Rna Synthesis And Processing

Front 1

what is the central dogma of DNA?

Back 1

DNA -- (transcription)-> RNA -- (translation) --> protein

DNA is duplicated using replication

Front 2

RNA properties

Back 2

-It is a ribonucleic acid
-it is a polymer of nucleotides
-the order of the bases leads to information
-the bases are attached to a ribose sugar
-they are linked together via phosphodiester bonds

Front 3

What does the 5' end of RNA have on it?

Back 3

it has a triphosphate end

Front 4

What direction is the template strand for RNA?

what is the direction of the mRNA?

what direction is RNA synthesized?

Back 4

the template strand is read 3' to 5'

the mRNA strand is 5' to 3'

RNA synthesized 5' to 3' and the protein is goes from the N terminus to the C terminus

Front 5

What direction does the RNA polymerase read the template strand?

Back 5

3' to 5'

Front 6

why is proofreading in RNA not that important compared to DNA?

Back 6

in DNA errors would be passed onto the next generation.

Front 7

what are the basic steps in making mRNA?

Back 7

1. initiation - RNA polymerase binds to the promoter of a gene and starts RNA synthesis
2. Elogation
3. Termination - RNA polymerase encounters the termination signal and falls of the DNA template

Front 8

what are the properties of the RNA polymerase? basically what makes up the core (alpha) (beta) (beta')

Back 8

it is a multisubunit enzyme of 400kDA
CORE:
- 2 alpha parts - which recognize the regulatory sequence in the promoter on the DNA
-beta - phosphodiester backbone formation in the 5' to 3' direction
-beta prime - holds onto the dna template

Front 9

what makes up the holoenyme of the RNA polymerase?

Back 9

the core -

the sigma factor which simultaneously decreases the holoenyme affinity for non promoter DNA while increasing affinity for the promoter DNA by 10000 fold.

Front 10

how does the drug Rifampicin work to kill the bacteria causing TB?

Back 10

it binds specifically to the beta subunit of RNA. Synthesis of the RNA proceeds only to the dinucleotide stage before stopping.

END RESULT - TRANSCIPTIONAL PARALYSIS

big problem is resitant but selecting for a mutation in the gene that creates the beta subunit

Front 11

Nomenclature and mechanics of RNA synthesis; what is the starting point referred to as? where is downstream? where is upstream?

Back 11

the starting point is the 5' end; position +1

downstream - the numbers increase as the sequence goes downstream

Position -1 is the nucleotide in the promoter adjacent to the transcription

as the negative number increases the sequence proceeds downstream

Front 12

What happens at the promoter region?

Back 12

transcription starts at the promoter - the RNA polymerase holenzyme binds to initiate transcription;

Front 13

what is the preinitiation complex?

Back 13

The PIC is the binding of the RNA polymerase holoenzyme to the teemplate DNA

the closed to open transition gives space for the formation of the first phosphodiester bond of the new RNA chain

Front 14

what is the frist phosphodiester bond?

how is the reaction done so it is very difficult to reverse it?

Back 14

it is the binding of the first 2 rNTPs in the active site of the beta subunit of the holoenzyme.

there is a triphosphate at the 5' end

there is the release of pyrophosphate PPi immediately degraded to 2Pi

Front 15

what are the 2 events associated with the end of initiation?

Back 15

1. the chain reaches 10 nt or so
2. the sigma factor is released from the holoenzyme; this changes the RNA polymerase affinity for the DNA

the sigma factor is recycled because there is only enough sigma factor for about 1/3 RNA polymerase core population to exist as holoenyzme

Front 16

what are the functions of the Topo I and Gyrase in the elongation phase?

Back 16

Topo I removes - coils

Gyrase adds (-) coils to relax DNA

DNA unwinding provides access for the appropriate and temporary base pairing to the template strand

Front 17

what are the 2 ways for termination? what is involved?

Back 17

1. intrinsic terminator - requires G+C rich palindrome in the sequence followed by a U-rich sequence (no protein involved

2. Rho-dependent terminator - no palindrome - protein p (rho) involved

Front 18

Monocistronic vs polycistronic?

Back 18

RNA transcribed from a single gene is moncistronic

RNA transcribed from several contiguous genes is polycistronic

Front 19

what is a drug that stops elogation in eukaryotic transcription?

Back 19

Actinomycin D that intercalates in DNA: distorts the template, halting RNA synthesis

Front 20

How is eukaryotic transcription more complex?

Back 20

-there are introns
-genes are much larger
-no operons (makes is simpler)
-eukaryotic RNA polymerases are veyr large multisubunit enzymes - 2 large subunits and 10 smaller subunits
-Location : Pol I -> nucleoli; Pol II and Pol III - > nucleoplasm

Front 21

What type of cells is transcription and translation coupled?

Back 21

in prokaryotic cells without the nucleus they are coupled.

in eukaryotic cells - transcription takes place within the nucleus and translation takes place in the cytoplasm and are not coupled

Front 22

what genes does RNA polymerase I transcribe?

Back 22

5.8S , 18 S, 28S rRNA genes

Front 23

what genes does RNA polymerase II transcribe?

Back 23

all protein - coding genes plus snoRNA genes, miRNA genes, siRNA genes and most snRNA genes

Front 24

what genes does RNA polymerase III?

Back 24

tRNA genes, 5S rRNA, some snRNA genes and genes for other small RNAs

Front 25

what makes synthesis of ribosomal RNAs (rRNAs)

Back 25

one large transcript is processed into 3 small transcripts (23s, 16s and 5s RNAs)

this ensures that they will be made in equal quantities

rRNAs are then incorporated into the ribosomes

Front 26

what is the C-terminal domain (CTD)

Back 26

CTD is the link between transcription and mRNA processing - capping, splicing, and polyadenylation

it is unique to pol II;

Front 27

what does the hepatotoxin alpha amanitin do?

Back 27

it inhibits the largest subunit of RNA polymerase II precluding RNA synthesis

Front 28

what is RNAPI?

Back 28

it a bipartite promoter- small core promoter element overlapping the +1 site upstream element

Front 29

what is RNAPIII

Back 29

a promoter located with the tRNA gene.

Front 30

what is the RNAPI

Back 30

this recognizes the 60 bp of DNA in the core promoter and initiates RNA synthesis from the +1 base located 25 bases downstream of the TATA box.

Front 31

what is the TATA box reponsible for?

Back 31

the TATA box is responsible for basal or constitutive transcription.

TATA box works on the downstream

non tata box promoters contain initiater regions (Inr's)

Front 32

4 key properties of the enhancer elements -

Back 32

1. enhancers are not required fro initiation of transcription while promoters are

2. enhancers can be positioned at a large distance from its gene; but promoters are located immediately 5' of the gene

3. Enhancers can be upstream, downstream or within the intron of gene but the promoter location is fixed at the 5' end of the gene
4. enhancers are orientation independent but promoters are orientation dependent ie they work downstream always

Front 33

what does TFIID do?

Back 33

TBP or tata box binding protein that recognizes and binds to the TATA box and many TAFs required for transcriptional initiation at the promoter

there is also B, F, E and H

Front 34

what are the three types of termination signals for 3 eukaryotic RNA polymerases ?

Back 34

1. RNAPI - terminator sequence + protein factor - 1000 bp downstream of coding region
2. RNAPII - termination signal unknown but it stops - linked with the polyadenylation of RNA
3. RNAPIII - similar to bacteria i.e run of U residues in GC rich region

Front 35

what adds the 5' cap and why? 3 reasons

Back 35

Guanylytransferase adds a 7-methyl G cap to the growing transcript

it is needed for 3 reasons
1. enhanced export of mRNA to the cytoplasm
2. protect mRNA from the 5' exonuclease degradation
3. recognition feature during translation

Front 36

what is polyadenylation? why does it happen

Back 36

CTD brings a Poly A polymerase in proximity for cleavage and the addition of upto 200 A residues - this is part of making the mRNA mature

the poly a tail is added to increase efficiency of translation to protein and protects the mRNA from 3' exonuclease attack

Front 37

splicing. what happens

Back 37

-removal of sequences of RNA and joining remaining sequences

-non coding RNA introns are tossed

-exons are kept.

Front 38

what does the ribozyme do?

Back 38

it does a nucleophilic attack from an A residue within the intron, initiates thje cut at the 5' splice site

- the 3' OH of the 5' exon attacks the 3' splice site

-Catalysis is RNA driven

Front 39

RNA editing...

Back 39

it is a post transcriptional modiciation and goes against thee central dogma; the genetic information can be changed at the mRNA level without affecting the DNA blueprint

Front 40

RNA interference (RNAi)

Back 40

look at the packet. i dont know.