MCB 102 - Survey of the

Principles of Biochemistry and

Molecular Biology
Lecture

Functions of Nucleotides and

Nucleic Acids
Nucleotide Functions:
Energy for metabolism (ATP)
Enzyme cofactors (NAD+)
Signal transduction (cAMP)

Nucleic Acid Functions:

Storage of genetic info (DNA)

Transmission of genetic info (mRNA)
Processing of genetic information (ribozymes)
Protein synthesis (tRNA and rRNA)

Nucleotides and Nucleosides

Nucleo'de =
Nitrogeneous base
Pentose
Phosphate

Nucleoside =
Nitrogeneous base
Pentose

Nucleobase =
Nitrogeneous base

Pyrimidine Bases
Cytosine is found in both DNA and RNA
Thymine is found only in DNA
Uracil is found only in RNA
All are good H-bond donors and acceptors
Neutral molecules at pH 7
Planar or almost planar
structures
Absorb UV light around
250270 nm

3
2

Purine Bases
Adenine and guanine are found in both RNA and
DNA
Also good H-bond donors and acceptors
1
Neutral molecules at pH 7
Planar or almost planar
structures
Absorb UV light around
250270 nm

Each Base Has Its Preferred

Tautomeric Form
Each of the bases exist in alternative tautomeric states,
which are in equilibrium with each other.
This equilibrium is biased towards the forms commonly
found in B-DNA.

The capacity to form

alternative tautomers is a
frequent source of error in
DNA synthesis.
Note: Book showed the OH in the
enol form of G as an acceptor, but
I corrected it to a donor.

Pentose in Nucleotides
-D-ribofuranose in RNA
-2-deoxy-D-ribofuranose in DNA
Dierent puckered conformaIons (4)
of the sugar ring are possible.
Phosphate

Base

5
1

4
3

RNA or DNA

In all conformations, four of the

five atoms are nearly in a
single plane.

-N-Glycosidic Bond
In nucleotides the pentose
ring is attached to the
nucleobase via N-glycosidic
bond.
The bond is formed to the
anomeric carbon of the sugar
in configuration
The bond is formed:
to position N1 in
pyrimidines
to position N9 in purines
This bond is quite stable
Bond cleavage is catalyzed by
acid.

Conformation around N-Glycosidic

Bond
Relatively free rotation can occur around
the N-glycosidic bond in free nucleotides
There is free rotation around 6 bonds,
with restrictions only around bond 4.
Conformation can be Syn or Anti.
Anti conformation is found in normal BDNA .

Phosphate Group
Negatively charged at neutral pH
Typically attached to 5 position
Nucleic acids are built using 5-triphosphates
ATP, GTP, TTP, CTP

Nucleic acids contain one phosphate moiety per nucleotide

May be attached to other positions

Nomenclature

DeoxyRibonucleotides
You need to know structures, names, and symbols
(both two-le>er (dA) and four-le>er (dAMP) codes)

Ribonucleotides
You need to know structures, names, and symbols
(both one-le>er and three-le>er codes)

UV Absorption Spectrum
The absorption
spectrum is independent
of ribose or deoxyribose
in free nucleotides

Minor Nucleosides in DNA

ModicaIon is done aPer DNA synthesis

5-Methylcytosine is common in eukaryotes, also found in

bacteria
N6-Methyladenosine is common in bacteria, not found in
eukaryotes
EpigeneIc marker
Way to mark own DNA so that cells can degrade foreign DNA
(prokaryotes)
Way to mark which genes should be acIve (eukaryotes)
Could the environment turn genes on and o in an inheritable
manner? MORE ON THIS LATER!!

Minor Nucleosides in DNA

Minor Nucleosides in RNA

Inosine sometimes found in the wobble position of the
anticodon in tRNA
Made by de-aminating adenosine
Provides richer genetic code
Pseudouridine ( ) found widely in tRNA and rRNA
More common in eukaryotes but found also in
eubacteria
Made from uridine by enzymatic isomerization after
RNA synthesis
May stabilize the structure of tRNA
May help in folding of rRNA

Minor Nucleosides in RNA

Polynucleotides
Covalent bonds formed via phosphodiester linkages (5P to 3-OH)
negatively charged backbone

Backbone is fairly
hydrophilic as the sugar
residues can form hydrogen
bonds with water.
Phosphate groups have pKa
near 0, so they are completely
ionized at pH 7.
The negative charges of the
backbone are neutralized by
ionic interactions with positive
charges in proteins, metal ions
and polyamines.

Polynucleotides
The DNA backbone is
stable.
The RNA backbone is
more unstable and can be
hydrolyzed at alkali
conditions (due to the
extra OH)
Polynucleotides are linear
polymers, with no
branching or side chains.
They have directionality,
and we read the sequence
from the 5 to 3.

Hydrogen-Bonding Interactions
Two bases can hydrogen bond to
form a base pair.
For monomers, large number of
base pairs is possible.
In polynucleotide, only few
possibilities exist
Watson-Crick base pairs
predominate in double-stranded
DNA
Purine pairs with pyrimidine
A pairs with T (2 Hydrogen Bonds)
C pairs with G (3 Hydrogen Bonds)

DNA is a double helix with

antiparallel polynucleotide strands

The sequence is read from 5 to 3.

The two chains dier in sequence.
The two chains are complementary.
The two chains run anIparallel.
The following base pairs are the only
ones allowed:

A= T
G C
Stability due mostly to the stacking of
the bases

Double Helical DNA strength in

numbers
Hydrogen-bonds between bases are
only slightly stronger than between
a base and H2O.
The packing of DNA bases doesnt
allow water molecules inside the
double helix.
In the absence of H2O between
bases >12 complementary base pairs
are sufficient to hold two DNA
strands together.
The cooperativity of the many
noncovalent links of a zipper are a
familiar model.

Why dont the bases usually

swivel around? Vertical sharing of
+

P-electron bonding is
similar to metallic bonds,
in which numerous atoms
share electrons.

aromatic delocalized pelectrons between bases

generates stacking bonds
(Zusman slide).
This vertical stacking
prevents the DNA bases
from rotating freely
away from the base
pairing with the
complementary strand.
(pi-stacking)

Further evidence for vertical

stacking: Aromatic dyes intercalate
between bases of DNA
Aromatic dyes like ethidium,
actinomycin intercalate,
stack in DNA:
The resulting fluorescence is
evidence for vertical bonding
by shared electrons
(Lehninger p960).

Intercalation of dyes in DNA

generates fluorescence in UV light
To a first approximation
Aromatic dyes, when they
absorb a photon can release
energy either as:
Thermal collision with the solution.
Fluorescence

Stacked in DNA pairs, it is

dehydrated, and has less
freedom of motion and is thus
less likely to release energy
through thermal collision and
more likely to release a photon.

DNA Fluoresces in Eth-Br buffer

(Agar gel electrophoresis)

Bases can Flip Out of the

Double Helix
Sometimes individual bases can
protrude from the double helix,
a phenomenon known as base
flipping.
This is important in DNA
methylation and DNA repair.
In fact, it is thought that
enzymes involved in
homologous recombination and
DNA repair scan DNA by
flipping out one base after
another.

Major and Minor Grooves

A result of the geometry of base
pairs.
The edges of each base pair are
exposed in the major and minor
grooves, creating a pattern of Hbond donors and acceptors and
of van der Waals surfaces that
can be recognized.

A= acceptor

D= donor

H= non-polar
hydrogens

M= methyl
groups

Major groove is extremely sensitive to the identity of the base

pairs inside.
AT A D A M (TA M A D A)
GC A A D H (CG H D A A)

Minor groove has similar hydrogen bonding patterns regardless

of the base pair.
AT A H A (TA A H A)
GC A D A (CG A D A)

Possible DNA Structures

DNA can exist in a variety of
structures as there is a
significant number of bonds
with free rotation.
All conformations contain the
following properties, first
defined by Watson and Crick:
Strand complementarity
Antiparallel strands
A= T and G C base pairs.

Possible DNA Structures

A form is
more
favorable
for DNARNA or
RNA-RNA

Most Common Form

B-DNA
Right handed
Diameter ~20A
10.5 base pairs per helical
turn.
Helix rise per base pair
3.4A
Almost planar base
orientation. They stack
together closely,
excluding water.
Major and minor grooves.
36A is a complete turn.