MODULE 3

NUCLEIC ACIDS

TARGET
After completing this module, you are expected to:
• Distinguish between a purine and a pyrimidine.
• Explain the differences among nucleoside, nucleotide and nucleic acid.
HOOK

HOOK

Imagine a world in which you could quickly, accurately, and cheaply remove or repair a
harmful gene. In this same world, you could also insert a needed gene into a cell that lacked it. This
sounds a bit like science fiction but that technology exists today. Gene editing, or genome editing,
includes a set of technologies that allow scientists to add, remove, or alter genes. One of the most
recent and exciting of these is called CRISPR-Cas9, which is short for clustered regularly
interspaced short palindromic repeats and CRISPR-associated protein 9.
This same technology allows the modification of any genome. Scientists think they could
treat or prevent single-gene disorders such as hemophilia, sickle cell disease, or cystic fibrosis.
Some think that CRISPR-Cas9 could even be used with more complex diseases, such as cancer or
heart disease. Of course, there are ethical concerns. It is one thing to modify body cells that are not
passed on from generation to generation. But, could a human fertilized egg be enhanced for athletic
ability or particular desired physical traits? Scientists and society at large need to think deeply about
the appropriate guidelines for the use of this technology.
But in order to even grasp an understanding of these recent technologies on molecular
genetics, one must first learn the fundamental concepts of nucleic acids in terms of its structure.
Here is a video that introduces you to the important concepts you need to learn about nucleic acids:

https://www.youtube.com/watch?v=MA-ouz1LtpM

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Chemistry 3: AY 2019 – 2020
 IGNITE

The Structure of the Nucleotide

Nucleic acids are macromolecules made up of units called nucleotides. DNA

(deoxyribonucleic acid) and RNA (ribonucleic acid) are long nucleic acid polymers composed of
nucleotides. A nucleotide consists of the following:
• Nitrogen-containing heterocyclic base (nitrogenous base)
Purine – adenine or guanine
Pyrimidine – cytosine, thymine, or uracil
• Five-carbon sugar (furanose) ring
Ribose – in RNA
Deoxyribose – in DNA
• Phosphoryl group

Nucleoside and Nucleotide Structures

Nucleosides have only the base and the sugar (no phosphate). Ring structures are found
in both the base and the sugar. Sugar ring numbers are given the designation ' or prime. The bond
between the base and the sugar is a β-N-glycosidic linkage joining the 1'-carbon of the sugar and a
nitrogen atom of the base. Nucleotides also have a covalent bond between the sugar and the
phosphoryl group - a phosphoester bond.

Nucleotide Sugars

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Chemistry 3: AY 2019 – 2020
Major Purine Bases

Nitrogenous bases are heterocyclic amines, cyclic compounds with at least one nitrogen atom in
the ring structure. Purines are a double ring structure – a six-membered ring fused to a five-
membered ring. The structures of adenine and guanine are given below.

6 7 6 7
5 1 5
1
8 8
2 2
4 9 4 9

3 3

Major Pyrimidine Bases

Pyrimidines consist of a single six-membered ring. The structures of thymine, uracil, and cytosine
are given below. Thymine is found only in DNA, while uracil is found only in RNA. Cytosine is
found in both DNA and RNA.

6 1 6
1 5 5

4 4

2 2
3 3

1 6
5

2
3

Nucleotides

A nucleotide is the repeating unit of the DNA or RNA polymer. The repeating unit of RNA is
called a ribonucleotide, while the one in DNA is called a deoxyribonucleotide. The nitrogenous
base is attached through a β-glycosidic bond to ribose in RNA, and to deoxyribose in DNA. The
phosphate group is attached through a phosphoester bond to carbon 5’ of the sugar.

PHILIPPINE SCIENCE HIGH SCHOOL CALABARZON REGION CAMPUS

Chemistry 3: AY 2019 – 2020
Ribonucleotides of Adenosine

Adenosine is the name of the molecule that has adenine attached to carbon 1’ of ribose. The
ribonucleotide forms differ by the number of phosphate groups joined to carbon 5’ of the ribose.

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Chemistry 3: AY 2019 – 2020
 Names and Abbreviations of the Ribonucleotides and
Deoxyribonucleotides Containing Adenosine.

Nucleic Acids

Nucleic acids are macromolecules made out of units called nucleotides, which come in two
naturally occurring varieties:

1. deoxyribonucleic acid (DNA)

2. ribonucleic acid (RNA).

Please watch these two videos that briefly compare and contrast DNA and RNA:

https://www.youtube.com/watch?v=ruUf7ntRCk8
https://www.youtube.com/watch?v=JQByjprj_mA&frags=wn

Nucleotides are joined by 3′–5′ phosphodiester bonds in both DNA and RNA. DNA is a
double helix, two strands of nucleotide polymers wound around one another with the sugar-
phosphate backbone on the outside and complementary pairs of bases extended into the center of
the helix. Base pairs are held together by hydrogen bonds. Adenine (A) base pairs with thymine
(T). Cytosine (C) base pairs with guanine (G). The two complementary strands of DNA are
antiparallel to one another. On the other hand, RNA is usually single-stranded. Instead of thymine,
uracil (U) is present as a pyrimidine base.

Prokaryotes are organisms with a simple cellular structure and in which there is no true
membrane-bound nucleus and no true membrane-bound organelles. Eukaryotes are organisms
that have cells containing a true nucleus with a nuclear membrane and a variety of organelles that
segregate a variety of cellular functions from one another. Eukaryotic chromosomes have a complex
structure with a first-level structure called the nucleosome. The genome is the complete set of
genetic information of an organism.

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 THE COVALENT PRIMARY STRUCTURE OF DNA

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 NAVIGATE

Solve the following problems on your notebook.

I. Concept Questions
1. What is a heterocyclic amine?
2. What components of nucleic acids are heterocyclic amines?
3. Draw the structure of the purine ring, and indicate the nitrogen that is bonded to sugars in
nucleotides.
4. a. Draw the ring structure of the pyrimidines.
b. In a nucleotide, which nitrogen atom of pyrimidine rings is bonded to the sugar?
5. ATP is the universal energy currency of the cell. What components make up the ATP nucleotide?
6. One of the energy-harvesting steps of the citric acid cycle results in the production of GTP. What
is the structure of the GTP nucleotide?

II. Draw the structures for nucleotides consisting of the following units:
1. Ribose, adenine, two phosphoryl groups
2. 2′-Deoxyribose, guanine, three phosphoryl groups

KNOT

In summary, here is a map fundamental to learning key concepts about nucleic acids:

Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are polymers of nucleotides.
Nucleosides are produced by the combination of a sugar, either ribose in RNA or 2′-deoxyribose in
DNA, and a nitrogenous base. Nucleotides are composed of a nucleoside bonded to one, two, or
three phosphoryl groups. There are two types of nitrogenous bases:
Purines (double ring structure): adenine and guanine
Pyrimidines (single 6-membered ring structure): cytosine, thymine, and uracil
Deoxyribonucleotides are the subunits of DNA while ribonucleotides are the subunits of RNA.
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References:

Smith, Janice (2017). Organic Chemistry 5th Edition. McGraw-Hill Education.

Denniston, Katherine, Topping, Joseph, Quirk Dorr, Danae. (2019). General, Organic, and
Biochemistry 10th Edition. McGraw-Hill Education.

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Chemistry 3: AY 2019 – 2020