midterm 1

Question 1

describe What’s the helical pitch of B-DNA?

Answer 1

• 35.7 A
• 3.4 A x 10.5
• axial rise x #bp/turn

Question 2

what is the twist angle of B-DNA?

Answer 2

34.3 degrees

• 360/10.5
• full rotation angle/ 3bp/turn

Question 3

what is the helix diameter of a B-DNA?

Answer 3

• 20 A

Question 4

what are 4 features of B-DNA?

Answer 4

• 10.5 bp/turn
• antiparallel base pairing
• right-handed helix
• major and minor groove

the B form DNA is the hydrated form.

B-DNA has a wide major groove and a narrow minor grooves

Question 5

what are the characteristics of A-DNA?

Answer 5

• A DNA is a right-handed helix
• compact with 11 bp/turn
• the major groove is narrower and deeper than B-DNA
• the minor groove is broader and shallower than B-DNA.
• the orientation of the base pairs is tilted in the A-DNA relative to the orientation of the helix
• available in less humid environments

Question 6

what are the characteristics of Z-DNA?

Answer 6

• left-handed helix
• the glycosidic bonds connecting the bases to the 1’ position of 2’deoxyribose is either in anti or syn conformation
• zigzag effect
• available in TC repeats

Question 7

what are the major grooves codes per base pair?

Answer 7

• AT: ADAM
• GC: AADH
• TA: MADA
• CG: HDAA

Question 8

What are the minor groove recognition sequences?

Answer 8

AT/TA: AHA

CG/GC : ADA

Question 9

DNA Topology equations

Answer 9

• L= Tw + Wr
• Lo= #bp/ 10.5 = Tw
• σ= delta L/Lo = (L-Lo)/Lo
• Delta G = (1100 RT/N) (L-Lo)²

R= 1.98 x 10^-3 kcal/mol/deg

N: number of bp

N has to be greater or equal to 2000 bp

Question 10

Type IA topoisomerase

Answer 10

removes negative supercoiling

• E coli TOPO I and III
• III becomes active when the amount f negatively supercoiled DNA reach a certain threshold

Question 11

Type IB topoisomerase

Answer 11

• removes positive OR negative supercoiling
• human TOPO I

Question 12

type II A atypical Topoisomerase

Answer 12

• E coli gyrase
• increases negative supercoiling
• essential bacterial enzyme

Question 13

TYPE IIA typical topoisomerase

Answer 13

• E coli TOPO IV
• eukaryotic TOPO II
• can relax positive or negative supercoiling but can NOT introduce supercoils

Question 14

TYPE IIB topoisomerase

Answer 14

• can relax positive or negative supercoils
• TOPO VI in archaea