6 - RNA tertiary structure

Question 1

In RNA, the primary structure is

Answer 1

the sequence of nucleotides

Question 2

In RNA, the secondary structure is

Answer 2

where WC base pairs form and where they don’t

Question 3

In RNA, the tertiary structure is

Answer 3

how the secondary structural elements pack together in 3-dimensions

Question 4

In RNA, P, J, and L stand for

Answer 4

paired region, junction, loop

Question 5

Compensatory mutagenesis makes

Answer 5

mutations to disrupt a potential helix

Question 6

For most RNAs, the tertiary structure is ______ dependent

Answer 6

metal ion

Question 7

Why is RNA better than DNA at forming complex tertiary interactions?

Answer 7

The ability of the 2’-hydroxyl groups to H-bond

Question 8

RNA structures are _______ cooperative than protein structures

Answer 8

less

Question 9

In RNA, tertiary structure interactions result from

Answer 9

base stacking and hydrogen bonding

Question 10

RNA is very prone to

Answer 10

misfolding

Question 11

RNA helix formation tends to be ________ driven

Answer 11

enthalpically

Question 12

A reverse G-U wobble dramatically

Answer 12

changes the nature of the minor groove

Question 13

In RNA, non-WC base pairs facilitate

Answer 13

tertiary structure formation

Question 14

A WC ______ base pair cannot substitute for a G-U wobble

Answer 14

G-C

Question 15

Minor groove - minor groove interactions in RNA are

Answer 15

very common

Question 16

Tetraloops can dock in

Answer 16

the minor groove of RNA helices

Question 17

The major groove is ______ for packing

Answer 17

inaccessible

Question 18

In a tetraloop, the G and N nucleotides are ____ bases away in the helical stack

Answer 18

2

Question 19

The G and A in a GNRA tetraloop form a

Answer 19

sheared pair

Question 20

In a G-A sheared pair, the A

Answer 20

slips below and across the G

Question 21

The tetraloop receptor makes specific contacts to _______ in the GAAA tetraloop

Answer 21

the first A

Question 22

The G-A sheared base pair positions an adenosine in

Answer 22

the minor groove of the RNA helix

Question 23

Adenosines have a shape complementary to the minor groove of a

Answer 23

G-C base pair

Question 24

Ribose zippers

Answer 24

H-bonds involving the 2’-hydroxyls on consecutive base pairs

Question 25

For RNA to fold, the dielectric constant of the solvent must be

Answer 25

sufficiently high to shield the close approach of the RNA backbone (cations serve this role)

Question 26

In an inside-out RNA loop, metal ions are coordinated directly to

Answer 26

phosphate groups in the RNA backbone

Question 27

Hydrated metal ions are found in the ______ of duplex RNAs

Answer 27

major groove