Nucleic acids

 Structure

 Classification

 Function

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 Nucleic acids
o Nucleic acids are molecules that store information for

cellular growth and reproduction.

o There are two types of nucleic acids:

- deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)

 DNA, the repository of genetic information, is present not

only in chromosomes in the nucleus of eukaryotic organisms,

but also in mitochondria .

 The genetic information found in DNA is copied and

transmitted to daughter cells through DNA replication.

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o Nucleic acids are polymers consisting of long chains of monomers

called nucleotides

o A nucleotide consists of a nitrogenous base, a pentose sugar and a

phosphate group.

 Glycosidic bond: The linkage of base & sugar (N-glycosidic bond)

for nucleosides involves distinct nitrogen atoms in purine &

pyrimidine ring.

 The linkage in purine nucleotide is between 1 of sugar ribose and 9

of purine bases.

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  The linkage in pyrimidine nucleotide is between 1 of sugar ribose
and 1 of pyrimidine bases.

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 Nitrogen Bases
 The nitrogen bases in nucleotides consist of two general types:

- purines: adenine (A) and guanine (G)

- pyrimidines: cytosine (C), thymine (T) and Uracil (U)

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 Nucleosides

 The addition of a pentose sugar to a base

produces a nucleoside.

 If the sugar is ribose, a ribonucleoside is

produced; if the sugar is 2-deoxyribose, a

deoxyribonucleoside is produced .

 Nucleosides with purine bases have the suffix

- sine, while pyrimidine nucleosides end with

- dine.

 The deoxyribonucleosides of A, G, C, and T

have the added prefix, “deoxy-,” for example,

6deoxyadenosine. 2/4/2024
 Nucleotides

 The addition of one or more phosphate groups to a nucleoside

produces a nucleotide.

 The first phosphate group is attached by an ester linkage to the 5'-

OH of the pentose.

 Such a compound is called a nucleoside 5'-phosphate or a 5'-

nucleotide.

 If a second or third phosphate is added to the nucleoside, a

nucleoside diphosphate or triphosphate results.

 The second and third phosphates are each connected to the

7 nucleotide by a “high-energy” bond. 2/4/2024

The phosphate groups are responsible for the negative charges
associated with nucleotides, and cause DNA and RNA to be referred to
as nucleic acids.

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 Physiological functions of nucleotides

1. Precursors for DNA and RNA synthesis

2. Essential carriers of chemical energy, especially ATP , GTP

3. Components of the cofactors NAD+, FAD, and coenzyme A

4. Formation of activated intermediates such as UDP-glucose .

5. cAMP and cGMP, are also cellular second messengers.

6. Allosteric regulation of various metabolic pathways e.g. ATP

inhibits PFK-1

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 The central dogma of molecular biology

 The biological information flows from

DNA to RNA, & from there to proteins.
 This is central dogma of life.

 The flow of information from DNA to

RNA to protein is termed the “central
dogma” of molecular biology, and is
descriptive of all organisms, with the
exception of some viruses that have
RNA as the repository of their genetic
information.
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 Primary Structure of DNA

o DNA is unbranched linear molecule.

o This structure which is created by 3’, 5’-phosphodiester bond

interlinking of NMP is the primary structure of DNA.

o Phosphodiester bonds join the 3′-hydroxyl group of the

deoxypentose of one nucleotide to the 5′-hydroxyl group of the
deoxypentose of an adjacent nucleotide through a phosphate group.

o 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).
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• The bases located along the resulting deoxyribose–phosphate
backbone are, by convention, always written in sequence from
the 5′-end of the chain to the 3′-end.

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 Secondary Structure of DNA

 DNA exists as a double-stranded (ds) molecule, in which the two

strands wind around each other, forming a double helix.

 F. Crick and J. Watson discovered native DNA is double stranded

molecule.

 In the double helix, the two chains are coiled around a common axis

called the axis of symmetry.

 The chains are paired in an antiparallel manner, that is, the 5′-end of

one strand is paired with the 3′-end of the other strand.

 The overall structure resembles a twisted ladder.

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  The spatial relationship between the two strands in the helix

creates a major (wide) groove and a minor (narrow) groove.

 These grooves provide access for the binding of regulatory

proteins to their specific recognition sequences along the DNA

chain.

 Certain anticancer drugs, such as dactinomycin (actinomycin D),

exert their cytotoxic effect by intercalating into the narrow groove

of the DNA double helix, thus interfering with DNA and RNA
synthesis

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  Watson - Crick have proposed a double helical model of DNA,
having the following important characteristic features.
1. Two helical polynucleotide chains are coiled around a common
axis. The chains run in opposite directions, (anti parallel)
2. The two anti-parallel polynucleotide chains are not identical, but
they are complimentary.
3. The purine, pyrimidine bases are on the inside of the helix, the
phosphate and deoxyribose groups are on the outside.
4. The diameter of the helix is 20 A0 adjacent bases are separated by
3.4 A0
5. The helical structure repeats after 10 residues on each chain.

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6. The two chains are held together by hydrogen bonds between pairs
of bases.
Adenine is always paired with thymine, Guanine always paired
with cytosine.
A to T is bonded by two hydrogen bonds (A= T), Guanine is
bonded to cytosine by three hydrogen bonds(G=C)
7. The double helix is stabilized by interaction between stacked bases
of the same strand.
8. Watson - Crick Model of DNA is also referred as B-DNA, which is
the most stable one under physiological conditions.

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 Base pairing

 The bases of one strand of DNA are paired with the bases of the

second strand, so that

 An adenine is always paired with a thymine

 A cytosine is always paired with a guanine

 Therefore, one polynucleotide chain of the DNA double helix is

always the complement of the other.

 Given the sequence of bases on one chain, the sequence of bases

on the complementary chain can be determined.

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The specific base pairing in DNA leads to the Chargaff Rule: In
any sample of dsDNA, the amount of adenine equals the amount of
thymine, the amount of guanine equals the amount of cytosine, and
the total amount of purines equals the total amount of pyrimidines.

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• The base pairs are held
together by hydrogen bonds:
• Two between A and T and
three between G and C.
• These hydrogen bonds, plus
the hydrophobic interactions
between the stacked bases,
stabilize the structure of the
double helix

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Tertiary structure
 ds-DNA is a very thin and long molecule. For instance human
DNA has thickness of 2nm and average length of 5cm.
 In this structure 147 bps of DNA is wrapped around a ball of
histone complex (H2A.H2B.H3.H4)2.
 Five classes of histones -H1, H2A, H2B, H3 & H4.

 This structure is called nucleosome.

 Histones are basic proteins rich in lysine and Arginine hence

neutralizes charge on DNA
 They form ionic bonds with negatively charged DNA.

 The DNA wrapped around histone generates a solenoid.

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Histone H1 of which there are several related species, is not found
in the nucleosome core, but instead binds to the linker DNA chain
between the nucleosome beads.
 Histone H1 facilitates the packing of nucleosomes into the more
compact structures.

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 Separation of the two DNA strands in the double helix

 The two strands of the double helix separate when hydrogen bonds

between the paired bases are disrupted.

 Disruption can occur in the laboratory if the pH of the DNA

solution is altered so that the nucleotide bases ionize, or if the

solution is heated.

 Note: Phosphodiester bonds are not broken by such treatment.

 When DNA is heated, the temperature at which one half of the

helical structure is lost is defined as the melting temperature (Tm).

 The loss of helical structure in DNA, called denaturation

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 Because there are three hydrogen bonds between G and C but only

two between A and T, DNA that contains high concentrations of A and

T denatures at a lower temperature than G- and C-rich DNA .

 Under appropriate conditions, complementary DNA strands can

reform the double helix by the process called renaturation (or

reannealing).

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 Structure of RNA

 There are three major types of RNA that

participate in the process of protein

synthesis: ribosomal RNA (rRNA),
transfer RNA (tRNA), and messenger
RNA (mRNA).

 Like DNA, these three types of RNA are

unbranched polymeric molecules

composed of nucleoside monophosphates
joined together by phosphodiester bonds.

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 However, they differ as a group from DNA in several ways, for

example, they are considerably smaller than DNA, and they contain
ribose instead of deoxyribose and uracil instead of thymine.

 Unlike DNA, most RNAs exist as single strands that are capable of

folding into complex structures.

 The three major types of RNA also differ from each other in size,

function, and special structural modifications.

 RNA chains are usually single-stranded and lack the continuous

helical structure of double-stranded DNA

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  However, RNA still has considerable secondary and tertiary

structure because base pairs can form in regions where the strand
loops back on itself.

 As in DNA, pairing between the bases is complementary and

antiparallel.

 But in RNA, adenine pairs with uracil rather than thymine.

 Base pairing in RNA can be extensive, and the irregular looped

structures generated are important for the binding of molecules,

such as enzymes, that interact with specific regions of the RNA.

 Some RNA molecules are capable of catalyzing reactions. Thus,

28 RNA, as well as protein, can have enzymatic activity. 2/4/2024

 Certain rRNA precursors can remove internal segments of

themselves, splicing the remaining fragments together.

 Because this RNA is changed by the reaction that it catalyzes, it is

not truly an enzyme and therefore has been termed a “ribozyme.”

 Other RNAs act as true catalysts, serving as ribonucleases that

cleave other RNA molecules or as a peptidyl transferase, the

enzyme in protein synthesis that catalyzes the formation of peptide

bonds.
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 A. Messenger RNA

 mRNA comprises only about 5% of the RNA in the cell, yet is by far the

most heterogeneous type of RNA in size and base sequence.

 The mRNA carries genetic information from the nuclear DNA to the

cytosol, where it is used as the template for protein synthesis.

 mRNA travels through nuclear pores to the cytoplasm, where it binds to

ribosomes and tRNAs and directs the sequential insertion of the

appropriate amino acids into a polypeptide chain.

 If the mRNA carries information from more than one gene, it is said to

be polycistronic.

 Polycistronic mRNA is characteristic of prokaryotes.

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 If the mRNA carries information from just one gene, it is said to be

monocistronic and is characteristic of eukaryotes.

 In addition to the protein coding regions that can be translated, mRNA

contains untranslated regions at its 5′- and 3′-ends.

 Special structural characteristics of eukaryotic (but not prokaryotic)

mRNA include a long sequence of adenine nucleotides (a “poly-A tail”)

on the 3′-end of the RNA chain, plus a “cap” on the 5′-end consisting of a
molecule of 7-methylguanosine attached “backward” (5′→5′) through a
triphosphate linkage.

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 Most of the leader sequence, all of the coding region, and most of
the trailer are formed by transcription of the complementary
nucleotide sequence in DNA
However, the terminal guanosine in the cap structure and the
poly(A) tail do not have complementary sequences; they are added
posttranscriptionally.

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B. Transfer RNA(tRNA)
 tRNA molecules are rather small compared with both mRNA and
the large rRNA molecules.
 On average, tRNA molecules contain approximately 80 nucleotides
and have a sedimentation coefficient of 4S.
 There is at least one specific type of tRNA molecule for each of the
twenty amino acids commonly found in proteins.
 Together, tRNA make up about 15% of the total RNA in the cell.

 tRNA molecules contain not only the usual nucleotides, but also
derivatives of these nucleotides that are produced by
posttranscriptional modifications.
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  The tRNA have extensive intrachain base-pairing that leads to

characteristic secondary and tertiary structure.

 Each tRNA serves as an “adaptor” molecule that carries its

specific amino acid—covalently attached to its 3′-end—to the site

of protein synthesis.

 There it recognizes the genetic code word on an mRNA, which

specifies the addition of its amino acid to the growing peptide

chain.

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 During protein synthesis, tRNA molecules carry amino acids to

ribosomes and ensure that they are incorporated into the

appropriate positions in the growing polypeptide chain.

 This is done through base-pairing of three bases of the tRNA (the

anticodon) with the three base codons within the coding region of
the mRNA.

 Therefore, cells contain at least 20 different tRNA molecules that

differ somewhat in nucleotide sequence, one for each of the amino

acids found in proteins.

 Many amino acids have more than one tRNA.

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 The acceptor arm: The 3-ACC amino acid acceptor sequence
 Anticodon : makes base pairs with codons on the mRNA during protein synthesis
 D loop is important for proper recognition a given tRNA by its amino acyl tRNA
synthetase.
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 The TψC loop –binding of amino acyl tRNA to ribosome during protein synthesis.
C. Ribosomal RNA(rRNA)

 rRNAs are found in association with several proteins as components of

the ribosomes the complex structures that serve as the sites for protein
synthesis.

 In the eukaryotic cytosol, there are four rRNA species (28S, 18S, 5.8S,

and 5S).

 “S” is the Svedberg unit, which is related to the molecular weight and

shape of the compound.

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  Prokaryotic and eukaryotic ribosomes are similar in structure,

and serve the same function, namely, as the “factories” in which

the synthesis of proteins occurs.

 The large ribosomal subunit catalyzes formation of the peptide

bonds that link amino acid residues in a protein.

 The small subunit binds mRNA and is responsible for the

accuracy of translation by ensuring correct base-pairing between

the codon in the mRNA and the anticodon of the tRNA.

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