DNA Final Presentation PDF

12-MBT-001 *DNA is a polymer of deoxyribonucleotides and is found in chromosomes, mitochondria and chloroplasts. *The nuclear DNA is found bound to basic proteins called histones. *DNA is present in every nucleated cell and carries the genetic information. * 1868 - Meischer isolate...

12-MBT-001 *DNA is a polymer of deoxyribonucleotides and is found in chromosomes, mitochondria and chloroplasts. *The nuclear DNA is found bound to basic proteins called histones. *DNA is present in every nucleated cell and carries the genetic information. * 1868 - Meischer isolated a phosphorous-rich material from a crude preparation of nuclei obtained from WBCs * Substance - ‘nuclein’ = nucleic acid + protein i.e. nucleoprotein * 1898 - Atlman isolated a protein-free preparation of nuclei - coined the term ‘Nucleic acid’ * The specific nucleic acid obtained from nuclei is called deoxyribonucleic acid (DNA). * Hydrolysis of DNA - nitrogenous bases, deoxypentose sugar, phosphate group.  PHOSPATE SUGAR BASE Ribose or PURINES PYRIMIDINES Deoxyribose Adenine Cytocine (C) (A) Thymine (T) Guanine( Uracil (U) G) NUCLEOTIDE © 2007 Paul Billiet ODWS *D-Ribose - RNA *2’-deoxy-D-ribose - DNA *Sugar units are attached to the nitrogenous bases to form nucleosides and are always present in the ring form *Both 2´ and 3´position have OH gp- attached to the sugar in RNA, OH gp – attached at 3 ´position in DNA  RIBOSE DEOXYRIBOSE CH2OH CH2OH O OH O OH C C C C H H H H H H H H C C C C OH OH OH H © 2007 Paul Billiet ODWS *The bases in DNA have C-N ring structures; because of the nitrogen atoms, they are called nitrogenous bases. *There are two types of ring structures. *Adenine & Guanine are Purines, each having two joined C-N rings but with different side chains. *Thymine & Cytosine are Pyrimidines; each has only one C-N ring and again differ in their side chains. *In polynucleotides - single negative charge is present between the O2 atoms. *Negative charge - acidity of NA *Rigid unit, no internal flexibility *Four O2 occupy tetrahedran, phosphorous center O O O P O *Base + 5-carbon sugar (ribose/deoxyribose) *Nucleosides - ribonucleosides/ deoxyribonucleosides *The linkage is between the C-1’ of the sugar and either atom N-1 (in Py) or N-9 (in Pu) of the base. *Linkage - glycosidic bond (since sugar is involved) *The type of chemical linkage between the monosaccharide units of disaccharides, and polysaccharides, which is formed by the removal of a molecule of water. *The bond is normally formed between the carbon-1 on one sugar and the carbon-4 on the other.  DNA Nucleotide Phosphate Group O 5 O=P-O CH2 O O N Nitrogenous base C4 C1 (A, G, C, or T) Sugar (deoxyribose) C3 C2 *Base + sugar + phosphate *Phosphate is linked to one of the free hydroxyl groups of sugar i.e. to C-3’ or C-5’ of ribose. *Nucleotides containing deoxyribose are called deoxyribonucleotides *Nucleotides containing ribose are called ribonucleotides *Deoxyribonucleotides - building blocks of DNA *Ribonucleotides - building blocks of RNA *In nucleic acids, nucleotides are joined together by phosphodiester bonds *Nucleotides of each of the two helical strands are bound to each other by covalent 3`-5` phosphodiester linkage. *Each such bond is formed by the ester linkages of a single phosphate residue with the 3`-OH (i.e. C-3`-OH group of the ribose sugar) of one nucleotide with the C-5`-OH group of ribose of the next nucleotide. *This kind of bonding gives rise to a linear polydeoxyribonucleotide strand with two free ends on both sides. *That end of the strand which bears a free 5` phosphate group without a phosphodiester linkage is called the 5`- end. *The opposite end bears a free 3`-hydroxyl or 3`- phosphate group is called the 3`-end. *MONONUCLEOTIDE - a nucleotide that is derived from one molecule each of a nitrogenous base, a sugar, and a phosphoric acid *DINUCLEOTIDE - a nucleotide consisting of two units each composed of a a nitrogenous base, a sugar and a phosphate group *POLYNUCLEOTIDE - A polymeric compound consisting of a number of nucleotides. - A polymer is a large molecule (macromolecule) composed of repeating structural units. Nucleotide Structure  P P P *The nucleotides are all orientated in the same direction *The phosphate group joins the 3rd P Carbon of one sugar to the 5th Carbon of the next in line. P P © 2007 Paul Billiet ODWS  P G P *The bases are attached to C the 1st Carbon *Their order is important P It determines the genetic C information of the molecule P A P T P T © 2007 Paul Billiet ODWS  Hydrogen bonds P G C P P C G P P C G P P A T P P T A P P T A © 2007 Paul Billiet ODWS P DNA Double Helix 1953 - Watson & Crick worked out the 3D structure of DNA based on X-Ray diffraction photographs taken by Franklin & Wilkins. DNA composed of two strands wound around each other to form a double helix with the bases inside and the sugar- phosphate backbones on the outside. Double helix - two DNA strands are organized in an antiparallel arrangement (i.e. one strand is oriented 5` 3` and the other 3` 5`) The bases form hydrogen bonds to each other, A pairs with T and G with C. This is called complementary base pairing  DNA Double Helix 5 O 3 3 O P 5 P 5 O 1 G C 3 2 4 4 2 1 3 5 P O P 5 T A 3 O O 25 5 P 3 P  Chargaff’s Rule * Adenine must pair with Thymine * Guanine must pair with Cytosine * Their amounts in a given DNA molecule will be about the same (1:1) * There are two hydrogen bonds present between Adenine & Thymine while three hydrogen bonds are present between Guanine & Cytosine. T A G C *In DNA, the glycosidic bonds between sugar and bases are not directly opposite each other and two grooves of unequal width form around the double helix. *The edge of the helix that measures more that 180º from glycosidic bond to glycosidic bond is called the major groove and if it is less than 180º it is called minor groove.  DNA double helix major groove 12 Å one helical turn 34 Å minor groove 6Å backbone: deoxyribose and phosphodiester linkage bases Importance of the Grooves: *Certain proteins bind to DNA to alter its structure or to regulate transcription or replication. *It is easier for these DNA binding proteins to interact with the bases (the internal parts of the DNA molecule) on the major groove side because the backbones are not in the way. *The narrowness of the minor groove means that the edges of the bases are more accessible in the major groove. *DNA can exist in several conformations depending upon the base composition and under different physical conditions. *In all these conformations the same base pairing rules apply, changes do not alter the information content of the DNA. *The conformation of DNA have been determined by X-ray crystallography. *By far, the most common conformation is B-DNA. * Right-handed helix B- DNA * Double helix completes one turn every 10.4 base pairs * One turn of the double helix spans a distance of 3.4nm. * This distance is the pitch of the helix. * Each base pair increases the length of the double helix by 0.33nm. * Diameter of the double helix is 2.37nm. * Minor groove is narrow. Major groove is wide * Right-handed helix. Wider and flatter than B-DNA. * When B-DNA crystals are dried or when salt content of the crystal is lowered, the long-thin B-DNA molecule becomes a short, stubby molecule and is called as A- DNA A-DNA. *The pitch of the helix is 2.46nm and the number of base pairs per turn is about 11. *Deep major and shallow minor groove  Z- DNA * A left-handed helix * Seen in conditions of high salt concentrations * Z-DNA is longer and thinner than B-DNA. * One complete turn has 12bp * The pitch of the double helix id 4.56nm * The diameter of the double helix is 1.84nm * The major groove in Z-DNA is no more a groove but a convex surface. * The minor groove is a deep cleft that spirals around the structure. DNA Polymorphism  Prokaryotic DNA Eukaryotic DNA * Prokaryotes - include bacteria and * Eukaryotes - more complex multicellular Archae organisms e.g. plants, animals, fungi, and * Lack a membrane bound nucleus also many single celled organisms e.g. enclosing the DNA amoeba, yeast * DNA is present as a single circular * Membrane-bound nucleus molecule called a Bacterial Chromosome * DNA bound with histone proteins * DNA is naked having no associated histone proteins phschool.com * Dr. R.D.J. Barker and Dr. C.K. Leach, 1991, Nucleic Acids, THE MOLECULAR FABRIC OF CELLS, pp: 72-89, Butterworth-Heinemann Ltd., Jordan Hill, Oxford. * Dr. J.J. Gaffney, Dr. J.S. Gartland, Dr. K.M.A. Gartland, Dr. P. Hooley, Dr. S.H. Kirk, Dr. C.A. Smith, 1993, DNA Structure and Replication in Prokaryotes and Viruses, GENOME MANAGEMENT IN PROKARYOTES, pp: 2-12, Butterworth - Heinemann Ltd., Jordan Hill, Oxford. * David Hames and Nigel Hooper, 2011, DNA Structure and Replication, BIOCHEMISTRY 4ed., pp: 173-177, Garland Science, New York & London. * Dr. M.N. Chatterjee and Dr. Rana Shinde, 2005, Chemistry of Nucleic Acids, DNA Replication and DNA Repair, TEXTBOOK OF MEDICAL BIOCHEMISTRY 6ed., pp: 216-218, Jaypee Brothers Medical Publishers (P) Ltd.. New Delhi