DNA structure, properties of DNA double helix

Question 1

Where are nucleotides added

Answer 1

Nucleotides are successively added to the 3’-OH group of the preceding nucleotide – gives the polymer directionality

Question 2

Phosphodiester bond

Answer 2

joins sugars and phosphates

Question 3

Acidic or basic

Answer 3

Acidic
Phosphate groups ionised
(pKa low), so carry negative charge at physiological pH

Question 4

Writing nucleic acids

Answer 4

Sequence of < 50 nt = oligonucleotide

Longer = polynucleotides or nucleic acid

Question 5

Structure

Answer 5

Primary– sequence of nts from 5’ to 3’

Secondary– two strands running antiparallel, B-DNA- right handed double helix

Question 6

Physical measurements

Answer 6

Xray measurements show regular structure: helix with complete turn every 3.4nm, diameter +- 2nm
Density measurements: helix must have two chains

Question 7

Chargaff’s rules

Answer 7

A and T is always found in a 1:1 ratio
G and C is always found in a 1:1 ratio
Number of Pyrimidine bases always equal the number of purine bases
amount of A= amount of T, & C=G…henceA+G=T+C

Question 8

Hydrogen bonds

Answer 8

between paired bases
A–T
C—G

Question 9

Double helix

Answer 9

Sugar-phosphate backbone on outside carries -ve charge neutralised by +ve ions/proteins in cell

Non-covalent interactions between the planar aromatic rings
Pi-bond – cloud of electrons formed by overlapping their p-orbitals

WIDE AND NARROW
GROOVE
Proteins needed for
replication and transcription of DNA interact with DNA at these grooves
Some proteins can recognize specific base sequences by ‘reading’ the pattern of H-bonding possibilities in these grooves

Question 10

Genome

Answer 10

46 chromosomes, 3.1 billion bp

Question 11

Glycosidic bond

Answer 11

connects base to backbone

Question 12

Denaturation… renaturation/anneal

Answer 12

Can reversibly denature, renature
H bonds and pi-pi interactions are disrupted. Double helix unwinds. This is reversible if the conditions are removed. Especially if >10 bases are still held together

Question 13

pH

Answer 13

Solutions of carefully isolated, native DNA are VERY viscous at pH 7.0 at room temperature.

Extremes of pH or temp lead to denaturation— decreased viscosity

high pH= deprotonation
low pH= protonation

Question 14

Hypo/er-chromism

Answer 14

Single-stranded DNA absorbs light more effectively than double- helical DNA.
UV absorbance consequence of π-electron transitions in bases
π-π stacking between bases diminishes UV absorbance

Question 15

Tm

Answer 15

Melting temp
temp at which sea has reached half total max denaturation
Can measure this by decrease in viscosity and increase in light absorbance

Differences in tm reflect base comp and length

Ions such as Na+ will interact with the negative charges on the phosphate backbone of DNA, suppressing the electrostatic repulsion between the negatively charged phosphates in the complementary strands of the helix, thus stabilising the duplex structure. Increases Tm

Question 16

Genes

Answer 16

gene structure
gene transcription (making RNA) translation (protein synthesis) regulation of gene expression

Upstream to the coding area is called promoter
Downstream terminates