Molecular Biology: General theory
Molecular Biology:
General Theory
Author: Dr Darshana Morar
Licensed under a Creative Commons Attribution license.
NUCLEIC ACIDS
DNA
DNA is made up of nucleotides. A nucleotide consists of a nitrogenous base (either a purine or a
pyrimidine), a five-carbon sugar (deoxyribose), and a phosphate group. The four nitrogenous bases found
in DNA are adenine (abbreviated A), cytosine (C), guanine (G) and thymine (T).
Figure 1 Basic structure of a nucleotide
(Adapted from http://www.duke.edu/web/MAT/jennifer_sohn/unit/translation_oh.htm)
DNA is composed of a series of nucleotides, held together in a long linear chain by a phosphodiester
linkage from the 3’ hydroxyl group of one sugar to the 5’ phosphate group of the next (a DNA strand or
polynucleotide therefore comprises a sugar-phosphate backbone with attached bases). Since the
phosphodiester bonds form between the third and fifth carbon atoms of adjacent sugars, a strand of DNA
has a direction or orientation.
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Molecular Biology: General theory
Most DNA is double-stranded: two chains that constitute a double helix. The two chains have opposite
orientations and are connected via hydrogen bridges between opposing base groups. Each type of base
on one strand forms a bond with just one type of base on the other strand. Adenine (purine) bonds only to
thymine (pyrimidine) by two hydrogen bonds, and guanine (purine) bonds only to cytosine (pyrimidine) by
three hydrogen bonds. This arrangement of two nucleotides binding together across the double helix is
called a base pair. The sequences of the two DNA chains are thus complementary.
Figure 2 Basic structure of DNA
By convention the upper strand is written from 5' (five prime) to 3' (three prime). If DNA is transcribed, the
upper strand (known as the sense strand) corresponds to the RNA sequence. If this is messenger RNA
(mRNA) it contains the triplets of the genetic code, the coding strand. Normally only this upper strand is
listed in publications and databases.
In schematic drawings of gene structure the DNA is often represented as a straight line (or a circle for a
plasmid). Left to right always corresponds to the 5' to 3' orientation of the upper strand.
5' _______________________ 3'
This representation does not do justice to the double-helix structure, but is nevertheless adequate to
understand the DNA manipulations described in the other modules.
Cleavage of DNA always generates one end with a phosphate group coupled to the fifth carbon atom in
the ribose sugar ring (the 5'-phosphate) and the other end with a hydroxyl group attached to the third
carbon atom in the ribose sugar ring (the free 3'-OH group):
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Molecular Biology: General theory
5'-phosphate________________________3'-OH
RNA Structure
RNA is a very labile molecule and, like DNA, it is made from a long chain of nucleotide units. Each
nucleotide consists of a nitrogenous base, a ribose sugar, and a phosphate. Note that the sugar
present in a DNA molecule is deoxyribose, while the sugar present in a molecule of RNA is ribose (in
deoxyribose there is no hydroxyl group attached to the second carbon atom in the ribose sugar ring). The
extra hydroxyl group makes RNA more prone to hydrolysis which is why it is less stable than DNA. The
four bases found in RNA are adenine (A), cytosine (C), guanine (G) and uracil (U) (replacing the thymine
(T) in DNA).
Figure 3 Deoxyribose versus ribose sugars
Although RNA is essentially single-stranded, most biologically active RNA molecules contain selfcomplementary sequences that allow parts of the molecule to fold and pair with itself to form double
helices. There are three major types of RNA: messenger RNA (mRNA), transfer RNA (tRNA) and
ribosomal RNA (rRNA). There are a number of other types of RNA present in smaller quantities as well,
including small nuclear RNA (snRNA), small nucleolar RNA (snoRNA) and the 4.5S signal recognition
particle (SRP) RNA. Novel species of RNA continue to be identified.
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