DNA Structure DNA is usually a double-helix and has two strands running in opposite directions. (There are some examples of viral DNA which are single-stranded). Each chain is a polymer of subunits called nucleotides (hence the name polynucleotide). Each strand has a backbone made up of (deoxy-ribose) sugar molecules linked together by phosphate groups. The 3' C of a sugar molecule is connected through a phosphate group to the 5' C of the next sugar. This linkage is also called 3'- 5' phosphodiester linkage. All DNA strands are read from the 5' to the 3' end where the 5' end terminates in a phosphate group and the 3' end terminates in a sugar molecule.

Each sugar molecule is covalently linked to one of 4 possible bases (Adenine, Guanine, Cytosine and Thymine). A and G are double-ringed larger molecules (calledpurines). C and T are single-ringed smaller molecules (called pyrimidines). In the double-stranded DNA, the two strands run in opposite directions and the bases pair up such that A always pairs with T and G always pairs with C. The A-T base-pair has 2 hydrogen bonds and the G-C base-pair has 3 hydrogen bonds. The G-C interaction is therefore stronger (by about 30%) than A-T, and A- T rich regions of DNA are more prone to thermal fluctuations. 

The bases are oriented perpendicular to the helix axis The bases are oriented perpendicular to the helix axis. They are hydrophobic in the direction perpendicular to the plane of the bases (cannot form hydrogen bonds with water). The interaction energy between two bases in a double-helical structure is therefore a combination of hydrogen-bonding between complementary bases, and hydrophobic interactions between the neighboring stacks of base-pairs. The backbone of polynucleotides are highly charged (1 unit negative charge for each phosphate group; 2 negative charges per base-pair). If there is no salt in the surrounding medium, there is a strong repulsion between the two strands and they will fall apart. Therefore counter-ions are essential for the double- helical structure. Counter-ions shield the charges on the sugar-phosphate backbone.

TYPES in nature DNA can form three structures, A-, B- and Z-DNA. depends on the hydration level, DNA sequence, the amount and direction of supercoiling, chemical modifications of the bases. A: a shorter more compact helical structure. occurs only in dehydrated samples of DNA, such as those used in crystallographic experiments Z: left-handed helix with a zig-zag phosphate backbone , The major and minor grooves, unlike A- and B-DNA, show little difference in width

Assignment 1 Define the 3 structure of DNA and mention the following terminologies after defining them. Helix Diameter                Rise / base-pair                 Base-pair / helical turn       Helix pitch                            Tilt of the bases 

RNA Structure RNA molecules are also polynucleotides with a sugar- phosphate backbone and four kinds of bases. 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) and has an –OH at the 2' C position highlighted in red in the figure below (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 shown in red in U.

RNA molecules do not have a regular helical structure like DNA 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.

Classes of RNA Messenger RNA (mRNA) which acts as a template for protein synthesis and has the same sequence of bases (read from the 5' to the 3' end) as the DNA strand that has the gene sequence. mRNA 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). tRNA molecules 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. All tRNA molecules are in the range ~70-90 nucleotides. They have a molecular weight of ~25,000 and have sedimentation constant ~ 4 Svedberg (S) units. Ribosomal RNA (rRNA) which make up an integral part of the ribosome, the protein synthesis machinery in the cell.

Secondary and tertiary structure of tRNA The crystal structures of several tRNA molecules have been determined. 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 secondary structure then folds up to form a 3-dimensional structure which looks like an inverted L. One end of one L arm (the 3' end of the chain) is the acceptor stem. 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-dimensional) 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 covalent attachment between the tRNA and its corresponding amino-acid is achieved by yet another adaptor molecule (this time a protein molecule called aminoacyl-tRNA synthetase) of which there are at least 20 varieties, one for each kind of amino-acid. The synthetases recognize the detailed shape and properties of a specific amino-acid and the detailed shape of the acceptor stem in the folded tRNA molecule and catalyze the covalent attachment between the amino-acid and its corresponding tRNA. 

Ribosomal RNA The ribosome is a large machinery (~ 20 nm in diameter, 70S sedimentation rate for bacterial ribosomes) and is made of two subunits: a large subunit (~50S) and a small subunit (~ 30S). The large subunit is in turn made of two ribosomal RNA (5S and 23S) and several (~34 proteins) whereas the small subunit has one ribosomal RNA (16S) and ~ 21 proteins. The 23S rRNA is ~ 3000 nucleotides long, and the 16S rRNA is ~ 1500 nucleotides long.

THE NUCLEOLUS The nucleolus (nucleoli) non-membrane bound structure composed of proteins and nucleic acids , transcribe ribosomal RNA (rRNA) and assemble it within the cell. takes up to about 25% of the nuclear volume. Three major components of the nucleolus are recognized: the fibrillar centers (FC), The DFC (dense fibrillar center) consists of newly transcribed rRNA bound to ribosomal proteins granular component (GC), contains RNA bound to ribosomal proteins that are beginning to assemble into ribosome. These different regions are thought to represent the sites of progressive stages of rRNA transcription, processing, and ribosome assembly.

The rRNA genes are located in the fibrillar centers, with transcription occurring primarily at the boundary of the fibrillar centers and dense fibrillar component. Processing of the pre-rRNA is initiated in the dense fibrillar component and continues in the granular component, where the rRNA is assembled with ribosomal proteins to form nearly completed preribosomal subunits, ready for export to the cytoplasm. Another structure identified within many nucleoli (particularly in plants) is a clear area in the center of the structure referred to as a nucleolar vacuole. Nucleoli of various plant species have been shown to have very high concentrations of iron in contrast to human and animal cell nucleoli.