Transcription & RNA Processing

Question 1

3 steps of transcription

Answer 1

initiation, elongation, termination

Question 2

define promoter

Answer 2

sequence of double stranded DNA where RNA polymerase binds

Question 3

when does initiation occur

Answer 3

when RNA polymerase binds to the promoter

Question 4

what helps RNA polymerase bind to the promoter in eukaryotes?

Answer 4

transcription factors

Question 5

transcription factors + RNA polymerase + promoter = ?

Answer 5

pre-initiation complex

Question 6

How much of your genome is replicated right before your cells divide?

Answer 6

all of it

Question 7

How much of your genome is converted to protein (transcribed, then translated)?

Answer 7

<2%

Question 8

How much of your genome is converted to RNA (transcribed)?

Answer 8

80%

Question 9

What are transcription factors?

Answer 9

proteins that bind to the promoter first and allow RNA polymerase to bind

Question 10

What sort of sequence does a promoter usually contain? Why is this helpful?

Answer 10

T-A rich sequences called TATA boxes; easier to seaparate because they have fewer hydrogen bonds

Question 11

What happens during elongation?

Answer 11

RNA polymerase starts moving along DNA strand and synthesizes the pre-mRNA transcript

Question 12

Where do transcription factors go during elongation?

Answer 12

stay at the promoter

Question 13

Why do transcription factors stay at the promoter? What does this allow?

Answer 13

allows another RNA polymerase to bind at the promoter and start transcribing another pre-mRNA transcript; this makes transcription faster and more efficient

Question 14

How fast does RNA polymerase add nucleotides?

Answer 14

10-100 nucleotides / sec

Question 15

What is the “sense” strand?

Answer 15

strand of DNA that is the same sequence as the pre-mRNA transcript

Question 16

What is the “antisense” or “template” strand?

Answer 16

the strand of DNA that serves as the template for RNA polymerase

Question 17

Which strand is “read” by RNA polymerase?

Answer 17

“antisense” strand

Question 18

all “sense” strands are…

Answer 18

5’ —> 3’

Question 19

What happens during elongation?

Answer 19

RNA polymerase untwists DNA and synthesizes mRNA by connecting free ribonucleotides to elongating strand

Question 20

Does RNA polymerase have proofreading activity?

Answer 20

no

Question 21

Does RNA polymerase need a primer to start synthesizing?

Answer 21

no

Question 22

What happens during termination?

Answer 22

RNA polymerase, DNA and RNA transcript dissociate

Question 23

How does RNA polymerase know when to stop in bacteria?

Answer 23

stops at “termination sequence” by itself

Question 24

How does RNA polymerase know when to stop in eukaryotes?

Answer 24

proteins/enzymes are needed to recognize DNA sequences and make RNA stop in the right place

Question 25

Does RNA polymerase need topoisomerase?

Answer 25

no, the double stranded DNA quickly rewinds into the double helix after being read by RNA polymerase

Question 26

When a single pre-mRNA molecule is made in one of our cells, how much information does it contain?

Answer 26

the genetic code for one allele from one chromosome

Question 27

What nucleotide does RNA use that is different from DNA?

Answer 27

uracil instead of thymidine

Question 28

what do most RNA transcripts code for?

Answer 28

some for protein, others for rRNA, tRNA, some mysterious

Question 29

transcripts that encode protein

Answer 29

pre-mRNA

Question 30

average human pre-mRNA transcript length

Answer 30

27,000 nucleotides

Question 31

average human protein length

Answer 31

400 amino acids (requires only 1200 nucleotides)

Question 32

exons

Answer 32

blocks of pre-mRNA transcripts or “primary transcripts” that are kept and encode for proteins and some regulatory sequences

Question 33

introns

Answer 33

intervening sequences that get cut out of pre-mRNA

Question 34

what are “UTRs”

Answer 34

untranslated regions at the 5’ and 3’ ends that are part of exons and are not translated into proteins

Question 35

purpose of the 5’UTR and 3’UTR sequences

Answer 35

regulate the lifespan of the mRNA, translation rate, and where in the cytoplasm the mRNA is placed

Question 36

what is splicing and what does it result in?

Answer 36

process of removing introns and ligating exons together to make mature mRNA (messenger RNA)

Question 37

what enzyme performs splicing and what is its structure?

Answer 37

spliceosome; made of several “small nuclear RNAs” or “snRNAs”

Question 38

how does the spliceosome accurately remove introns?

Answer 38

recognizes the “splice donor” and “splice acceptor” sites at the 5’ and 3’ ends of each intron

Question 39

what consequence might mutating the DNA sequences encoding the splice donor or splice acceptor have?

Answer 39

prevents splicing

Question 40

how might we make different splice forms of the same gene? what is this process called?

Answer 40

by removing exons; called alternative splicing

Question 41

what does alternative splicing allow?

Answer 41

allows a single gene to code for several mRNAs, and thus make several different proteins

Question 42

after splicing, what two modifications are made to the ends of mRNA?

Answer 42

5’ cap and poly-A tail

Question 43

what is the 5’ cap? how is it accomplished? purpose?

Answer 43

a modified guanine nucleotide added to the 5’ end by capping enzymes; needed for stabilization and ribosome binding

Question 44

what is the poly-A tail? purpose?

Answer 44

50-250 adenine nucleotides are added to the 3’ end; needed for stabilization and ribosome binding

Question 45

how is the poly-A tail added to the transcript?

Answer 45

ribonuclease recognizes the AAUAAA (polyadenylation signal) in the primary transcript and cleaves 11-30 nucleotides 3’ to that sequence; then poly(A) polymerase can add As

Question 46

how long does it take to make a single 10,000 nucleotide primary transcript?

Answer 46

2 minutes