DNA and RNA Molecular Biology Notes | PDF

DNA and RNA DNA The Primary Agent of Genetic Material The important features of the DNA model are:- 2 helical polynucleotide chains are coiled around a common axis. The chains run in opposite directions The purine and pyrimidine bases are on the inside of the helix. The phos...

DNA and RNA DNA The Primary Agent of Genetic Material The important features of the DNA model are:- 2 helical polynucleotide chains are coiled around a common axis. The chains run in opposite directions The purine and pyrimidine bases are on the inside of the helix. The phosphate and deoxyribose units are on the outside The diameter of the helix is 20Ao (2 nm). Adjacent bases are separated by 3.4 Ao (0.34 nm) along the helix. i.e. stacked 0.34 nm apart. The helix makes one full turn every 3.4 nm along its length. Therefore there are 10 layers of base pairs/rungs on the ladder in each turn of the helix. The two chains are held together by hydrogen bonds between pairs of bases.  Adenine is always paired with thymine and guanine is always paired with cytosine The most important aspect of the DNA double helix is the specificity of the pairing of bases. Adenine must pair with thymine because of steric and hydrogen bonding factors. – i.e. the regular helical nature of the sugar- phosphate backbone restricts the bonding of the base pairs. – The gycosidic bonds that are attached to a bonded pair of bases are always 10.85 Ao apart.  – The purine-pyrimidine base pair fits perfectly in this space. However, there is insufficient room for two purines. Also, there is too much room for two pyrimidines and they would be too far apart to for hydrogen bonds. Therefore one base must always be a purine and the other a pyrimidine. The base pairing is further restricted by hydrogen bonding requirements. – The hydrogen atoms in the purine and pyrimidine bases have well defined positions. Eg. Adenine cannot bond to cytosine because there would be two hydrogens near one of the bonding positions and none near the other. – Similarly, thymine cannot bond with guanine. – However, adenine forms two hydrogen bonds with thymine and cytosine forms three bonds with guanine. – The orientations and distances of these hydrogen bonds are optimal for achieving strong attraction between the bases. The base pairing is further restricted by hydrogen bonding requirements. The hydrogen atoms in the purine and pyrimidine bases have well defined positions. Eg. Adenine cannot bond to cytosine because there would be two hydrogens near one of the bonding positions and none near the other. Similarly, thymine cannot bond with guanine. However, adenine forms two hydrogen bonds with thymine and cytosine forms three bonds with guanine. The orientations and distances of these hydrogen bonds are optimal for achieving strong attraction between the bases. Much more structural information can be obtained from x- ray analyses of the DNA crystals. The bases rotate in opposite directions about their long axis (called propeller twisting) This feature enhances the stacking of bases in each strand The base pairs tilt relative to their neighbours (called base roll) (the variability of the double helix depends on the DNA sequence to facilitate a protein searching for a specific target sequence in DNA) The helix can be smoothly bent into an arc or supercoiled with little change in local structure (this enables circular DNA to be formed and allows DNA to be wrapped around proteins) A-DNA appears when the relative humidity is reduced to below 75% (i.e. when the DNA is dehydrated) is a right-handed double helix made up of antiparallel strands held together by Watson and Crick base pairing is wider and shorter than the B-helix the base pairs are tilted rather than normal to the helix axis (as in the B-helix) double stranded regions of RNA (e.g hairpins) and RNA- DNA hybrids adopt a form very similar to that of A-DNA. the 2’ –OH of ribose prevents the RNA from forming the B-helix Z-DNA Forms antiparallel strands held together by Watson and Crick base pairing. Differences: left handed double helix  The phosphates in the backbone zig-zag (to give the name Z-DNA) (It zig-zags because the repeat unit is a dinucleoitde of alternating pyrimidines and purines e.g. CGCGCG) It contains only one deep helical groove. A stretch of Z-DNA can occur in B-DNA by flipping the base pairs 180o and rotating the sugars of the purine residues. The negative supercoiling of naturally occurring DNA molecules also promotes the transition to Z-DNA. RNA RNA molecules are also polynucleotides with a sugar-phosphate backbone and four kinds of bases A,U,C,G. The main differences between RNA and DNA are: RNA molecules are single-stranded The sugar in RNA is a ribose sugar – as opposed to deoxy-ribose has an –OH at the 2' C position – DNA sugars have –H at that position Thymine in DNA is replaced by Uracil in RNA. – T has a methyl (-CH3) group instead of the H atom.  RNA molecules do not have a regular helical structure like DNA. Instead, they can form complicated 3- dimensional structures where the strands can loop back and form intra-strand base-pairs from self- complementary regions along the chain There are three classes of RNA molecules: messenger RNA (mRNA) – acts as a template for protein synthesis – has the same sequence of bases (read from the 5' to the 3' end) as the DNA strand that has the gene sequence – can range from ~300 nucleotides to ~7000 nucleotides, depending on the size and the number of proteins that they are coding for. – transfer RNA (tRNA) – one for each triplet codon that codes for a specific amino-acid (the building blocks of proteins). – are covalently attached to the corresponding amino-acid at one end, and at the other end they have a triplet sequence (called the anti-codon) that is complementary to the triplet codon on the mRNA. – are in the range ~70-90 nucleotides. – have a molecular weight of ~25,000 and have sedimentation constant ~ 4 Svedberg (S) units. – ribosomal RNA (rRNA) – ribsomal RNA (rRNA) and protein combine to form a nucleoprotein called a ribosome.  – The ribosome serves as the site and carries the enzymes necessary for protein synthesis. All tRNA molecules have very similar secondary structures in which the single-stranded chain is folded in a 'clover-leaf' structure that has three hairpins and an acceptor stem where the amino-acid is covalently attached. The acceptor stem is the 3' end of the chain and always terminates in the sequence 5'-CCA-3'. The other end of the L is the anti-codon loop that has to match the codon on the mRNA. The distance between the two ends of the L is ~ 7 nm. The corner of the L is used for correct positioning on the ribosome where the protein synthesis takes place.  In the tertiary (3-Dl) structures of RNA, bases sometimes make hydrogen bonds with more than one partner. These extra hydrogen bonds compensate for the distortion in the double-stranded helical regions when the RNA folds up and help stabilize the tertiary structure.  The ribosome is large – ~ 20 nm in diameter – 70S sedimentation rate for bacterial ribosomes) is made of two subunits: – a large subunit (~50S) in turn made of two ribosomal RNA (5S and 23S) ~34 proteins – a small subunit (~ 30S). has one ribosomal RNA (16S) ~ 21 proteins.