step
What are the requirements of the virus?
- Attachment to the host cell
- Penetration
- Uncoating of the viral genome
- Replication of the viral genome
- Assembly of a new virion
- Exit the host cell
- Transmission to another host or cell
What are the steps for viral replication?
- Receptor mediated
- Attachment and Entry
- Uncoating
- Genome replications
- RNA and Protein synthesis
- Assembly of nucleocapsid and maturation
- Release from the cell
What is Reverse Transcriptase?
RNA-dependent DNA Polymerase
What types of cells can a virus enter and replicate in?
- Susceptible: has a receptor for a virus
- Resistant: does not have the receptor for a virus
- Permissive: can replicate the virus
- Susceptible & Permissive: the virus can enter the cell and replicate
What are the Steps for attachment and entry in Viral Replication?
- Virions have to diffuse across the plasma membrane and then release the genome
- Step:
-
Adhere to the cell surface
- Not specific, happens by chance
-
Attach to a receptor
- specific receptors on the cell
- Made for proteins that the cell normally needs
- specific receptors on the cell
- Genome is then transferred into the cell
-
Adhere to the cell surface
What are the mechanisms of virus entry?
- Macropinocytosis
- Cavsolin/lipid raft
- Phagocytosis
- IL-2
- Clathrin-mediated endocytosis
What is Viral Fusion?
- Endosome and Envelop Protein bind
- Change from a Dimer to a Trimer
- Allows the nucleic acid to come out of the virus and is released into the cytoplasm
What is uncoating?
- Acidic condition in the endosome triggers changes in viral structural proteins resulting in uncoating and release of the viral genome
What information does the viral genome contain?
- Replication
- Assembly and packaging
- Regulation of the replication cycle
- Modulation of host defense
- Spread
How are viral genes transcripted?
- DNA genome viruses:
- Host or virus DNA-dependent RNA polymerase generates viral mRNA
- mRNA is translated into viral proteins using cellular machinery
- RNA genome viruses:
- Require a viral-encoded RNA-dependent RNA polymerase (RdRp) to make mRNA (and genomic RNA)
- Virus must possess of synthesize RdRp
How is viral mRNA translated to viral proteins?
- Translate the mRNA into proteins
- protein synthesis
- Compare to cell mRNA
- 5’ cap UTR AUG ORF Stopp UTR AAAAAA 3’
- Ribosomes are needed for Transltion
- tRNA also needed to add the correct the AA
- Translation also needs:
- Initiation proteins
- Elongation proteins
- Termination proteins
How are viral proteins named?
- Named based on timing of synthesis
- Early translation products
- “immediate early” or “early”
- mostly nonstructural proteins (polymerases, regulatory proteins)
- Late translation products
- “late proteins”
- Structural proteins (capsid proteins, envelope glycoproteins)
- Early translation products
What is Post translational modification of proteins?
- Further processing of viral proteins
- RNA viruses frequently synthesize polyproteins that are cleaved by viral proteases
- The first cleavage is an autocleavage to release a protease, which cleaves other proteins
What happens during assembly of nucleocapsids and virus maturation?
-
Self assembly of the capsid
- Many viral proteins assemble on their own
-
Assisted assembly:
- Some need scaffolds and chaperones from the cell to form the viral structure
-
All Viruses need to:
- Form the protein shell from one or many viral proteins
- Assemble the protein shell
- Release the virion from the host cell
-
Some:
- Acquire an envelope
- Go through virion maturation
How can viruses exit the cell?
- Budding - Acquires membrane
- Lysis - break the cell open and release the virion
- Release virus without lysis (poliovirus)
- Move from cell to cell without cell lysis
How do dsDNA viruses replicate?
- Replicate in the nucleus
- Protein vhs - cuts up the host cell mRNA which blocks host cell defenses (cell cannot make protein from mRNA)
- Protein VP16 - facilitates the transcription of herpesvirus RNA
What types of mRNA are produced by dsDNA viruses?
- 3 types:
- a - immediate early
- B - early
- y - late
What types of proteins are produced by dsDNA virus?
- 3 types of proteins:
- Immediate early
- Early
- Late
How are +RNA viruses (ie coronavirus) replicated?
- Replicates in the cytoplasm (NOT the host cell nucleus)
- Buds in the ER/golgi
- Only makes 8 viral proteins
How are Retroviruses replicated?
- Have a provirus step
- Replicate in the nucleus for the DNA step
- When the host cell divides the virus divides with it because of the provirus
