Assignment

Topic: Nucleic acids: DNA and RNA

Course Code: PHR213; Section: 02

Course Title: Biochemistry and Cell Biology

Submitted To:

Dr. Md. Hasanuzzaman Shohag

Assistant Professor,

Department of Pharmaceutical Sciences

North South University

Submitted By:

Name: Israt Jahan Surovy

ID: 1512006046
 Nucleic Acids: DNA and RNA

The molecules of nucleic acids labeled chromosomes, remain repose about the genetic

particulars of eukaryotes or prokaryotes, are cell’s molecules larger than any other that can

accommodate innumerable genes and substantial tracts through the intergenic regions of

DNA. [17]

Nucleic acids classified into deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) those

have the common component nucleotide which is the basic unit of nucleic acid and

storehouse of the genetical information according to the code of the molecules. Information

about each protein, complex biomolecules, are scheduled as codes in the nucleotides. The

rudimentary postulate of living things is to reserve and convey genetical attributes from

generation to generation. [15]

 Nucleotides are the structural constituents of Nucleic Acids

 The DNA of a cell particularizes the nucleotide chain in RNA and the patterns of

amino acids constructing protein in a cell, by using its nucleotide chain. A gene is a

fragment of a DNA molecule that supplies information or instruction via codes for

synthesizing any biological complex like amino acid chain - protein or nucleotide

chain present in RNA. A cell cytoplasm houses the nucleus that contains chromosome

that contains DNA that incline to be enormous storing innumerable genes carrying

diverse attributes. Storing genes and conveying the genetical information via

replication, transcription and translation are the cardinal role of DNA. [15]

 The process of conveying genetic material to offsprings and cellular functioning are

DNA’s purposes. 2 polydeoxynucleotide strands makes up a double helix. The

instruction and information is converted into codes from nitrogenous purine and

pyrimidine base sequences. DNA replication, is the synthesis process that requires
 complementary purine base and pyrimidine base coupling betwixt the parental and the

newly manufactured strand. [16]

 The synthesis of RNA initiates the process of decoding of genetical datas and governs

the cellular activities. RNA synthesis process denoted as transcription requires

ribonucleotide bases with DNA bases to be complementarily paired. Each molecules

of RNA which are newly manufactured are designated as transcript. [16]

 Nucleotides along with Nucleic acids have idiosyncratic Bases, Pentoses and

Phosphate groups

Nucleotides are made up of 3 basic constituents: (1) a nitrogen containing framework

( purine or pyrimidine bases), (2) a pentose, and (3) a phosphate.

Figure: General structure showing the numbering convention for Figure: A nucleotide skeleton
the pentose ring. This is a ribonucleotide. In deoxyribonucleotides
the -OH group on the 2 carbon (in red) is replaced with -H.
 In deoxyribo nucleic acid (DNA) and ribonucleic acid (RNA) there are 2 variations of

Pentose sugar.

a). Deoxyribose in DNA and b). Ribose in RNA

Figure: Pentose sugars in DNA and RNA

  Pyrimidine and purine are two skeletons of nitrogenous bases. Adenine, Guanine,

Cytosine, thymine and Uracil are their derivatives. Any nucleotide has the bases and

pentoses which are heterocyclic compounds. The parent compound carrying carbon

and nitrogen are numbered traditionally for facilitating entitlement and identifying

compounds derived from them. [15]

Figure: Purine and Pyrimidine base and their derivatives

Deoxyribonucleotides and ribonucleotides are nucleic acid derivatives. A, G, T, C, dA, dG,

dT, and dC are representations of deoxyribonucleotide units; A, G, U, and C are

representations of ribonucleotide units. The abbreviations for deoxyribonucleotides and

ribonucleotides when they are independent are respectively dAMP, dGMP, dTMP, dCMP;

and AMP, GMP, UMP, and CMP. The phosphate group remains at the 5’position in all the

abbreviated forms. [15]

Figure: Nucleotide
structures –
Deoxyribonucleotides and
Ribonucleotides

The molecules without the phosphate group are called nucleosides. [15.16]

Purine Base
Nucleosides

Adenosine Deoxyadenosine Guanosine Deoxyguanosine

Pyrimidine Base
Nucleosides

Cytidine Deoxycytidine Uridine

Deoxythymidine

 At the 5’-monophosphate end of nucleosides extra phosphate group or groups can be

attached to compose diphosphtes and triphosphates. The vital source of power and

energy to carry out functions of cell is ATP (Adenosine Tri Phosphate) [15, 16]
 Primary and Secondary Structure of DNA

Nucleotides make a segment to form biopolymeric nucleic acids by joining with

phosphodiester bond. The base segments in the sequence of nucleic acid forms the basic

DNA and RNA structure. The base sequences are read in according to the direction from 5′

end → 3′ end. The 3′-OH group that belongs to the pentose sugar of the previous nucleotide,

and the 5′-carbon that belongs to the pentose sugar of the following nucleotide create an ester

bond with the group that contains phosphate of the preceding nucleotide. We can read the

sequence from the free 5’-end using the letters of the bases upto the last 3’-OH group of the

last pentose sugar in the sequence. Example: 5’—A—C—G—T—3’ [6, 13, 15]

The complementary base pairs of nucleotides yield secondary nucleic acid structure. This

structure is designated as ‘Watson‐Crick pairing’ in double stranded DNA or RNA. [6, 13,
15] The intramolecular pair of bases in the middle of complementary pair of bases ascertain

the secondary configuration of the single stranded DNA or RNA molecule. [15] 

 DNA Is a Double Helix (Secondary DNA Structure)

 A three dimensional configuration of DNA molecule was hypothesized in 1953 by

two scientists Watson and Crick that served a rational explanation of all the available

data.

 The DNA molecules are comprised of two spiral shaped DNA biopolymer sequences

winding around each other on a vertical axis which in consequence forms right-

handed double helix.

o Between the 2 twisting strand the base pairs arrays themselves like

stairs

o The twisting strands that are wound togeter runs from 5’→3’ and

3’→5’ direction which is opposite to each other.

 Substituting deoxyribose and phosphate groups have a hydrophilic skeleton at the

exterior of the double helix surrounding by water and fronting towards. Every

deoxyribose that contains furanose ring structure remains in the C-2ʹ endo (closest)

isomeric conformation. [15]

 Both the strands of a double helix have their purine and pyrimidine bases arranged in

a neat stack resulting in ring structure which is hydrophobic in nature and almost

planer and endure perpendicularly with the vertical axis persisting as close as

possible. The counteracting nature of the pair in the helix generates major groove and

minor groove on the plane. [6, 13, 15]

 The individual nucleotide bases of each strand is paired with the complementary

individual nucleotide bases of the other strand (A-T & G-C) and must persist in the
 same plane that is coplaner which appear to be a stair like structure in between the

twisted helix. [6,13,15,16]

 Watson and Crick discovered that the nucleotide pairs, G and C; A and T are fused

via hydrogen bonds. They were unanimous in accordance with Chargaff’s postulation

about G= C and A=T in any DNA. Three hydrogen bonds and two hydrogen bonds

represented as G≡C and A=T respectively between G and C, A and T are formed.

This in consequence makes it difficult for the bond to be broken in DNA base pairs

and seperate them. Higher the ratio of G≡C to A=T more troublesome to break the

bond. Other pairing of bases inclined to weaken the double helix thus they don’t exist.

[6,13,15]

 While constructing the DNA model Watson and Crick they couldn’t decide if the

DNA should be parallel or antiparallel; both the strands in the helix should run from

5ʹ→3ʹ directions or 3ʹ→5ʹdirection. With the help of X-ray difraction studies of

Wilkins and Rosalind Franklin on DNA fibres they came to a resolution that DNA

double helix is antiparallel in direction. [6,13]

 Watson and Crick developed the model that appeared as a formation where nucleotide

bases that are vertically arranged in the double helix are 3.4 Å away from each other;
 They also observed 10 nucleotide base pair in one whole twist (apex to apex or crown

to crown) of the double helix model that measures the distance of 34 Å. 10.5

nucleotide base pairs in per spin of the helix can be seen if the media is liquid. [15]

 The polynucleotide chains that construct the double-helix have neither similarity in

physical appearance nor in chemical composition. Rather complementary to each

other. Always Adenine appears to complement Thymine and Guanine complements

Cytosine. [6, 13, 15]

 DNA Molecules Have Distinctive Base Compositions

3 H bonds in G-C and 2 H bonds in A-T comprise the double helix. According to Chargaff’s

postulation the quantity of adenosine precipitate is equivalent to the quantity of thymidine

precipitate (A=T). Similarly, quantity of guanosine precipitate equivalent to cytidine

precipitate (G=C). As a result the sum total precipitate of purine and pyrimidine are equal that

is A+G=T+C. [6, 13, 15]

 Phosphodiester Bonds connect the neighboring Nucleotides in Nucleic Acids

In DNA and RNA the 5ʹ phosphate group of the previous nucleotide is fused with the 3ʹ

hydroxyl group of the successing nucleotide which has a covalent bond of phosphate-group

bridges, that eventually yeild in a phosphodiester linkage. Consequently, the structural

framework of nucleic acid is covalently bonded comprising of permutable phosphate group

along with pentose precipitates. The left over nitrogenous bases are attached to the structural

framework as side chain functional group maintaining a uniform gap. The sugar-phosphate

backbone that makes up DNA and RNA has hydrophilic nature. OH¯ group that yields from

the sugar precipitate are bonded with water by hydrogen bonding. The pKa of phosphate

groups are almost 0, are dissociated into ions and have negative charges with a pH level of 7.

The phosphate anions (occurred due to dissociation) are counterbalanced by interacting with

positively charged protein ions, polyamines and metal ions (cations). The direction of the

phosphodiester bonds throughout the chain remains same providing individual nucleic acid

strand which appears to be linear definite 5’ end and 3’ end and polar nature. [6, 13, 15]

Figure: Watson and Crick’s patterns of hydrogen-bonding in the nucleotide base

pairs. The blue lines represent hydrogen bonds..

 Replication of DNA

 Beginning of replication at the locus of chromosome, Prolongation of polynucleotide

chains, and Cessation of replication are the 3 steps of DNA replication. A definite

chromosomal locus is the starting point of DNA replication, and continues in series to

the end point. [4, 7, 9, 10, 11].

 The two daughter strands at the same time are replicated in a semiconservative

manner on two sides of the fork shaped parent strand after it got unwinded.
 As both the strands of DNA double helix complement one another and are

antiparallel, one daughter strand grows toward 5’ to 3’ direction while the other

grows toward 3’ to 5’ direction and they have opposite polarity. This opposite polarity

for polymerization is essential for the uninterrupted synthesis of daughter strands. [13]

 Each daughter strand has now become templates for synthesizing their own

complementary base pairs leading to a totally new DNA double strand construction

which can be catalyzed by an enzyme primase. [15]

 Replication construct two indistinguishable DNA double helix carries one parent

strand and another freshly synthesized from parent turning into daughter template.

[25, 27]

 DNA polymerase enzymes so far have been distinguished to give permission to add

nucleotide monomers outside of living organism only in 5’ to 3’ direction. [12]

 As there are contradictory theories regarding the different polarities of DNA

replication in vivo and in vitro the idea of discontinuous DNA replication [1, 2, 18]

was set on. The ‘Okazaki fragment’ theory of temporary intermediate replication

fragments was applied for E.coli and bacteriophage T4 DNA replication process. [1,

2, 18] The proposal was, replication will continue by attaching temporary fragments
 of DNA which are uniquely synthesized by polymerization of nucleotides from 5'

towards 3'. The other daughter strand become longer advancing from 3' towards 5'

conceivably reversely synthesized. [8, 19, 20, 21] We can conclude that the process of

DNA replication is semiconservative in nature. Every strand located in the double

helix functions as template for a complementary and novel strand to be produced.

 Activity of Enzymes and proteins in DNA replication

 The unzipping of parent DNA double strands ascertains the projection of advancing

the replication fork. The Helicase enzyme unzips the parent double strand and

replication fork is formed. [4, 24, 25,27]. The antiparallel structure of DNA let one

new daughter strand being synthesized uninterruptedly in the advancing projection of

the fork denoted as leading strand. The other new daughter strand designated as

lagging strand, advances in the projection opposite from the fork. On this strand, short

intermediate segments of DNA, called Okazaki fragments, are synthesized from RNA

primers. The RNA primers are withdrawn while replication and the discrete fragments

are attached together to form the lagging strand. [22]

 Proteins named single-strand binding (ssb) proteins overlay the unwinded strands

of DNA where the replication fork begins separation. It refrains the splitted strand

from merging again with the double strand. [26]

 New DNA starnd is constructed by enzymes called DNA polymerases, which need a

template called a primer (or starter), an already existing chain or short segment of

 nucleotides and synthesize DNA in the 5' to 3' direction. Enzyme DNA primase

makes the primers for proofreading, or checking if any "wrong" nucleotides are

getting accidentally attached to the new chain. Through the replication process one

new strand namely the leading strand is produced uninterruptedly by means of DNA

polymerase enzyme. The other new strand namely the lagging strand is built in small

fragments. [23]

 In prokaryotic cells two major DNA polymerases: DNA pol III (the major DNA-

maker), and DNA pol I, engaged in DNA replication which portrays a crucial role by

providing support. [27]

 The maintenance and cleanup crew: A protein called the sliding clamp clutches the

DNA polymerase III molecules in its position as they functions in synthesizing DNA.

Sliding clamp protein appears to be ring-shaped functions by keeping away the DNA

polymerase enzyme that belongs to the lagging strand from gliding off when it new

Okazaki fragment starts synthesizing. [26]

 Exonuclease enzyme removes all the RNA primers used before not only from

lagging strand but also from leading strand

 Topoisomerase portrays essential maintenance role as well during DNA replication.

This enzyme blocks the DNA double helix from being winded compactly to move

forward the replication fork as it got unzipped by helicase. It functions by making

intermediate nicks in the double helix to free the tension, afterwards sealing off the

nicks to keep DNA away from malfunctioning. [24.25,26,27]

 Finally, for gap and RNA free DNA, RNA primers are withdrawn and substituted by

DNA by the means of DNA polymerase I, another polymerase enzyme engaged in

 replication. Still some nicks remain as the primers got replaced. DNA ligase enzyme

seals them off. [24, 25, 26]

 Differences between DNA and RNA

 The pentose sugar of RNA is ribose where deoxyribose in DNA. The existance of

the 2’-OH group of ribose makes RNA more reactive than DNA.

 The nitrogenous base uracil is used in RNA which is different from those

thymine used in DNA.

 RNA is found as a single strand where DNA is double stranded.

 RNA has unique and complex structure with diversity where DNA is double helix

‘stair like’ structure

 RNA are more available in nature than DNA

 RNA molecules are smaller than that of DNA. [28]

 Primary structure of RNA

RNA is synthesized by the transcription process of DNA sequences and it portrays crucial

role in protein synthesis.

In RNA, nucleotide bases A, C, G, and U are connected by 3’-5’ester bonds within ribose and

phosphate [15]

 Secondary Structure of RNA

There are various types of secondary structure that occur in RNA molecules. Hairpin loops

form when there are at least four bases that form base pairs. Internal loops form when both

sides of a double-stranded segment cannot form base pairs. Stable stem loops are formed

between the length of four and eight bases. [28]

 Ribosomal RNAs (rRNAs)

They are components of ribosome, a cellular organelle. They have a complex

structure that implement proteins synthesis.[15] Ribosomal RNA (rRNA) is the most

available configuration of RNA in living organisms. Since rRNA is present in all

living organisms, its sequences have been used to characterize the evolutionary

relationships between organisms. rRNA possess a remarkably complex structure.

Even though there are differences in types in the primary nucleotide sequences of

rRNA, all inclusively the three-dimensional structure of rRNA is preserved.

Prokaryotic ribosomes represented ad 70S are composed of a 50S subunit and a 30S

subunit. On the other hand, ribosomes of eukaryotes represented as 80S consist of 60S
 subunit and a 40S subunit. Several types of rRNA and protein are housed in each type

of ribosomal subunit. [30]

Figure: 3-D structure of rRNA

 MessengerRNAs (mRNAs)

They carries genetic information from one or a few genes to a ribosome and are intermediate

structure. Protein corresponding with mRNA can be formed in the process of protein

synthesis. [15] mRNA molecule holds three-base sequences, together denoted as codons, that

determines corresponding amino acids in the subsequently synthesized protein. Open

reading frame (ORF) is a base segment inside mRNA which is used in coding polypeptide.

By beginning through an initiation codon and ending through a termination or stop codon an

ORF functions. mRNAs can vary widely in length. For example, the number of bases in

mRNA from E. coli varies from 500 to 6000. ORFs are flanked by untranslated sequences

that are referred to as the 59UTR (upstream of the ORF) and the 39UTR. [30]

 Transfer RNAs (tRNAs)

They are adapter molecules of RNA that loyally translate the informations in mRNA into

a specific sequence of amino acids. [15] Transfer RNA (tRNA) molecules transport

amino acids to ribosomes for assembly into proteins. The length of tRNA molecules

varies from 75 to more than 90 nucleotides. Each tRNA molecule becomes bound to a

specific amino acid. Consequently, cells possess at least one type of tRNA for each of the

20 standard amino acids.

Figure: 3-D structure
of tRNA
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