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• Nucleic Acids

2006-2007
Nucleic acids

2006-2007
 Nucleic Acids
 Nucleic acids are biopolymers, or small
bio-molecules, essential to all known forms of life.
They are composed of nucleotides, which are
monomers made of three components: a 5-
carbon sugar a phosphate group and a
nitrogenous base.
If the sugar is a compound ribose, the polymer is
RNA (ribonucleic acid);
if the sugar is derived from ribose as
deoxyribose, the polymer is DNA
(deoxyribonucleic acid).
 The sweet side of life: The sugars
 The 5-carbon sugars found in the nucleic acids are
D-ribose and D-deoxyribose.
 The difference between these two sugars is that
deoxyribose is missing an oxygen atom on carbon
atom number 2’. The structures for these two
sugars carbon atom number 1’, the anomeric
carbon. This is where the nitrogen base will attach.
 Both sugars adopt the β form of the furanose ring.
Numbering of the sugar begins with the anomeric
carbon (1') and proceeds clockwise with the
 –CH2OH carbon being 5'.
 The bitter side of life: nitrogen bases
 The bases fall into two
categories, the general defining
structures of which are:
1. The purines (adenine and
guanine), composed of two
fused rings incorporating two
nitrogen atoms in each ring and
2. The pyramidines (cytosine,
thymine, and uracil), composed
of a single ring with two
nitrogen atoms in the ring
structure
 Types of nitrogen bases
Purine = AG
• 2 types of nitrogen bases Pure silver!
– different nitrogen bases
– purines
• double ring N base
• adenine (A)
• guanine (G)
– pyrimidines
• single ring N base
• cytosine (C)
• thymine (T)
• uracil (U)
 The sour side of life: Phosphoric acid
• The third component
of a nucleotide is a
phosphoric At
physiological pH it
does not exist in the
fully protonated form
shown in the figure.
• It is responsible for
the “acid” in nucleic
acid.
 Tracing the Process: From Nucleoside
to Nucleotide to Nucleic Acid
Naturally; first joins a nitrogen base
and a 5-carbon sugar to form a
nucleoside;
 then that nucleoside joins with
phosphoric acid to form a nucleotide;
finally, the combination of these
nucleotides produces a nucleic acid.
 First reaction: Nitrogen base +
5-carbon sugar = nucleoside
The combination of a nitrogen base with
a 5-carbon sugar is a nucleoside. The
general reaction appears in the Figure.
Here a compound containing hydrogen
(the nitrogen base) approaches another
molecule containing an –OH group (a
sugar). The hydrogen combines with the
–OH to form water, which is expelled.
 Second reaction: Phosphoric acid +
nucleoside = nucleotide
 The combination of a phosphoric acid with a nucleoside
produces a nucleotide, which is a phosphate ester.
 The formation involves a condensation reaction between
the phosphoric acid and the alcohol group on carbon
number 5, the –CH2OH.
 Adenosine monophosphate (AMP) is an example of a
nucleotide.
 Nucleotides are the monomers from which nucleic acids
form.
 AMP is not only one of the “combination” that makes RNA
but is also very much involved in the energy transfer
process in the cells (from AMP to ADP to ATP).
 Nucleotides
• 3 parts
– nitrogen base (C-N ring)
– pentose sugar (5C) Nitrogen base
I’m the
• ribose in RNA A,T,C,G or U
• deoxyribose in DNA part!

– phosphate (PO4) group

Are nucleic acids

charged molecules?
 Third reaction: Nucleotide
becomes nucleic acid
Nucleic acids form by joining nucleotides
using the same condensation reactions.
This condensation reaction involves the
phosphate of one nucleotide reacting
with the alcohol group on carbon atom
number 3' of another nucleotide. The
starting end of the polymer is 5', whereas
the terminal end is 3'.
• Nucleic Acids
Information
storage

2006-2007
 Nucleic Acids
• Function:
– genetic material
• stores information
– genes
– blueprint for building proteins
» DNA  RNA  proteins
DNA • transfers information
– blueprint for new cells
– blueprint for next generation

proteins
A Primer on Nucleic Acids
• Nucleic acids are responsible for storing and
directing the information our cells use for
reproduction and growth. They are large
molecules found in the cell’s nucleus. The
genetic information is contained in the DNA, in
terms of its primary and secondary structure. As
a cell divides and reproduces, the genetic
information in the cell is replicated to the new
cells, which must be done accurately and
precisely — no mistakes must be made. RNA’s
role is to create proteins via translation.
 Function:
1. DNA has two direct purposes:
 It must generate new DNA (replication) so
that new generations of cells will have the
information necessary to their survival.
 And it must generate RNA (ribonucleic
acid).
2. The RNA is involved in the direct synthesis
of proteins, called translation. These
proteins are essential for the maintenance
of life.
 T
G A
T C
C A
A G

G
A
T
C
 Nucleic Acids
• Examples:
– RNA (ribonucleic acid)
• single helix
– DNA (deoxyribonucleic acid)
• double helix
• Structure:
– monomers = nucleotides

DN RN
A A
 Nucleic polymer
• Backbone
– sugar to PO4 bond
– phosphodiester bond
• new base added to sugar of previous
base
• polymer grows in one direction
– N bases hang off the
sugar-phosphate backbone

Dangling bases?
Why is this important?
 Pairing of nucleotides
• Nucleotides bond between
DNA strands
– H bonds
– purine :: pyrimidine
– A :: T
• 2 H bonds
– G :: C
• 3 H bonds

Matching bases?
Why is this important?
 DNA molecule
• Double helix
– H bonds between bases join
the 2 strands
• A :: T
• C :: G

H bonds?
Why is this important?
 Copying DNA
• Replication
– 2 strands of DNA helix are
complementary
• have one, can build other
• have one, can rebuild the whole

Matching halves?
Why is this
a good system?
 When does a cell copy DNA?
• When in the life of a cell does DNA have to
be copied?
– cell reproduction
• mitosis
– gamete production
• meiosis
HELIXHELIX
 Nucleic acids
• Structure / monomer
– nucleotide
• Function
– information storage
& transfer
• Examples
– DNA, RNA

phosphodiester bond
Let’s build
some DNA, baby!
 RNA & DNA
• RNA
– single nucleotide chain
• DNA
– double nucleotide chain
• N bases bond in pairs
across chains
– spiraled in a double helix
• double helix 1st proposed as structure of DNA in 1953
by James Watson & Francis Crick
(just celebrated 50th anniversary in 2003!)
 Information polymer
• Function
– series of bases encodes information
• like the letters of a book
– stored information is passed
from parent to offspring
• need to copy accurately
– stored information = genes
• genetic information

Passing on information?
Why is this important?
BYE-Hussein