CHEM 205 LECTURE 5: NUCLEOTIDES AND
NUCLEIC ACIDS
(derived from Voet, 2011)
Friedrich Miescher in 1869
• isolated what he called nuclein from the
nuclei of pus cells
• Nuclein was shown to have acidic properties,
hence it became called nucleic acid
© 2007 Paul Billiet ODWS
Two types of nucleic acid are found
• Deoxyribonucleic acid (DNA)
• Ribonucleic acid (RNA)
© 2007 Paul Billiet ODWS
The distribution of nucleic acids in the
eukaryotic cell
• DNA is found in the nucleus
with small amounts in mitochondria and
chloroplasts
• RNA is found throughout the cell
© 2007 Paul Billiet ODWS
DNA as genetic material: The
circumstantial evidence
1. Present in all cells and virtually restricted to the nucleus
2. The amount of DNA in somatic cells (body cells) of any given
species is constant (like the number of chromosomes)
3. The DNA content of gametes (sex cells) is half that of somatic
cells.
In cases of polyploidy (multiple sets of chromosomes) the DNA
content increases by a proportional factor
4. The mutagenic effect of UV light peaks at 253.7nm. The peak for
the absorption of UV light by DNA
© 2007 Paul Billiet ODWS
NUCLEIC ACID STRUCTURE
• Nucleic acids are polynucleotides
• Their building blocks are nucleotides
© 2007 Paul Billiet ODWS
NUCLEOTIDE STRUCTURE
PHOSPATE SUGAR BASE
PURINES PYRIMIDINES
Ribose or
Deoxyribose Adenine (A) Cytocine (C)
Guanine(G) Thymine (T)
Uracil (U)
NUCLEOTIDE
© 2007 Paul Billiet ODWS
Ribose is a pentose
C5
C4 C1
C3 C2
© 2007 Paul Billiet ODWS
Spot the difference
RIBOSE DEOXYRIBOSE
CH2OH CH2OH
O OH O OH
C C C C
H H H H H H H H
C C C C
OH OH OH H
© 2007 Paul Billiet ODWS
Purines & Pyrimidines
Adenine Thymine
Guanine Cytosine
© 2007 Paul Billiet ODWS
Structure of Nucleotides
Major Bases of Nucleic Acids
The Pentoses of Nucleotides
P
THE SUGAR-PHOSPHATE
BACKBONE P
• The nucleotides are all
P
orientated in the same
direction
• The phosphate group joins the P
3rd Carbon of one sugar to the
P
5th Carbon of the next in line.
© 2007 Paul Billiet ODWS
P
G
ADDING IN THE BASES P
C
• The bases are
P
attached to the 1st C
Carbon
• Their order is P
important A
It determines the
P
genetic information T
of the molecule
P
T
© 2007 Paul Billiet ODWS
Hydrogen bonds
P
G
DNA IS MADE OF
C
TWO STRANDS OF P
POLYNUCLEOTIDE
C G
P
C G
P
A T
P
T A
P
T A
© 2007 Paul Billiet ODWS
P
DNA IS MADE OF TWO STRANDS OF
POLYNUCLEOTIDE
• The sister strands of the DNA molecule run in opposite
directions (antiparallel)
• They are joined by the bases
• Each base is paired with a specific partner:
A is always paired with T
G is always paired with C
Purine with Pyrimidine
• This the sister strands are complementary but not
identical
• The bases are joined by hydrogen bonds, individually
weak but collectively strong
© 2007 Paul Billiet ODWS
Erwin Chargaff’s Data (1950-51)
Wilkins & Franklin (1952): X-ray crystallography
© Norman Collection on the History of Molecular Biology in Novato, CA
Watson & Crick Base pairing
© 2007 Paul Billiet ODWS
Nomenclature of Nucleosides & Nucleotides
The names of the nucleosides and nucleotides containing the five
common bases are listed in Table 8-1.
Deoxyribonucleotides of DNA
The structures and names of the four major deoxyribonucleotides
(deoxyribonucleoside 5’-monophosphates) of DNA are shown below
(Fig. 8-4a). All nucleotides are shown in their free form at pH
7.0. The deoxyribonucleotide units of DNA are usually symbolized
as A, G, T, and C, and sometimes as dA, dG, dT, and dC. In their
free forms, the deoxyribonucleotides are commonly abbreviated
dAMP, dGMP, cTMP, and dCMP. For each nucleotide in the figure,
the more common name is followed by the complete name in
parentheses. All abbreviations assume that the phosphate group is
at the 5’ position. The nucleoside portion of each molecule is
shaded in light red.
Ribonucleotides of RNA
The structures and names of the four major ribonucleotides
(ribonucleoside 5’-monophosphates) of RNA are shown below (Fig.
8-4b). All nucleotides are shown in their free form at pH 7.0.
The ribonucleotide units of RNA are usually symbolized as A, G,
U, and C. In their free forms, the ribonucleotides are commonly
abbreviated AMP, GMP, UMP, and CMP. For each nucleotide in
the figure, the more common name is followed by the complete
name in parentheses. All abbreviations assume that the phosphate
group is at the 5’ position. The nucleoside portion of each
molecule is shaded in light red.
Minor Bases
Both DNA and RNA also contain some
minor bases (Fig. 8-5). In DNA, the
most common of these are methylated
forms of the major bases (Panel a).
Minor bases of many types occur in
tRNAs (Panel b). If the modification
occurs directly on one of the ring
atoms of the pyrimidine or purine base,
the convention is to simply indicate the
ring position of the substituent by its
number, e.g., 5-methylcytidine. The
convention changes when the
substituent atom is exocyclic (not
within the ring structure). In this case
the type of atom is identified and the
ring position to which it is attached is
denoted with a superscript, e.g., N6-
methyladenosine.
Some Adenosine Monophosphates
Cells also contain nucleotides with phosphate groups in positions
other than on the 5’ carbon of the pentose ring (Fig. 8-6). For
example, ribonucleoside 2’,3’-cyclic monophosphates are isolatable
intermediates, and ribonucleoside 3’ & 2’-monophosphates are end
products of the hydrolysis of RNA by certain ribonucleases.
Other variants are adenosine 3’,5’-cyclic monophosphate (cAMP),
which is a very important molecule in some signal transduction
pathways.
Phosphodiester Linkages in the Covalent
Backbone of DNA and RNA
The successive
nucleotides in DNA and
RNA are covalently
linked through
phosphate-group bridges
in which the 5’-
phosphate of one
nucleotide unit is joined
to the 3’-hydroxyl group
of the next, creating a
phosphodiester linkage.
Hydrolysis of RNA by Alkali
The covalent backbone of DNA and RNA is subject to slow,
nonenzymatic hydrolysis of its phosphodiester bonds.
Tautomeric Forms of Uracil
Free pyrimidine and purine bases may exist in two or more
tautomeric forms depending on the pH. Uracil, for example,
occurs in lactam, lactim, and double lactim forms depending on
the pH Certain tautomeric forms predominate at neutral pH,
and these are the structures shown for the five common
purines and pyrimidines in Fig. 8-2. These are the tautomers
that are present in the bases in DNA and RNA.
Nucleotide Absorption Spectra
All nucleotide bases absorb UV light, and nucleic acids are
characterized by a strong absorption at wavelengths near 260 nm
(Fig. 8-10). Plotted in this figure is the variation in molar
extinction coefficient, , as a function of wavelength. The molar
extinction coefficients at 260 nm are listed in the attached table.
The spectra of corresponding ribonucleotides and
deoxyribonucleotides are essentially identical. For mixtures of
nucleotides, a wavelength of 260 nm is used for absorption
measurements.
The Double Helix (1953)
Public Domain image
© Dr Kalju Kahn USBC Chemistry and Biochemistry
Watson and Crick Base-pairing in DNA
Double-helical Strand Complementarity
The two antiparallel chains of
double-helical DNA are not
identical in either base sequence
or composition. Instead, they
are complementary to one
another. Wherever adenine
occurs in one chain, thymine
occurs in the other. Similarly,
guanine occurs opposite cytosine
in the two chains (Fig.8-14).
Watson-Crick Model for DNA Replication
The model for DNA structure
immediately suggested to Watson and
Crick a mechanism for the transmission
of genetic information. The essential
feature of the model is the
complementarity of the two DNA strands
in the double helix. As Watson and Crick
were able to see, well before
confirmatory data became available, this
structure could logically be replicated by
separating the two strands, and
synthesizing a complementary strand for
each (Fig. 8-15). Because nucleotides in
each strand are joined in a sequence
specified by the base-pairing rules
stated above, each preexisting strand
functions as a template to guide the
synthesis of one complementary strand.
The A, B, and Z Forms of DNA (I)
The Watson-Crick structure of DNA
is also referred to as B-form DNA,
or B-DNA. B-DNA is the most stable
structure for a random-sequence DNA
molecule under physiological conditions
and is therefore the standard
structural reference in any study of
the properties of DNA. Two
structural variants that have been well
characterized in crystal structures
are the A- and Z-forms of DNA. The
properties of these forms are
summarized in the Fig. 8-17 table
(next slide). In general, A-DNA is a
dehydrated form of DNA that may
not occur in cells. A similar type of
structure does occur in double helical
RNA. There is evidence for some
short tracts of Z-DNA in bacterial
and eukaryotic cells. These Z-DNA
tracts may play a role (as yet
unidentified) in regulating the
expression of some genes or in genetic
recombination.
The A, B, and Z Forms of DNA (II)
The DNA backbone of Z-DNA takes on a zigzag conformation.
Certain nucleotide sequences fold into left-handed Z helices much
more readily than others. Prominent examples are sequences in
which pyrimidines alternate with purines, especially alternating C
and G or 5-methyl-C and G residues. To form the left-handed
helix in Z-DNA, the purine residues flip to the syn conformation,
alternating with pyrimidines in the anti conformation.
DNA Palindromes and Mirror Repeats
