nucleic acids aditya asopa

8/7/2019 NUCLEIC ACIDS Aditya Asopa

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NUCLEIC ACIDS

COMPILED BY ADITYA ASOPA,

UNDER GUIDANCE OF: DR. ANIL MOOLCHANDANI

DR. MEENAXI SAREEN

DEPARTMENT OF VETERINARY BIOCHEMISTRY

BIKANER, INDIA


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Nucleic Acids are giant polymeric molecules that are

responsible for carrying genetic information fromgenerations to generations as well as for producing all the

proteins present in a cell which are very essential for life of

a cell.

Nucleic acids are universal in nature i.e. they are found in all

the living cells and viruses.

Nucleic acids were first discovered by Friedrich Miescher.

CHEMICAL NATURE OF NUCLEIC ACIDS

The monomers from which nucleic acids are constructed

are called Nucleotides.

Each nucleotide consists of three components.

i) A nitrogenous heterocyclic base,

ii) A pentose sugar and

iii)A phosphate molecule.


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NITROGENOUS BASE

These molecules are the backbone of nucleic acid molecule

to which other components of nucleic acid is bonded. These

are nitrogen containing heterocyclic aromatic molecules

which are of two types: Pyrimidine and Purine.

Pyrimidine

It is the class of nitrogenous base containing only a

single nitrogenous heterocyclic ring.It has three main examples, cytosine, uracil and

thymine.

These bases are designated by T, U and C

respectively.


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Pyrimidines exhibit keto-enol and amino-imine

tautomerism but oxo and amine from prevails at

physiological Ph.Apart from these three pyrimidine bases, there are

some modified pyrimidines also as 5, 6-Dihydrouracil,

5-methylcytosine etc.


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Purines

It is the class of nitrogenous base containing two rings

in the molecule; a five carbon and a six membered

ring. This class has two naturally occurring bases,

adenine and guanine.

These bases are designated by A and G respectively.

Apart from these naturally occurring purines there are

some modified purine bases, for instance

hypoxanthine, xanthineand 7-methylguanineetc.

Purines exhibit keto-enol and amino-iminetautomerism but oxo and amine from prevails at

physiological Ph.

GUANINE

ADENINE


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PENTOSE SUGAR

It is a five carbon sugar molecule which binds with the

nitrogenous bases and makes the characteristics of

the nucleic acids.

In nucleic acids there are two types of sugar

molecules found in general. They are ribose and

deoxyribose.

Ribose

It is the 5-carbon nitrogenous base made up of cyclic

structure of D-ribose sugar.

RIBOSE


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Deoxyribose

It is the deoxidized form of ribose sugar (2-deoxy-D-Ribose). It is also a five carbon molecule having a

hydrogen atom instead of hydroxyl group at second

carbon.

Phosphate Molecule

It is simply the molecule of phosphoric acid which is

binds with the sugar molecule and is responsible for

acidity of nucleic acid.

DEOXYRIBOSE MOLECULE

PHOSPHORIC ACID


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Building Blocks of Nucleic Acid

Nucleic acids are polymers having monomer units as

Nucleotides. Nucleotides are further made up ofnucleosides and phosphate molecule.

Nucleosides are derivatives of purines and

pyrimidines that have a sugar linked to a ring nitrogen.

The sugar is linked to the heterocyclic base via a -N-glycosidic bond, almost always to N-1 of a

pyrimidine or to N-9 of a purine.

Mononucleotides are nucleosides with a phosphoryl

group esterified to a hydroxyl group of the sugar. The

3- and 5-nucleotides are nucleosides with a

phosphoryl group on the 3- or 5-hydroxyl group of the

sugar, respectively. Since most nucleotides are 5-,the prefix 5- is usually omitted when naming them.

Additional phosphoryl groups linked to the phosphoryl

group of a mononucleotide (by acid anhydride

bonds) form diphosphates and triphosphates.

Sterioisomerism of nucleotides

Steric hindrance by the base restricts rotation about

the -N-glycosidic bond of nucleotides andnucleosides. Both therefore exist as syn or anti

conformers but anti conformers predominates in

nature.


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RIBONUCLEOTIDES

Syn Anti


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DEOXY RIBONUCLEOTIDES


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Role of nucleotides

Nucleotides form a part of many coenzymes and

serve as donors of phosphoryl groups (e.g. ATP or

GTP), sugars (e.g. UDP or GDP sugars), or of lipid

(e.g. CDP-acylglycerol). Regulatory nucleotides

include the second messengers, cAMP and cGMP,

the control by ADP of oxidative phosphorylation, andallosteric regulation of enzyme activity by ATP, AMP,

and CTP. Synthetic purine and pyrimidine analogs

that contain halogens, thiols, or additional nitrogen are

employed for chemotherapy of cancer and AIDS and

as suppressors of the immune response during organ

transplantation.

Classification of Nucleic Acids

Nucleic acids are divided on the basis of ingredients

in two important classes. One is Deoxyribose Nucleic

Acidand other is Ribose Nucleic Acid.


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Deoxyribose Nucleic Acid

As the name suggest deoxyribonucleic acid or DNAas they are popularly called contains 2-deoxyribose

as pentose sugar.

This polymeric molecule, DNA, is the chemical basis

of heredity and is organized into genes, the

fundamental units of genetic information. DNA directs

the synthesis of RNA, which in turn directs protein

synthesis.

In DNA monomeric units i.e. Deoxyribonucleotides are

held by 3-5-phosphodiester bridges constituting a

single strand forming a polymeric giant molecule.

A DNA is always written in the direction 5 to

3direction i.e. one end has a 5- hydroxyl or

phosphate terminal and other end has 3-phosphate

or hydroxyl terminal. This polarity is evident during

transcription of genetic information.


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A segment of one strand of a DNA molecule in which the purine and pyrimidine bases G, C, T and A are held

together by phosphodiester backbone between 2-deoxyribosyl moieties attached to nucleobases by N-glycosidicbond. Note that back bone has a direction. Conventionally DNA sequence is written in the 5 to 3direction.

In the above mentioned way one strand of DNA is

created. But DNA is a double stranded molecule, so

the complementary strand runs anti parallel to the

main strand and both strands are joined by thehydrogen bonds which are forces between

nitrogenous bases.

Each nitrogenous base has its specific partner to

which it binds. Thus adenine binds with thymine by


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double hydrogen bonds and guanine binds with

cytosine by triple hydrogen bonds.


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BONDING IN DEOXYRIBONUCLEIC ACIDS


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DNA stores genetic information in the form of order of

nucleotide base pairs. These base pairs at the time ofprotein synthesis encodes for the specific amino acids

which in the course of synthesis joins to form protein.

Thus each segment has a unique order of bases and

thus encodes for specific protein chains and enzymes.

STRUCTURE OF DNA

DNA exists in the form of double helix in which the

two strands run antiparallel to each other. This

structure of DNA was proposed by James Watson

and Francis Crick which won them Nobel Prize.


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DNA is found in many structures but there are five most

occurring structures which are arbitrarily assigned name A,B, C, D and Z-DNA. In these all DNA structures B-DNA is

most common and it was this structure which was studied

by Watson and Crick. Hence we will take B-DNA first into

account.

B-DNA: It is right handed form of DNA which always

predominates in living world. It is the standard point of

reference in study of DNA. In this DNA there are 10.5 base

pairs per turn which are tilted at an angle of 1 to helical

axis. Its diameter is 23.7 .

A-DNA: In very high humidity the crystallographic

structure of B-DNA changes to A-form. A form is more

compact than B form having 11 base pairs per turn of

helix. Its base pairs are not perpendicular to the axis

but tilted at an angle of 20

with respect to the helicalaxis. In addition the A- form has a central hole. Like B

-DNA, A-DNA is a right handed double helix. The

diameter of A-DNA helix is 25.5 .


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C-DNA: This form of DNA is also right handed which

has 9.33 base pairs per turn of the helix. The C-DNAhelix has the diameter of 19 . The tilt of base pairs is7.8. This type of DNA is formed at 66% relative

humidity in presence of Li+ ions.

D-DNA: It has 8 base pairs per turn of the helix. The

tilting of base pairs from the axis of the helix is 16.7.

D-DNA is also right handed double helical structure.

Z-DNA: It is a left handed helix and has a zigzag

(hence Z) appearance. It was discovered by R.

Nordheim and Wang in 1984. Z-DNA is known to

occur in nature, most often when there are repeated

purine and pyrimidine G-C sequences (especially CG

CG CG). Its function is not certain; it may play a role

in gene expression. Z-DNA contains 12 base pairs perturn of the helix which are inclined at 9 with the axis.

The diameter of the Z-DNA molecule is 18.4 .

A particularly exotic DNA structure, known as H-DNA,

is found in polypyrimidine or polypurine tracts that


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also incorporate a mirror repeat. A simple example is

a long stretch of alternating T and C residues.

The H-DNA structure features the triple-stranded form

illustrated in. Two of the three strands in the H-DNA

triple helix contain pyrimidines and the third contains

purines.

DNA Supercoiling

Triple Helix


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DNA can be twisted like a rope in a process called

DNA supercoiling. With DNA in its "relaxed" state, a

strand usually circles the axis of the double helix onceevery 10.4 base pairs, but if the DNA is twisted the

strands become more tightly or more loosely wound. If

the DNA is twisted in the direction of the helix, this is

positive supercoiling, and the bases are held more

tightly together. If they are twisted in the opposite

direction, this is negative supercoiling, and the basescome apart more easily. In nature, most DNA has

slight negative supercoiling that is introduced by

enzymes called topoisomerases. These enzymes are

also needed to relieve the twisting stresses introduced

into DNA strands during processes such as

transcription and DNA replication.

Biological Functions

DNA usually occurs as linear chromosomes in

eukaryotes, and circular chromosomes in prokaryotes.

The set of chromosomes in a cell makes up itsgenome; the human genome has approximately 3

billion base pairs of DNA arranged into 46

chromosomes. The information carried by DNA is held

in the sequence of pieces of DNA called genes.

Transmission of genetic information in genes is

achieved via complementary base pairing. For


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example, in transcription, when a cell uses the

information in a gene, the DNA sequence is copied

into a complementary RNA sequence through theattraction between the DNA and the correct RNA

nucleotides. Usually, this RNA copy is then used to

make a matching protein sequence in a process

called translation which depends on the same

interaction between RNA nucleotides. Alternatively, a

cell may simply copy its genetic information in aprocess called DNA replication. The details of these

functions are covered in other articles; here we focus

on the interactions between DNA and other molecules

that mediate the function of the genome.

Genomic DNA is located in the cell nucleus ofeukaryotes, as well as small amounts in mitochondria

and chloroplasts. In prokaryotes, the DNA is held

within an irregularly shaped body in the cytoplasm

called the nucleoid. The genetic information in a

genome is held within genes, and the complete set of

this information in an organism is called its genotype.

A gene is a unit of heredity and is a region of DNA

that influences a particular characteristic in an

organism. Genes contain an open reading frame that

can be transcribed, as well as regulatory sequences


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such as promoters and enhancers, which control the

transcription of the open reading frame.

In many species, only a small fraction of the totalsequence of the genome encodes protein. For

example, only about 1.5% of the human genome

consists of protein-coding exons, with over 50% of

human DNA consisting of non-coding repetitive

sequences. The reasons for the presence of so much

non-coding DNA in eukaryotic genomes and the

extraordinary differences in genome size, or C-value,

among species represent a long-standing puzzle

known as the "C-value enigma." However, DNA

sequences that do not code protein may still encode

functional non-coding RNA molecules, which areinvolved in the regulation of gene expression.

Ribose Nucleic Acid

Ribonucleic acid (RNA) is a nucleic acid that consists

of a long chain of nucleotide units. Each nucleotide

consists of a nitrogenous base, a ribose sugar, and a

phosphate.

RNA is transcribed from DNA by enzymes called RNA

polymerases and is generally further processed by


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other enzymes. RNA is central to the synthesis of

proteins.


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Structure of RNA

RNA is composed by polymerization of

ribonucleotides. There is a main difference between


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composition of RNA and DNA; in RNA there is base

uracil which replaces base thymine.

Thus in RNA adenine binds with uracil and guaninebinds with cytosine respectively with double and triple

hydrogen bonds.

Due to the presence of ribose instead of deoxy-ribose,

there is a change in conformation of RNA. It is rather

like A-form DNA instead of B-DNA having deep and

narrow major groove and shallow and flat minorgroove.

RNA is transcribed with only four bases (adenine,cytosine, guanine and uracil), but there are numerous

modified bases and sugars in mature RNAs.

Pseudouridine (), in which the linkage between

uracil and ribose is changed from a CN bond to a C

C bond, and ribothymidine (T), are found in various

places (most notably in the TC loop of tRNA).

Typical right handed stacking

pattern of single stranded

RNA. The bases are shown in

white.


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Another notable modified base is hypoxanthine, a

deaminated adenine base whose nucleoside is called

inosine.

Synthesis of RNA

Synthesis of RNA is usually catalyzed by an

enzymeRNA polymeraseusing DNA as a

template, a process known as transcription.The DNA

double helix is unwound by the helicase activity of the

enzyme. The enzyme then progresses along the

template strand in the 3 to 5 direction, synthesizing a

complementary RNA molecule with elongation

occurring in the 5 to 3 direction. The DNA sequencealso dictates where termination of RNA synthesis will

occur.

Types of Ribonucleic Acids

Messenger RNA


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It is the commonest form of RNA, formed as a result

of transcription from the DNA. IT carries information

from DNA to ribosome, the site of protein formation inthe cell. The coding sequence of RNA determines the

sequence of amino acids in the protein chain. It

serves as a template for the protein synthesis. It can

also form DNA inversely with the help of enzyme

reverse transcriptase which is found in certain viruses.

Once it is formed it migrates to ribosomes andattaches itself to it where the protein synthesis starts.

Messenger RNAs, particularly in eukaryotes, have

some unique chemical characteristics. The 5 terminal


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of mRNA is capped by a 7-methylguanosine

triphosphate. The protein-synthesizing machinery

begins translating the mRNA into proteins beginningdownstream of the 5 or capped terminal.

Transfer RNA

tRNA molecules vary in length from 74 to 95

nucleotides. They also are generated by nuclear

processing of a precursor molecule (Chapter 37). The

tRNA molecules serve as adapters for the translation

of the information in the sequence of nucleotides of

the mRNA into specific amino acids.


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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 structurei.e., the nucleotide

sequenceof all tRNA molecules allows extensive


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folding and intrastrand complementarity to generate a

secondary structure that appears like a cloverleaf. All

tRNA molecules contain four main arms. The acceptorarm terminates in the nucleotides CpCpAOH. These

three nucleotides are added post transcriptionally.

The tRNA-appropriate amino acid is attached to the

3-OH group of the A moiety of the acceptor arm. The

D, TC, and extra arms help define a specific tRNA.

Although tRNAs are quite stable in prokaryotes, theyare somewhat less stable in eukaryotes. The opposite

is true for mRNAs, which are quite unstable in

prokaryotes but generally stable in eukaryotic

organisms.

Ribosomal RNA

A ribosome is a cytoplasmic nucleoprotein structure

that acts as the machinery for the synthesis ofproteins from the mRNA templates. On the

ribosomes, the mRNA and tRNA molecules interact to

translate into a specific protein molecule information

transcribed from the gene. In active protein synthesis,

many ribosomes are associated with an mRNA

molecule in an assembly called the polysome. The


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distinct polypeptide chains. All of the ribosomal RNA

molecules except the 5S rRNA are processed from a

single 45S precursor RNA molecule in the nucleolus.5S rRNA is independently transcribed. The highly

methylated ribosomal RNA molecules are packaged

in the nucleolus with the specific ribosomal proteins.

In the cytoplasm, the ribosomes remain quite stable

and capable of many translation cycles. The functions

of the ribosomal RNA molecules in the ribosomalparticle are not fully understood, but they are

necessary for ribosomal assembly and seem to play

key roles in the binding of mRNA to ribosomes and its

translation. Recent studies suggest that an rRNA

component performs the peptidyl transferase activity

and thus is an enzyme (a ribozyme).


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Double-stranded RNA

Double-stranded RNA (dsRNA) is RNA with two

complementary strands, similar to the DNA found in allcells. dsRNA forms the genetic material of some

viruses (double-stranded RNA viruses). Double-

stranded RNA such as viral RNA or siRNA can trigger

RNA interference in eukaryotes, as well as interferon

response in vertebrates.

FUNCTIONS OF RNA

RNA Genomes

Like DNA, RNA can carry genetic information. RNA

viruses have genomes composed of RNA, plus avariety of proteins encoded by that genome. The viral

genome is replicated by some of those proteins, while

other proteins protect the genome as the virus particle

moves to a new host cell. Viroids are another group of

pathogens, but they consist only of RNA, do not

encode any protein and are replicated by a host plant

cell's polymerase.

Regulatory RNA

Several types of RNA can downregulate gene

expression by being complementary to a part of an


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mRNA or a gene's DNA. MicroRNAs are found in

eukaryotes and act through RNA interference (RNAi),

where an effecter complex of miRNA and enzymes canbreak down mRNA which the miRNA is

complementary to, block the mRNA from being

translated, or accelerate its degradation. While small

interfering RNAs (siRNA; 20-25 nt) are often produced

by breakdown of viral RNA, there are also endogenous

sources of siRNAs. siRNAs act through RNAinterference in a fashion similar to miRNAs. Some

miRNAs and siRNAs can cause genes they target to

be methylated, thereby decreasing or increasing

transcription of those genes. Animals have Piwi-

interacting RNAs (piRNA; 29-30 nt) which are active in

germ line cells and are thought to be a defense against

transposons and play a role in gametogenesis.

Antisense RNAs are widespread among bacteria; most

downregulate a gene, but a few are activators of

transcription. One way antisense RNA can act is by

binding to an mRNA, forming double-stranded RNAthat is enzymatically degraded.


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Comparison with DNA

RNA and DNA differ in three main ways.

First, unlike DNA which is double-stranded, RNA is a

single-stranded molecule in most of its biological roles

and has a much shorter chain of nucleotides.

Second, while DNA contains deoxyribose, RNA

contains ribose, (there is no hydroxyl group attached to

the pentose ring in the 2' position in DNA). These

hydroxyl groups make RNA less stable than DNA

because it is more prone to hydrolysis.

Third, the complementary base to adenine is not

thymine, as it is in DNA, but rather uracil, which is an

demethylated form of thymine.

Like DNA, most biologically active RNAs including

tRNA, rRNA, snRNAs and other, non-coding RNAs are

extensively base paired to form double helices.Structural analysis of these RNAs has revealed that

they are highly structured. Unlike DNA, this structure is

not long double helices but rather collections of short

helices packed together into structures akin to

proteins. In this fashion, RNAs can achieve chemical

catalysis, like enzymes. For instance, determination of


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the structure of the ribosomean enzyme that

catalyzes peptide bond formationrevealed that its

active site is composed entirely of RNA.


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No. DNA RNA

1 It is genetic material for all living organisms. RNA is genetic material in only some viruses and virusoids.

2 Deoxy ribose is the parent sugar. Ribose is parent sugar.

3 It can replicate itself. It cannot replicate except in RNA viruses.

4 It is generally double stranded. It is generally single stranded.

5 It doesnt possesses unusual bases. Some unusual bases like pseudouridine are found.

6 It gives positive Feulgen Test. It gives Pyronin Test specifically.

7 DNA is regularly helical. It is not regular generally.

8 it is the largest macromolecule It is medium-sized to small sized macromolecule

9 It shows positive Feulgen test (Schiffs reagent) Feulgen test id negative.

0 Pyronin test is negative. Pyronin test is Specific for RNA.

1 DNA is regularly coiled helically. A regular helical coiling is rare.

2 Sugar percent in DNA is deoxyribose (C5H10O4) Sugar percent in RNA is ribose (C5H10O5)

3 Nitrogen bases of DNA are Adenine, Guanine

(Purines) ,Cytosine , Thymine (Pyrimidines).

Nitrogen bases of RNA are Adenine, Guanine (Purines) ,Cytosine

,Uracil(Pyrimidines).

4 Purines &Pyrimidines bases are always in equal

number.

There is not fixed ratio between Purines &

Pyrimidines.

5 There is replication and equitable distribution of

DNA at each cell division.

Though there is increased transcription of RNA , an equitable

distribution does not occur at the time of cell division.

6 DNA controls heredity, variations and metabolism

of cell.

RNA controls metabolism of cells.


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