The Structure of Nucleotides and Nucleic Acids

Morning on the other side of planet Earth

Zhongshan, Guangdong Province, China

There are two basic kinds of nucleic acids

Deoxyribonucleic acid, DNA
storage of genetic information, genes and regulatory sequences that control
expression of genes.
Ribonucleic Acid, RNA
involved in the expression of genetic information in the processes of
transcription (mRNA) and translation (tRNA, rRNA).
A variety of small RNA molecules also play gene expression regulatory
roles in the cell.

All cellular life forms on earth use DNA to store genetic information.
Many viruses use RNA instead of DNA to store genetic information.

Whats in a Name
The terms nitrogenous base, nucleoside, and nucleotide have precise meanings
Nitrogenous base

Adenine

Nucleoside

Adenosine

in common speech, we frequently use the

term adenine when referring to the
nucleotide version as well.

Nucleotide

Adenosine
monophosphate, AMP
Adenosine diphosphate, ADP
Adenosine triphosphate, ATP

Nitrogenous bases
the bases in nucleotides or nucleic acids are derivatives of either purine or
pyrimidine.
the rings in in both base types are referred to as Heterocyclic meaning they
contain elements other than carbon (e.g. nitrogen).
the ring structure of purines are a fusion between a 6C pyrimidine ring and
a 5C imidazole ring
Have you encountered
atoms making up molecules are numbered as indicated
an imidazole ring
elsewhere?

What is the
difference
between
uracil and thymine?

Two purines participate in the formation of nucleic acids but many other purines
exist in nature

Chemistry of Nitrogenous Bases

the bases are aromatic (have resonance structures) and are relatively hydrophobic.
the bases are planar, can engage in stacking interactions with each other and
with other aromatic groups like the side chains on certain amino acids.
because of their aromaticity, the nitrogenous bases absorb UV radiation at
260 nm very strongly. This is why we measure DNA concentrations in solution
at 260 nm.

Nitrogenous base groups that can participate in Hydrogen bonding

Nucleosides
nucleosides are compounds formed when a base is covalently linked to a
5C sugar called ribose.

it is the absence of an oxygen atom

on the 2 (pronounced two prime)
carbon atom that results in name
deoxyribonucleic acid.

The nucleosides used in ribonucleic acid (RNA)

Nelson p812

nitrogenous bases and certain nucleotides are used extensively in cells

for purposes other than nucleic acid synthesis but the nucleosides not so much.

Adenosine is an interesting exception it acts as a sort of hormone.

in mammals adenosine has a variety of hormonal functions in the body

blood vessel dilation

smooth muscle contraction
neurotransmitter release
metabolism of fat

for example, after extensive exercise adenosine levels rise in muscle tissue
causing blood vessel dilation and increased blood flow to muscle cells.
Adenosine also regulates sleep:
upon prolonged wakefulness, adenosine levels rise and promote
sleepiness by interacting with neuron receptors

adenosine

Caffeine, which is a structural mimic of adenosine, blocks adenosine function

by binding to the same neuronal receptors.

Nucleotides
A nucleotide results when phosphoric acid is linked to the sugar of a nucleoside
by an ester linkage.
the ester linkage occurs on the 5 carbon of the sugar

Nelson p813

Formation of di- and tri-phosphate nucleotides

phosphate groups linked by phosphoanhydride linkages
ATP is an energy carrier in cell and contributes needed energy to many reactions
because of the energy carried in the anhydride bonds.
in the cell, the tri-phosphate forms are used to build nucleic acids (ATP or dATP)

Nelson p814

Nucleic acids are polymers of nucleoside monophosphates

nucleic acids have directionality called

5 to 3, this is the order in which DNA
is read.
fragments also begin with 5 phosphate
and end with 3 OH group.
nucleic acids have a net negative charge.
the ribose of each nucleotide is joined by
a phosphodiester bond.

If the molecule to the right was RNA

instead of DNA, what would it look like?
moran p580

Why are nucleic acids called acids?

pKa = 2

H+

HOO

-O

5
4
[acid]=[conjugate base]

3
pH

2
1
-

OHO

at physiological pH
this form exists

Complementary strands of DNA form Double-stranded DNA

note the antiparallel directions of opposing strands
note the base pairing rules and the H bonding patterns
identify the components of each participating nucleotide

moran p581

A short segment of DNA

5-ATCGTAGCCGATGCCGCTACGTGCGTAGCTAGCGATGCTAGTA-3
3-TAGCATCGGCTACGGCGATGCACGCATCGATCGCTACGATCAT-5

Notice:
5 to 3 directionality of top strand of DNA
the complementarity of the nucleotides in each strand
(A always basepairs with T)
(G always basepairs with C)
the anti-parallel directionality of bottom strand (3 to 5)

How many nucleotides make up your DNA?

Double-stranded DNA forms a helical structure

the helix is the result of several intra-molecular interactions and forms
spontaneously in water

Stabilizing Features of double-stranded helical DNA

ds DNA is stabilized by 3 major interactions types
Hydrogen bonding between bases on opposite strands
these are widely thought to be the major stabilizing force in DNA
structure. But they provide only small contribution to stability.
The Hydrophobic effect
the nitrogenous bases are hydrophobic. It is entropically favorable
to shield these from contact with water molecules.
Stacking interactions between bases on same strand
mainly van der Waals forces between adjacent planar bases
these are the main contributors to DNA helix stability.

Hydrogen bonding occurs between base pairs on opposite strands

what are the donors and acceptors in these bonds?

predominant form
at pH 7

predominant form
above pH 9.7

hence, pH can influence the stability of double-stranded nucleic acids.

The Hydrophobic Effect

Double stranded DNA adopts a compact structure where the hydrophobic bases
are largely shielded from contact with water molecules.

Adjacent base pairs stack together along the helix

each adjacent pair is separated by a distance that is ideal for the formation of
van der Waals interactions

these are the interactions in ds DNA that

contribute the most stability to the
helix, not H bonding as is commonly
thought.

3. Induced dipole-induced dipole. Random

fluctuations in electron distribution in one
molecule sets up temporary dipole. This induces
dipole in adjacent molecule, resulting in
interaction. Weak but very important to the
cohesiveness of everything.
Also known as London Dispersion Forces.

Alternative views of the stacking arrangement

of bases in DNA

note the substantially hydrophobic

core to the helix

The Overall Topology of Double-stranded DNA (B-form)

right-handed helix
width 2.4 nm
rise
0.33 nm
pitch 3.4 nm
there are 10-11 nucleotides
per complete turn of DNA

about 4,000 DNA strands laid side by side

would equal the width of a human hair
moran pg 583

The geometry of the base pairs explain the origin of

major and minor grooves

Nelson p840

Many Proteins bind DNA in a base sequence-dependent fashion

e.g. proteins involved in DNA replication and gene expression regulating proteins
these proteins usually make contact with the major groove where functional groups
on the bases are exposed. This is how a specific nucleotide sequence is
recognized by a protein. Consequently nucleotide recognition sites are often
about 10-11 nucleotides apart.

lambda bacteriophage cII DNA binding protein (cII)

Relevant Dimensions
Major groove
Minor groove
-helix

10
5

5-AAACGTTGCGTTTGTTTGCCACGAACCATA-3
3-TTTGCAACGCAAACAAACGGTGCTTGGTAT-5

5
recognition/binding site (red) in DNA for lambda cII protein

molecular interaction
pattern matching

BIOL3073
Biochemistry of Gene Expression

Major and minor groove groups available for molecular interaction

So, the major groove is the primary site of specific

interaction by DNA binding proteins because:
-dimension of major groove vs minor groove fits a protein -helix
-more information exposed (i.e. more molecular interaction sites)

-more diversity in pattern of molecular interaction sites

In this discussion of nucleotide and nucleic acid structure,

notice how you needed knowledge of:

-molecular interactions
-acid base concepts