VISHAL KUMAR 2020/2021
I. DNA and RNA
1. Chemical structure of nucleotides;
primary and secondary structure of nucleic
acids (DNA and different types of RNA)
- Nucleoside: nucleobase + pentose
- Nucleotide: nucleoside + 1 phosphate group
(at least)
CHEMICAL STRUCTURE OF NUCLEOTIDES
Nucleobases:
N-containing heteroaromatic compounds,
substituted purine or pyrimidine rings.
Purines and pyrimidines are nitrogen-
containing heterocycles. They contain, in
addition to carbon, other (hetero) atoms,
such as nitrogen. Their six-atom rings are
numbered in opposite direction
- Pyrimidines: with the clock
- Purines: against the clock
Oxo-enol tautomerism of nucleobases
Tautomers are isomers of a compound which differ only
in the position of protons (H) and electrons.
- The oxo and amino groups of purines and
pyrimidines exhibit oxo-enol and amine-imine
tautomerism
- Physiological conditions favor oxo + amino forms
,VISHAL KUMAR 2020/2021
Pentose (sugar)
In RNA, the sugar moiety to which the phosphates and
purine + pyrimidine bases are attached to is ribose,
rather than the 2’ deoxyribose of DNA.
Phosphate
Bonds between the phosphates: ester bond, and 2 acid
anhydride bonds
- Acid anhydride bonds are considered as
macroergic bonds (store high energy)
- Cleavage of an acid anhydride bond may be
coupled with other processes
CHEMICAL STRUCUTRE OF NUCLEOSIDES
Nucleosides are derivatives of purines and pyrimidines, only have a sugar linked to a ring
nitrogen of a purine / pyrimidine
- Numerals with a prime (e.g. 2’ or 3’ on a
sugar) distinguish atoms of the sugar
from those of the heterocycle
- Both sugars are linked to the
heterocycle by a N-glycosidic bond,
usually to the N-1 of a pyrimidine or to
a N-9 of a purine
Syn- and anti-conformation of nucleotides
- Heterocyclic N-glycosides exist as syn- and
anti-conformers
- Steric hindrance by the heterocycle
dictates that there is no freedom of
rotation about the beta-N-glycosidic bond
of nucleosides/nucleotides
- Therefore, both exist as non-
interconvertible syn- or anti-conformers
- Anti-conformers predominate
(energetically more favorable)
,VISHAL KUMAR 2020/2021
Nucleic acids are polynucleotides specialized for information storage and transmission. They
are composed of multiple nucleotide units connected by phosphodiester bonds.
Primary structure of the polynucleotide chain
DNA and RNA are chemically very similar polynucleotides.
The primary structures of both polymers consist of linear
chain, composed of nucleotide monomers
DNA – deoxyribonucleic acid RNA – ribonucleic acid
Deoxyribose Ribose
Thymine Uracil
Double-stranded Single-stranded
5’ -> 3’ direction:
- The 5’- phosphoryl group of a mono-nucleotide can
esterify a second hydroxyl group, forming a
phosphodiester bond
- This second hydroxyl group is the 3’-OH of the
pentose of a second nucleotide
- This forms a dinucleotide in which the pentose
moieties are linked by a 3’,5’-phosphodiester bond
to form the backbone of RNA and DNA
The secondary (3D) structure
Base pairing:
- A-T base pair: 2 hydrogen bonds
- G-C base pair: 3 hydrogen bonds (stronger
interaction)
Two polynucleotide strands run antiparallel to each
other
- Base pairs are perpendicular to the sugar-
phosphate backbone (actually, base inclination is 6 degrees)
- The purine-pyrimidine pairing ensure the constant width of the helix (2nm)
Adjacent base pairs are rotated by 36 degrees relative to each
other, therefore both strands wind around each other, forming
the well-known right-handed double helix
, VISHAL KUMAR 2020/2021
I. DNA and RNA
1. Chemical structure of nucleotides;
primary and secondary structure of nucleic
acids (DNA and different types of RNA)
- Nucleoside: nucleobase + pentose
- Nucleotide: nucleoside + 1 phosphate group
(at least)
CHEMICAL STRUCTURE OF NUCLEOTIDES
Nucleobases:
N-containing heteroaromatic compounds,
substituted purine or pyrimidine rings.
Purines and pyrimidines are nitrogen-
containing heterocycles. They contain, in
addition to carbon, other (hetero) atoms,
such as nitrogen. Their six-atom rings are
numbered in opposite direction
- Pyrimidines: with the clock
- Purines: against the clock
Oxo-enol tautomerism of nucleobases
Tautomers are isomers of a compound which differ only
in the position of protons (H) and electrons.
- The oxo and amino groups of purines and
pyrimidines exhibit oxo-enol and amine-imine
tautomerism
- Physiological conditions favor oxo + amino forms
,VISHAL KUMAR 2020/2021
Pentose (sugar)
In RNA, the sugar moiety to which the phosphates and
purine + pyrimidine bases are attached to is ribose,
rather than the 2’ deoxyribose of DNA.
Phosphate
Bonds between the phosphates: ester bond, and 2 acid
anhydride bonds
- Acid anhydride bonds are considered as
macroergic bonds (store high energy)
- Cleavage of an acid anhydride bond may be
coupled with other processes
CHEMICAL STRUCUTRE OF NUCLEOSIDES
Nucleosides are derivatives of purines and pyrimidines, only have a sugar linked to a ring
nitrogen of a purine / pyrimidine
- Numerals with a prime (e.g. 2’ or 3’ on a
sugar) distinguish atoms of the sugar
from those of the heterocycle
- Both sugars are linked to the
heterocycle by a N-glycosidic bond,
usually to the N-1 of a pyrimidine or to
a N-9 of a purine
Syn- and anti-conformation of nucleotides
- Heterocyclic N-glycosides exist as syn- and
anti-conformers
- Steric hindrance by the heterocycle
dictates that there is no freedom of
rotation about the beta-N-glycosidic bond
of nucleosides/nucleotides
- Therefore, both exist as non-
interconvertible syn- or anti-conformers
- Anti-conformers predominate
(energetically more favorable)
,VISHAL KUMAR 2020/2021
Nucleic acids are polynucleotides specialized for information storage and transmission. They
are composed of multiple nucleotide units connected by phosphodiester bonds.
Primary structure of the polynucleotide chain
DNA and RNA are chemically very similar polynucleotides.
The primary structures of both polymers consist of linear
chain, composed of nucleotide monomers
DNA – deoxyribonucleic acid RNA – ribonucleic acid
Deoxyribose Ribose
Thymine Uracil
Double-stranded Single-stranded
5’ -> 3’ direction:
- The 5’- phosphoryl group of a mono-nucleotide can
esterify a second hydroxyl group, forming a
phosphodiester bond
- This second hydroxyl group is the 3’-OH of the
pentose of a second nucleotide
- This forms a dinucleotide in which the pentose
moieties are linked by a 3’,5’-phosphodiester bond
to form the backbone of RNA and DNA
The secondary (3D) structure
Base pairing:
- A-T base pair: 2 hydrogen bonds
- G-C base pair: 3 hydrogen bonds (stronger
interaction)
Two polynucleotide strands run antiparallel to each
other
- Base pairs are perpendicular to the sugar-
phosphate backbone (actually, base inclination is 6 degrees)
- The purine-pyrimidine pairing ensure the constant width of the helix (2nm)
Adjacent base pairs are rotated by 36 degrees relative to each
other, therefore both strands wind around each other, forming
the well-known right-handed double helix
, VISHAL KUMAR 2020/2021
