NUCLEOTIDES

AND
NUCLEIC ACIDS

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 AT THE END OF THE SESSION, THE STUDENTS SHOULD BE ABLE TO
ANSWER THE FOLLOWING :

1. What are the different functions of nucleotides and how can you explain them?
2. Identify / Describe :
2.1 the chemical structures of purine and pyrimidine nitrogenous
bases that are present in nucleic acids.
2.2 the chemical structures of ribose and deoxyribose that serve
as the bases for naming nucleic acids.
3. Describe / Identify :
3.1 How nucleosides are formed from the interaction between the
nitrogenous base and sugar and the manner by which they are named.
3.2 Describe how nucleotides are formed from the interaction between
specific nucleoside and phosphoric acid and the different ways by which
they are named.
4. Identify how these monophosphate nucleotides are converted to nucleoside
diphosphates (NDP’s) and nucleoside triphosphates (NTP’s).
5. Describe / Identify the assembly of nucleic acids from mononucleotides.
5.1 Phosphodiester linkage as the covalent backbone.
5.2 Manner by which the nitrogenous bases, sugars and phosphoric acid
are arranged in space.
6. What are findings and conclusions can you draw from the experiments of
Chargaff regarding DNA?
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 Nucleotides and Nucleic Acids
Nucleotides are the building blocks of Nucleic Acids

Nucleotide
RNA DNA

Nucleotides also play other important roles in the cell

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 Roles of Nucleotides

• Building blocks of nucleic acids (RNA, DNA)

•Analogous to amino acid role in proteins
• Energy currency in cellular metabolism
(ATP: Adenosine TriPhosphate)
• Allosteric effectors (c-AMP; GMP)

• Structural components of many enzyme

cofactors (NAD; FAD; CoASH)

• Secondary messengers (c-AMP)

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 Roles of Nucleic Acids

DNA
• DNA contains the information needed to
synthesize functional proteins and RNAs

• DNA contains segments that play a role in

regulation of gene expression (promoters)

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RNA
• Ribosomal RNAs (rRNAs) are
components of ribosomes, playing a
role in protein synthesis

• Messenger RNAs (mRNAs) carry genetic

information from a gene to the ribosome

• Transfer RNAs (tRNAs) translate

information in mRNA into an amino acid
sequence

RNAs have other functions, and can in some cases,

perform catalysis
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 BIOMEDICAL IMPORTANCE
- Synthetic Pyrimidines : 5-iodo-2’-
deoxyuridine; 5-fluorouracil; 6-azauridine and
Purine Analogs (8-azaguanine; 6-mercapto-
purine; 6-thioguanine; allopurinol) that contain
Halogens, Thiols, or additional Nitrogen are
employed for Chemotherapy of Cancer and
AIDS
- As suppressors of the immune response
during organ

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 Structure of Nucleotides

Nucleotides have three characteristic components:

A Nitrogenous Base
A Phosphate Group (Pyrimidines or Purines)

A Pentose ugar

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 Structure of Nucleosides

Remove the Phosphate Group, and you have a Nucleoside.

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Naming Conventions
 Nucleosides:
 Purine Nucleosides end in “-sine”
 Adenosine, Guanosine
 Pyrimidine Nucleosides end in “-dine”
 Thymidine, Cytidine, Uridine
 Nucleotides:
 Start with the Nucleoside name from above
and add “Mono-”, “Di-”, or “Triphosphate”
 Adenosine Monophosphate, Cytidine Triphosphate,
Deoxythymidine Diphosphate

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 ATP is a Nucleotide - energy currency

Base (adenine)
triphosphate
Ribose sugar

DG = -50 kJ/mol

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 NAD is an important Enzyme Cofactor

Nicotinamide

NADH is a hydride transfer agent,

or a reducing agent.
Derived from Niacin

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 Nucleotides play roles in regulation

The covalent attachment of another molecule

can modify the activity of enzymes and many
other proteins. In these instances, a donor
ADP-ribosylation is the addition of
molecule provides a functional moiety that
one or more ADP-ribose moieties to a
modifies the properties of the enzyme.
protein.

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 Structure of Nucleotides
Below is the General Structure of a Nucleotide.
The Base, Pentose Sugar, and the Phosphate
Moieties all show variations among nucleotides.

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 The Ribose sugar

2’-Deoxyribose

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 Ribose

• Ribose (b-D-furanose)
is a pentose sugar
(5-membered ring). 5’
4’ 1’
• Note numbering of the
carbons. In a nucleotide, 3’ 2’
"prime" is used
(to differentiate from
base numbering).

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 Ribose

• An important derivative
of ribose is
2'-Deoxyribose, or just
Deoxyribose, in which the
2' OH is replaced with H.

• The sugar prefers

different puckers in DNA
(C-2' endo) and RNA
C-3' endo).

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 The Purine or Pyrimidine Base

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 Pyrimidines and Purines

Nucleotide bases in nucleic acids are pyrimidines or purines.

Imidazole Ring

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 6 7
1 5
8
4 N10-Formyl THF
2
3 9

N10-Formyl THF

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 4
3 5

2 6
1

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 Imidazole Ring
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 Major Bases in Nucleic Acids
• The bases are
abbreviated by their
first letters
6 6

(A, G, C, T, U).
• The Purines (A, G) occur
2

in both RNA and DNA

6-aminopurine 2-amino-6-oxypurine

• Among the Pyrimidines, C 4 4

5
4

occurs in both RNA and

DNA, but 2 2 2

• T occurs in DNA, and

U occurs in RNA 2-oxy-4-amino- 2,4-dioxy-5-methyl 2,4-dioxy
pyrimidine pyrimidine pyrimidine

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 Some Minor Bases

• 5-Methylcytidine occurs in DNA of animals and higher plants

• N6-methyladenosine occurs in bacterial DNA

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 The Phosphate

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 Variation in Phosphate Group
• Adenosine 3', 5'-Cyclic
Monophosphate is an
important regulatory
nucleotide.

• In hydrolysis of RNA by
some enzymes,
Ribonucleoside 2',3'-Cyclic
Monophosphates are
isolable intermediates;
Ribonucleoside 3'-Mono-
phosphates are end
products

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 Nucleotides in Nucleic Acids
• Bases attach to the C-1' of ribose or deoxyribose
• The Pyrimidines attach to the pentose via the N-1
position of the pyrimidine ring
• The Purines attach through the N-9 position
• Some Minor Bases may have different attachments.
N9
N1

N-C Glycosidic Bond

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 Deoxyribonucleotides
N-C Glycosidic Bond
2'-Deoxyribose Sugar
with a base (here, a Purine,
Adenine or Guanine)
N9
attached to the C-1' 5’
position is a C1
Deoxyribonucleoside
(here Deoxyadenosine
and Deoxyguanosine).

Phosphorylate the 5' position

and you have a Nucleotide
(here, Deoxyadenylate or
Deoxyguanylate)

Deoxyribonucleotides are abbreviated (for example) A, or dA

(deoxyA), or dAMP (deoxyadenosine monophosphate)
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 The Major Deoxyribonucleotides
N-C Gycosidic Bond

N9

1’

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 Ribonucleotides
N-C Glycosidic Bond
• The base (here, a
Pyrimidine, Uracil or
Cytosine) is attached to 1
the ribose C-1' position
1’
• Phosphorylate the 5'
position and you have a
ribonucleotide (here,
uridylate or cytidylate)

• Ribonucleotides are abbreviated (for example) U, or

UMP (uridine monophosphate)

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 The Major Ribonucleotides

N-C Gycosidic Bond

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 Nucleotide Nomenclature

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 Nucleotide Nomenclature

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 Nucleic Acids
Nucleotide Monomers
can be linked together via a
Phosphodiester Linkage
formed between the 3'-OH
of a nucleotide
and the phosphate of the
next nucleotide.

Two ends of the resulting poly-

or oligonucleotide are defined:
The 5' end lacks a nucleotide
at the 5' position,
and the 3' end lacks a
nucleotide at the 3' end
position.
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 Sugar-Phosphate Backbone

5’- 3’-

• The polynucleotide or Nucleic Acid backbone thus consists of

alternating pentose and phosphate residues.
• The bases are analogous to side chains of amino acids; they
vary without changing the covalent backbone structure.
• Sequence is written from the 5' to 3' end: 5'-ATGCTAGC-3‘
• Note that the backbone is polyanionic. Phosphate groups
pKa ~ 0.
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 The Bases can take syn or anti positions

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 Sugar phosphate backbone conformation
• Polynucleotides have
unrestricted rotation about
most backbone bones (within
limits of sterics)

• with the exception of the sugar

ring bond

• This behavior contrasts with

the peptide backbone.

• Also in contrast with proteins,

specific, predictable
interactions between bases are
often formed: A with T, and G
with C.

• These interactions can be

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 Compare Polynucleotides and Polypeptides

• As in proteins, the sequence of side chains

(Bases in Nucleic Acids) plays an important
role in function.

• Nucleic Acid structure depends on the

sequence of bases and on the type of ribose
sugar (ribose, or 2'-deoxyribose).

• Hydrogen Bonding interactions are

especially important in Nucleic Acids.

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A STRAND
OF RNA

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A STRAND
OF DNA

T G C A

40
 Class Activity

1. Draw the structures of all the two purine and three

pyrimidine bases.
2. Draw the structures of :
a) dAMP d) dTMP
b) ATP e) UDP
c) GMP
3. Draw the following Polynucleotide :
a) dAMP-dGMP-dTMP-dCMP
b) UMP-GMP-CMP-AMP

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Interstrand H-bonding between DNA bases

4
H-Bond 6
3 1
1
9

4
H-Bond
6 3 1
1 2

9 2

Watson-Crick Base Pairing

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 DNA structure determination

• Franklin collected X-ray

Diffraction data (early 1950s)
that indicated 2 periodicities
for DNA: 3.4 Å and 34 Å.

• Watson and Crick proposed a

3-D model accounting for the
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data. 43
 DNA Structure
• DNA consists of two helical
chains wound around the same 3’ 5’
axis in a right-handed fashion - -
aligned in an antiparallel
fashion. - -

• There are 10.5 Base Pairs, - -

or 36 Å, per turn of the 10 Base Pairs
helix. - -
• Alternating Deoxyribose and - -
Phosphate groups on the
backbone form the outside of
the helix.
• The planar Purine and
Pyrimidine bases of both
strands are stacked inside 3’ 5’
the helix.
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 DNA Structure

• The furanose ring usually is

puckered in a C-2' endo
conformation in DNA.
• The offset of the
relationship of the base
pairs to the strands gives a
major and a minor groove.
• In B-form DNA (most
common) the depths of the
major and minor grooves
are similar to each other.

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 Base stacking in DNA
H-Bond

• C-G (red) and A-T (blue) base

pairs are isosteric (same shape
and size), allowing stacking
•Base pairs stack
along a helical axis for any
inside the helix.
sequence.

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 DNA strands
H-Bond

• The antiparallel strands of DNA are

not identical, but are complementary.
• This means that they are positioned
to align complementary base pairs:
C with G, and A with T.
• So you can predict the sequence of
one strand given the sequence of its
complement.
• Useful for information storage and
transfer!

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 Nucleic Acids
• B form - The most common
36 base pairs
conformation for DNA. Backbone - blue;
• A form - common for RNA Bases- gray
because of different sugar
pucker. Deeper minor groove,
shallow major groove
• A form is favored in conditions
of low water.
• Z form - narrow, deep minor
groove. Major groove hardly
existent. Can form for some
DNA sequences; requires
alternating syn and anti base
configurations.
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 Nucleic Acids : DNA

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 Eukaryotic DNA

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 Eukaryotic Cell Nucleus

Mircotubules
DNA

10 mm

Heterochromatin Euchromatin Nucleolus

Chromatin organization of higher eukaryotes

DNA
 Chromatin in the Nucleus
• In 1884, Albrecht Kossel coined the term “Histone” to
describe the proteins he found by extracting avian erythrocyte
nuclei using diluted acids
• In 1973, Olins, et al and Woodcock, et al observed
that chromatin shows a “beads on a string” structure by EM

• treatment of chromatin with micrococcal nuclease preferentially

cuts between the beads
 Nucleosome Structure
Roger Kornberg
• based on EM images, nuclease digestion patterns, X-ray diffraction
data, and purification of nucleoprotein complexes, proposed that the
nucleosome is the repeating unit of chromatin and that every ~200 bp
of DNA forms a complex with four histone pairs (1974)

H1 Nucleosome

core Histone octamer =

2 copies each of

H2A
H2B
DNA H3
H4
 Core Histones
• core histones (H2A, H2B, H3 and H4) are small (11 to 14 kD), highly
basic proteins

• they are evolutionarily highly conserved (from yeast to humans)

• they all share similar structural motifs

N C

N-terminal tail helicies C-term tail

histone fold

= “hand shake” motif

 Assembly of a Nucleosome
• histones can dimerize through their “hand shake motifs”

• H3 can only dimerize with H4 and H2A always dimerizes with H2B
• Nucleosome assembly starts with two H3-H4 dimers forming a tetramer

• This followed by addition of two H2A-H2B dimers to form the octamer

• DNA is wrapped around the histone octamer

H3 Nucleosome Crystal Structure
H4

Luger et al, Nature, 1997

 Nucleosome Crystal Structure
H3 H2A
H4 H2B

Luger et al, Nature, 1997

 Why is Chromatin folding important in the cell?

DNA/Chromatin has to condense and decondense during the Cell Cycle

Stable cell line expressing H3-GFP

 How does chromatin folding affect Nuclear Functions?

• Nucleosomes inherently function as barrier to nuclear factors that need to

access and bind to DNA elements

• e.g. Chromatinized template inhibits transcription of underlying genes

• Also affects other DNA-templated processes such as DNA replication,

repair etc.

• In order to activate gene expression, the cell has developed ways to “open”
up chromatin

a. ATP-dependent chromatin remodeling factors

b. histone modifying enzymes
c. insert histone variants at strategic locations within genome
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 RNA has a rich and varied structure
Watson-Crick base
pairs (helical segments;
Usually A-form). Helix
is secondary structure.
Note A-U pairs in
RNA.

DNA can
form
structures
like this as
well.

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RNA displays interesting Tertiary Structure

Single-
Yeast tRNAPhe
stranded
(1TRA)
RNA
right-
handed
helix
Hammerhead Ribozyme
(1MME)

T. thermophila intron,
A Ribozyme (RNA enzyme)
(1GRZ)

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 t-RNA

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Chargaff’s Rule

• A with T: the purine adenine (A) always

pairs with the pyrimidine thymine (T)

• C with G: the pyrimidine cytosine (C)

always pairs with the purine guanine (G)

Sum of Purines = Sum of Pyrimidines

A + G = T +C
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 The Mother of all Biomolecules
(Proteins at least) Large Subunit of the Ribosome

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