Transcription

Question 1

What synthesizes RNA?

Answer 1

RNA polymerases

Question 2

What things are necessary for RNA synthesis?

Answer 2

DNA template
Ribonucleotide triphosphates
Mg2+ cofactor

Question 3

What are the two complementary base pairs in RNA?

Answer 3

CG

AU

Question 4

Is a primer needed to initiate RNA synthesis?

Answer 4

No

Question 5

Why is error in RNA polymerization higher than in DNA polymerization?

Answer 5

They don’t proofread - there are a lot of mRNA copies, so the occasional error doesn’t matter

Question 6

How many RNA polymerases doe E. coli use for transcript synthesis?

Answer 6

1

Question 7

What does primase do in E. coli?

Answer 7

Makes short primers that never leave the template

Question 8

How many subunits does the core of E. coli polymerase have?

Answer 8

5 - 2 alpha-subunits, 1 beta, 1 beta’ and 1 omega

Question 9

What is the sixth subunit of E. coli that is required for efficient initiation?

Answer 9

Sigma Factor

Question 10

What is the complete enzyme called that starts E. coli RNA polymerase?

Answer 10

RNA polymerase holoenzyme

Question 11

What are the three stages of RNA synthesis?

Answer 11

Initiation
Elongation
Termination

Question 12

Where is RNA synthesis initiated?

Answer 12

At promoters

Question 13

Where is the site of transcription?

Answer 13

5’ upstream of position of translational initiation codon in the gene

Question 14

What is the transcription start site?

Answer 14

The first base copied on the template transcribed/sense strand

Question 15

What is the number of the transcription start site?

Answer 15

+1

Question 16

In reference to numbering, what are the values of the upstream bases?

Answer 16

Negative (-)

Question 17

E. coli uses variations in __ and __ sequences to creat promoters of different efficiencies.

Answer 17

• 35

- 10

Question 18

What does the commonality of promoter sequences suggest?

Answer 18

Functional importance

Question 19

Where does the RNA polymerase holoenzyme first bind to the DNA in E. coli?

Answer 19

Weakly binds and slides to the -35 site; then binds tightly and forms a closed complex

Question 20

After binding to the -35 site, RNA polymerase binds to the ___ site and unwinds how many base pairs?

Answer 20

-10 site

Unwinds about 17 base pairs; binds tightly to form open complex

Question 21

What is the first nucleotide brought into the active site?

Answer 21

Almost always a purine

Question 22

Why is a sigma subunit required?

Answer 22

To ensure specific, efficient recognition of the promoter

Question 23

When is the sigma subunit lost?

Answer 23

Once several bases are incorporated

Question 24

Why are there different sigma subunits?

Answer 24

To allow different promoters to be used

Question 25

What facilitates the unwinding of DNA?

Answer 25

-ve supercoiling

Question 26

At termination, why does RNA polymerase dissociate from the template?

Answer 26

It lacks a sigma subunit, not promoter and is not elongating a chain; it can't bind to DNA without those things

Question 27

What are the 2 mechanisms for transcriptional termination in prokaryotes?

Answer 27

Rho dependent | Rho independent

Question 28

How does Rho dependent termination work?

Answer 28

Rho protein binds to poorly characterized sequences in the 3' region of the transcript; uses ATP to break H bonds holding transcript to template

Question 29

What drives Rho independent termination?

Answer 29

Secondary structure formation of RNA transcript and thermodynamics

Question 30

In Rho independent termination, what reduces the base pairing template?

Answer 30

The region of transcript folds into a hairpin loop

Question 31

After RNA forms a hairpin loop, what causes the DNA to rewind?

Answer 31

A U-rich environment that causes poor hydrogen bonding to template

Question 32

In eukaryotes, typical mRNA promoter has what?

Answer 32

TATA box about 25 bases upstream of the +1 transcription start site

Question 33

In eukaryotes, what does Pol II do?

Answer 33

Catalyzes RNA synthesis

Question 34

In eukaryotes, what does TBP do?

Answer 34

Recognizes the TATA box

Question 35

In eukaryotes, what does TFIIA do?

Answer 35

Stabilizes TFIIB and TBP binding to promoter

Question 36

In eukaryotes, what does TFIIB do?

Answer 36

Binds TBP | Recruits Pol II-TFIIF complex

Question 37

In eukaryotes, what does TFIIE do?

Answer 37

Recruits TFIIH | Has ATPase and helicase activities

Question 38

In eukaryotes, what does TFIIF do?

Answer 38

Binds Pol II | Binds TFIIB and prevents nonspecific binding of Pol II

Question 39

In eukaryotes, what does TFIIH do?

Answer 39

Unwinds DNA at promoter | Phosphorylates Pol II within CTD

Question 40

What is a newly synthesized RNA molecule called?

Answer 40

Primary transcript

Question 41

What are constitutive genes?

Answer 41

Genes that are involved in making things that we need all the time, like the enzymes of glycolysis and the TCA cycle

Question 42

What are the core promotor proteins?

Answer 42

Pol II, TBP, TFIIA, TIFFB, TFIIE, TFIIF, TFIIH

Question 43

What does TBP stand for?

Answer 43

TATA binding protein

Question 44

What shape is tRNA usually in?

Answer 44

Cloverleaf

Question 45

Where is the anticodon region of tRNA usually found?

Answer 45

Across from the "open"end

Question 46

What is always found at the 3' end of every tRNA?

Answer 46

A CCA

Question 47

Why is it important to have a CCA on the 3' end of tRNA?

Answer 47

That is where the amino acids bind

Question 48

What does the tRNA anticodon base pair with?

Answer 48

The RNA template

Question 49

RNA is transcribed as one big precursor. What happens to get all the forms of RNA?

Answer 49

Primary transcripts must be cleaved into functional fragments

Question 50

Where are tandem arrays of rRNA found?

Answer 50

Nucleolar regions

Question 51

When are tandem arrays of rRNA processed?

Answer 51

Post-transcriptionally

Question 52

What chromosomes make up the nucleolar regions?

Answer 52

13-15, 21, 22

Question 53

What is the "ribosomal factory"?

Answer 53

Nucleoli

Question 54

After being arranged into subunits, where are rRNA and ribosomal proteins shipped?

Answer 54

To the cytoplasm

Question 55

What 3 thing are required to make a mature mRNA?

Answer 55

5' cap 3' polyA tail Introns spliced out

Question 56

What is the poly A addition signal?

Answer 56

AAUAAA

Question 57

When the PolyA addition signals is recognized by the enzyme complex, what happens?

Answer 57

The enzyme complex cleaves the transcript 10-30 nucleotides 3' to signal

Question 58

What tethers mRNA to CTD of Pol II?

Answer 58

Cap binding complex

Question 59

In mRNA splicing, what is the cap tethered to?

Answer 59

RNA polymerase

Question 60

What mediates mRNA splicing?

Answer 60

snRNA (called U1-U6)

Question 61

snRNA's come together to form what?

Answer 61

Spliceosome complex

Question 62

How do mRNAs get spliced?

Answer 62

snRNAs build spliceosome, then bring in 5' splice junction next to the branch point adenosine, form a loop, cut off both sides and allow them to ligate (I think)

Question 63

What is usually larger, introns or exons?

Answer 63

Introns

Question 64

Often, the introns spliced out are not junk. What are they/why are they spliced out?

Answer 64

Tissues can decide what do splice; usually introns that are spiced out are for use in different tissues

Question 65

What type of RNA is most commonly edited?

Answer 65

In mitochondrial transcripts

Question 66

What is rifamycin (rifampicin)?

Answer 66

Antibiotic that inhibits prokaryote RNA polymerase

Question 67

How does rifamycin work?

Answer 67

Blocks the initiation of transcription

Question 68

What does rifamycin treat?

Answer 68

TB

Question 69

What does alpha-amanitin affect?

Answer 69

RNA Pol II | Blocks mRNA synthesis