Unwinding Mechanisms

Question 1

What mechanism do SF1 and SF2 helicases use to move along DNA/RNA?

Answer 1

Inchworm mechanism

Question 2

What mechanism do SF3-6 helicases use to move along DNA/RNA?

Answer 2

Rotary hexomeric ring

Question 3

What kind of folds do SF1 and SF2 contain?

Answer 3

tandem RecA folds

Question 4

What kind of folds do SF3-6 helicases contain?

Answer 4

RecA/AAA+ folds

Question 5

Can SF2-6 helicases move along dsDNA?

Answer 5

Yes

Question 6

Do SF2-6 helicases move along and unwind dsDNA?

Answer 6

No they move but do not unwind

Question 7

In the inchworm helicase mechanism which amino acid residues help to co-ordinate Mg²⁺?

Answer 7

T and D

Question 8

In the inchworm helicase mechanism which amino acid residue cradles the phosphates of ATP?

Answer 8

K

Question 9

In the inchworm helicase mechanism which amino acid residue activates water?

Answer 9

E

Question 10

What is the function of the arginine finger in the inchworm helicase mechanism?

Answer 10

Senses the gamma phosphate and plays a role in controlling relative conformation of C and N core domains

Question 11

What does Mg²⁺ co-ordinate in the helicase inchworm mechanism?

Answer 11

the beta and gamma phosphates via charge interaction

Question 12

Once ATP has been hydrolysed why does the C core motif stretch forwards?

Answer 12

• Gamma phosphate no longer there
• Arg-ATP interaction lost
• Causes change in conformation

Question 13

What happens to the C core domain once ADP+ Pi diffuse out of the active site?

Answer 13

• ATP can rebind
• C core domain returns to position

Question 14

How does directionality come about in the helicase inchworm mechanism?

Answer 14

As a result of ATP controlling relative grip of domains on DNA

Question 15

In the inchworm helicase mechanism in the ATP-free form which core domain has a tighter grip?

Answer 15

The tail domain

Question 16

In the inchworm helicase mechanism what happens when ATP binds?

Answer 16

• Alters relative affinity of tail and head for DNA
• Tail loses some grip and the head has increased affinity
• Entire tail moves forwards relative to ssDNA

Question 17

In the inchworm helicase mechanism what happens once ATP has been hydrolysed?

Answer 17

• Head has a loose grip and tail has strong grip
• Head skips forward

Question 18

In the inchworm helicase mechanism how is the DNA unwound?

Answer 18

The head core domain has a pin attached which acts as a hydrophobic wedge

Question 19

How does a helicase rotary motor unwind DNA?

Answer 19

One strand of DNA moves through the centre of the ring whilst the other strand is displaced

Question 20

What is thought to be the benefit of the helicase rotary motor being hexameric?

Answer 20

It gives the helicase high processivity as the helicase is toplogically engaged with one of the strands so it is very difficult for it to fall off

Question 21

Where does the hexameric helicase bind the DNA bases?

Answer 21

Each subunit binds one DNA base via a central loop

Question 22

In hexameric helicases which loop has the tightest ATP binding pocket?

Answer 22

The highest loop

Question 23

In hexameric helicases what is the step size?

Answer 23

1 base per ATP

Question 24

In hexameric helicases what happens when ATP binds?

Answer 24

Causes DNA binding loop to flip to the top

Question 25

In hexameric helicases which binding pocket will be the 1st to bind to a new ATP?

Answer 25

The most empty

Question 26

In hexameric helicases why do DNA binding loops flip to the top of the subunit?

Answer 26

In order to anticipate binding at the next nucleobase

Question 27

In hexameric helicases why when one subunit flips to the top of each subunit does every other subunit have to push down a little?

Answer 27

Because all loops are allosterically coupled