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MB 461 > Quiz 2 > Flashcards

Quiz 2 Flashcards

1
Q

What is a protein

A

-polymer of amino acids (bunch of amino acids joined together)

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2
Q

Characteristic of a protein

A

-directionality- always grow in a certain direction. Amino acids get joined on the c-termini

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3
Q

Codon

A

a triplet of nucleotides that code for a given amino acid

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4
Q

initiation (start) codon

A
  • generally AUG

- 5’ cap structure and where ribosome and mRNA get together

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5
Q

Open Reading Frame

A
  • 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)
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6
Q

What are the two arrangements of open reading frame?

A

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

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7
Q

Glycosylation

A

Post-translation modification:

  • addition of sugars
  • viral spikes always have sugars on them
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8
Q

(specific) proteolytic cleavage

A

Post-translation modification:

-cleavage by protease to change the function of the protein

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9
Q

Ribosome scanning mechanism

A

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)

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10
Q

Strain

A

anything that is different between the two. (varies from one virus to another)

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11
Q

serotype

A

strain distinguished from other strain by reactivity with antibody (protein)

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12
Q

type

A

same but do not distinguish by antibody but instead distinguish by the nucleic acid (example-genome sequencing)

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13
Q

Why can’t RNA polymerase be used for proofreading?

A

1) doesn’t need a primer so continuously copying without proofreading
2) no 3’-5’ exonuclease activity

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14
Q

Proofreading mechanism

A
  • 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
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15
Q

What does recombination require from the two viruses involved?

A

they must be in the same cell

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16
Q

DNA Recombination

A
  • 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

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17
Q

Rate of change for recombination vs. mutation

A

mutation- gradual change

recombination-rapid change

18
Q

Recombination in RNA ssRNA viral genomes

A

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
19
Q

What does pseudo recombination require?

A

requires mixed infection of SAME CELL with two distinct viruses that have a SEGMENTED GENOME

20
Q

Characteristics of pseudorecombination?

A

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

21
Q

Species

A

a population of viruses sharing a pool of genes distinct from the gene pools of other viruses

22
Q

What taxonomic entity is virales?

A

order

23
Q

What taxonomic entity is viridae

A

family

24
Q

What taxonomic entity is virinae?

A

subfamily

25
Q

what taxonomic entity is virus?

A

genus

26
Q

How do you classify viruses into families?

A

-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

27
Q

What classification is only used for genus and species level?

A

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

28
Q

Virion

A

virus particle

29
Q

Genome

A

all the genetic material of the virus

30
Q

Capsid

A

protein coat on non-enveloped virus that surrounds nucleic acid

31
Q

Nucleoprotein

A

nucleic acid and protein in enveloped and non-eveloped viruses

32
Q

Envelope

A

lipid membrane and spikes (anything that is stuck on the membrane)

33
Q

Nucleocapsid

A

Nucleic acid and protein core in an enveloped virus

always in a enveloped virus

34
Q

Assembly/disassembly

A

process for building virus particles and taking them apart

35
Q

Viral protein

A

protein encoded by the genome of the virus (structural or non-structural protein)

36
Q

Virion protein

A

structural protein dealing with virus particle

37
Q

Stability vs. instability (virus structure)

A
  • 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

38
Q

Assembly vs disassembly (virus structure)

A
  • 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
39
Q

What are the two basic structural forms of a viral nucleoprotein? and characteristics of both

A

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

40
Q

What are the two different viral assembly mechanisms?

A

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

41
Q

OAS

A

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)

MB 461 (15 decks)

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