Nucleic Acids Biochem 4511 Chapter 3 Figures from Essentials of Biochemistry 3rd Ed OSU Custom Edition Lehninger Principles of Biochemistry 4th 5th Ed Voet Voet Biochemistry 3E Voet Voet Pratt Fundamentals of Biochemistry 2E Nucleic Acids Related topics including nucleic acid properties transcription and translation are covered extensively in Molgen 4500 taken by the majority of our students Here we cover nucleic acids as biomolecules to provide foundational knowledge Nucleotides Nucleosides and Bases Nucleotides Nucleosides and Bases Base Aromatic heterocyclic molecules that provide the name and identity for different nucleotides Nucleosides Bases plus a 5 membered sugar ring derivative ribose which differs between DNA deoxyribonucleic acid and RNA ribonucleic acid Nucleotides Base plus ribose plus phosphate group that links nucleotides together through the phosphate backbone Know these and their structures Bases Base Aromatic heterocyclic molecules that are different between the nucleotides 2 primary types Purines and Pyrimidines Purine Pyrimidine PURINES Bases Adenine Guanine Same bases rotate 180 PYRIMIDINES DNA Bases PYRIMIDINES RNA Cytosine Uracil Nucleosides Nucleosides Bases plus a pentose derivative Nucleotides Nucleotides Includes phosphate at C3 and or C5 positions Nucleotides are the monomer unit of DNA and RNA Nucleotides Most often 5 phosphate Nucleotides Don t memorize but derive cAMP Nucleotide derivatives CoA will see often in metabolism Citric acid cycle Fatty acid metabolism Etc Don t memorize just concept Oxidation reduction NAD NADH Electron transfer Cofactor in other enzyme pathways Nucleic Acids Default 5 3 Individual nucleotide formally called a residue Phosphodiester bond Dinucleotide 2 nucleotides Trinucleotide 3 nucleotides Oligonucleotide many RNA vs DNA Stability RNA is readily hydrolyzed in basic conditions History DNA carries genetic information 1952 Hershey Chase Experiment Two batches 32P labeled DNA 35S labeled protein 32P was found in infected cells producing progeny phage 32S was not DNA is the hereditary information For history History Chargaff Base Content Rules 1 Base composition of DNA varies from one species to another 2 DNA specimens from different tissues of one species have the same base composition 3 Base composition of DNA in a given species does not change with 4 age nutritional state or environment In all cellular DNA the percentage composition A T and G C In addition and related the total purine total pyrimidine ie A G T C For fun and history Enol Keto tautomers In 1953 crystallographer Jerry Donahue provides evidence that bases are primarily in keto forms in DNA This is important for hydrogen bonding and for hydrophobic effect For fun and history Searching for the Double Helix For fun and history DNA Double Helix B form DNA Major Groove Two strands wrapping around a common axis with right handed twist to form a double helix Minor Groove Bases occupy the core of the helix sugar phosphate chains are on the outside Each base has a Watson Crick pairing to generate a planar H bonded pair DNA Double Helix Antiparallel strands note 3 and 5 Diameter 20 Rise per turn 34 and 10bp base pairs Negative charge of phosphate repulses Mg2 and Mn2 can stabilize Bases stack in middle Watson Crick Pairings Major Groove Minor Groove DNA Replication It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material Watson Crick Nature 1953 Base pairing supports information transfer by templating Parent strand contains all information required for formation of daughter strand 5 3 Meselson Stahl 1958 DNA replication is semi conservative Analysis by 15N labeling and ultracentrifugation Density gradient equilibrium sedimentation in cesium chloride For history and awesomeness DNA damage Pyrimidine Dimers Many types of DNA damage interfere with accurate replication Forces in DNA Hydrogen Bonding Note the register of hydrogen bonding donors line up with acceptors AT 2 H bonds GC 3 H bonds Forces in DNA base stacking Bases in double helix are stacked Distance between bases is 3 4 same size as predicted by van der Waals interactions stacking DNA Detection Intercalation Ethidium Bromide with Br counterion DNA on agarose gel Highly aromatic compounds can intercalate slip in between the stacked bases sharing stacking Ethidium becomes much more fluorescent after intercalation can be visualized under UV light Intercalating compounds are carcenogenic interfere with DNA polymerase during replication No need to memorize just very interesting N NH2H2N Forces in DNA Hydrophobic Effect Hydrophobic bases excluded from water Hydrophilic phosphate sugar backbone interacts with water DNA double helix can be denatured Monitoring DNA structure UV detection Hyperchromic effect Environment of the base affects UV absorbance Implications of Hydrogen Bonding Don t memorize numbers but be able to predict pattern Implications of Hydrogen Bonding Tm 4 of G C pairs 2 of A T pairs Don t memorize numbers but be able to predict pattern Other Nucleic Acid Structures Left tRNA Right DNA RNA hybrid helix Structural variance in DNA RNA backbone Ring pucker don t memorize this Ribose is puckered 2 hydroxyl changes conformational preferences DNA vs RNA Syn anti base configurations Don t memorize this either Other nucleic acid double strand helices Don t need to memorize this Non helical DNA Self complementary Hoogsteen pairing Extra Don t need to memorize this Complex Functional Ribosome Ribosome ribonucleoprotein complex carries out transcription Other functional RNAs Ribozymes catalyze reactions What does it mean to go from genes to proteins Central dogma simple view Genes are sequences of DNA Replication copying DNA Transcription converting DNA into RNA Reverse transcription converting RNA into DNA Translation making proteins from an RNA template Transcription Translation Transcription RNA polymerase makes transcription bubble Coding sense strand separates from noncoding antisense strand RNA transcript is complementary to antisense strand same as coding strand RNA produced is messenger RNA or mRNA Translation tRNA Aminoacylation covalently link amino acid Anticodon which amino acid Translation Genetic Code Codon Chart Do not memorize PCR Polymerase Chain Reaction Very important in molecular biology biotechnology medicine genome sequencing forensic chemistry to be an educated citizen And we aren t discussing