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Repeating Units Of Nucleotides Biology Essay

Differentiate between structures and functions of DNA and various RNAs. How does the structure of each particular nucleic acid make it ideally suited for its functions.

Nucleic acids are made up of repeating units of nucleotides. Each nucleotide is made up of a nitrogenous base attached to a pentose sugar at 1´end a phosphate group at5´end. The nucleotides can be deoxyribonucleotides or ribonucleotides depending on the type of pentose sugar they contain. Deoxyribonucleotides contain deoxyribose sugar with –O- attached to 3´carbon of sugar while ribonucleotides contain ribose sugar with –OH group attached at 3´ end of ribose sugar.

Base composition is also quite different in deoxyribonucleotides and ribonucleotides. Deoxyribonucleotides will have bases adenine (A), guanine (G), cytosine (C), and thymine (T), where as ribonucleotides will have adenine, guanine, cytosine and uracil (U).

Deoxyribonucleotides and ribonucleotides forms phosphodiester linkages between the phosphate and hydroxyl groups at 3´ and 5´ carbons of the sugar resulting in the synthesis of deoxyribonucleic acid (DNA) and ribonucleic acid respectively. DNA and RNA with some differences in their chemical structures, they differ greatly in their final three dimensional structures and functions.

Thus, the structures and functions of DNA and RNA ( rRNA, mRNA and tRNA ) are discussed in the following topics in regard to their differences.

Deoxyribonucleic Acid

The formal study regarding DNA was started by Friedricgh Miescher in 1868. (Nelson and Cox, 2000).

He isolated a phosphorus containing substance from the nuclei of pus cells to which he called it as

“nuclein”. In that nuclein he found some acidic substance which can be said as DNA and a basic part as

protein. But DNA as the bearer of genetic information was proved by Avery, MacLeod and McCarty in

1944. (Nelson and Cox, 2000). James Watson and Francis Crick were remembered for their discovery

of structure of DNAin 1953. They worked out the three dimensional structure of DNA from X-ray

diffraction photograph taken by Franklin and Wilkins. (Hames and Hooper, 2005).

Structure of DNA

Deoxyribonucleic acid (DNA) consists of four bases namely Adenine(A), Guanine(G), Thymine(T)

and Cytosine(C). These bases combine with the deoxyribose sugar to form deoxynucleosides like

deoxyadenosine, deoxyguanosine, deoxythymidine (thymidine) and deoxycytidine. These

deoxyribonucleosides when attached to the phosphate(s) on the hydroxyl at C-5 of the deoxyribose sugar

form deoxyribonucleotides.

(Source; Nelson and Cox, 2000)

Nucleotides are covalently bonded to form a long polymer chain in DNA. The phosphate group on the

5´ portion of the sugar is attached to the hydroxyl on the 3´ portion of the sugar of the next nucleotide

through a covalent bond. This covalent bond formed between the phosphate and hydroxyl of two

nucleotide is called 3´5´ phosphodiester bond. So excepting for the first and the last nucleotide, all

nucleotides in a chain are involved in the phosphodiester bond formation. All the phosphate groups in a

nucleic acid are charged. The terminal phosphate group has a net charge of 2- while the rest will have 1­-

net charge each.

The linear sequence of deoxyribonucleotides in a chain accounts for the primary structure of DNA.

By convention nucleotide sequence are always written from the 5´ end to the 3´end of the

polynucleotide. Each nucleotide can be thought of a single letter represented by their respective bases of

A, G, C and T. Also the deoxyribonucleotides in a DNA molecule differ only in their bases so it can be

called as base sequence. For example, AGCGAACTG

The secondary structure of DNA can be thought of two complementary single strands of DNA

molecules coming together to form a double stranded helical structure. In a double helix, two

(Source; Nelson and Cox, 2000).

complementary single strands of DNA twists together around a common axis to form a right handed

helical structure. The two chains run antiparallel to each other –one from 5´-3´while the other from 3´-

5´. The formation of double stranded helix is possible only because of the H-bonding between the

complementary base pairs.

In a DNA double helix two H-bonds are formed between adenine (A) and thymine (T) while three

H-bonds are formed between guanine(G) and cytosine(C).

The double stranded helix has its sugar phosphate bonds charged and thus they are exposed so that they

can interact with the aqueous environment. On the other hand bases are nearly perpendicular to the axis,

and staked on top of each other. Staking of bases helps the stability of DNA molecule by excluding the

water molecules from the spaces between the base pairs.(Griffiths, 2008). Double helical structure is

formed as a result of base stacking. It forms two distinct grooves running in spiral; the major groove

and the minor groove. One helical turn of double stranded right handed DNA has 10 base pairs each

being twisted by 36o. The diameter of the helix is 20Å and the distance per turn is 34Å.

(S. Patel, Lecture Notes; 10th March, 2010.)

Functions of DNA

DNA is essential in protein synthesis and particularly mRNA synthesis.

Transcription cannot happen in absence of DNA. During transcription, RNA polymerase binds to

the DNA molecule and thus unwinds the double stranded helical structure. Now one of the

strands serves as template for the RNA synthesis which then initiates translation.

During the process of transcription DNA directs RNA polymerase where on gene to begin

transcribing and where to finish. (Alberts, et al, 2008).

Also during transcription the genetic information present in DNA are copied to mRNA. The

information is still coded in same nucleotide sequence as in DNA.(Becker et al, 2008). Thus,

DNA is indirectly responsible for protein synthesis.

DNA contain genetic information as nucleotide sequence. Inheritance of parental genotype and

phenotypes are possible only with the presence of DNA. Replication of DNA separates the two

strands and copies information in each strand to another new strand during cell division. This is

called semiconservative replication because each daughter helix has one parental strand.

Besides the inheritance of parental genes in the offspring, they don’t look alike to their parents

phenotypically or genotypically. This could because of the genetic crossing over between

paternal and maternal chromosomes which would lead to genetic diversity.

Though there is always conservation of parental characters on one hand but on the other hand

mutations occur that it leads to genetic diversity. But too much mutations would lead to different

genetic diseases so DNA must able to resist some of the harmful mutations but let helpful

mutations to occur.

Structure of DNA makes it suitable for its functions.

The double helical structure of DNA with its sugar phosphate backbones (hydrophilic)

exposed and the bases (hydrophobic) enclosed by the backbones make it suitable to keep

on functioning even in the presence of aqueous environment.

DNA stores information and it needs to pass it on to the other generations. For this

process the double stranded and the complementary base pairing has its role to play.

During DNA replication each strand of DNA acts as a template for the synthesis of other

strand and complementary base pairing aids genetic information to copy accurately.

Structure of Ribonucleic acid (RNA)

The structure of ribonucleic acid (RNA) can be discussed under the following points.

RNA is usually single-stranded nucleotide chain, not a double stranded helix like DNA. The

advantage of being single stranded over double stranded is it becomes more flexible and can

form much greater diversity of complex three dimensional structures.

RNA can bend in such a way that some of its own bases pair with each other forming looped

structures. These intra-molecular H-bonding is important for determining RNA shape.

RNA has ribose sugar in its nucleotide while DNA has deoxyribose. The presence of –OH group

at 2’carbon atom helps the action of RNA in many important cellular activities.

RNA strand is formed of a sugar phosphate backbone like that in individual DNA strand, with a

base covalently linked at 1’ position to each other. The sugar phosphate linkages are made at 5’

and 3’position of the sugar as in DNA. Thus, like DNA, RNA chains also have 5’ end and 3’

end.

RNA nucleotides (ribonuceotides) contain bases adenine, guanine, cytosine and uracil(U).

thymine of DNA is replaced by uracil in RNA. It forms two H-bonds with adenine like thymine

of DNA.

During protein folding uracil forms base pair with guanine which are weaker than that formed

between adenine and uracil. The ability of uracil to form bonds both with adenine and uracil is

one of the reasons why RNA can form extensive and complicated structures, many of which are

important in biological activities. (Griffiths, et al 2008).

Griffiths in 2008 states that,unlike DNA, RNA acts like a protein , catalyzing biological

reactions. The name ribozyme was coined for the RNA molecules that function like enzymes.

(Source; Hames and Hooper, 2005).

RNA exists in different forms like rRNA, mRNA and tRNA.

Ribosomal RNA (rRNA)

Ribosomal RNA (RNA) is the major component of robosomes while DNA occurs in the

chromosomes of nucleus. Prokaryotes have 70S robosomes (S=sedimentation coefficient) with two

smaller sub units;50S and 30S. The 50S subunit has two rRNAs, 5S and 23S with 120 and 2094

nucleotides respectively where as 30S subunit contain 16S rRNA with

1541 nucleotides.

Eukaryotes on the other hand have larger complex ribosomes. The 80S ribosome monomer

consists of 60S and 40S sub units. The larger 60S sub unit consists of three rRNAs – 5S, 5.8S and 28S

of 120, 150 and 5050nucleotides respectively. The smaller 40S subunit has 18S rRNA with 2100

nucleotides. (Bhagavan, 2002).

Functions of rRNA

The various rRNA tightly folded and base pair extremely with each other to form the core of

ribosomal sub units with protein restricted to the surface and filling gaps between RNA folds.

The rRNA also form the three main binding sites (A, P and E sites) for binding tRNA involved

in protein synthesis.(Bhagavan,2002).

The 23S rRNA from the catalytic site for peptide bond formation in protein synthesis.

(Bhagavan,2002)

Assembly of amino acid chain by mRNA and tRNA is guided by the rRNA.

Messenger RNA(mRNA)

All messenger RNAs (mRNA) contain the same four nucleotides A, C, G and U and utilize the

codon AUG as the start codon and codon UAG, UGG and UAA as stop codons. Some prokaryotic

and eukaryotic mRNAs looks structurally similar but differ in other aspects. Prokaryotic mRNAs are

polycistronic and usually carries information for the synthesis of several polypeptides from a single

mRNA. But eukaryotic genes invariably contains information for only a single polypeptide from the

ribosome. The eukaryotic mRNA has exons and introns where as prokaryotes have only exons.

Exons are the coding sequences while the introns the non-coding sequences of genes. At the 5’end,

mRNA is capped with a methyl guanosine nucleotide and at the 3’ end a poly A tail (-AAAnAOH) is

added.

(Source – Bhagavan, 2002)

Functions of mRNA

The mRNA binds to ribosome in the translation process of protein synthesis. mRNA carries the

information transcribed from DNA in the form of three base code words each of which specifies a

particular amino acid.

Transfer RNA (tRNA)

Transfer RNA was first discovered by Hoagland(1884-18850. (Becker, et al, 2006). The tRNA molecule range

in size from73-93 nucleotides (Bhagavan,2002).

All tRNAs form double stranded regions representing secondary structures which resembles the

clover leaf where open loops are connected by double stranded stems. The stem loops of clover leaf

like structure are known as arms. There are four arms observed in the tRNA structure;

Anticodon arm which contains nucleotides at its anticodon region. Anticodon forms base pairing

with mRNA during translation.

DHU arm contains dihydrouracil, an unusual pyrimidine in its D loop.

T- arm with T- loop contains unusual base, pseudouracil in the sequence.

Some tRNAs may contain variable (optional)areas with 3-21nucleotides.

(Hames and Hooper, 2005).

The amino acid acceptor stem contains a site called amino acid acceptor site at the 3’ end of

the nucleotide sequence. Once amino acids attached to tRNA they are called heminoacyltRNA.

By convention the name of the amino acid attached to the tRNA is written as superscript.

Example Alanine attached to tRNA can be written as tRNA­­­Ala.. tRNA also form tertiary

structures. Here the amino acid attachment site is at one end and the anticodon is at the other end.

Transfer RNA carries amino acids to the messenger RNA and codes for the polypeptides.

(Source; Becker, et al 2006.)

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