Outline of Next Six Lectures Tues. Nov. 1: Structures of DNA and RNA Fri. Nov. 4: Recombinant DNA Tues. Nov. 8: Prokaryotic DNA Replication I Fri. Nov. 11: Prokaryotic DNA Replication II Tues. Nov. 15: Eukaryotic DNA Replication I Fri. Nov. 18 TEST #3 (on Lectures 14-19) Tues. Nov. 22: Eukaryotic DNA Replication II Lecture 16 Lecture 17 Lecture 18 Lecture 19 Lecture 20 Lecture 21

MBB 694:407 & 115:511 Lecture 16: Structures of DNA and RNA Nov. 1, 2005

The Beginning of the DNA Era DNA has a cool shape!

I. Landmark Experiments in the Study of the Genetic Material A Gregor Mendel—physical traits are inherited as discrete units Streptococcus pneumoniae Polysaccharide capsule B Frederick Griffith —discovers a hereditary molecule that is transmissible between bacteria: “Transforming Principle” Conclusion: “Heat-killed Type S bacteria can transform live Type R bacteria into the virulent Type S form.”

C Avery, MacLeod, McCarty —treated heat-killed Type-S bacterial extracts prior to addition to live Type-R bacteria Treatment Transformation? Proteases DNase RNase Yes No Yes Lipases Yes Conclusion: “ The “transforming principle” is DNA

Purines/Pyrimidines D Erwin Chargaff—DNA molecules Have Distinctive Base Compositions Chargaff’s rules: [A] = [T]; [G] = [C]; [purines] = [pyrimidines] A+G = C+T 1. The base composition of DNA varies from one species to another. 2. DNA specimens from different tissues of the same species have the same base composition. 3. The base composition doesn’t change with age, nutritional state, or changing environment. 4. In all cellular DNAs, regardless of species, the number of adenosine residues is the same as the number of thymidine residues and #guanosine=#cytosine residues. Conclusion: DNA has the characteristics expected of genetic material (A+G/C+T)

E Hershey and Chase —”blender experiment” Proved that DNA is the hereditary molecule of bacteriophage DNA, not protein, enters bacterial cells and directs the synthesis of new viruses

DNA is the Genetic Material of Living Cells Now what? Solve the 3D Structure of DNA

Using X-ray Crystallography to Solve the Structure of DNA Structure A of DNA (Taken by Maurice Wilkins) Structure B of DNA (Taken by Rosalind Franklin) Two distinct forms of DNA exist: Crystalline Occurs at 75% rel. humidity Contains 30% water Paracrystalline Occurs at >75% rel. humidity Contains >30% water Natural DNA

F. 1953—Watson and Crick Discover the Structure of DNA (Interpret X-ray data using molecular models)

1953—Watson and Crick propose a structure for DNA I. How DNA stores genetic information II. How DNA is replicated Base complementarity: each strand serves as a template for a new strand The sequence of the nucleotides encodes information about proteins

II. Nucleotides 2’-deoxyribose Nitrogenous base Base + Ribose Nucleoside + phosphate Not very soluble Soluble

The Common Nitrogenous Bases DNA only RNA only (Watson & Crick bases) Found in dsDNA

Purines Pyrimidines Adenine Guanine AdenosineAdenylate Thymine Cytosine GuanosineGuanylate Uracil (Thymidine) or (Deoxythmidine) Cytidine Uridine (Thymidylate) or (Deoxythmidylate) Cytidylate Uridylate Base Nucleoside Nucleotide Nucleic Acid (Deoxyadenosine)(Deoxyadenylate) (Deoxyguanosine)(Deoxyguanylate) (Deoxycytidine)(Deoxycytidylate) RNA (DNA) Nomenclature of the nucleotides

Nucleotides contain only the cyclic form 1’ 2’3’ 4’ 5’ Ribose can exist in four different “puckered” conformations D-ribose

Nucleotides consist of: 1. a nitrogenous base 2. a ribose sugar 3. a phosphate group (or more) N-glycosidic bond phosphoester bond

Nucleotides are formed by the removal of water phosphoester bond N-glycosidic bond

Conformations of Bases when attached to Ribose Purines in syn or anti when attached to ribose (only anti in DNA) Pyrimidines only in anti when attached to ribose

Hydrolysis of phosphoanhydrides  30kJ/mol Hydrolysis of phosphoester  14kJ/mol phosphoester bond Nucleoside monophosphates (NMPs) can become NDPs and NTPs phosphoanhydride bonds

Functions of nucleotides Deoxyribonucleotides —dNTPs are building blocks for making DNA Ribonucleotides —NTPs are building blocks for making RNA —ATP drives many reactions —GTP for protein synthesis (initiation and elongation) —CTP for lipid synthesis (CDP supplies the phosphate group in glycerophospholipids —UTP for carbohydrate metabolism (UDP-glucose + fructose  sucrose) —Cyclic nucleotides (cAMP and cGMP) are signal molecules (epinephrine pathway)

Unusual bases of RNA Inosine -non W-C base-pairing  ”wobble” -can hydrogen bond w/ A, C, U