Lecture 6 - DNA virus macromolecular synthesis

Question 1

What are the 3 main steps of macromolecular synthesis?

Answer 1

Transcription, translation and genome replication

Question 2

List 4 examples of trans acting factors

Answer 2

DNA-dependent DNA polymerase, DNA-dependent RNA polymerase, capping, splicing and polyA enzymes, ribosomes

Question 3

List 4 examples of cis acting elements

Answer 3

Ori, promoters and enhancers, ORF, TL start sites

Question 4

What is one way Retroviruses and Hepadnaviruses have broken the central dogma of molecular biology rules?

Answer 4

They encode a reverse transcriptase, which is an RNA-dependent DNA polymerase.

Question 5

Where must DNA viruses replicate their genomes and why?

Answer 5

They must replicate their genomes in the nucleus because host machinery for transcription and genome replication is located there.

Question 6

If a DNA virus is dependent on host machinery for genome replication, what must it do the cell cycle for gen rep?

Answer 6

It must induce S phase to gain access to host DNA replication machinery

Question 7

What two phases is MMS divided into?

Answer 7

Early phase and late phase

Question 8

In some DNA viruses, the early phase can be further subdivided into what two phases?

Answer 8

Immediate early phase and early phase

Question 9

What type of factors do IE genes generally produce? What is another name for these in respect to cancer?

Answer 9

Transcription factors, oncoproteins

Question 10

What type of factors do E genes generally produce?

Answer 10

DNA replication factors

Question 11

What is the function of early phase genes?

Answer 11

To produce transcription factors that induce S phase and lead to expression of viral and cellular enzymes required for vDNA replication

Question 12

What is the function of late phase genes?

Answer 12

To produce progeny virus genomes, structural proteins and progeny virions

Question 13

What is the nucleotide sequence for a strong translation start site?

Answer 13

A/GnnAUGG

Question 14

What is leaky scanning? Why do viruses use it?

Answer 14

A translational mechanism where a ribosomal subunit is able to scan mRNA and bypass initial start codons and start translation at downstream start codons. Viruses use leaky scanning to produce several proteins from a single gene in order to maximize genetic economy - cope with selection pressure

Question 15

Why do most DNA viruses deregulate the cell cycle?

Answer 15

Because most cells never divide and viruses need to induce S phase to replicate their genomes

Question 16

What are two groups of DNA viruses that are associated with cancer and what are the cancers associated with each group

Answer 16

Papillomaviruses: cervical carcinoma
Herpesviruses: B cell lymphoma and nasopharyngeal carcinoma

Question 17

What are the 4 constraints viruses face for gene expression?

Answer 17

1) their genomes have limited coding capacity
2) need to temporally and quantitatively control their gene expression
3) eukaryotes can’t translate polycistronic mRNA
4) must outcompete host for biosynthetic machinery

Question 18

What is the purpose of terminal structures in viral genomes? Give 5 types

Answer 18

Save ends of the genome from degradation after replication.

• direct repeats
• inverted repeats
• palindromes
• viral protein genome-linked
• no ends (circular)

Question 19

What is the role of primers for DNA synthesis?

Answer 19

To supply a free 3’ hydroxyl to the polymerase complex when initiating the first 3’ - 5’ phosphodiester linkage between the primer 3’ -OH and 5’ phosphate of the first incorporated nucleotide

Question 20

What are 3 examples of primers viruses use for DNA replication?

Answer 20

• small RNA fragments
• nucleotide and protein
• self -priming hairpin loops

Question 21

Are larger DNA viruses or smaller DNA viruses more dependent on host machinery for genome replication and why?

Answer 21

Smaller DNA viruses are more dependent because their smaller genome doesn’t typically encode any replication enzymes whereas larger DNA viruses may encode some replication machinery