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Nucleotides and DNA Structure
C483 Spring 2013
1. Purine(s) which are found mainly in both deoxyribonucleotides and ribonucleotides are
A) thymine and cytosine.
B) cytosine and uracil.
C) cytosine.
D) guanine and cytosine.
E) adenine and guanine.
2. The abbreviation dGp indicates
A) 5' deoxyguanylate.
B) 3' deoxyguanylate.
C) 3', 5' deoxyguanylate.
D) 5', 3'deoxyguanylate.
E) dGMP
3. Much of the stability of the double stranded helical DNA structure is the result of
A) hydrogen bonding between purines.
B) the phosphodiester backbone.
C) Ionic nucleobase attraction.
D) the stacking interactions between base pairs.
All five histones are rich in ________ amino acid residues whose positive charges allow
binding to the sugar-phosphate backbone of DNA.
A) lysine and alanine
B) lysine and arginine
C) leucine and alanine
D) leucine and arginine
Which does not apply to most bacterial DNA?
A) Circular.
B) Relaxed.
C) Not packed into nucleosomes.
D) Supercoiled.
Which best describes the structure of a nucleosome core particle?
A) A histone octamer with DNA threaded through its center.
B) About 50 bp of DNA associated with one histone H1 molecule.
C) One nucleosome plus one histone H1 and linker DNA.
D) A histone octamer wrapped approximately two times around with DNA.
Nucleic Acid Structure
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Nucleobase
Nucleoside
Nucleotide
Nucleic acid
Chromatin
Chromosome
Base Structure
• Purines and
pyrimidines
• Aromatic
• Tautomers
• H-bonding
Nucleosides
• Ribonucleosides and deoxyribonucleoside
• Purine = osine; pyrimidine = idine (watch cytosine)
Nucleotides
• Phosphorylated on 2’, 3’, or 5’
• 5’ unless noted
• Draw these:
– dA
– ADP
– ppAp
– ApAp
• pA is normally called _______
or _______________
Polynucleotides
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Phosphate diesters
polyanion
directionality
5’  3’
Abbreviation is
pdApdGpdTpdC
• tetranucleotide
Double Stranded DNA
• Chargaff’ Rule: %A =%T and %G = %C
• (C + G) not necessarily equal to (A + T)
Complementary Base Pairs
Mismatching may occur with tautomers
Antiparallel
• Inaccuracy of twodimensional
drawing: bases
are perpendicular
to the paper
• “ladder”
• H-bonding
Helix
• Maximization of
base pair stacking
• More compact
• Major and minor
groove
• How do we explain
major/minor
grooves?
Major/Minor Groove
• Many pictures
show ladder with
backbone at 180o
• Actually a
distorted ladder
with poles closer
to each other, on
one side
Weak Forces Stabilize Double Helix
• Stacking interactions
(vdW forces)
• Hydrogen bonding
• Hydrophobic effect
• Charge-charge
Denaturation
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Melting point
Melting curve
UV-absorption
cooperative
A/T Rich and G/C Rich strands
• GC rich strands harder to
denature due to STACKING (not
H-bonds)
• Cooperativity due to initial
unstacking, which exposes bases
to water, which destabilizes Hbonds, which leads to further
denaturation
Supercoiling
• Bacterial DNA
• Closed, circular DNA
• Topology and topoisomerases
Eukaryotic DNA
• Chromatin
• 8000x packing ratio
– Nucleosomes (10x)
– 30nm chromatin fiber
(4x)
– RNA/Protein scaffold
holds loops (200x
condensation of DNA
length
Nucleosomes
• Beads on string
• Histones form octamer
• Core particle
Unpacking
• Histones serve as negative
supercoiling
• Histone acyltransferases
(HATS)
• Necessary for expression
Chromosome
• Scaffold of RNA and
protein
• 30nm fibers are looped
many times
• Picture of histonedepleted chromosome:
DNA strands have fallen
off of scaffold
Answers
1.
2.
3.
4.
5.
6.
E
B
D
B
B
D