Nucleotide Structure
3 Components of a Nucleotide
base
sugar
phosphate / PO4
Both glycosidic and
phosphodiester bonds
Therefore, these bonds facilitate
nucleotide structural features
Base Structure and Nomenclature
purine (Pu) base
pyrimidine (Pyr) base
(two rings – 9 constituent atoms)
(one ring – 6 constituent atoms)
N
N
N
N
N
N
Ring numbering designates specific ring atoms
(note: Pu and Pyr rings are numbered differently)
(note: not all ring atoms are carbons)
1
BASE STRUCTURE and CHEMISTRY
1. Ring Chemistry and Structure
Pu and Pyr rings
aromatic in character ??
What are you looking for??
benzene ring
(note: all
ring atoms
are carbon)
C
C
C
C
How does non-carbon
atoms affect ring structure??
Pu / Pyr ring nitrogens
Pu / Pyr rings aromatic?
b
benzene
ring
i structure
t
t
Pu & Pyr ring structure
Pu / Pyr ring C and N atoms
Note: electron distribution is uneven thus affecting
the chemical and reactive properties of the
constituent ring atoms
2
3
2. Base Solubility
solvent of cells and living organisms
pseudoaromatic Pu / Pyr bases
hydrophobic interaction
between Pu / Pyr bases
important consequence for
nucleic acid structure and
base interaction with water
3 Base Exocyclic Modifications
3.
three types of exocyclic base modifications
O
NH2
CH3
C
C
C
guanine (Pu)
NH2 (2)
adenine ((Pu))
NH2 ((6))
cytosine (Pyr)
O
(2)
NH2 (4)
thymine (Pyr)
O (2)
O (4)
uracil
O (2)
O (4)
(Pyr)
O (6)
(numbers in parentheses indicate position of exocyclic modification)
CH3 (5)
How do these exocyclic modifications affect the
chemical character / reactivity of each base ??
???
4
4. Base Tautomeric Forms
O
OH
H
N
N
exocyclic
carbonyl
ratio
+
NH2
NH2
H
N
exocyclic
amine
N
5 IIonizable
5.
i bl Base
B
Groups
G
“base” = ionizable
with
values
(protons on ring N)
H
+
N
pKa ~
=
H
N
pKa ~
=
At physiological pH (7.0)
N
( Which forms are
found in bases? )
-N
Base charge ?
Ribose / Deoxyribose Sugar Structure
specific sugar carbons are
defined by
designation
Ribose
base
C5
CH2
HO
5
C4
O
( beta configuration at
the C1’ carbon with
free 360 rotation )
C C1
C
C3 C
OH
free rotation
described by
C C2
OH
ribose
deoxyribose
sugar ring carbons (C2’ and C3’)
can twist out of the plane or
Sugar Ring Structure
flat planar ring not
stabilized by resonance
carbon out of sugar plane towards base
carbon out of sugar plane away from base
exo
endo
O
O
C
C
C
C
C
C
C
DNA (typically) =
RNA (typically) =
C
??? Why does DNA and RNA exhibit different puckers?
6
Sugar – Base Linkage:
free 360 degree rotation around glycosidic bond
range of motion/angles around P angle
Base Configuration Around the Glycosidic Bond
N
N
N
N
N
N
N
purine
O
O
C
C
C
C
C
C
C
C
N
N
N
N
pyrimidine
O
O
C
C
C
N
C
C
C
C
C
is energetically/sterically favorable
Phosphate Groups
7
ionization state / protonation dependent upon pH
PO4 addition makes the nucleotide more soluble
O
O
O
+
H O P O P O
pKa =
p
P
O
CH2
O
H+
O
H+
O
H+
base
O
C
C
C
pKa =
C
What is the sugar -- PO4 backbone charge (pH 7)??
N
nucleotide flexibility
N
O
(ribose)
O
P
N
O
O
CH2
O
C
C
C
covalent bonds
of free rotation per
nucleotide
N
C
O
O
P
O
CH2
(ribose)
nucleotide flexibility built into the nt’s structure
8
Important physical property of nucleotides/nucleic acids
ablilty to absorb incident
radiation or
base ring
nt base is a
absorb UV light
(
(conjugated
j
t dd
double
bl b
bonds)
d )
ground to
excited state
nt / nucleic acid absorption spectrum
(nucleotides and
nucleic acids)
(proteins)
220
240
260
λ
280
300
320
A260
A280
ratio =
(nts / nucleic acids)
?? What happens to A260/A280 ratio with protein contamination?