RNA structure + transcription

Question 1

Describe the structure of RNA

Answer 1

-ribose, base, phosphates

Question 2

Where do the bases and phosphates join the ribose in RNA?

Answer 2

-bases join at the 1’ carbon
-phosphates join at the 5’ carbon

Question 3

Where do the phosphates of a nucleotide join to the adjacent RNA ribose?

Answer 3

At the 3’ carbon

Question 4

What is a nucleoside?

Answer 4

When the phosphate group has been removed

Question 5

What are the RNA base names and their corresponding nucleoside names?

Answer 5

-uracil –> uridine
-adenine –> adenosine
-guanine –> guanosine
-cytosine –> cytidine

Question 6

What is the difference between ribose and deoxyribose?

Answer 6

Ribose has an OH group, whereas deoxyribose only has an H group

Question 7

Where are the phosphate and hydroxyl groups typically in cellular RNA?

Answer 7

-5’ phosphate group
-3’ hydroxyl group

Question 8

What forms as a result of intramolecular base-pairing within RNA?

Answer 8

Short helices - many are stem-loops (secondary structure)

Question 9

Are RNA helices normally regular or irregular and why?

Answer 9

Irregular - can have different base pairs from C-G and A-U

Question 10

Describe the major and minor groove in RNA

Answer 10

-major groove is narrow
-many interactions with RNA involve the minor groove - molecules can access base pairings

Question 11

What are the Watson and Crick base pairings and how many bonds does each form?

Answer 11

Cytosine and guanine - 3 hydrogen bonds
Uracil and adenine - 2 hydrogen bonds

Question 12

What is the “wobble” base pair and what is its importance?

Answer 12

Guanine and uracil - important for decoding information

Question 13

Describe the tertiary structure of RNA

Answer 13

-interactions connect regions of RNA that are separated in secondary structure
-folds into 3 dimensions
-a minor motif

Question 14

What is a minor motif?

Answer 14

Consists of 2 adjacent A residues in the minor groove that interact with the edge of a G-C base pair

Question 15

How is RNA made?

Answer 15

-by (DNA-dependent) RNA polymerases (RNAP)
-nucleotide triphosphates (NTPs) selected by base-pairing with the template strand and added to the 3’ end of the extending RNA strand

Question 16

What does the RNAP active site contain?

Answer 16

A short RNA/DNA heteroduplex - a double stranded nucleotide structure containing 1 DNA and 1 RNA

Question 17

What regions start and end RNA polymerase action?

Answer 17

Promotor and terminator

Question 18

What are regulatory sequences?

Answer 18

Sequence of DNA that’s bound by a protein that promote the activity of polymerases
-typically found upstream to promotor regions

Question 19

Which direction does RNA polymerase move in?

Answer 19

5’ carbon to 3’ carbon

Question 20

What are the subunits of an E. coli RNA polymerase enzyme and what are they for?

Answer 20

2 alpha subunits (identical) - where it binds to transcription factors
2 beta subunits (different) - used in making RNA
Omega subunit - for assembly + stability

Question 21

Where does DNA bind to E. coli RNA polymerase?

Answer 21

Between the 2 beta subunits - DNA binding groove

Question 22

In prokaryotes, what do sigma factors do?

Answer 22

-provide specificity to the RNAP for the gene promotor
-RNAPs can start transcription without additional primase activity
-sigma factor released from RNAP as it moves away from promotor

Question 23

How many RNA polymerases are in eukaryotic cells + what do they do?

Answer 23

RNA polymerase I - synthesise rRNA
RNA polymerase II - synthesis mRNA + noncoding RNAs
RNA polymerase III - synthesises tRNA + 5S rRNA

Question 24

How is RNA polymerase II assembled onto gene promotors and why is it needed?

Answer 24

-eukaryotic cells don’t express sigma factors
-general transcription factors (gTF) complexes are required to put RNAP II onto promoters