Nucleic Acids

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15.1 Types of Nucleic Acids

Nucleic acids are unbranched polymers composed of repeating monomers called

nucleotides. There are two types of nucleic acids.

The nucleotide monomers that compose DNA and RNA consist of three components—a
monosaccharide (a pentose sugar), a nitrogen-containing base, and a phosphate group. A
block structural diagram for a nucleotide is

DNA molecules contain several million nucleotides while RNA molecules are much
smaller, containing perhaps a few thousand nucleotides. DNA is contained in the chromosomes
of the nucleus, each chromosome having a different type of DNA. The number of chromosomes
differs from species to species. Humans have 46 chromosomes (23 pairs). An individual
chromosome is composed of many genes. A gene is a portion of the DNA molecule
responsible for the synthesis of a single protein.

15.2 Nucleosides—Joining A Sugar And A Base

15.2.1 Pentose Sugars
The nucleotides of both DNA and RNA contain a five-membered ring monosaccharide,
often called simply the sugar component.
In RNA the sugar unit is ribose—hence the R in RNA. In DNA the sugar unit is 2-
deoxyribose—hence the D in DNA.

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Structurally, the only difference between these two sugars occurs at carbon 2’. The —OH
group present on this carbon in ribose becomes a —H atom in 2’-deoxyribose. (The prefix deoxy
means “without oxygen.”)

The systems for numbering the atoms in the pentose and nitrogen-containing base subunits of
a nucleotide are important and will be used extensively in later sections of this module. The
convention is that
1. Pentose ring atoms are designated with primed numbers (‘).
2. Nitrogen-containing base ring atoms are designated with unprimed numbers.

15.2.2 Nitrogen-containing Bases

Only five common nitrogen-containing bases are present in nucleic acids. Three bases
with one ring (cytosine, uracil, and thymine) are derived from the parent compound pyrimidine.
Two bases with two rings (adenine and guanine) are derived from the parent compound
purine.

Each base is designated by a one-letter abbreviation as shown.

Uracil (U) occurs only in RNA, while thymine (T) occurs only in DNA. As a result:

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15.2.3 Nucleoside Formation

A nucleoside is formed by joining the anomeric carbon of the sugar with a nitrogen atom
of the base. The bond connecting the sugar and base is a β-N-glycosidic linkage.

With pyrimidine bases, the nitrogen atom at the 1 position bonds with the 1' carbon of
the sugar. With purine bases, the nitrogen atom at the 9 position bonds with the 1' carbon of the
sugar. For example, joining cytosine with ribose forms the ribonucleoside cytidine. Joining
adenine with 2’-deoxyribose forms the deoxyribonucleoside deoxyadenosine.

Nucleosides are named as derivatives of the bases from which they are formed.

Sample Problem 15.1

The Sugar & Base in a Nucleotide

Identify the sugar and base used to form the following nucleoside, and then name it.

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 The sugar portion of a nucleoside contains the five-membered ring. If there is an OH

group at C2', the sugar is ribose, and if there is no OH group at C2', the sugar is
deoxyribose.
 A pyrimidine base has one ring, and is derived from either cytosine, uracil, or thymine.
A purine base has two rings, and is derived from either adenine or guanine.
 Nucleosides derived from pyrimidines end in the suffix -idine. Nucleosides derived from
purines end in the suffix -osine.

The sugar contains no OH at C2', so it is derived

from deoxyribose. The base is thymine. To name
the deoxyribonucleoside, change the suffix of
the base to -idine and add the prefix deoxy; thus,
thymine → deoxythymidine.

Problem 1

Problem 2

15.3 Nucleotides—Joining A Nucleoside and A Phosphate Group

15.3.1 Nucleotide Formation
Nucleotides are formed by adding a phosphate group to the 5'-OH of a nucleoside.
The phosphate group is attached to the sugar at the C-5’ position through a phosphate–ester
linkage. Nucleotides are named by adding the term 5'-monophosphate to the name of the
nucleoside from which they are derived. Ribonucleotides are derived from ribose, while
deoxyribonucleotides are derived from 2-deoxyribose.

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Because of the lengthy names of nucleotides, three- or four-letter abbreviations are

commonly used instead. Thus, cytidine 5'-monophosphate is CMP and deoxyadenosine 5'-
monophosphate is dAMP.
Table 1 summarizes the information about nucleic acids and their components learned
thus far.

Table 1 Summary of the Components of Nucleosides, Nucleotides, and Nucleic Acids

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There are four possible RNA nucleotides, differing in the base present (A, C, G, or U),
and four possible DNA nucleotides, differing in the base present (A, C, G, or T).

Table 2 The Names of the Eight Nucleotides Found in DNA and RNA

Di- and triphosphates can also be prepared from nucleosides by adding two and three
phosphate groups, respectively, to the 5'-OH. For example, adenosine can be converted to
adenosine 5'-diphosphate and adenosine 5'-triphosphate, abbreviated as ADP and ATP,
respectively.

Sample Problem 15.2

Nucleotide Structure

Draw the structure of the nucleotide GMP.

 Translate the abbreviation to a name; GMP is guanosine 5'-monophosphate.

 First, draw the sugar. Since there is no deoxy prefix in the name, GMP is a
ribonucleotide and the sugar is ribose.
 Then draw the base, in this case guanine, bonded to C1' of the sugar ring.
 Finally, add the phosphate. GMP has one phosphate group bonded to the 5'-OH of the
nucleoside.

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Problem 3

Problem 4

Problem 5

15.4 Nucleic Acid Structure

Nucleic acids—both DNA and RNA—are polymers of nucleotides (polynucleotide),
formed by joining the 3'-OH group of one nucleotide with the 5'-phosphate of a second
nucleotide in a phosphodiester linkage.
For example, joining the 3'-OH group of dCMP (deoxycytidine 5'-monophosphate) and
the 5'-phosphate of dAMP (deoxyadenosine 5'-monophosphate) forms a dinucleotide that
contains a 5'-phosphate on one end (called the 5' end) and a 3'-OH group on the other end
(called the 3' end).

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For DNA molecules, the backbone consists of alternating phosphate and deoxyribose
sugar units; for RNA molecules, the backbone consists of alternating phosphate and ribose sugar
units.

The primary structure of a polynucleotide is the sequence of nucleotides that it contains.

This sequence, which is determined by the identity of the bases, is unique to a nucleic acid.
Only four types of bases are found in any given nucleic acid structure. In both RNA and DNA,
adenine, guanine, and cytosine are encountered as side-chain components; thymine is found
mainly in DNA, and uracil is found only in RNA.

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Polynucleotides are named by the sequence of the bases they contain, beginning at the 5'
end and using the one-letter abbreviation for the bases. Figure 1 illustrates the structure of a
polynucleotide formed from four different nucleotides. This polynucleotide contains the bases
cytosine, adenine, thymine, and guanine, in order from the 5' end; thus, it is named CATG.

Figure 1 Sample Primary Structure of a Polynucleotide

Sample Problem 15.3

Dinucleotide Structure

a) Draw the structure of a dinucleotide formed by joining the 3'-OH group of AMP to the 5'-
phosphate in GMP.
b) Label the 5' and 3' ends.
c) Name the dinucleotide.

 Draw the structure of each nucleotide, including the sugar, the phosphate bonded to C5',
and the base at C1'. In this case the sugar is ribose since the names of the
mononucleotides do not contain the prefix deoxy.
 Bond the 3'-OH group to the 5'-phosphate to form the phosphodiester bond.
 The name of the dinucleotide begins with the nucleotide that contains the free
phosphate at the 5' end.

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Problem 6

Problem 7

Problem 8

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