Quiz 2 Flashcards
What is a protein
-polymer of amino acids (bunch of amino acids joined together)
Characteristic of a protein
-directionality- always grow in a certain direction. Amino acids get joined on the c-termini
Codon
a triplet of nucleotides that code for a given amino acid
initiation (start) codon
- generally AUG
- 5’ cap structure and where ribosome and mRNA get together
Open Reading Frame
- has to have start codon (AUG) to be able to “open” and to stop it needs a STOP codon
- ONLY 3 reading frames on mRNA (3 ways RNA can be coded)
- it sometimes doesn’t translate at first AUG (start codon)
What are the two arrangements of open reading frame?
Nested ORF- is contained in the same register as the first ORF
Overlapping ORF- the second frame is in a different register as the first
Glycosylation
Post-translation modification:
- addition of sugars
- viral spikes always have sugars on them
(specific) proteolytic cleavage
Post-translation modification:
-cleavage by protease to change the function of the protein
Ribosome scanning mechanism
1) small 40s subunit actually does the scanning
2) 40s wants to bind to cap but can’t so needs a protein adaptor
3) once attached it starts scanning 5’ to 3’ one nucleotide at a time by GTP hydrolysis until it gets to the start codon (AUG) then the i-tRNA binds and the the 60s subunit binds
4) then scans three nucleotides at a time (translation is happening)
Strain
anything that is different between the two. (varies from one virus to another)
serotype
strain distinguished from other strain by reactivity with antibody (protein)
type
same but do not distinguish by antibody but instead distinguish by the nucleic acid (example-genome sequencing)
Why can’t RNA polymerase be used for proofreading?
1) doesn’t need a primer so continuously copying without proofreading
2) no 3’-5’ exonuclease activity
Proofreading mechanism
- Only done by DNA polymerase
- DNA polymerase senses bump and goes back and proofread every base
- polymerase is much faster than exonuclease activity, so when the wrong base is detected the DNA polymerase stalls allowing the exonuclease to do its job
- exonuclease activity is 3’-5’ to take off the wrong part
What does recombination require from the two viruses involved?
they must be in the same cell
DNA Recombination
- analogous to crossing over during meiosis
- CALLED cutting and joining of dsDNA
- ssDNA makes dsDNA intermediate (substrate for recombination)
-homologous sequence- alike sequence (better success)
-non-homologous sequence- will mess up chromosomes
and are conjoined NON-like sequence
Rate of change for recombination vs. mutation
mutation- gradual change
recombination-rapid change
Recombination in RNA ssRNA viral genomes
Copy choice
- output is the same as with DNA recombination (homologous or non homologous)
- Process happens during replication of nucleic acid
- RNA polymerase binds to 3’end
- Copies template
- detaches from template still holding strain
- net output depends if it binds back to same analogous region
- Binds back to different region- Non homologous and results in deletion or duplication
- Binds to same region- Homologous and results in two copies of the same segment
What does pseudo recombination require?
requires mixed infection of SAME CELL with two distinct viruses that have a SEGMENTED GENOME
Characteristics of pseudorecombination?
viable pseudo recombinants generally formed only from strains of the same virus (produce infectious virus)(interaction between different species will not produce infectious virus)
- Pseudorcombination results from shuffling of parental genome segments in viral progeny
- More likely to result in viable progeny then random recombination
- Novel gene combinations in progeny can result in rapid change in viral trait
mixed up genomes from parents but haven’t changed the sequences
Species
a population of viruses sharing a pool of genes distinct from the gene pools of other viruses
What taxonomic entity is virales?
order
What taxonomic entity is viridae
family
What taxonomic entity is virinae?
subfamily
what taxonomic entity is virus?
genus
How do you classify viruses into families?
-primarily on genome and other virion characteristics
1) morphology- shape and size of virions
-presence/absence of envelope
2)structural proteins: Molecular weights (size)/number of distinct proteins
3)Genome properties-type of nucleic acid: DNA, RNA, ds,ss+/-
-size and number of nucleic acid molecules
-structural features= DNA (ss or ds); circular or linear
+/- ssRNA, 5-cap/VPg/poly(A) tail
-nucleotide sequence
What classification is only used for genus and species level?
nucleotide sequence relatedness and biological criteria
Ex: tissue tropism (being in the nose or gut) is a good way to distinguish a genus or species BUT NOT A FAMILY
Or what host they affect is good way to distinguish a genus or species
Virion
virus particle
Genome
all the genetic material of the virus
Capsid
protein coat on non-enveloped virus that surrounds nucleic acid
Nucleoprotein
nucleic acid and protein in enveloped and non-eveloped viruses
Envelope
lipid membrane and spikes (anything that is stuck on the membrane)
Nucleocapsid
Nucleic acid and protein core in an enveloped virus
always in a enveloped virus
Assembly/disassembly
process for building virus particles and taking them apart
Viral protein
protein encoded by the genome of the virus (structural or non-structural protein)
Virion protein
structural protein dealing with virus particle
Stability vs. instability (virus structure)
- when outside a cell in the virus particle form- must be stable to protect the genome (be able to hold together)
- when virus enters a new cell, virus particle must be able to be unstable (be able to dissociate easily/come apart)-goal is to spread the virus genome into infected cell
- Chemical bonding (non-covalent determine balance)-hydrogen bonding
GOAL=metastable- make a virus particle that isn’t to stable but at the same time won’t come apart when transferring from cell to cell
Assembly vs disassembly (virus structure)
- both occur during an infection cycle
- disassembly is kinetically and/or energetically favored at the BEGINNING of the cycle
- Assembly is favored at the end of the cycle (builds new virus particle to be transferred from host)
- spatial compartments determine balance ( help get reactions going at different times. Don’t necessarily happen in the same compartment
What are the two basic structural forms of a viral nucleoprotein? and characteristics of both
Rodshaped- protein subunits wrap around nucleic acid, nuclei protein is helical symmetry, and may be inside spherical enveloped, can be stiff or flexible
Spherical - spherical shell encloses the nucleic acid, has icoshaderal symmetry
What are the two different viral assembly mechanisms?
Nucleation (like growing crystals)- nucleic acid sequence and/or structure is recognized by viral protein (subunit or oligomer) then protein sub unites added subsequently until all nucleic acid is covered.
-mech applies to all rod shaped and most spherical viruses
Shell-stuffing- empty (no nucleic acid) capsid completely assembled, then nucleic acid is inserted (stuffed)
-mech applies to some spherical viruses ONLY
OAS
origin of assembly sequence=place where the nucleic acid will be bound by the protein initially
-then more subunit protein will come and bind (elongation phase not OAS)
