Lecture 6 - DNA virus macromolecular synthesis Flashcards
What are the 3 main steps of macromolecular synthesis?
Transcription, translation and genome replication
List 4 examples of trans acting factors
DNA-dependent DNA polymerase, DNA-dependent RNA polymerase, capping, splicing and polyA enzymes, ribosomes
List 4 examples of cis acting elements
Ori, promoters and enhancers, ORF, TL start sites
What is one way Retroviruses and Hepadnaviruses have broken the central dogma of molecular biology rules?
They encode a reverse transcriptase, which is an RNA-dependent DNA polymerase.
Where must DNA viruses replicate their genomes and why?
They must replicate their genomes in the nucleus because host machinery for transcription and genome replication is located there.
If a DNA virus is dependent on host machinery for genome replication, what must it do the cell cycle for gen rep?
It must induce S phase to gain access to host DNA replication machinery
What two phases is MMS divided into?
Early phase and late phase
In some DNA viruses, the early phase can be further subdivided into what two phases?
Immediate early phase and early phase
What type of factors do IE genes generally produce? What is another name for these in respect to cancer?
Transcription factors, oncoproteins
What type of factors do E genes generally produce?
DNA replication factors
What is the function of early phase genes?
To produce transcription factors that induce S phase and lead to expression of viral and cellular enzymes required for vDNA replication
What is the function of late phase genes?
To produce progeny virus genomes, structural proteins and progeny virions
What is the nucleotide sequence for a strong translation start site?
A/GnnAUGG
What is leaky scanning? Why do viruses use it?
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
Why do most DNA viruses deregulate the cell cycle?
Because most cells never divide and viruses need to induce S phase to replicate their genomes
What are two groups of DNA viruses that are associated with cancer and what are the cancers associated with each group
Papillomaviruses: cervical carcinoma
Herpesviruses: B cell lymphoma and nasopharyngeal carcinoma
What are the 4 constraints viruses face for gene expression?
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
What is the purpose of terminal structures in viral genomes? Give 5 types
Save ends of the genome from degradation after replication.
- direct repeats
- inverted repeats
- palindromes
- viral protein genome-linked
- no ends (circular)
What is the role of primers for DNA synthesis?
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
What are 3 examples of primers viruses use for DNA replication?
- small RNA fragments
- nucleotide and protein
- self -priming hairpin loops
Are larger DNA viruses or smaller DNA viruses more dependent on host machinery for genome replication and why?
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
