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Home , Deoxyribonucleotide, Nucleotide, Ribose, Thymine, Uracil

Nucleotides and Nucleic Acids Definitions

Nucleic acids are of Nucleotides are ring structures containing nitrogen linked to a 5- carbon (a )

5-carbon sugar is either a ribose or a deoxy-ribose making the either a or a

In eukaryotic cells nucleic acids are either:

Deoxyribose nucleic acids (DNA) Ribose nucleic acids (RNA)

Messenger RNA (mRNA) Transfer RNA (tRNA) Ribosomal RNA (tRNA) Function

DNA Genetic material - sequence of nucleotides encodes different amino acids

RNA Involved in the / of genetic material (DNA) Genetic material of some viruses Nucleotide Function

Building blocks for DNA and RNA

Intracellular source of energy - triphosphate (ATP)

Second messengers - Involved in intracellular signaling (e.g. cyclic [cAMP])

Intracellular signaling switches (e.g. G-) Nucleotide Structure

Despite the complexity and diversity of the structure of DNA is dependent on only 4 different nucleotides

Diversity is dependent on the nucleotide sequence

All nucleotides are 2 ring structures composed of: 5-carbon sugar : -D-ribose (RNA) -D- (DNA)

Base

Phosphate group A nucleotide WITHOUT a group is a Nucleotide Structure - 1 HOCH OH 2 O Generic Ribose Structure Ribose 5’ HOCH2 O OH OH 4’ 1’

3’ 2’ HOCH OH 2 O

N.B. are given numberings as a Deoxyribose OH H Nucleotide Structure - 2 Bases -

NH2

N N A N N N 6 H 7 5 1 N 8 9 4 2 O N 3 N N N H G N N NH2 H Nucleotide Structure - 3 Bases - O

H C 3 NH T

N O 4 3 5 N H

2 6 NH2 1 N N C N O H Nucleotide Structure - 4 Bases - Pyrimidines

Thymine is found ONLY in DNA. In RNA, thymine is replaced by Uracil and Thymine are structurally similar

Uracil O

4 3 N NH 5 U 2 6 1 N N O H Nucleotide Structure - 4 Phosphate Groups

Phosphate groups are what makes a nucleoside a nucleotide Phosphate groups are essential for nucleotide polymerization

Basic structure:

O

O P O X

O Nucleotide Structure - 4 Phosphate Groups

Number of phosphate groups determines nomenclature

Monophosphate O e.g. AMP O P O CH Free = inorganic 2 phosphate (Pi) O

Diphosphate O O e.g. ADP O P O P O CH2 Free = Pyro- O O phosphate (PPi) Nucleotide Structure - 4 Phosphate Groups

Triphosphate O O O e.g. ATP

O P O P O P O CH2 No Free form exists O O O Nucleotide Structure - 4 2- Base-Sugar-PO4

4 3 5 N

2 6 O 1 N 5’ O P O C O

O 4’ 1’

3’ 2’

OH

Monophosphate Polymerization

P P P N P P P N

C C S Phosphodiesterase S

P N + P P C (PPi) S P P P N

C S Nucleic Acid Structure Polymerization

Nucleotide Sugar Phosphate “backbone” Nucleic Acid Structure Polymerization

5’ 3’ Sugar Phosphate “backbone” T A G C A C Bases

5’ 3’ TAGCAC Nucleic Acid Structure “Base Pairing”

RNA [normally] exists as a single stranded DNA exists as a double stranded polymer

DNA double strand is created by bonds between nucleotides Nucleotides always bind to complementary nucleotides

A T (2 H-bonds)

G C (3 H-bonds) Nucleic Acid Structure “Base Pairing” Nucleic Acid Structure “Base Pairing”

RNA is [usually] single stranded Base pairing can occur in RNA but is usually within the same strand Nucleic Acid Structure “Base Pairing”

DNA base-pairing is antiparallel i.e. 5’ - 3’ (l-r) on top : 5’ - 3’ (r-l) on 5’ 3’

T A G C A C A T C G T G

3’ 5’ Nucleic Acid Structure Antiparallel Base Pairing

Why antiparallel DNA base-pairing? - Need to shield the genetic information -Istheonly conformational structure to allow double helix formation Nucleic Acid Structure The double helix

First determined by Watson & Crick in 1953

Most energy favorable conformation for double stranded DNA to form

Shape and size is uniform for all life (i.e. DNA is identical)

Without anti-parallel base pairing this conformation could not exist

Structure consists of “major” grooves and “minor” grooves

Major grooves are critical for binding proteins that regulate DNA function Nucleic Acid Structure The double helix

Minor Groove

Major Groove