Module Title: INMED

Course Content: Biochemistry

By:Ebsa Tofik(BSc,MSc)

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 NUCLEIC ACIDS
Nucleic Acids:

 have been the subject of biochemical investigations since 1869 .

 In 1869 Friedrich Miescher, a 25-year old Swiss chemist,

 isolated nuclei from pus cells and

 found that they contained unknown phosphate-rich substance which he

named nuclein.

 This substance was quite different from the carbohydrates, proteins and

fats.

 Later, it was found that the nuclein had acid properties and hence,

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 Altmann introduced the term nucleic acid to replace nuclein in 1899,

NUCLEIC ACIDS

 Named b/c initial discovery within the nucleus & for the presence of

phosphate groups.

 are the hereditary determinants of living organisms.

 are the macromolecules present in most living cells either:

 in the free state or bound to proteins as nucleoproteins.

 are biopolymers of high molecular weight with mononucleotide as their

repeating units.

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 NUCLEIC ACIDS….
 contain carbon, hydrogen, oxygen, nitrogen and phosphorus

 most important of all biomolecules.

 found in all living things and is the overall name for DNA & RNA

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Nucleosides

 Result from linking one of the sugars with a purine or pyrimidine base

through an N-glycosidic linkage

 Purines bond to the C1‟ carbon of the sugar at their N9 atoms

 Pyrimidines bond to the C1‟ carbon of the sugar at their N1 atoms

Thymidine

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Phosphoric acid

 mono-, di- or triphosphates

 phosphates can be bonded to either c3 or c5 atoms of the sugar

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Nitrogenous bases

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Pyrimidines

 Single heterocyclic ring structures

 Cytosine(both in RNA& DNA)

 Thymine(only in DNA),

 Uracil( only in RNA)

 In nucleotide base carbons denoted as 1,2.. Etc

 All pyrimidine bases can exist in lactam & Lactim form.

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 If the group is –HN–CO–Lactam(keto),

 if it isomerizes to –N=C–OHLactim(enol).

 At physiological pH, the lactam form is predominant.

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Cytosine

 Chemically it is 2-deoxy-4-amino pyrimidine,

 can exist in both lactam or lactim forms.

 found in all NAs except in DNA of certain viruses.

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Uracil

 Chemically it is 2,4-dideoxy Pyrimidine.

 Confined to RNA only

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Thymine(5-methyl-Uracil)

 2,4-dideoxy-5-methyl pyrimidine.

 found only in DNA,

 Minor amounts have recently been found in t-RNA.

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Purines

 heterocyclic double ring structures

 product of fusion of pyrimidine ring with imidazole ring.

 Adenine & Guanine(found in both DNA&RNA).

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Adenine

 Chemically it is 6-aminopurine

Guanine

 2-amino-6-oxypurine.

 can exist as lactam & lactim forms by isomerization

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Minor Bases

 Unusual & can exist with no known fun.

 Some found in NAs of bacteria & viruses.

 many found in DNA & tRNAs of both pro& eukaryotes.

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Examples:

 bacteriophages contain 5-hydroxy methyl cytosine.

 in mRNA of mammalian cells like N6– methyl adenine,N7–methyl guanine

& N6–N6–dimethyl adenine.

In plants:-many purine derivatives are found:like;

 - Theophylline:-1,3-dimethyl xanthine in tea.

 - Theobromine:-3,7-dimethyl xanthine in cocoa.

 - Caffeine:-1,3,7-trimethyl xanthine in coffee.

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Pentose Sugar

 Numbering of carbon is “primed”

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Nucleotides

 Result from linking one or more phosphates with a nucleoside onto the 5‟

end of the molecule through esterification

Naming

Nucleosides:

Purine nucleosides end in “-sine”

 Adenosine, Guanosine

Pyrimidine nucleosides end in “-dine”

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Nucleotides:

 Start with the nucleoside name from above and add “mono-”, “di-”, or

“triphosphate”

Adenosine Monophosphate, Cytidine Triphosphate, Deoxythymidine

Diphosphate

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Common Nucleotides

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Importance of Nucleotides & Nucleosides

 Out of DNA & RNA, they have diverse functions.

Adenosine nucleotides

 ATP,ADP,AMP & cAMP.

ATP(storage battery of tissues)

 Energy currency of the cell.

 It is storehouse of energy.

 has 2~P& releases energy(7.6Kcal)endergonic rxns.

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 in gluconeogenesis,FA,Creatine,SAM synthesis etc.

 for phosphotransferases

 to synthesize „active‟ sulfate(PAPS).

 Converted to ADP,AMP & 3‟,5‟-cAMP

Adenosinediphosphate(ADP)

 1o Pi acceptor in oxidative phosphorylation(OP)ADP+Pi=ATP

 control cellular respiration, muscle contraction,etc.

 activator of the enzyme Glutamate dehydrogenase.

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3-phosphoadenosine-5-phosphosulfate (PAPS)

 the sulfate donor for proteoglycans & conjugations of drugs

S-adenosylmethionine

 the methyl group donor

GTP

 serves as an allosteric regulator &

 an energy source for protein synthesis

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The second messengers (cAMP, cGMP) :

cAMP

 secondary messengers for the action of many hormones

cGMP

 serves as a 2nd messenger in response to nitric oxide

 during relaxation of smooth muscles

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UDP-sugar derivatives participate in:

Sugar epimerization

Biosynthesis of:

 glycogen & glucosyl disaccharides

 the oligosaccharides of glycoproteins & proteoglycans

UDP-glucuronic acid forms

 the urinary glucuronide of bilirubin

 conjugates of many drugs such as aspirin

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CTP participates in biosynthesis of:

 phosphoglycerides, sphingomyelin, & other substituted sphingosines

Synthetic Nucleotide Analogs Are Used in Chemotherapy

 Synthetic analogs of purines, pyrimidines, nucleosides, & nucleotides

altered in;

 either the heterocyclic ring or the sugar moiety

 have numerous applications in clinical medicine:

 Their toxic effects reflect either inhibition of enzymes essential for NA

synthesis or

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 or their incorporation into nucleic acids,

 with resulting disruption of base-pairing

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The purine analog allopurinol

 used in treatment of hyperuricemia & gout

 Inhibits: purine biosynthesis & xanthine oxidase activity

Cytarabine

 is used in chemotherapy of cancer

Azathioprine

 which is catabolized to 6-mercaptopurine

 is employed during organ transplantation

 to suppress immunologic rejection

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Function of Nucleic acids

 serve as genetic material of living organisms.

 are involved in the storage, transfer and expression of genetic information.

 contain all the necessary information required for the formation of

individual or organism.

 determines physical fitness of an individual to life.

 Some acts as enzymes and coenzymes.

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 nucleic acids are polynucleotides

Polynucleotides (Nucleic acids) characteristics

Polynucleotides are directional macromolecules:

 Phosphodiester bonds link the 3'- & 5'-C‟s of adjacent monomers

 Each end of a nucleotide polymer thus is distinct

 refer to the "5'- end" or the "3'- end" of polynucleotides,

 the 5'- end being the one with a free or phosphorylated 5„-OH.

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 Where all the phosphodiester bonds are 5„3',

a more compact notation is possible:

 pGpGpApTpCpA

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 This representation indicates that

the 5'-OH,but not the 3'-OH, is phosphorylated

 The most compact representation shows

only the base sequence with:

 the 5'- end on the left &

 the 3'- end on the right

 The phosphoryl groups are assumed but not shown:

 GGATCA

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 The 5'-phosphoryl group of a mononucleotide can esterify

the 3'-OH of the pentose of a 2nd nucleotide

 forming a phosphodiester

 This forms a dinucleotide in w/c the pentose moieties are

linked by a 3„5' phosphodiester bond to form;

 the "backbone" of RNA & DNA

 The formation of a dinucleotide may be represented as

the elimination of water b/n two mononucleotides

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Nucleic Acids(NAs) :two types in living organisms: DNA & RNA

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DNA Structure

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 Primary structure of DNA is the linear sequence of its building nucleotide

units that are as follows

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 The phosphate and sugar form the backbone of the DNA molecule

 whereas the bases form the “rungs”

There are four types of nitrogenous bases

which bounds with its specific base in two poly peptide run in

opposite direction

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 Each base will only bond with one other specific base.

A T

Adenine Thymine

C G

Cytosine Guanine

Because of this complementary base pairing, the order of the bases in one

strand determines the order of the bases in the other strand.

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Base pairing

The bases of one strand of DNA are paired with the bases of the second

strand

 A is always paired with T &

 C is always paired with G.

 The base pairs are perpendicular to the axis of the helix

 one polynucleotide chain of the DNA double helix is always the

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complement of the other
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The specific base pairing in DNA leads to the Chargaff Rule:

 In any sample of dsDNA,

the amount of A equals the amount of T

 the amount of G equals the amount of C

 the total amount of purines equals the total

amount of pyrimidines.

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Erwin Chargaff – (1905-2002)

 Columbia University, NY

 Investigated the composition of DNA

 His findings by 1950 strongly suggested the base-pairings of A-T & G-C

 Met with Watson and Crick in 1952 and shared his findings

 “Chargaff‟s rule” A = T & C = G

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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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Double helix

James Watson (1928) and Francis Crick (1916-2004)

 Worked together at Cavendish Laboratory in Cambridge to determine the

structure of DNA

Used work from Franklin, Wilkins, and Chargaff to determine the double

helix shape

The two chains are

 coiled around a common axis called the axis of symmetry

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 paired in an antiparallel manner.

 The hydrophilic deoxyribose–phosphate backbone of each chain is on the

outside of the molecule, whereas

The hydrophobic bases are stacked inside.

The overall structure resembles a twisted ladder

spatial relationship between the two strands in the helix creates

 a major (wide) groove and

 a minor (narrow) groove

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 These grooves provide access for the binding of regulatory proteins

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ORGANIZATION OF EUKARYOTIC DNA

Eukaryotic DNA is associated with tightly bound basic proteins, called histones.

 These serve to order the DNA into fundamental structural units called

nucleosomes

 Nucleosomes are further arranged into increasingly more complex structures

that organize and condense the long DNA molecules into,

 chromosomes that can be segregated during cell division.

 The complex of DNA and protein found inside the nuclei of eukaryotic cells is

called chromatin

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There are five classes of histones

H1, H2A, H2B, H3and H4.

These small proteins are positively charged at physiologic pH as a result of

their high content of lysine and arginine

 Because of their positive charge, they form ionic bonds with negatively

charged DNA

 Histones, along with positively charged ions such as Mg2

 help neutralize the negatively charged DNA phosphate

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groups.
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RNA-Ribonucleic acid

 Base-Cytosine, guanine, adenine and uracil

 Single stranded

Functions

rRNA-ribosomal RNA

 makes up about 60% of ribosomal structure

mRNA-messenger RNA

 record information from DNA and carry it to ribosomes

tRNA-transfer RNA

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 delivers amino acids to proteins at the ribosome to extend the chains
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RNA Structure

Primary Structure : Sequence of ribonucleotides in chain.

Secondary Structure

Even though most RNAs are single stranded, they exhibit extensive

secondary structures, including intramolecular double-stranded region

that are important to their function

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These secondary structures,

one of the most common of w/c is called a hairpin loop

are the product of intramolecular base pairing

that occurs b/n complementary nucleotides within a single RNA molecule

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Tertiary Structures

 Involves the folding of the molecule into 3D-structure.

 Stabilised by hydrophobic & H-bonds producing a compactly coiled

globular structure.

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Types of RNAs

Messenger RNA (m-RNA)

 the most heterogeneous class of RNA in size & stability.

 Mwt=3×104-2×106 /1000-10,000 ribonucleotides.

 formed from DNA template strand(3‟–5‟)during transcription.

 mRNA carries a specific sequence of nucleotides in “triplets”.

 called codons, responsible for specific protein synthesis.

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rRNA-ribosomal RNA

 80% the total cellular RNA.

 Ribosome is a nucleoprotein found in cytoplasm.

 On ribosome the mRNA & rRNA interact during translation

 Mammalian ribosomes are made up of 2-subunits:

larger-60S(~60% rRNA)

 combination of 5S r-RNA,5.8S r-RNA & 28S r-RNA.

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smaller-40S r-RNA

 carries 18S r-RNA & 33-d/t proteins.

 the fun of rRNA in ribosomes isn‟t clearly known.

 but play a role in binding of mRNA to ribosomes during translation.

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Transfer RNA (t- RNA)

 smallest of three major species of RNA molecules

 have 74-95 nucleotide residues

 are synthesized by the nuclear processing of a precursor molecule

 transfer the amino acids from cytoplasm to the protein synthesizing

machinery,

 hence the name t RNA.

 are easily soluble ,hence called “Soluble RNA or s RNA

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 are also called Adapter molecules,

 since they act as adapters for the translation of the sequence of nucleotides

of the m RNA in to specific amino acids

There are at least 20 species of t RNA one corresponding to each of the 20

amino acids required for protein synthesis

Structural characteristics of t- RNA

 The nucleotide sequence of all the t RNA molecules allows extensive

complimentarity that generates a secondary structure.

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Secondary structure

 Each single t- RNA shows extensive internal base pairing and acquires a

clover leaf like structure.

 The structure is stabilized by hydrogen bonding between the bases and is a

consistent feature.

 All t-RNA contain 5 main arms or loops

a) Acceptor arm
b) Anticodon arm
c) D HU arm
d) TΨ C arm

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e) Extra arm
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 Bases that commonly occur in a particular position

are indicated by letters

 The locations of the modified bases are indicated

Dihydrouridine (D),

Ribothymidine (T) &

Pseudouridine ()

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Acceptor arm

 The acceptor arm is at 3‟ end

 It has 7 base pairs

 The end sequence is unpaired Cytosine,Cytosine-Adenine at the 3‟ end

 The 3‟ OH group terminal of Adenine binds with carboxyl group of amino

acids

 The tRNA bound with amino acid is called Amino acyl t RNA

 CCA attachment is done post transcriptionally

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 The carboxyl group of amino acid is attached to 3‟OH group of Adenine

nucleotide of the acceptor arm.

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 The anticodon arm base pairs with the codon present on the m- RNA
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Anticodon arm

 Lies at the opposite end of acceptor arm

5 base pairs long

Recognizes the triplet codon present in the m RNA

Base sequence of anticodon arm is complementary to the base

• sequence of m RNA codon.

 Due to complimentarity it can bind specifically with m RNA by

• hydrogen bonds.

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DHU arm

 It has 3-4 base pairs

Serves as the recognition site for the enzyme (amino acyl t RNA synthetase)

that adds the amino acid to the acceptor arm.

ΨC arm

This arm is opposite to DHU arm

Since it contains pseudo uridine that is why it is so named

 It is involved in the binding of t RNA to the ribosomes

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Extra arm or Variable arm

 About 75 % of t RNA molecules possess a short extra arm

If about 3-5 base pairs are present the t-RNA is class 1.

 Majority t -RNA belong to class 1.

 The t –RNA belonging to class 2 have long extra arm, 13-21 base pairs in

length.

Tertiary structure of t- RNA

The L shaped tertiary structure is formed by further folding of the clover leaf
due to hydrogen bonds between T and D arms.

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 The base paired double helical stems get arranged in to two double helical

columns, continuous and perpendicular to one another

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The Differences Between DNA & RNA

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