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DNA and RNA are chain like molecules composed of sub-units called nucleotides . The nucleotides contain a base, linked to the 1´-positon of a sugar (deoxyribose in DNA and ribose in RNA) and a phosphate group. The phosphate joins the sugar in DNA or RNA chain through their 5´- and 3´- hydroxyl groups by phosphodiester bond.
DNA as genetic information carrier came to known by the end of 1940s (Weaver, 2002). However its structure was never understood. It was when, Rosalind Franklin X-rayed (1952) the crystallized DNA solution, that have started the suggestion about the structure of DNA. Churgaff also did have an information regarding DNA. He has seen the amount of purine and pyrimidine in a nucleic acid was always roughly equal. (Weaver, 2002)
In the later year, James Watson and Francis Crick related the two above information. According to them DNA must be double helix with its sugar-phosphate backbone on the outer side and its bases in the inner side. Two helix must have paired their bases such that purine on one strands always pairing with a pyrimidine on other strand (adenine with thymine and guanine with cytosine) so that helix is uniform. (Weaver, 2002). This was their crucial understanding, the key to the structure of DNA.
DNA is a structural sequences of nucleic acid in which information are coded in a unit called genes. The information to be passed to the offspring cannot be done by DNA alone .This process is accompanied by various RNAs.The information contained in the four base language of DNA i.e. A, G, U & T is copied into four base language of RNA, i.e. A, G, C & U, through a process called Transcription . This RNA contains the exact information that will specify the correct order of amino acids during protein synthesis through a process called translation (Lodish et al, 2008). Different genetic information carrier have their structure determining specific functions
Structure of DNA
Watson and Crick in 1953, proposed the first correct three-dimensional structure of DNA molecule in Cambridge University (Hartl et al, 2001).Their structure proposed, is a double stranded helix, each twisted around the other. The double helix is right-handed, following clockwise pathway when it is viewed along the imaginary axis of the helix. The sub-units of each strand are nucleotides. Each nucleotide contains any one of the four base attached to a phosphorylated molecule of the 5-carbon sugar deoxyribose. The four bases of DNA includes: Adenine (A) & Guanine (G), consisting purine, and Cytosine (C) & Thymine (T) making pyrimidine.
Structure of A and G (b) Structure of C and T
Fig.1 Bases of DNA (Introduction to DNA Structure n.d)
Each strand of DNA is a sugar-phosphate strand, oriented in antiparallel direction. Thus the 5′-phosphate end of one strand lies next to the 3Î„-hydroxyl end of the complementary strand. This antiparallel orientation creates a situation, such that if one strand reads a sequence of bases in 5′ to 3′ direction, the other reads its complementary bases from 3′ to 5′ direction. The two strands in a helix are complementary to each other, such that A bonded to T with two H-bonds and G bonded to C with three H-bonds.
Fig.2 Base pairing in DNA(The sugar-phosphate backbone is on the outside and the four different bases on the inner side of the DNA molecule)
(DNA helix, n.d)
In complementary strands, the sequence of bases
in one strand directs the other strand’s base sequence.
However the sequence of bases in one strand is not restricted,
so any sequence can be present along a single strand.
(Hartl et al, 2001 & Bhagavan, 2002).
Each base pair in a double helix lies in a plane
almost flat, stacked on top of one another, perpendicular
to the axis of the helix. Adjacent pairs of basses in DNA
are separated by 0.34nm. Each turn of the helix repeats
every 3.4nm in which, includes 10 base pair. Each base
pair is rotated by 60 degree with respect to one another Fig.3 Double helix DNA molecule
in each turn. (Hartl et al, 2001). The double helix structure (Double helix structure of DNA, n.d)
of DNA reveals two grooves: major and minor groove, which runs along the length of the entire molecule. Major grooves are wider (22Å) and deeper compare to minor groove, which are narrow (12Å) and shallow (Bhagavan, 2002 and Freifelder et al, 1998). There are two other types of DNA viz., A-DNA (right-handed) and Z-DNA (left-handed) besides B-DNA. (Lodish, 2008)
Function of DNA
DNA is an informational molecule that contains the sequence of nucleotides with all information to build all the proteins of an organism thus it is a medium of long-term storage and transmission of genetic information.(Lodish, 2008). DNA also helps to solve some problems regarding the phylogenetic relationship between different organisms. This is based on the fact of % GC content in the related organisms are similar. (Black, 2008)
Functions of DNA determined by its structure
The fact of base pairing A with T and G with C in the two polynucleotide chain makes the possibility of exact duplication of DNA molecule, which in turn will conserve the accurate information present in DNA that is to be inherited by daughter cells. The DNA molecule of being double helix, results in the formation of two complementary helix by unwinding and separation during transcription process. Thus it is a semi conservative replication.
The requirement of genetic material to have the capacity to carry all of the information needed to direct the organization and metabolic activities of the cell is achieved by the nature of DNA being made protein molecules. Proteins are sequence of amino acids determining the physical and chemical properties of DNA. A long DNA chain helps direct the synthesis of verities of protein molecules. (Hart et al, 2001).
The grooves in DNA molecule provide space for the attachment of other strands of nucleic acids and regulating proteins. (Bhagavan, 2002).
DNA with deoxyribose sugar has H at 2Î„ position which prevents OH-catalysis of phosphodiester bond at neutral pH. This stability suits critically to the function of DNA to store genetic information for long term.(Lodish, 2008). The presence of thymine with methyl group (unreactive) contributes to the stability of DNA molecule. DNA is devoid of OH-group at 2Î„ so it is prevented from the formation of cyclic phosphate ester, so the DNA is not hydrolyzed by alkali. The complementary of the helical structure serve as template to specify the base sequence of newly synthesized complementary strand. As a result in synthesis of daughter DNA molecules, it each will be precisely identical to that of the parent DNA. (Conn et al, 1076).
Ribonucleic acids (RNA)
The structure of RNA molecule differ from DNA as: RNA being single stranded unlike DNA has a much shorter chain of nucleotides than DNA; RNA contains ribose (there is hydroxyl group attached to the pentose ring in the 2′ position in RNA) instead of deoxyribose in DNA; OH-group at 2Î„ carbon in place of H in DNA; and presence of uracil in place of thymine in DNA .(Lodish, 2008).
Chemically RNA contains a ribose sugar, with carbons numbered 1′ through 5′. A base is attached to the 1′ position, generally adenine (A), cytosine (C), guanine (G) or uracil (U). Adenine and guanine are purine, cytosine and uracil are pyrimidine. A phosphate group is attached to the 3′ position of one ribose and the 5′ position of the next. . The bases form hydrogen bonds between cytosine and guanine, between adenine and uracil.
Fig.4 Chemical structure of RNA
(Chemical structure of RNA n.d)
Functions of RNA
The function of RNA is to translate genetic information stored in DAN into the amino acid sequence of protein. In RNA virus it takes up the function of DNA. Messenger rRNA carries genetic information transcribed from DNA and is used as a template for protein synthesis. Transfer RNA carrying particular amino acid participates in translation where it adds the amino acid to the terminal end of the polypeptide chain. Ribosomal RNA is major components of the ribosome where protein synthesis occurs. (Hartl, 2001).
The flexibility of single stranded backbone permits the RNA strands to bend back on itself to allow one part of the molecule to form weak bonds with other part of the same molecule. This cause the RNA chains to fold up into specific shape that is directed by its sequence. The shape of the RNA molecule in turn may enable to recognize other molecule by binding them selectively. (Alberts et al 2008). RNA is necessary for DNA to get started replication because the DNA-polymerase cannot initiate replication on its own. The initiation is brought about by free 3Î„ hydroxyl group of segment of RNA. (Hartl et al, 2001). RNA has ribose sugar with OH-group at the 2Î„ position which makes RNA chemically labile for translation. This, also facilitated by the presence of uracil (without methyl group)
RNA is of three types:
Messenger RNA (mRNA),
Transfer RNA (tRNA) and
Ribosomal RNA (rRNA).
Messenger RNA (mRNA) structure
The DNA molecule to transfer information in it, under goes transcription and its template is called
primary transcript. In prokaryotes primary transcript acts directly as mRAN. In eukaryotes primary transcript under goes processing to become mRNA (Hartl et al, 2001). Messenger RNA are single stranded. The simplest and most common secondary structure of mRNA is formed by pairing of complementary bases within a linear sequence; the structure called “Hair-pins” and “stem loops”. This is formed by pairing of 5-10 nucleotides. Stem loop formed by pairing of bases more than 10 nucleotides. In many cases pairing follows Watson- Crick base pairs, however in some cases mismatch base pair occurs which result the base to bulge out of loop. Tertiary structure are formed by cooperative folding of simple secondary structure called “pseudoknot”. (Lodish et al, 2008)
Hair-pin (b)Stem loop (c) Pseudoknot
Fig.5 Structures of mRNA: (a) & (b) are primary and (c) is secondary structure. (Lodish et al,2008)
Functions of mRNA
Messenger RNA has 5Î„ cap which helps to bind the ribosome to begin protein synthesis. The 3Î„- terminus act as substrate for the addition of polyadenylate sequence (Hartl et al, 2001). Messenger RNA have start codon, AUG for methionine at 5Î„ that facilitates the growth of polypeptide chain from 5Î„ to 3Î„. Stop codon (UAA, UGA &UAG) is present at 3Î„ end that terminates the further protein synthesis. (Lodishet al, 2008).
Transfer RNA (tRNA) structure
Transfer RNA discovered by Zamencnik and coworker (1957) has complex structure including primary, secondary and tertiary structure (Weaver, 2002). Primary structure includes the linear sequence of bases in the RNA. The secondary structure is the base pairing of the different regions of the tRNA. Tertiary structure is the overall 3-dimensional shape of the molecule.
The secondary structure is seen when in the solution which form a stem-loop arrangement due to base pairing within the molecule. It resembles “clover leaf” when drawn in 2-dimension. (Lodishet al, 2008).
(b) tRNA in 3-dimension
Fig.6. tRNA structures (Transfer RNA structure n.d)
The clover leaf has four base paired stems that define the four major regions of the molecules called stems. Three of the four loop stems have loops containing seven or eight base at their ends, while one loop contains the free 3Î„and 5Î„ ends of the chain. The 1st stem at the top is the acceptor stem. This includes the two ends of the tRNA which are base-paired to each other, i.e. 3Î„ and 5Î„ end. The 3Î„end bears the invariant base sequence CCA and protrudes beyond the 5Î„end. Next is the dihydrouracil loop (D loop) always containing modified uracil base. At the bottom is the anticodon loop containing all important anticodons at its apex. The last stem is the T-loop possessing nearly invariant of three bases: TÎ¨C, Î¨ is modified nucleotides in the tRNA called pseudouradine. The region between the anticodon loop and T-loop is called the variable loop- it varies its length from 4-13 nucleotides. (Weaver, 2002).
Tertiary structure of tRNA was made known by Alexander Rich (1970s) using X-ray diffraction technique. It has folded structure in inverted L-shape, with the anticodon loop and accepter stem forming the two ends of the loop. (Lodish et al,2008). The horizontal region comprises of accepter and T-stem. Vertical axis of the molecule includes anticodon and D-stem above. The base paired stem of the molecule are RNA-RNA double helix similar to the A-helix form of the DNA. It has around 11 base pairs. (Weaver, 2002).
Functions of tRNA
The folded structure of tRNA promotes its decoding functions (Lodish, 2008). The tRNA becomes chemically linked to particular amino acid by forming high-energy bond. The anticodon region (folded end) of tRNA, base pairs with a codon in mRNA and activated amino acid is added to the growing polypeptide chain. Transfer RNA and associated enzyme aminoacyl-tRNA synthetases helps information in DNA to get translate into mRNA. The modified bases help to bind amino acids. It was found that tRNA with unmodified bases made invitro unable to bind amino acids. The L-shaped tertiary structure maximizes the length of its base-paired stem by stacking them in two sets, forming relatively long extended base paired regions. The two parts of each stem are not aligned perfectly and thus stem bend slightly. This alignment allows the base pair to stack on each other and therefore provide stability (Weaver, 2002).
The tertiary structure of tRNA having anticodon bases stacked, are projecting out, away from the backbone of tRNA. This places them in a position to interact with the bases of the codon in mRNA. The twisted nature of the anticodon backbone into particular helix shape, facilitate base pairing with corresponding codons. (Weaver, 2002). The specific anticodon ensures the correct placement of the amino acids in a growing polypeptide chain. (Conn et al, 1976)
Ribosomal RNA ( rRNA)
RNA in the ribosome is called rRNA. There are three types in prokaryotes and four in eukaryotes. For prokaryotes E .coli rRNA are used as sized standards; they have sedimentation coefficients of 5s, 16s and 23s. The rRNA in E. coli have been sequenced and contain 120, 1541 and 2904 nucleotides respectively. In addition to prokaryotes rRNA, eukaryotes have 5s rRNA with 120 nucleotides. (Bhagavan,2002). Ribosomal RNA has helical structure resulting from folding back of a single stranded polymer at areas where is possible- because of short length complementary structure. But it never exists in double stranded polymer as that of DNA.
Ribosomal RNA does not have extremely rigid and stable helical structure. They exists in single stranded conformation at high temperature. At low ionic strength, a compact rod with regularly arranged helical regions can exist, and at high ionic strength a compact coil will occure. (Conn et al, 1976)
Functions of rRNA
The rRNA are major constituents of the cell
organelle, ribosome. It is a complex structure which move along an mRNA
molecule and catalyze the assembly of amino
acids into polypeptide chains.They also bind
tRNA and other accessory proteins for protein
synthesis. (Lodish et al, 2008) They have
binding site at which 5´ end of mRNA binds.
Transfer RNA carrying amino acid for the
growing polypeptide chain attaches at
peptidyl site of the rRNA.
(Becker et al, 2006) Fig.7. Structure of various rRNA (rRNA structure, n.d)
DNA, the macromolecule composed of two polynucleotide chain, is the carrier of genetic information in all cells and many viruses. The information contained in DNA get expressed in the daughter cell with the help of RNAs. The transfer of information follow a route called “Central Dogma” of molecular genetics. Both DNA and RNA, to carry out their functions, have particular structures which facilitates their activities. DNA is double helix, so that it is able to store more genetic information for long period. Messenger RNA is single stranded so that information transcribed from DNA can be easily get expressed during protein synthesis.
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