Biochemistry

Nucleotides & Nucleic Acids

Likando Chababa
 NUCLEOTIDES
 Nucleotides have a variety of roles in cellular metabolism.
1. Energy currency in metabolic transactions, t
2. Essential chemical links in the response of cells to hormones and other
extracellular stimuli.
3. Structural components of an array of enzyme cofactors and metabolic
intermediates.
4. Constituents of nucleic acids: deoxyribonucleic acid (DNA) and
ribonucleic acid (RNA), the molecular storehouses of genetic
information.
 The structure of every protein, and ultimately of every biomolecule and
cellular component, is a product of information programmed into the
nucleotide sequence of a cell's nucleic acids.
 Ability to store and transmit genetic information from one generation to the
next is a fundamental condition for life.
 NUCLEOTIDES

 Nucleotides have three characteristic components:

 Nitrogenous (nitrogen-containing) base,
 A pentose sugar, and
 A phosphate group.
 The molecule without the phosphate group is called a nucleoside.
 The nitrogenous bases are derivatives of two parent compounds, pyrimidine
and purine.
 The bases and pentose sugars of the common nucleotides are heterocyclic
compounds
 Base of a nucleotide is joined covalently (at N-1of pyrimidines and N-9 of
purines) in an N-β-glycosidic bond to the 1' carbon of the pentose, and the
phosphate is esterified to the 5' carbon.
 The N-β-glycosidic bond is formed by removal of the elements of water (a
hydroxyl group from the pentose and hydrogen from the base).
 NUCLEOTIDES
 Both DNA and RNA contain two major purine bases, adenine (A) and
guanine (G), and two major pyrimidines.
 In both DNA and RNA one of the pyrimidines is cytosine (C), but the
second major pyrimidine is not the same in both:
 Thymine (T) in DNA and
 Uracil (U) in RNA.
 Nucleic acids have two kinds of pentose sugars. The recurring
deoxyribonucleotide units of DNA contain 2'-deoxy-l-ribose, and the
ribonucleotide units of RNA contain o-ribose.
 Phosphodiester Linkages
 Successive nucleotides of both DNA and RNA are covalently linked
through phosphate-group "bridges."
 5'-phosphate group of one nucleotide unit is joined to the 3'-hydroxyl
group of the next nucleotide, creating a phosphodiester linkage.
 Covalent backbones of nucleic acids consist of alternating phosphate and
pentose residues.
 Nitrogenous bases may be regarded as side groups joined to the
backbone at regular intervals.
 The backbones of both DNA and RNA are hydrophilic.
 Hydroxyl groups of the sugar residues form hydrogen bonds with water.
 Phosphodiester Linkages
 Key convention is that the phosphodiester linkages in DNA and RNA have
the same orientation along the chain, giving each linear nucleic acid
strand a specific polarity and distinct 5' and 3' ends.
 By definition, the 5' end lacks a nucleotide at the 5' position and the 3'
end lacks a nucleotide at the 3' position.
 The resulting long, unbranched chain has polarity, with both a 5'-end (the
end with the free phosphate) and a 3'-end (the end with the free hydroxyl)
that is not attached to other nucleotides.
 Bases along the resulting deoxyribose-phosphate backbone are, by
convention, always written in sequence from the 5'-end of the chain to the
3'-end.
 Phosphodiester linkages between nucleotides (in DNA or RNA) can be
cleaved hydrolytically by chemicals, or hydrolyzed by a family of
nucleases: deoxyribonucleases for DNA and ribonucleases for RNA.
Phosphodiester Linkages
 NUCEIC ACIDS

 The discovery that genetic information is coded along the length of a

polymeric molecule composed of only four types of monomeric units
was one of the major scientific achievements of the twentieth century.
 This polymeric molecule, DNA, is the chemical basis of heredity and is
organized into genes, the fundamental units of genetic information.
 The basic information pathway i.e., DNA directs the synthesis of RNA,
which in turn directs protein synthesis has been elucidated.
DEOXYRIBONUCLEIC ACID
 The chemical nature of the monomeric deoxynucleotide units of DNA:
1. deoxyadenylate, deoxyguanylate, deoxycytidylate and thymidylate
have already been described.
 Genetic information resides in the order of the monomeric units within the
polymers, and there is a mechanism of reproducing or replicating this
specific information with a high degree of fidelity.
 This requirement, together with x-ray diffraction data from the DNA
molecule and the observation of Chargaff that in DNA molecules:
1. Concentration of deoxyadenosine (A) nucleotides equals that of
thymidine (T) nucleotides (A = T),
2. Concentration of deoxyguanosine (G) nucleotides equals that of
deoxycytidine (C) nucleotides (G = C).
 This led Watson, Crick, and Wilkins to propose in the early 1950s a
model of a double-stranded DNA molecule.
DNA
 The two strands of this double-stranded helix are held in register by
hydrogen bonds between the purine and pyrimidine bases of the
respective linear molecules.
 The pairings between the purine and pyrimidine nucleotides on the
opposite strands are very specific and are dependent upon hydrogen
bonding of A with T and G with C.
 This common form of DNA is said to be right-handed because as one
looks down the double helix the base residues form a spiral in a
clockwise direction.
 In the double-stranded molecule, restrictions imposed by the rotation
about the phosphodiester bond and the favoured anti configuration of
the glycosidic allow A to pair only with T and G only with C.
 This base-pairing restriction explains the earlier observation that in a
double-stranded DNA molecule the content of A equals that of T and
the content of G equals that of C.
DNA – Helix & Hydrogen Bonding
DNA – Helix & Hydrogen Bonding
 Diagrammatic representation of the Watson and Crick model of the
double-helical structure of DNA.
 The horizontal arrow indicates the width of the double helix (20 Å), and
the vertical arrow indicates the distance spanned by one complete turn of
the double helix (34 Å).
 One turn of DNA includes ten base pairs (bp), so the rise is 3.4 Å per bp.
 The central axis of the double helix is indicated by the vertical rod.
 The short arrows designate the polarity of the antiparallel strands.
 Base pairing between deoxyadenosine and thymidine involves the
formation of two hydrogen bonds.
 Three bonds form between deoxycytidine and deoxyguanosine.
 Thus, the G–C bonds are much more resistant to denaturation, or
“melting,” than A–T-rich regions.
DNA – Helix & Hydrogen Bonding
 This specific base pairing in DNA leads to Chargaffs’s rules:
1. Any sample of double-stranded DNA, the amount of adenine
equals the amount of thymine, the amount of guanine equals
the amount of cytosine and,
2. The total amount of purines equals the total amount of
pyrimidines
 The two strands of the double-helical molecule, each of which
possesses a polarity, are antiparallel; i.e., one strand runs in the 5′ to
3′ direction and the other in the 3′ to 5′ direction.
 This is analogous to two parallel streets, each running one way but
carrying traffic in opposite directions.
 DNA – Helix & Hydrogen Bonding
 In the double-stranded DNA molecules, the genetic information resides in
the sequence of nucleotides on one strand, the template strand.
 This is the strand of DNA that is copied during nucleic acid synthesis. It is
sometimes referred to as the noncoding strand.
 The opposite strand is considered the coding strand because it matches
the RNA transcript that encodes the protein.
Salient features of DNA by Watson and Crick
1. DNA has two chains are twisted and coiled around each other in a right
handed double helix.
2. Base pairing rule: A is always paired with T, G always paired with C.
 Thus the two strands are said to be complementary to each other
and are not identical.
3. The two chains are held together by hydrogen bonds between pairs of
bases. A to T is bonded by two hydrogen bonds; G is bonded to C by
three hydrogen bonds.
 H bonds together with hydrophobic interactions between the bases
stabilize the molecule of DNA.
4. Two strands of DNA are antiparallel i.e. one strand runs in the 5’ to 3’
direction while the other runs in the 3’ to 5’ direction.
 The 5’ end of one strand pairs with the 3’ end of the other strand.
Salient features of DNA by Watson and Crick
5. DNA is spiral with a pitch of 34Å per turn and within a single turn 10
base pairs are seen.
6. There is a major and minor groove wind along the molecule parallel
to the phosphodiester backbone.
7. The diameter of the helix is 20Å.
RIBONUCLEIC ACID (RNA)
 RIBONUCLEIC ACID
 Ribonucleic acid (RNA) is a polymer of purine and pyrimidine
ribonucleotides linked together by 3′,5′- phosphodiester bridges
analogous to those in DNA.
 Although sharing many features with DNA, RNA possesses several
specific differences:
1. In RNA, the sugar moiety to which the phosphates and purine and
pyrimidine bases are attached is ribose rather than the 2′-
deoxyribose of DNA.
2. RNA contains the ribonucleotides of adenine, guanine, and
cytosine, it does not possess thymine. Instead of thymine, RNA
contains the ribonucleotide of uracil.
3. RNA exists as a single strand, whereas DNA exists as a double-
stranded helical molecule.
 RIBONUCLEIC ACID
4. Since the RNA molecule is a single strand complementary to
only one of the two strands of a gene, its guanine content does
not necessarily equal its cytosine content, nor does its adenine
content necessarily equal its uracil content.
5. RNA can be hydrolyzed by alkali to 2′,3′ cyclic diesters of the
mononucleotides, compounds that cannot be formed from
alkali-treated DNA because of the absence of a 2′-hydroxyl
group.
 RIBONUCLEIC ACID
 RNA exists in three different forms.
1. Cytoplasmic RNA molecules that serve as templates for protein
synthesis (i.e. that transfer genetic information from DNA to the
protein-synthesizing machinery) are designated messenger RNAs, or
mRNAs.
2. Many other cytoplasmic RNA molecules (ribosomal RNAs; rRNAs)
have structural roles wherein they contribute to the formation and
function of ribosomes (the organellar machinery for protein synthesis)
3. Serve as adapter molecules (transfer RNAs; tRNAs) for the translation
of RNA information into specific sequences of polymerized amino
acids.
Messenger RNA (mRNA)
 This class is the most heterogeneous in size and stability.
 Function as messengers conveying the information in a gene to the
protein synthesizing machinery.
 Where each serves as a template on which a specific sequence of
amino acids is polymerized to form a specific protein molecule, the
ultimate gene product.
 Messenger RNAs, particularly in eukaryotes, have some unique chemical
characteristics.
1. 5′ terminal of mRNA is “capped” by a 7-methylguanosine
triphosphate.
 The cap is involved in:
a) Recognition of mRNA by the translating machinery, and
b) Helps stabilize the mRNA by preventing the attack of 5′-
exonucleases.
Messenger RNA (mRNA)
 Protein-synthesizing machinery begins translating the mRNA
into proteins beginning downstream of the 5′ or capped
terminal.
2. The other end of most mRNA molecules, the 3′-hydroxyl terminal,
has an attached polymer of adenylate residues 20–250 nucleotides
in length.
 Specific function of the “poly(A) tail” at the 3′-hydroxyl terminal of
mRNAs is not fully understood, but it seems that it maintains the
intracellular stability of the specific mRNA by preventing the
attack of 3′-exonucleases.
Transfer RNA (tRNA)
 Molecules vary in length from 74 to 95 nucleotides.
 The tRNA molecules serve as adapters for the translation of the
information in the sequence of nucleotides of the mRNA into specific
amino acids.
 There are at least 20 species of tRNA molecules in every cell, at least one
(and often several) corresponding to each of the 20 amino acids required
for protein synthesis.
 Although each specific tRNA differs from the others in its sequence of
nucleotides, the tRNA molecules as a class have many features in
common.
 The primary structure—i.e. the nucleotide sequence—of all tRNA
molecules allows extensive folding and intra-strand complementarity to
generate a secondary structure that appears like a cloverleaf.
Transfer RNA (tRNA)
 All tRNA molecules contain four main arms.
1. The acceptor arm: where an appropriate amino acid is attached.
2. The DHU arm: binds with active centre of the enzyme aminoacyl
tRNA synthetase.
3. The TψC arm: the one that binds to ribosome during protein
synthesis.
4. The Anticodon arm: which pairs with the codon of mRNA during
protein synthesis.

Transfer RNA (tRNA)
Ribosomal RNA (rRNA)
 A ribosome is a cytoplasmic nucleoprotein structure that acts as the
machinery for the synthesis of proteins from the mRNA templates.
 rRNA participates in the structure of ribosome.
 rRNA, ribosomal proteins and Mg2+ constitute ribosome.
 On the ribosomes, the mRNA and tRNA molecules interact to
translate into specific protein molecule information transcribed from
the gene.
 The ribosome is made of two subunits big and small.
 In active protein synthesis, many ribosomes are associated with an
mRNA molecule in an assembly called the polysome.