Nitrogenous bases, nucleotides, nucleic acids

Christine Carrington
Biochemistry Unit, Bldg 36, Rm 102
christine.carrington@sta.uwi.edu
The nitrogenous bases
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
four
atoms
carbons
in the
in double
ring ring structure (4
• Five carbons and one nitrogen
structure nitrogen, 5 carbon)
Important
purines Found in DNA and RNA Products of purine degradation

Isomer of
guanine formed
by oxidative
Found in damage to DNA
chocolate

Found in coffee; Product of purine

high concentrations in degradation; excreted
FMS students in urine
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
NicotinamideOROR
Niacinamide
Niacin
OR
Member of vitamin
vitaminBB3group
of water soluble vitamins
Nucleosides
Nucleosides = nitrogenous base + 5 carbon sugar
• Sugar may be ribose or deoxyribose

Nitrogenous Base
CH2OH O
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’
Sugar
Phosphate H H
H H
group 3’ 2’
OH OH in ribose
/ H in deoxyribose
Nucleotides can have up to 3 phosphate
groups
 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. deoxyadenosine)

• 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)
Part of the genome of SARS-CoV-2
• >nCoV2019|Wuhan-Hu-1|MN908947|China|Wuhan|2019-12

• ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACA

GGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTC

AGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGGCTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTA

TGTGTTCATCAAACGTTCGGATGCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACTCGAAGGCATTCAGTACGGTCGTAGTGGTGAGACACTTGGTGTCCTTGTCCCTCATGTGGGCGAAATACCAGTGGCTTACCGCA

AGGTTCTTCTTCGTAAGAACGGTAATAAAGGAGCTGGTGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTAGGCGACGAGCTTGGCACTGATCCTTATGAAGATTTTCAAGAAAACTGGAACACTAAACATAGCAGTGGTGTTACCCG

TGAACTCATGCGTGAGCTTAACGGAGGGGCATACACTCGCTATGTCGATAACAACTTCTGTGGCCCTGATGGCTACCCTCTTGAGTGCATTAAAGACCTTCTAGCACGTGCTGGTAAAGCTTCATGCACTTTGTCCGAACAACTGGACTTTATTGA
CACTAAGAGGGGTGTATACTGCTGCCGTGAACATGAGCATGAAATTGCTTGGTACACGGAACGTTCTGAAAAGAGCTATGAATTGCAGACACCTTTTGAAATTAAATTGGCAAAGAAATTTGACACCTTCAATGGGGAATGTCCAAATTTTGTAT

TTCCCTTAAATTCCATAATCAAGACTATTCAACCAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCACCAAATGAATGCAACCAAATGTGCCTTTCAACTCTCATGAAGTGTGATCATTGTG

GTGAAACTTCATGGCAGACGGGCGATTTTGTTAAAGCCACTTGCGAATTTTGTGGCACTGAGAATTTGACTAAAGAAGGTGCCACTACTTGTGGTTACTTACCCCAAAATGCTGTTGTTAAAATTTATTGTCCAGCATGTCACAATTCAGAAGTAG

GACCTGAGCATAGTCTTGCCGAATACCATAATGAATCTGGCTTGAAAACCATTCTTCGTAAGGGTGGTCGCACTATTGCCTTTGGAGGCTGTGTGTTCTCTTATGTTGGTTGCCATAACAAGTGTGCCTATTGGGTTCCACGTGCTAGCGCTAACA

TAGGTTGTAACCATACAGGTGTTGTTGGAGAAGGTTCCGAAGGTCTTAATGACAACCTTCTTGAAATACTCCAAAAAGAGAAAGTCAACATCAATATTGTTGGTGACTTTAAACTTAATGAAGAGATCGCCATTATTTTGGCATCTTTTTCTGCTTC

CACAAGTGCTTTTGTGGAAACTGTGAAAGGTTTGGATTATAAAGCATTCAAACAAATTGTTGAATCCTGTGGTAATTTTAAAGTTACAAAAGGAAAAGCTAAAAAAGGTGCCTGGAATATTGGTGAACAGAAATCAATACTGAGTCCTCTTTATG

CATTTGCATCAGAGGCTGCTCGTGTTGTACGATCAATTTTCTCCCGCACTCTTGAAACTGCTCAAAATTCTGTGCGTGTTTTACAGAAGGCCGCTATAACAATACTAGATGGAATTTCACAGTATTCACTGAGACTCATTGATGCTATGATGTTCAC

ATCTGATTTGGCTACTAACAATCTAGTTGTAATGGCCTACATTACAGGTGGTGTTGTTCAGTTGACTTCGCAGTGGCTAACTAACATCTTTGGCACTGTTTATGAAAAACTCAAACCCGTCCTTGATTGGCTTGAAGAGAAGTTTAAGGAAGGTGT

AGAGTTTCTTAGAGACGGTTGGGAAATTGTTAAATTTATCTCAACCTGTGCTTGTGAAATTGTCGGTGGACAAATTGTCACCTGTGCAAAGGAAATTAAGGAGAGTGTTCAGACATTCTTTAAGCTTGTAAATAAATTTTTGGCTTTGTGTGCTGA

CTCTATCATTATTGGTGGAGCTAAACTTAAAGCCTTGAATTTAGGTGAAACATTTGTCACGCACTCAAAGGGATTGTACAGAAAGTGTGTTAAATCCAGAGAAGAAACTGGCCTACTCATGCCTCTAAAAGCCCCAAAAGAAATTATCTTCTTAGA

GGGAGAAACACTTCCCACAGAAGTGTTAACAGAGGAAGTTGTCTTGAAAACTGGTGATTTACAACCATTAGAACAACCTACTAGTGAAGCTGTTGAAGCTCCATTGGTTGGTACACCAGTTTGTATTAACGGGCTTATGTTGCTCGAAATCAAAG
ACACAGAAAAGTACTGTGCCCTTGCACCTAATATGATGGTAACAAACAATACCTTCACACTCAAAGGCGGTGCACCAACAAAGGTTACTTTTGGTGATGACACTGTGATAGAAGTGCAAGGTTACAAGAGTGTGAATATCACTTTTGAACTTGAT

GAAAGGATTGATAAAGTACTTAATGAGAAGTGCTCTGCCTATACAGTTGAACTCGGTACAGAAGTAAATGAGTTCGCCTGTGTTGTGGCAGATGCTGTCATAAAAACTTTGCAACCAGTATCTGAATTACTTACACCACTGGGCATTGATTTAGA

TGAGTGGAGTATGGCTACATACTACTTATTTGATGAGTCTGGTGAGTTTAAATTGGCTTCACATATGTATTGTTCTTTCTACCCTCC
Roles of nucleotides and their derivatives

• Serve as coenzymes in cellular Coenzymes

signaling and metabolism. Organic
• E.g. compounds
• Coenzyme A (CoA) (vitamins or vitamin
• flavin adenine dinucleotide (FAD) derivatives) that
• flavin mononucleotide (FMN) facilitate transfer of
• nicotinamide adenine dinucleotide electrons and
phosphate (NADP). hydrogens released
by catabolic
pathways
Nicotinamide adenine dinucleotide (NAD)
• Coenzyme found in all cells (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.
 Nicotinamide adenine dinucleotide (NAD)

• 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).
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 (vitamin B2).
• Involved in several important
reactions in metabolism.
• Many oxidoreductases (flavoenzymes /
flavoproteins) require FAD as a
prosthetic group.
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)

Roles of nucleotides and their derivatives

Source of chemical energy

• Adenosine 5’ triphosphate (ATP)
ATP
• Guanosine triphosphate (GTP)

Adenosine-5'-triphosphate (ATP)
Transports chemical energy within cells
Produced by photosynthesis & cellular respiration
consumed by many enzymes, cellular processes

http://www.zymes.com/knowledge-center/coenzyme-q10/what-does-coq10-do/coq10-is-required-to-produce-energy-atp/
 Roles of nucleotides and their derivatives

• Participate in cell signaling

• Cyclic AMP
• Cyclic GMP Cell signaling
Part of the complex
communication system that
governs and coordinates basic
cellular activities.
Mediates the ability of cells to
perceive and correctly respond
to their microenvironment.
Basis of development, tissue
repair, and immunity as well as
normal tissue homeostasis.
Roles of nucleotides and their derivatives
• Nucleotides are the structural units of RNA and DNA.
• RNA is made up of ribonucleotides
• DNA is made up of deoxyribonucleotides
• Nucleotides are held together by phosphodiester bonds.

Five nitrogenous bases in nucleic acids

• DNA – deoxyribonucleotides with A, T, C, G

• 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
Antiparallel strands held together by
H-bonds between complimentary
bases on adjacent strands

• A forms two hydrogen bonds with T

• G forms three hydrogen bonds with C
The DNA double helix
Dimensions (B-type DNA ):

i) Diameter = 20Å.

ii) Rotation between adjacent bases = 360;

10 bases per 3600 turn.

iii) 3.4Å between adjacent bases on same

strand; rise of 34Å per turn
DNA Packaging
DNA is much longer than the space into which it must fit

Prokaryotes: genomic DNA is circular and

forms a single bacterial chromosome.

Eukaryotes: linear stretches of supercoiled

DNA forms several chromosomes.
Packaging of eukaryotic DNA into chromosomes

Source: http://www.78stepshealth.us/plasma-membrane/eukaryotic-chromosomes.html
RNA structure
• Ribose instead of deoxyribose
• Single stranded (except in some viruses)
• Not as long as DNA
• Intramolecular base pairing à complex
secondary structures
There are many different types of RNA
• Messenger RNA (mRNA)

• Non-coding RNAs
• transfer RNA (tRNA)
• ribosomal RNA (rRNA)
• Regulatory RNAs
• Small nuclear RNAs

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