Nitrogenous bases, nucleotides,

nucleic acids

Christine Carrington
Biochemistry Unit, Bldg 36, Rm 102
christine.carrington@sta.uwi.edu
 The nitrogenous bases
Nitrogenous bases are organic compounds containing nitrogen that have the
properties of a base. They include:

• One 6 member ring

• Two rings ( 5-member and 6 member)
• One 6 member ring
• Two nitrogens and
• Nine
fouratoms
carbonsin in
thering
double ring structure (4
• Five carbons and one nitrogen
structure nitrogen, 5 carbon)
Important purines
Found in DNA
 Pyrimidines
• Found in DNA and RNA
– Cytosine (in DNA and RNA)
– Uracil (in RNA only)
– Thymine (in DNA only)
 Pyridines
• The pyridine ring occurs
in many important
compounds

Nicotinic acid
OR
Nicotinamide OR Niacinamide
Niacin
Member of vitaminOR B group of
vitamin
water soluble B3
vitamins
 Nucleosides
• Nucleosides = nitrogenous base + 5 carbon sugar
• Sugar may be ribose or deoxyribose

O
Nitrogenous Base
CH2OH
5’ N
4’
Sugar 1’

H
H H
H
Glycosidic bond
3’ 2’
OH OH in ribose
/ H in deoxyribose
 Nucleosides containing adenine
• Adenosine Deoxyadenosine

Glycosidic bond
Purine and pyrimidine
bases and their
corresponding ribo-
and
deoxyribonucleosides

Note: The nitrogenous base

in a nucleoside may also be a
pyridine
 Nucleotide
• Nucleosides can be phosphorylated by cellular
kinases to produce nucleotides
• Nucleotides = nucleoside + phosphate group(s)
O
O Nitrogenous Base
P O CH2 O
5’ N
O 4’ 1’
Phosphate group Sugar
H H
H H
3’ 2’
OH OH in ribose
/ H in deoxyribose
Nucleotide
Nucleotides
 Terminology and abbreviations

• N = any nitrogenous base (A, T, C, G, U)

• Nucleosides:
– Use suffix “-osine” for purine nucleosides (eg. adenosine, guanosine)
– Use suffix “idine” for pyrimidine nucleosides (eg. uridine, cytidine)
– Add prefix “deoxy” for deoxyribonucleosides (eg. deoxysdenosine)

• Nucleotides
– NMP = any ribonucleoside monophosphate (e.g. adenosine monophosphate / AMP)
– NDP = any ribonucleoside diphosphate (e.g. adenosine diphosphate / ADP)
– NTP = any ribonucleoside triphosphates ((e.g. adenosine triphosphate / ATP)
– dNTP = any deoxyribonucleoside triphosphates (e.g deoxyadenosine triphosphate)
Likewise for deoxyribonucleoside monophosphates (dNMP) and diphosphates (dNDP)
 Roles of nucleotides
• Nucleotides are the structural units of RNA and DNA.
– those A, G, C, T found in DNA
– A, G, C, U found in RNA

• They also serve as important cofactors in cellular

signaling and metabolism. Eg.
– Coenzyme A (CoA)
– flavin adenine dinucleotide (FAD)
– flavin mononucleotide (FMN)
– adenosine triphosphate (ATP)
– nicotinamide adenine dinucleotide phosphate (NADP).
 Coenzyme A (CoA)
• Plays an important role in the synthesis and
oxidation of fatty acids, and the oxidation of
pyruvate in the citric acid cycle.
 Flavin adenine dinucleotide (FAD)
• Derived from riboflavin, or
vitamin B2.
• A redox cofactor involved in
several important reactions
in metabolism.
– Many oxidoreductases
(flavoenzymes / flavoproteins)
require FAD as a prosthetic
group.
• Exist in two redox states
 FAD redox
• FAD can be reduced to the FADH2, whereby it
accepts two hydrogen atoms:
 Flavin mononucleotide (FMN)
• Also known as riboflavin-5-phosphate
– Produced from riboflavin (vitamin B2)
– more soluble than riboflavin
– main form of riboflavin found in cells &
tissues.

• Functions as prosthetic group of various

oxidoreductases
– During catalysis there is reversible
interconversion of oxidized (FMN),
semiquinone (FMNH•) and reduced
(FMNH2).
– Thus can take part in both one and two
electron transfer.s

• Used as a food dye (E101a)

 Adenosine-5'-triphosphate (ATP)
Transports chemical energy within cells for
metabolism
– Produced during photosynthesis and
cellular respiration
– consumed by many enzymes and cellular
processes.

Nucleic acid synthesis

– Incorporated into nucleic acids by polymerases during DNA replication
and transcription.
– For DNA, ribose sugar is first converted to deoxyribose by
ribonucleotide reductase.

Signal transduction pathways

- used as a substrate by kinases that phosphorylate proteins and lipids
- used by adenylate cyclase, to produce the 2nd messenger cyclic AMP.
Nicotinamide adenine dinucleotide (NAD)
• Coenzyme found in all cells (it is a dinucleotide)

• Involved in redox reactions

– NAD+ (oxidizing agent) accepts electrons from other
molecules and becomes reduce to NADH (reducing
agent) which can then donate electrons to other
molecules.

• Also used in other cellular processes as substrate of

enzymes that add or remove chemical groups from
proteins.

• Organisms can synthesise NAD+ from tryptophan or

aspartic acid OR components of the coenzymes are
taken up from food as the vitamin niacin.
 Nicotinamide adenine dinucleotide
phosphate (NADP)

• Involved in redox reactions

– NADPH is the reduced form
and NADP+ is the oxidized
form.
– NADP+ used in anabolic
reactions (eg. lipid and nucleic
acid synthesis).
 Structure of Nucleic Acids

• DNA and RNA are polynucleotides

– basic subunits are nucleotides.
– RNA is made up of ribonucleotides
– DNA is made up of deoxyribonucleotides

• Nucleotides are held together by phosphodiester

bonds.
 Nucleic Acids
• Five nitrogenous bases found in nucleic acids
• In DNA – deoxyribonucleotides with A, T, C, G
• In RNA – ribonucleotides with A, U, C, G
 Nucleic acid polymerisation
In RNA there would
be –OH in this
position

5’ phosphate group
Phosphodiester
bond

3’ OH group
 Structure of DNA

the strands are

antiparallel and are
held together by
hydrogen bonds
between
complimentary
bases on adjacent
strands
 Complimentary base pairing

• Adenine forms
two hydrogen
bonds with
thymine
• Guanine forms
three hydrogen
bonds with
cytosine.
 The DNA double helix
Dimensions (B-type DNA ):

I) Diameter = 20Å.

II) Rotation between adjacent

bases = 360 so 10 bases
per 3600 turn.

III) 3.4Å between adjacent

bases on same strand so
rise of 34Å per turn
 The double helix
.
Minor groove
Major groove
base

Phosphate sugar backbone

 DNA Packaging

DNA is much longer than the space into which

it must fit so it is very compactly packaged by
successive levels of coiling.

Eukaryotes: linear stretches of supercoiled DNA forms

several chromosomes.

Prokaryotes: genomic DNA is circular and forms a

single bacterial chromosome.
 Packaging of
eukaryotic DNA
into chromosomes

library.thinkquest.org/C004535/
chromosomes.html
 RNA structure
• Ribose instead of
deoxyribose
• Single stranded (except
in some viruses)
• Not as long as DNA
• Intramolecular base
pairing results in
complex secondary
structures
RNA structure
• Example of the
complex
secondary
structure seen in
RNA molecules
There are many different types of RNA
• Messenger RNA (mRNA)
– carries information from DNA to the ribosome in cytoplasm where protein
synthesis occurs.
– sequence of bases in mRNA encodes the aminoacid sequence of a
polypepetide.

• Non-coding RNAs
– transfer RNA (tRNA) and ribosomal RNA (rRNA) involved in protein synthesis
– Regulatory RNAs involved in gene regulation (modulate gene expression)
– Small nuclear RNAs involved in processing of RNA molecules (catalyse
chemical reactions such as cutting and ligating other RNA molecules)
– Ribozymes catalyse peptide bond formation in the ribosome

• RNA genomes
– Many viruses have genomes made up of RNA instead of DNA