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18
Nucleotides and Nucleic Acids
Chapter Summary
Nucleic acids, the carriers of genetic information, are macromolecules that are composed
of and can be hydrolyzed to nucleotide units. Hydrolysis of a nucleotide gives one
equivalent each of a nucleoside and phosphoric acid. Further hydrolysis of a nucleoside
gives one equivalent each of a sugar and a heterocyclic base.
The DNA sugar is 2-deoxy-D-ribose. The four heterocyclic bases in DNA are
cytosine, thymine, adenine, and guanine. The first two bases are pyrimidines, and the
latter two are purines. In nucleosides, the bases are attached to the anomeric carbon (C-1)
of the sugar as β-N-glycosides. In nucleotides, the hydroxyl group (–OH) at C-3 or C-5 of
the sugar is present as a phosphate ester.
The primary structure of DNA consists of nucleotides linked by a phosphodiester
bond between the 5'–OH of one unit and the 3'–OH of the next unit. To fully describe a DNA
molecule, the base sequence must be known. Methods for sequencing have been developed,
and, at present, over 150 bases can be sequenced per day. The counterpart of sequencing,
the synthesis of oligonucleotides having known base sequences, is also highly developed.
The secondary structure of DNA is a double helix. Two helical polynucleotide
chains coil around a common axis. In B-DNA, the predominant form, each helix is
right-handed, and the two strands run in opposite directions with respect to their 3' and 5'
ends. The bases are located inside the double helix, in planes perpendicular to the helix
axis. They are paired (A–T and G–C) by hydrogen bonds, which hold the two chains
together. The sugar-phosphate backbones form the exterior surface of the double helix.
Genetic information is passed on when the double helix uncoils and each strand acts as a
template for binding and linking nucleotides to form the next generation. Other forms of
DNA include A-DNA (a right-handed double helix in which base pairs are tilted to the helical
axis) and Z-DNA (a left-handed double helix).
RNA differs from DNA in three ways: the sugar is D-ribose, the pyrimidine uracil
replaces thymine (the other three bases are the same), and the molecules are mainly
single-stranded. The three principal types of RNA are messenger RNA (involved in
transcribing the genetic code), transfer RNA (which carries a specific amino acid to the site
of protein synthesis), and ribosomal RNA.
The genetic code involves sequences of three bases called codons, each of which
translates to a specific amino acid. The code is degenerate (that is, there is more than one
codon per amino acid), and some codons are "stop" signals that terminate synthesis.
Protein biosynthesis is the process by which the message carried in the base sequence is
transformed into an amino acid sequence in a peptide or protein.
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Chapter 18
In addition to their role in genetics, nucleotides play other important roles in
biochemistry. Key enzymes and coenzymes such as nicotinamide adenine dinucleotide
(NAD), flavin adenine dinucleotide (FAD), and vitamin B12 also include nucleotides as
part of their structures. Also, the major component of viruses is DNA.
Reaction Summary
Hydrolysis of Nucleic Acids
O
_
O
H
_
N
H O
O
Base
P
O
O
H O
H2 O
H
O
P
O
_
enzyme
H
H 2O
_
HO
H
OH
HO
Base
H O
H
H
O
N
Base
O
H
DNA segment
HO
H
H
OH
O
OH
Base
H
H 2O H +
+
H
OH
N
nucleoside
nucleotide
O
O
N
HN-Base
heterocyclic
base
2-deoxy- D-ribose
.
Learning Objectives
1.
Know the meaning of: nucleic acid, nucleotide, nucleoside.
2.
Know the structures of: cytosine, thymine, adenine, guanine, uracil,
2-deoxy-D-ribose, D-ribose.
3.
Know the meaning of: DNA, RNA, N-glycoside, pyrimidine base, purine base.
4.
Given the name, draw the structure of a specific nucleoside.
5.
Write an equation for the hydrolysis of a specific nucleoside by aqueous acid. Write
the steps in the reaction mechanism.
6.
Given the name, draw the structure of a specific nucleotide.
7.
Write an equation for the hydrolysis of a specific nucleotide by aqueous base.
8.
Draw the structure of an N-glycoside and an O-glycoside.
9.
Given the name or abbreviation for a DNA or RNA nucleotide or nucleoside, draw its
structure.
10.
Draw the primary structure of a segment of an RNA or DNA chain.
11.
Explain why only pyrimidine-purine base pairing is permissible in the double helix
structure.
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