Old Quiz 2 questions

Question 1

What are two distinct kinds of post-translational modification that may occur
during the process of protein maturation in eukaryotic cells?

Answer 1

glycosylation - addition of sugars

specific proteolytic cleavage - cutting of proteins by proteases to change the function of proteins.

Question 2

In the nomenclature of virus structure, what is meant by the term ‘nucleocapsid’?

Answer 2

nucleic acid and protein core of an enveloped virus

Question 3

To what taxonomic entity (i.e. order, family, subfamily, genus, or species) does each of the following belong?

(i) Herpesviridae: (ii) Enterovirus:

Answer 3

i) Family

ii) Genus

Question 4

What fundamental characteristic of all DNA polymerases allows some of them to carry out “proof-reading” during DNA synthesis?

Answer 4

DNA polymerases need a primer so they can sense bad bases.

Question 5

Why does treatment with a chemical cross-linking agent, as used in the manufacture of inactivated viral vaccines, make virus particles non-infectious?

Answer 5

-They make the virus very stable (don’t allow them to come apart) so the virus can’t come apart and the genetic material stays dormant. (Can’t do anything to the cytoplasm of the cell its trying to infect)

Question 6

By what two mechanisms can genetic variability be introduced into any kind of
virus?

Answer 6

mutation

recombination

Question 7

What are two morphological characteristics of a virus particle that can be used to classify it at the family level?

Answer 7

• shape and size of virions

- presence/absence of envelope (membrane)

Question 8

Briefly explain the ‘copy-choice’ mechanism that leads to recombination between ssRNA viruses.

Answer 8

1) RNA polymerase binds to 3’ end and starts replicating nucleic acid
2) Starts copying the template
3) Detaches from template still holding strand (Doesn’t have to detach)
4) attaches to new or old template
5) output depends if it binds back to same homologous region (if it binds to different regions it results in deletion or duplication=NON Homologous since the genetic sequence doesn’t match). Not really homologous pairing. The result looks like it is a homologous event.

Question 9

To what taxonomic entity (i.e. order, family, subfamily, genus, or species) does
each of the following belong? (i) Simian virus 40:
(ii) Gammaherpesvirinae:

Answer 9

i) species

ii) subfamily

Question 10

In the context of a virus, what is meant by the term ‘segmented genome’?

Answer 10

-multiple nucleic acid molecules that collectively make up the genome

Question 11

Which structural forms of viral nucleoprotein can be assembled by each of the following mechanisms?
(i) nucleation: (ii) shell-stuffing:

Answer 11

nucleation- all rod-shaped viruses and most spherical viruses

Shell-stuffing- some spherical viruses

Question 12

Briefly outline the mechanism by which “proof-reading” occurs during DNA synthesis.

Answer 12

• DNA polymerase senses bump and goes back and proofreads every base put in
• The polymerase is much faster than exonuclease activity. When wrong base is sensed the DNA polyermase stalls and the exonuclease increases kinetics.
• exonuclease activity 3’-5’
• Allows exonuclease to take off the wrong base.
• Results in a change in sequence in individual molecule

Question 13

To what taxonomic entity (i.e. order, family, subfamily, genus, or species) does
each of the following belong? (i) Alphavirus:
(ii) Orthoretrovirinae:

Answer 13

i) Genus

ii) Sub family

Question 14

In virology, what is meant by the term ‘host range’?

Answer 14

The spectrum of species that can be infected by a virus.

Question 15

What are the two fundamental mechanisms by which viral nucleoproteins can be assembled?

Answer 15

• nucleation

- shell-stuffing

Question 16

What is the name given to the mechanism by which recombination occurs during the replication of (+)-strand ssRNA-containing viruses?

Answer 16

copy-choice

Question 17

What is the molecular mechanism that leads to “leaky scanning”, a phenomenon in which translation fails to initiate at the 5’-proximal AUG codon of an mRNA molecule in a eukaryotic cell?

Answer 17

• leaky initiation of translation
• failure to initiate translation at first AUG (start codon)
• leaky aspect is actually due to the 40s subunit.
• before initiator tRNA, it moves along by one base.
• 40s subunit will not start translating until later
• To allow translation to happen immediately we need to change the bases upstream and downstream. We need a good kozak consensus sequence to most likely favor translation.
• This allows 40s subunit to pause long enough to initiator tRNA to get there and bind.

Question 18

Why are biological properties of viruses, such as mode of transmission, not
generally useful criteria for assigning them to specific families?

Answer 18

It’s a very general distinction because you end up grouping viruses as same when in fact they differ in many characteristics.

Question 19

Briefly describe (i) the process of ribosome scanning (2 points), and (ii) what occurs during ‘leaky scanning’ (2 points). What determines the likelihood that ‘leaky scanning’ will occur?

Answer 19

i) 40s subunit binds to the cap with help from an initiation factor. Once bound ribosome scanning begins moving 5’-3’ one nucleotide at a time. Making its way to AUG (start codon). Once we get to the AUG in the A-site the itRNA binds and then the 60s subunit binds and we can begin translation.
ii) Leaky scanning is the failure to initiate translation. The 40s subunit moves along by one base at a time past the AUG before the initiator tRNA can get to the site.
iii) the likelihood of leaky scanning occurring depends on a good kozak consensus sequence (if you have a good kozak sequence then leaky scanning will not occur), because it favors translation. Therefore it allows the 40s subunit to pause allowing the initiator tRNA to get there and bind resulting in translation.

Question 20

Define what is meant by the term ‘open reading frame’ (ORF).

Answer 20

combination of nucleotide triplets that begin with a start codon and end with a stop codon.

Question 21

Non-segmented (+)-ssRNA genomes, such as that of HEV, can acquire genetic variability through RNA recombination. Briefly explain the mechanism underlying this process. (2 points). What is the name given to this mechanism?

Answer 21

Copy-choice

• RNA polymerase binds to 3’ end
• starts copying the template
• detaches from template still holding strand
• attaches to new or old template
• net output depends if it binds back to same analogous region
• if it does bind back to same region then it is homologous
• if you attach to a different analogous region then its called non homologous and deletion or duplication is a result

Question 23

What structural form of viral nucleoprotein is optimal for each of the following? (i) packaging efficiency (i.e. has minimum possible number of protein molecules
per virion):
(ii) packaging adaptability (i.e. readily able to accommodate different-sized nucleic acid molecules into virions):

Answer 23

i) spherical

ii) rod

Question 24

vPG

Answer 24

protein attached to the 5’ end where the cap would be attached
(other things that help distinguish between families)