DNA Structure Lecture Notes PDF

DNA STRUCTURE Mahmoud Alfaqih BDS PhD Department of Medical Biochemistry College of Medicine and Health Sciences Arabian Gulf University Lecture objectives Describe the structure of nucleotides Describe the structure of DNA Describe the chemical bonds involved in maintaining...

DNA STRUCTURE Mahmoud Alfaqih BDS PhD Department of Medical Biochemistry College of Medicine and Health Sciences Arabian Gulf University Lecture objectives Describe the structure of nucleotides Describe the structure of DNA Describe the chemical bonds involved in maintaining DNA structure Apply Watson Crick Base pairing rules Explain Chargaff’s rule Crick 1953 Watson Franklin Publication that first described the structure of DNA Only two pages in length (900 words) Deoxyribo-Nucleic Acid Ribo-Nucleic Acid DNA RNA 1. DNA has deooxyribose while RNA has ribose 2. DNA is double stranded while RNA is single stranded 3. DNA has Thymine (T) while RNA has Uracil (U)  DNA, RNA A polymer of nucleotides Nitrogenous base Phosphate Pentose sugar Deoxyribose in DNA Ribose in RNA Sugar + Base + one phosphate group Sugar + Base = Nucleoside Nucleoside + one phosphate group = nucleoside monophosphate Nucleoside + two phosphate groups = nucleoside diphosphate Nucleoside + three phosphate groups = nucleoside triphosphate  Structure of nucleotides Phosphate Pentose sugar Nitrogenous base Pyrimidines (one ring): C, T , U Purines (Two rings); A, G Glycosidic linkage Deoxy-adenosine monophosphate Glycosidic linkage  3’ → 5’ phosphodiester bonds Joins the 3’-hydroxyl group of the deoxypentose of one nucleotide to the 5’- hydroxyl group of an adjacent nucleotide through a phosphoryl group Can be hydrolyzed by nucleases, deoxyribonucleases for DNA and ribonucleases for RNA. Can be broken down by chemicals.  DNA is double stranded DNA exists as a double stranded molecule (dsDNA) The two strands are held together by hydrogen bonds thru complementary base pairing In DNA Guanine (G) pairs with Cytosine (C) (three hydrogen bonds) while Adenine pairs with Thymine (T) The two strands will then form double helix DNA sequence is a primary structure and the DNA helix is a secondary structure  DNA ends are polar 3’ end of DNA has a hydroxyl group at the 3’ position on the deoxyribose sugar 5’ end of the DNA has a phosphate group at the 5’ position on the deoxyribose sugar DNA strands run in opposite directions (Antiparallel) 3’ end of DNA has a hydroxyl group at the 3’ position on the deoxyribose sugar 5’ end of the DNA has a phosphate group at the 5’ position on the deoxyribose sugar  DNA double helix ▪ The two DNA chains are coiled around a common axis called the helical axis ▪ The chains are paired in an anti-parallel manner ▪ The hydrophilic deoxyribose-phosphate backbones is on the outside ▪ The hydrophobic bases are stacked inside ▪ The spatial relationship between the two strands in the helix creates a major (wide) groove and a minor (narrow) groove. ▪ Each helical turn contains 10 bps. ▪ The distance between the bases (helical rise) is 0.34 nanometer. ▪ The grooves provide space for the binding of regulatory proteins What contributes to the stability of DNA double helix? ▪ Hydrogen bonds between complementary base pair. ▪ Hydrophobic interactions between the stacked nitrogen bases ▪ Hydrophilic interaction between sugar phosphate backbone and the solution  Chargaff rule In dsDNA: ▪ The amount of A equals to the amount of T ▪ The amount of G equals to the amount of C ▪ The total amount of purines (A+G) equals the amount of pyrimidine (T+C)  Denaturation Occurs when the hydrogen bonds between the paired bases are disrupted This may occur in a lab setting in the following conditions: change in pH, heat (note: covalent phosphodiester bonds are not broken by such treatments) Tm (Melting Temperature): Is the temperature at which one half of the helical structure is lost This leads to loss of helical structure in DNA DNA that contains high concentration of A and T denatures at a lower temperature than does G and C-rich DNA Right handed vs. left handed helix  II. DNA structure Structural forms (B form, A form, and the Z form) The B form: is a right-handed helix with 10 bps per 360◦ turn, and with the planes of the bases perpendicular to the helical axis Chromosomal DNA is thought to consist primarily of B-DNA The A form Produced by moderately dehydrating the B form Also right-handed helix, but there are 11 bp per turn, and the planes of the base pairs are tilted 20 ◦ away from the perpendicular axis of the helix The Z form Is a left-handed helix that contains 12 bp per turn Can occur naturally in regions of DNA that have a sequence of alternating purine and pyrimidines (for e.g poly GC or poly AT) Transition between B and Z form of DNA may play a role in regulation of gene expression  Quiz If adenine makes 30% of a double stranded DNA molecule, what will be the percentage of guanine? A. 20% B. 10% C. 40% D. 5% E. 30%