Bentzen 2 - DNA Structure

Question 1

What type of bonds link nucleotides together?

Answer 1

3’-5’ phosphodiester bonds

Question 2

What is the secondary structure of DNA?

Answer 2

The antiparallel double stranded DNA, both strands being complementary to each other.

It can also be the hairpin and stem type secondary structure

Question 3

What are the two alternating components of the backbone of polynucleotide chains?

Answer 3

Sugar and phosphate residues

Question 4

How many base pairs are there per turn of a DNA double helix? They are flatly stacked ____ apart

Answer 4

10. Stacked .34 nm apart

Question 5

In DNA, is the structure more conserved than the sequence? Or is the sequence more conserved than the structure?

Answer 5

The structure is more conserved than the sequence.

Question 6

What is the A form of DNA? How many bases per turn? What hand turn? What is special about the major groove?

It is found where?

Answer 6

Right hand turn
11 bases per turn
Narrower major groove
Forms under low humidity
Found in DNA-protein complexes

Question 7

What is the B form of DNA? Where is it formed?

Answer 7

The B form of DNA is found in cells and has a right hand turn (10 bp per turn)

Question 8

What is the Z form of DNA?

Answer 8

Left hand turns
12 residues per turn
No major grooves (only minor, because of zigzagging).

Question 9

What is the difference between a hairpin and stem secondary structure of DNA?

Answer 9

The hairpin has both a loop and stem, the stem is just a stem.

Both occur in SINGLE stranded DNA with inverted complementary sequence

Question 10

What is a cruciform in secondary structure DNA?

Answer 10

Only occurs in double stranded DNA, it is two hairpins.

Question 11

Single stranded RNA can form many secondary structures. What are three of these and what causes them?

Answer 11

Hairpins
Stems
COmplex secondary structures

This happens because of hydrophobic bases and unconventional base pairing (eg. C-U triple bases). Important for biological functions, can reach complexity seen in protiens

Question 12

When must DNA melting occur? (4 processes)

Answer 12

DNA replication
Transcription
recombination
repair

It can also be used to allow artifical molecuels to form (with strands from different sources, like in hybridization)

Question 13

What are four ways to melt DNA?

Answer 13

Increase temperature
Reduce salt concentration
Increase pH
Add solvents

Question 14

What is melting temperature? (Tm)

Answer 14

Temperature at which half of a given polynucleotide is hybridized to its complementary strand

An indication of the stability of the hybridized DNA molecule. (higher Tm = more stable DNA molecule

Question 15

How can DNA melting be monitored?

Answer 15

Absorbance.

Question 16

What is hyperchromatic shift in DNA melting?

Answer 16

When monitoring DNA melting with absorbance, a hyperchromatic shift is the absorbance increase as the DNA duplex separates.

Question 17

What factors affect melting temperature? (3)

Answer 17

GC content (% G + C)

Salt concentration in solution
- Because the negatively charged sugar-phosphate backbone repel each other, but these charges are shielded by cations in solution (stabilizing the helix)

Length of DNA molecule

Question 18

What effect does increasing pH and organic solvent concentration (eg. formamide and dimethyl sulfoxide -DMSO) have on melting temperature?

Answer 18

It decreases melting temperature by destabilizing DNA