Lec 6: Transcription, Translation, & Genome Replication Flashcards
DNA viruses transcription can occur:
in nucleus or cytoplasm
only animal cells have nucleus so viruses can go there
RNA viruses transcription can occur:
in cytoplasm only
Virus genomes: (7)
*note:
ss linear DNA
ds linear DNA
ss circular DNA
ds circular DNA
ss linear RNA
ds linear RNA
ss circular RNA
*note: NO ds circular RNA virus genome yet discovered
7 Baltimore classes of virus genomes:
Class 1: ds DNA Class 2: (+) DNA or (-) DNA Class 3: ds RNA Class 4: (+) RNA Class 5: (-) RNA Class 6: (+) RNA (rev-transc) Class 7: ds DNA (rev-transc)
Reverse transcription =
mRNA –> DNA
Transcription of virus genomes classes: (7)
Class 1: ds DNA –> (+) mRNA
Class 2: (+) DNA –> ds DNA –> (+) mRNA
or (-) DNA –> ds DNA –> (+) mRNA
Class 3: ds RNA –> (+) mRNA
Class 4: (+) RNA –> (-) RNA –> (+) mRNA
Class 5: (-) RNA –> (+) mRNA
Class 6: (+) RNA (rev-transc) –> (-) DNA –> ds DNA –> (+) mRNA
Class 7: ds DNA (rev-transc) –> (+) mRNA
OR
ds DNA (rev-transc) –> (+) RNA –> (-) DNA –> dsDNA –> (+) mRNA
virus mRNA, is always designated
mRNA =
(+)
mRNA = (+) RNA
- A nucleic acid strand that has the same sequence as mRNA is labelled =
- and a nucleic acid strand that has the sequence complementary to the mRNA is labelled =
(+)
-
5’ AUGGCCUAA 3’ =
mRNA / “(+) RNA”
3’ UACCGGAUU 5’ =
(-) RNA
The viruses with (+) RNA genomes =
& have…
However, only…
= (Classes 4 and 6)
…& have the same sequence as the virus mRNA.
…only the Class 4 genomes can function as mRNA.
class 4 viruses aka “_____” must…
“retroviruses”
…must first reverse transcribe their ssRNA genomes to dsDNA before mRNA can be transcribed (+RNA > -DNA > dsDNA > mRNA)
(+) RNA and (+) DNA have the same sequence as
the mRNA (except that in DNA thymine replaces uracil).
(−) RNA and (−) DNA have the
sequence complementary to the mRNA (except that in DNA thymine replaces uracil).
ambisense genomes
Some ssDNA viruses and some ssRNA viruses have ambisense genomes. This means that that the polarity of the genome is part (+) and part (−).
DNA or RNA can only be synthesized from
5’ to 3’ (starting from 3’ end on the template (-) strand)
coding strand =
(+) DNA strand (leading)
5’-3’
template strand =
(-) DNA strand (lagging/okazaki)
3’-5’
mRNA strand =
(+) mRNA strand
3’-5’
(same as template but with uracil)
Anything opposite of mRNA =
Anything similar to mRNA =
(-) strand
(+) strand
If template is (+): immediate product =
If template is (-): immediate product =
(-)
+
a few single-stranded nucleic acids of viruses have a mixture of
(+) and (−) polarity within the strand, in other words there are open reading frames (ORFs) in both directions.
+ RNA –>
proteins
- RNA –>
+ RNA –> proteins
Ambisense viruses usually have
two hosts in which they can replicat
- In their vector or reservoir host, infection is usually =
- However, in another host, multiplication of the virus can be =
- asymptomatic.
- lethal
central dogma vs. mod.’d central dogma
mod.’d central dogma includes reverse transcription & RNA genome replication
viruses must use
host cell translational machinery
Virus molecules synthesized in the infected cell must also be transported to…
- virus mRNAs are transported…
- Virus proteins may be transported…
…particular sites.
- …from nucleus to cytoplasm
- …to various locations, including the nucleus
transport vesicles –>
apical plasma membrane
Golgi –>
basolateral plasma membrane
Locations of virus genome replication in eukaryotic cells:
Cytoplasm:
- some dsDNA
- dsRNA
- (+) RNA
- (-) RNA (non-segmented genomes)
- retroviruses & pararetroviruses (ssRNA –> dsDNA)
Nucleus:
- some dsDNA
- ssDNA
- (-) RNA (segmented genomes)
- retroviruses & pararetroviruses (dsDNA –> ssRNA)
(Initiation of Genome replication)
Nucleic acid replication requires…
…priming = first reaction of a nucleotide with an –OH group on a molecule at the initiation site
(Initiation of Genome replication)
Some ssDNA viruses, such as parvoviruses, use…
…self-priming. At the 3 end of the DNA there are regions with complementary sequences that can base pair.
Synthesis of DNA needs RNA as a primer?
- Okazaki fragments primer = short mRNA fragments
- Viruses can also use protein as a primer
For some viruses the primer for initiation of nucleic acid replication is
the –OH group on a serine or tyrosine residue in a protein.
Protein primers are not…
…removed once their role is performed and they are found linked to the 5’ ends of the genomes in virions.
Enzymes used by viruses to replicate their genomes:
Virus Enzymes:
- DNA dep DNA pol
- RNA dep RNA pol
- RNA dep DNA pol (rev-trans)
Cell Enzymes:
- DNA dep DNA pol
- DNA dep RNA pol (RNA pol II)
Ori =
AT rich = easier to break bonds (only 2 H bonds in AT link)
Semi conservative =
Conservative =
= 1 old + 1 new AND 1 old + 1 new
= 2 old AND 2 new
ssRNA is replicated by
- both…
synthesis of complementary strands of RNA that are then used as templates for synthesis of new copies of the genome
- …both (+) and (−) strands of RNA accumulate in the infected cell not in equal amounts
(+) RNA viruses accumulate…
an excess of (+) RNA over (−) RNA, and for minus strand RNA viruses the reverse is true.
- Some RNA viruses replicate their genomes..
- Some DNA viruses replicate their genomes…
- Both modes of genome replication involve…
- …via a DNA intermediate.
- …via an RNA intermediate.
- …reverse transcription, which has two major steps:
synthesis of (−) DNA from a (+) RNA template
AND
synthesis of a second DNA strand
REPLICATION of virus genomes in the seven Baltimore Classes:
Class 1: dsDNA –> dsDNA
Class 2: (+) DNA –> dsDNA –> (+) DNA
or (-) DNA –> dsDNA –> (-) DNA
Class 3: dsRNA –> dsRNA
or dsRNA –> (+) RNA –> dsRNA
Class 4: (+) RNA –> (-) RNA –> (+) RNA
Class 5: (-) RNA–> (+) RNA –> (-) RNA
Class 6 (rev-transc): (+) RNA –> (-) DNA –> dsDNA –> (+) RNA
Class 7 (rev-transc): dsDNA –> (+) RNA –> (-) DNA –> dsDNA
