ch 8 RNA transcription, processing, and decay

Question 1

pulse-chase experiment

Answer 1

method of labelling molecules with specific markers to determine where they are found
1. pulse label a eukaryotic cell with 32P UTP
2. then chase away the label with an excess of non-radioactive UTP

Question 2

conclusion of pulse-chase experiment

Answer 2

label first appears in nucleus
after chase moves to Cytoplasm
signal is then lost (RNA turnover)

Question 3

informational RNA

Answer 3

RNA which is used as a template for protein synthesis (mRNA)
carries the ‘genetic message’ from genes in the nucleus to the ribosome in the cytoplasm

Question 4

functional RNA

Answer 4

RNA that is functional as an RNA molecule and is not translated into a protein
- tRNA, rRNA, snRNA, miRNA, siRNA

Question 5

transfer RNA (tRNA)

Answer 5

transport of aa to the ribosome

Question 6

ribosomal RNA (rRNA)

Answer 6

component of the ribosome

Question 7

small nuclear RNA (snRNA)

Answer 7

RNA processing

Question 8

microRNA (miRNA)

Answer 8

inhibit gene expression

Question 9

small interfering RNA (siRNA)

Answer 9

genome integrity

Question 10

gene (molecular terminology)

Answer 10

a segment of DNA that can be transcribed into RNA and the regulatory sequence that makes transcription possible

Question 11

transcription

Answer 11

production of any RNA from a DNA template

Question 12

typical prokaryotic gene

Answer 12

transcribed = coding sequence -> RNA -> protein
regulatory regions = promoter and terminator

Question 13

typical eukaryotic gene

Answer 13

transcribed region and regulatory region
transcribed region = introns (noncoding sequence) and exons (coding sequence)

Question 14

RNA is complementary to the

Answer 14

template strand

Question 15

template strand =

Answer 15

non-coding strand

Question 16

non-template strand =

Answer 16

coding strand

Question 17

3 stages of transcription

Answer 17

1. initiation - binding to template
2. elongation - synthesis of RNA
3. termination - release of RNA transcript

Question 18

RNA polymerase

Answer 18

the enzyme which transcribes DNA into RNA

Question 19

how does RNA polymerase know where to start transcription?

Answer 19

consensus sequences
- strong promoters, those with high levels of RNA transcription, are closer matches to the consensus

Question 20

holoenzyme

Answer 20

RNA polymerase binding to promoter

Question 21

sigma factor

Answer 21

attached to the holoenzyme
- recognizes and binds to the -35 and -10 regions
- opens helix at the -10 region (AT rich)

Question 22

core enzyme

Answer 22

initiation
- no sigma factor
first nucleotide transcribed at +1

Question 23

elongation

Answer 23

transcription bubble moves with polymerase
addition of new bases is always to the 3’ end of the growing chain

Question 24

hairpin loop

Answer 24

internal base pairing of G and C forms helical stem

Question 25

Poly-U stretch

Answer 25

follows the hairpin - forms spontaneously

Question 26

termination - intrinsic

Answer 26

intrinsic - factor-independent stop point defined by newly synthesized RNA sequence of hairpin loop and ploy-u stretch hairpin loop destabilizes DNA-RNA hybrid - RNA dissociates from DNA template

Question 27

termination - rho dependent

Answer 27

- rho protein binds to RNA at rut site, moves towards RNA polymerase - nearby sequence causes polymerase to pause - rho catches up and causes RNA dissociation

Question 28

why does mRNA decay

Answer 28

for control - respond to changing environment, pathway feedback

Question 29

how does mRNA decay

Answer 29

5'PPP -> 5'P endonuclease activity to cleave mRNA exonuclease activity to degrade mRNA, processively 3' -> 5'

Question 30

activator

Answer 30

a protein that binds to a DNA element and activates transcription

Question 31

repressor

Answer 31

a protein that binds to a DNA element and prevent transcription

Question 32

operon

Answer 32

multigeneic segment of DNA sharing regulatory regions - predominantly found in prokaryotes

Question 33

transcription of eukaryotes - increased complexity:

Answer 33

larger genomes - comprised of chromatin multicellular organisms gene composition - more genes - significantly longer - have non-coding regions (introns)

Question 34

3 eukaryotic RNA polymerases

Answer 34

RNA pol I - rRNA RNA pol II - mRNA RNA pol III - tRNA and 5S rRNA

Question 35

general transcription factors (GTFs)

Answer 35

needed bc RNA polymerase complex does not recognize and bind to promoters on its own - recognize promoter elements - may modify polymerase activity

Question 36

TATA box

Answer 36

initiation site of eukaryotes similar to -10 region in prokaryotes

Question 37

TFIID

Answer 37

multi-protein complex including TATA box binding protein

Question 38

pre-initiation complex

Answer 38

TFIIs recruited DNA helix opened (TFIIH) RNA polymerase bound

Question 39

what happens to get from initiation to elongation

Answer 39

TFIIH phosphorylates RNA pol II RNA synthesis begins transcriptions factors dissociate

Question 40

co-transcriptional modification

Answer 40

mRNA processing - within the eukaryotic nucleus 5' cap = addition pf 7-methylguanosine removal of introns, splicing together of exons polyA tail added to 3' end

Question 41

5' cap

Answer 41

guanylyltransferase adds 7-methylguanosine to the 5' end

Question 42

poly(A) tail

Answer 42

endonuclease recognizes the polyadenylation site (AAUAA) mRNA is cleaved on the 3' side of site 50-250 A's are added by poly (A) polymerase (PAP)

Question 43

splicing

Answer 43

introns, transcribed in the primary transcript, are removed and exons are spliced together

Question 44

branch point

Answer 44

conserved sequences - key nucleotide = A

Question 45

spliceosome

Answer 45

an RNA/protein complex responsible for splicing - composed of snRNA and protein = snRNPs

Question 46

roles of the spliceosome

Answer 46

- recognize the conserved intron sequence - help fold the intron into the correct 3d shape - regulate the spicing process (alternative splicing)

Question 47

3 steps of the 2 transesterification reactions

Answer 47

1. 2' OH pf branch point A attacks 5' splice site, releases 5' exon (3' OH exposed) first transesterification 2. A is now involved in 3'-5' bond and 2'-5' bond second transesterification 3. 3' OH of 5' exon attacks 3' splice site, joining together the 2 exons

Question 48

2 methods of mRNA decay in eukaryotes

Answer 48

both start with deadenylation (poly(A) tail removal) 1. decapping by Dcp1/Dcp2 - 5' -> 3' exonuclease 2. 3' -> 5' exonuclease - DcpS releases 5'm2Gp

Question 49

ribozymes

Answer 49

RNA with enzymatic activity - self splicing introns - free GTP attacks phosphodiester bond at 5' splice site, 5' exon joins 3' exon