Long Linear Chain Polymers Biology Essay

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DNA and RNA are long linear chain polymers, called nucleic acids, composed of monomers called nucleotides. It is found in all the organisms which act as genetic information carrying molecules that can be passed from one generation to the next. These macromolecules consisted of a large number of linked nucleotides, each nucleic acid composed of furanose (pentose) sugar, a phosphate, and a base (purines or pyrimidines). The sugars are linked to each other by glycosidic bond, forming a common backbone for structural role. The bases sequence in both molecules carries genetic information.

DNA is a double helix molecule. During the replication, one of strand acts as template forming complementary linear strand of RNA and transferred information to the mRNA (transcription). From here the information was carried for the synthesis of protein through the exact sequences of amino acids (translation). Therefore, we can confirm that DNA is information carrying molecules and RNA as a catalyst/intermediate for the protein synthesis. Thus, the flow of genetic information, gene expression in normal cell is

DNA and RNA are the nucleic acid present in the nucleus and cytoplasm of an organism but DNA is also found in the chloroplast of plant, which acts as genetic information carrying molecules in the exact sequence of their nucleotides. These molecules are linear polymers composed of monomers called nucleotides. Both the molecules have three main components in the structures- pentose sugar, nitrogenous bases, and the phosphate group attached at 5 carbon, as mentioned above. The chemical structure of single stranded DNA and RNA shows hydroxyl group at 3´ end and a phosphate group at 5´ end of carbon. The adjacent nucleotides are linked to each other by phosphodiester bond, one on the 5´ side of the phosphate and another on the 3´ side of the hydroxyl group. (Lodish et al, 2008) The structure of DNA is similar to RNA, but not identical to each other. In 1953, James D. Watson and Francis H. C. Crick proposed that DNA has a double helix molecule, based on analysis of x-ray diffraction patterns. DNA consists of two associated polynucleotide strands that wind together to form a double helix. The two sugar phosphate backbones are on the outside of the double helix, and bases project into the interior. The adjoining bases in each strand stack on top one another in parallel planes but the orientation of two strands are in anti-parallel, that is, their 5´ to 3´ directions are opposite. (Nelson & Cox, 2000) But RNA exists in single stranded. Their nucleotides are in the linear forms which has codon at 5 . The furanose sugar present in DNA is deoxyribose, whereas RNA has ribose sugar. The deoxyribose sugar contained hydrogen at 2 carbon of DNA which makes different from ribose sugar which contained OH-group at 2  in RNA. The common bases present in the DNA and RNA are adenine (A) and guanine (G) - purines, which contain a pair of fused rings, and the bases cytosine(C) - pyrimidines, having a single ring. But DNA contained thymine instead of uracil in RNA. In the complementary strand, adenine always pairs thymine/uracil with two hydrogen bonds and guanine pair's cytosine with three hydrogen bonds. The bases are on the 1  carbon of pentose sugar. (Berg et al, 2006)

Figure2: Chemical structure of DNA. Figure 3: Chemical structure of RNA.

(Interactive Concepts in Biochemistry, 2002) (Interactive Concepts in Biochemistry, 2002)

In normal form of DNA, the spaces between the intertwined strands form two helical grooves of different widths, major grooves (larger) and minor grooves (smaller). The DNA duplex is held together by two forces; hydrogen bond between complementary base pairs and base stacking interactions or hydrophobic interactions. Since RNA is a single stranded molecule it does have grooves in its structure. (Berg et al, 2006). The normal DNA in the cells is a right handed helix. The x-ray diffraction pattern of DNA reveals that the stacked of bases are regularly spaced 3.4Å apart along the helix axis. The helix makes a complete turn every 34Å and 10 base pairs per turn. There is a rotation of 36 degree per base (360 degrees per full turn/ 10 bases per turn. DNA can occur in different three dimensional forms since it is a flexible molecule. The secondary and tertiary structure of DNA is A-, B-, C-and H-forms, classified according to their characteristic structures or helixes. All plays the same functions in the regulation of expression of genes or genetic information.(Nelson & Cox, 2000) RNA also forms 3-dimensional structures, by the complementary base pairing within a linear sequence; G pairs with C and A pairs with U forming the secondary structures like hairpin loop, stem loop, and tertiary structure like pseudoknot and so on. Weak interactions, especially base-stacking interactions play a major role in stabilizing RNA structures. A-form right handed double helix (complementary sequence) and Z- form like DNA have been existed but B-form of RNA has not been observed. RNA is found in three forms (mRNA, tRNA, and rRNA) and their differences in structures and functions are given below. (Lodish et al, 2008)

Figure4: DNA double helix. Figure 5: Secondary Structure of RNA

(Interactive Concepts in Biochemistry, 2002) (Secondary Structure of RNA, n.d)

Function of DNA and RNA based on its structure

General function of DNA and RNA

DNA is a genetic material that controls all the cell activities. From the concept of Central Dogma of Molecular Biology, DNA stores the genetic information for protein synthesis. In the process of transcription, one of the DNA double strands acts as a template for the synthesis of complementary strand of RNA by replacing all thymine by uracil. Transcription of DNA is carried out by RNA polymerase, which adds one ribonucleotide at a time the 3´ of growing RNA chain. The sequence of the template DNA strand determines the order in which ribonucleotides are polymerized to form an RNA chain. (Hartl& Jones, 2005) The main function of RNA is to synthesize the proteins by exact sequencing of amino acids. The information stored in DNA is copied into ribonucleic acid during transcription, and then to the protein by translation. Translation is the process by which the linear nucleotides sequence of an mRNA is used as a template to join the amino acids in a polypeptide chain in the correct order. Three types of RNA take parts to perform different but cooperative functions in the protein synthesis. (Alberts et al, 2008)

Hydrogen at 2´carbon in deoxyribose and OH-group at 2  in ribose

DNA evolved as carrier of genetic information or its function in long term storage of genetic information because the hydrogen at 2´position in the deoxyribose of DNA makes it far more stable molecule than RNA. Hydrogen cannot attack and hydrolysis the phosphodiester bond, preventing the formation of the cyclic phosphate ester. Therefore, stability of DNA structure will be maintained in order to store information for longer time. Whereas, RNA have an OH-group attached at the 2´carbon of ribose. These 2´-hydroxyl groups in RNA act as nucleophile, attacking the phosphodiester bond. It results in less chance of storing the information. (Lodish et al, 2008) But this hydroxyl group on C2 of ribose makes RNA more chemically labile by attacking and hydrolysis the phosphodiester bond at neutral pH. This stability cleaves RNA into mononucleotides by alkaline solution. The C2 hydroxyl group of RNA provides a chemically reactive group that takes part in RNA- mediated catalysis. As a result, RNA like ribosomal RNA plays a catalytic role in the formation of peptide bond, by exact sequencing the amino acids during protein synthesis. Hence, flow of information is accurate. (Lodish et al, 2008)

Thymine in DNA and uracil in RNA

Thymine is more important in DNA because it contains methyl group (-CH3) which remains neutral. By having thymine in DNA in place of uracil (in RNA), cells ensures to repair damaged DNA, caused by the deamination of cytosine to uracil without causing other changes in the DNA molecule. It will also improve the long term stability of DNA structures, since thymine is inactive base. Therefore, genetic information gets store for longer time. If uracil is present in the DNA, it prevents the repairing of damaged DNA and error will occur during transcription. (Becker et al, 2006) Presence of uracil in RNA also plays important roles (absent in DNA). RNA easily gets folded forming secondary structure. During folding, uracil gets pair with adenine in which they will stabilize the secondary structure of RNA. Presence of uracil helps in enhancing the smooth flow of genetic information in the exact sequence of amino acids during protein synthesis. Uracil is also a reactive base since it does not have a methyl group that prevents the renaturation of helix. In that way organism receives immediate genetic information. (Lodish et al, 2008)

DNA function base on grooves

We know that secondary and tertiary structure of DNA contain two different grooves; major (larger) and minor (smaller) grooves. These grooves provide space for other strands of nucleic acid and also for binding of regulatory proteins. (Bhagavan, 2002) Whereas RNA does have grooves since it is single stranded molecule.

DNA is a double helix and RNA a single stranded molecule

The double helix facilitates the accurate transmission of hereditary information. The double helix structure and presence of specific base pairs replicates the genetic information accurately. The base sequence of one strand determines the sequence of other strand such that guanine of one strand always pairs with cytosine of other strand and so on. Therefore, if double helix separated into two component chains it results two single strand templates. For this, new double helices could be constructed, each of having the same bases sequence as the parent double helix. In a way, as DNA is replicated one of the chains of each daughter DNA molecule is synthesized, and other passed unchanged from the parent DNA molecule. Hence, a character is maintained between the two which means accurate transmission of information is occurred through double helix of DNA. (Berg et al, 2006) RNA is a single strand linear chain molecule. This single strand backbone is flexible. Therefore, the polymer chain can bend back on itself to allow one part of the molecule to form weak bond with another part of the same molecule, resulting folding of RNA chain which then into a specific shape based on its exact sequence. Then the shape of RNA recognizes other molecules by selective binding and even catalyzes chemical changes in the molecules that are bound. Exact sequencing of nucleotides, that is, sequence of amino acid in the polypeptide chain results in accurate transfer of genetic information during protein synthesis. (Alberts et al, 2008)

Double helix of DNA hides the bases inside because of hydrophobic in nature, which means it does not allow water molecules to get enter into the structure. Presence of deoxyribose sugar and base stacking will prevent the DNA structure from chemical attack. In that case, stability of structure will be maintain and stores information for longer time. (Nelson & Cox, 2008) The presence of single strand and ribose sugar in RNA is helpful in rapid transferring of information for the protein synthesis. (Alberts et al, 2008)

Three types of RNA - structures and its functions

Structures of RNAs

Messenger RNA is the template form for protein synthesis. It is a heterogeneous class of molecules with an average length of 1.2kilobases. The mRNA exists in linear polymers with codon for protein synthesis. In 5´ or N-terminus of linear polymers, methionine, AUG codon act as start codon and stop codon at 3´ or C-terminus with UAA, UAG and UGA three codons. Between this two points, present the reading frame, where sequencing of amino acid occurs. 5΄ cap is found at N-terminus which binds with proteins and poly A-tail at C-terminus of linear mRNA. The mRNA has secondary structure, stem loop formed by complementary base pairs of linear base sequence. (Lodish et al, 2008)

Figure7: - Structure of mRNA. (Interactive Concepts in Biochemistry, 2002)

Here in transfer RNA, it is a small RNA species independent of ribosome that is charged with an amino acid at one end (3´end) and another end coated with anticodon. The tRNA exist in all levels; primary (linear), secondary (stem loops) and tertiary structure (3-dimension). All tRNAs share a common structure during the function, represented by cloverleaf. They have four base-paired stems, having three stem loops- dihydrouracil loop (D loop) on left, antidon loop at bottom having three letters, anticodon at its apex T loop with sequence of the bases the acceptor stem and acceptor loop on the top.(Weaver, 2002). The tRNAs shares a common three dimensional shape, which resembles an inverted L. This shape maximizes stability of lining up the base pairs in the D stem with those in the anticodon stem, and the bases T stem pairs with those of acceptor stem. The aniticodon bases are stacked and projecting out to the right from the side of anticodon loops and twisted into a shape in order to base pairs with complementary codon of mRNA. The structure of tRNA is stabilized by tertiary interactions like base-base, base- backbone and backbone. (Weaver, 2002)

Figure6: Secondary structure of tRNA. (Secondary Structure of tRNA, n.d)

In the case of Ribosomal RNA, it forms a core of ribosome, cell's essential protein factory. It is found most abundantly and stable form, represents about 70-80% of total cellular RNA. Three types of rRNAs found in prokaryotes are 5s, 16s and 23s, base on their sedimentation behavior. (Lodish et al, 2008) In eukaryotes, four different size of rRNA is found- 5s, 5.8s, 18s and 28s. The rRNA exists as helical structure formed by folding of a single stranded polymer but does not exist as a double stranded polymer. The rRNA exists in several conformations because of no rigid and stable double helical structure like DNA. In prokaryotes, ribosome binds to the mRNA close to the translation start site. That ribosome binding site is referred to as Shine-Dalgarno sequence or as the ribosome recognition element. In eukaryotes, ribosome binds at 5´ end of the mRNA and scan down the mRNA until they encounter a suitable codon. (Weaver, 2002)

Function of mRNA

During transcription, information stored in DNA is copied into mRNA. The mRNA carries information from DNA in a codon to the ribosome. The translation begins at start codon, methionine (AUG). The translation begins from the 5´end, where codon runs from the specific start codon to a stop codon which is in 3´or c- terminus of polypeptide chain, called reading frame. Each amino acid is encoded by one or three codons in mRNA and each codon specifies one amino acid. The methionine, AUG codon (start codon) specified amino acid at 5´ but three stop codons (UAA, UAG, UGA) specified no amino acids, which is termination of translation. The uninterrupted codon sequence in tRNA (reading frame) between the start codon and stop codon is translated into linear sequence of amino acids which in turn result in protein synthesis. (Lodish et al, 2008)

Functions of tRNA

tRNA is mainly for decoding function.

1) tRNA charging - As discussed in structure, tRNA has two main end; one end with acceptor stem and other with anticodon. The acceptor stem accepts and covalently bound to specific amino acids, called tRNA charging (charged with amino acids). Charging takes place by two steps, both catalyzed by the enzyme, aminocyl- tRNA synthetase.

Amino acid is activated using ATP, forms an aminoacyl-AMP and pyrophosphate.

Energy stored in aminoacyl-AMP is used to transfer energy from amino acid to tRNA resulting formation of aminocyl-tRNA. This role was played by aminoacyl-tRNA synthetase but it also determines the charge specificity. Only 20 synthetases existed, one for each amino acid which is very specific. If acceptor stem receives wrong amino acids, it results more error in protein synthesis. (Weaver, 2002)

2) Anticodon- Anticodon loop is present at bottom of tRNA secondary structure with anticodons. Anticodons of tRNA get paired with codons of mRNA. The activated amino acid (encoded by codons in mRNA) can be added to the growing polypeptide chain. This is specific and regulated by an enzyme, aminoacyl-tRNA synthetase. Usually, base pairing between two RNA occurs in third (3´) base in an mRNA codon and the first (5´) base in tRNA anticodon. If wrong amino acid is getting attached to tRNA, there occurs immediate removal of amino acids. Specific or cognate tRNA with amino acid delivers correct protein synthesis. (Lodish et al, 2008)

Function of rRNA

As mentioned in its structure, it is used in building up of ribosome, the complex structure which moves along an mRNA molecule. Usually ribosome is bind with mRNA at 5´ end. (Weaver, 2002) This binding checks the suitable codon of mRNA. The rRNA catalyzes the assembly of amino acids into polypeptide chains. They also bind tRNA and other accessory proteins for protein synthesis. The rRNA also plays a catalytic role in the formation of peptide bonds during protein synthesis. (Lodish et al, 2008)

However, DNA and RNA both are macromolecules having similar structures. But they are not identical to each other. Each of their structures play a particular function. Both occur in three dimensional structures but RNA exists in three forms, each form differing from other, having different structures and functions. Over all, they perform different functions, but for the protein synthesis. Hence, DNA and RNA are nucleic acids found in all living organisms, which act as information carrying molecules for the protein synthesis.