Lec 6: Transcription, Translation, & Genome Replication

Question 1

DNA viruses transcription can occur:

Answer 1

in nucleus or cytoplasm

only animal cells have nucleus so viruses can go there

Question 2

RNA viruses transcription can occur:

Answer 2

in cytoplasm only

Question 3

Virus genomes: (7)

*note:

Answer 3

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

Question 4

7 Baltimore classes of virus genomes:

Answer 4

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)

Question 5

Reverse transcription =

Answer 5

mRNA –> DNA

Question 6

Transcription of virus genomes classes: (7)

Answer 6

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

Question 7

virus mRNA, is always designated

mRNA =

Answer 7

(+)

mRNA = (+) RNA

Question 8

• 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 =

Answer 8

(+)

-

Question 9

5’ AUGGCCUAA 3’ =

Answer 9

mRNA / “(+) RNA”

Question 10

3’ UACCGGAUU 5’ =

Answer 10

(-) RNA

Question 11

The viruses with (+) RNA genomes =
& have…
However, only…

Answer 11

= (Classes 4 and 6)
…& have the same sequence as the virus mRNA.
…only the Class 4 genomes can function as mRNA.

Question 12

class 4 viruses aka “_____” must…

Answer 12

“retroviruses”

…must first reverse transcribe their ssRNA genomes to dsDNA before mRNA can be transcribed (+RNA > -DNA > dsDNA > mRNA)

Question 13

(+) RNA and (+) DNA have the same sequence as

Answer 13

the mRNA (except that in DNA thymine replaces uracil).

Question 14

(−) RNA and (−) DNA have the

Answer 14

sequence complementary to the mRNA (except that in DNA thymine replaces uracil).

Question 15

ambisense genomes

Answer 15

Some ssDNA viruses and some ssRNA viruses have ambisense genomes. This means that that the polarity of the genome is part (+) and part (−).

Question 16

DNA or RNA can only be synthesized from

Answer 16

5’ to 3’ (starting from 3’ end on the template (-) strand)

Question 17

coding strand =

Answer 17

(+) DNA strand (leading)

5’-3’

Question 18

template strand =

Answer 18

(-) DNA strand (lagging/okazaki)

3’-5’

Question 19

mRNA strand =

Answer 19

(+) mRNA strand
3’-5’
(same as template but with uracil)

Question 20

Anything opposite of mRNA =

Anything similar to mRNA =

Answer 20

(-) strand

(+) strand

Question 21

If template is (+): immediate product =

If template is (-): immediate product =

Answer 21

(-)

+

Question 22

a few single-stranded nucleic acids of viruses have a mixture of

Answer 22

(+) and (−) polarity within the strand, in other words there are open reading frames (ORFs) in both directions.

Question 23

+ RNA –>

Answer 23

proteins

Question 24

• RNA –>

Answer 24

+ RNA –> proteins

Question 25

Ambisense viruses usually have

Answer 25

two hosts in which they can replicat

Question 26

- In their vector or reservoir host, infection is usually = | - However, in another host, multiplication of the virus can be =

Answer 26

- asymptomatic. | - lethal

Question 27

central dogma vs. mod.'d central dogma

Answer 27

mod.'d central dogma includes reverse transcription & RNA genome replication

Question 28

viruses must use

Answer 28

host cell translational machinery

Question 29

Virus molecules synthesized in the infected cell must also be transported to... - virus mRNAs are transported... - Virus proteins may be transported...

Answer 29

...particular sites. - ...from nucleus to cytoplasm - ...to various locations, including the nucleus

Question 30

transport vesicles -->

Answer 30

apical plasma membrane

Question 31

Golgi -->

Answer 31

basolateral plasma membrane

Question 32

Locations of virus genome replication in eukaryotic cells:

Answer 32

Cytoplasm: - some dsDNA - dsRNA - (+) RNA - (-) RNA (non-segmented genomes) - retroviruses & pararetroviruses (ssRNA --> dsDNA) Nucleus: - some dsDNA - ssDNA - (-) RNA (segmented genomes) - retroviruses & pararetroviruses (dsDNA --> ssRNA)

Question 33

(Initiation of Genome replication) | Nucleic acid replication requires...

Answer 33

...priming = first reaction of a nucleotide with an –OH group on a molecule at the initiation site

Question 34

(Initiation of Genome replication) | Some ssDNA viruses, such as parvoviruses, use...

Answer 34

...self-priming. At the 3 end of the DNA there are regions with complementary sequences that can base pair.

Question 35

Synthesis of DNA needs RNA as a primer?

Answer 35

- Okazaki fragments  primer = short mRNA fragments | - Viruses can also use  protein as a primer

Question 36

For some viruses the primer for initiation of nucleic acid replication is

Answer 36

the –OH group on a serine or tyrosine residue in a protein.

Question 37

Protein primers are not...

Answer 37

...removed once their role is performed and they are found linked to the 5’ ends of the genomes in virions.

Question 38

Enzymes used by viruses to replicate their genomes:

Answer 38

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)

Question 39

Ori =

Answer 39

AT rich = easier to break bonds (only 2 H bonds in AT link)

Question 40

Semi conservative = | Conservative =

Answer 40

= 1 old + 1 new AND 1 old + 1 new | = 2 old AND 2 new

Question 41

ssRNA is replicated by | - both...

Answer 41

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

Question 42

(+) RNA viruses accumulate...

Answer 42

an excess of (+) RNA over (−) RNA, and for minus strand RNA viruses the reverse is true.

Question 43

- Some RNA viruses replicate their genomes.. - Some DNA viruses replicate their genomes... - Both modes of genome replication involve...

Answer 43

- ...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

Question 44

REPLICATION of virus genomes in the seven Baltimore Classes:

Answer 44

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