TRANSCRIPTIONTRANSLATIONBIG PICTURESMisunderstandings About GenesNext Class:BENG 500BENG 500--1111CSCE 510CSCE 510--33INTRODUCTION TO COMPUTATIONAL BIOLOGYINTRODUCTION TO COMPUTATIONAL BIOLOGYMolecular Biology Review IIMolecular Biology Review IIJin-Woo KimDepartment of Biological and Agricultural EngineeringThe University of Arkansas – FayettevilleGenetic/Molecular Biological TermsGenetic/Molecular Biological Terms••Class Class Webpage Webpage ––“Terms in “Terms in Mological Mological Biology”Biology”oror••Dictionary of Genetic TermsDictionary of Genetic Termshttp://www.http://www.ornlornl..govgov//hgmishgmis//publicatpublicat/primer2001/glossary.html/primer2001/glossary.htmlDNA DNA is the Genetic Material of All Life on Earth.is the Genetic Material of All Life on Earth.STRUCTURE OF DNASTRUCTURE OF DNA• Nucleotide (deoxynucleotide) – the essential building block of the DNA molecule• Only six components• A sugar molecule – deoxyribose• A phosphate group• Four different nitrogen-containing bases – adenine, guanine, cytosine, and thymine.- All information is in the four bases• Polynucleotide – strings of nucleotides attached together by ‘phosphodiester bond’Structural elements – sugar-phosphate backboneNucleotideNucleotidePolynucleotidePolynucleotideThe Genetic MaterialThe Genetic Material••Complementary base pairsComplementary base pairs• The key to the transmission of genetic information lies in a characteristic of the bases: A and T together form a stable chemical pair, and C and G form a second stable pair.• Hydrogen bonds• AntiparallelDNA FUNCTIONDNA FUNCTION••Faithful ReplicationFaithful ReplicationCentral Player = DNA DNA polymerasepolymerase- Correct mistakes by itself – Proofreading- Error: 1 per 109 bpCentral DogmaDNA FUNCTIONDNA FUNCTION• Information Transmission“Central Dogma of Molecular Biology”TRANSCRIPTIONTRANSCRIPTIONCentral Player = RNA RNA polymerasepolymerasePROMOTORPROMOTOR– A special sequence of DNA bases that tells the RNA polymerase to start sythesize RNABacterial PromoterBacterial Promoter*Eukaryotic promotorsEukaryotic promotors are more variable and complicated.• TATA box: 30 bases upstream (Yeast); 60 bases upstream (mammals)• CCAAT and GC-rich sequence: Further upstreamGene Expression RegulationGene Expression RegulationGENE SPLICINGGENE SPLICING––Occurring in Occurring in EUKAYRYOTIC CELLSEUKAYRYOTIC CELLS; NOT in bacteria; NOT in bacteriaBacteria Bacteria -->90% Coding DNA; Human >90% Coding DNA; Human --<10% Coding DNA<10% Coding DNA––IntronsIntrons – Noncoding DNA––Exon Exon – Coding DNAAnother Difference:Another Difference:• Prokaryotic mRNA = PolycistronicPolycistronic [w/information for more than one protein]• Eukaryotic mRNA = MonocistronicMonocistronic [w/information for only one protein]DNA vs. RNADNA vs. RNATRANSLATIONTRANSLATIONCentral Players = Ribosome and Ribosome and tRNAtRNA* Open Reading Frames (ORFs) = Strings of codons uninterrupted by stop codons20 Amino Acids20 Amino AcidsAmino AcidsAmino AcidsGeneral Structure of Amino AcidsCoding Assignments of the 64 Triplet Coding Assignments of the 64 Triplet CodonsCodonsStart Codon = AUG (Methionine)Stop Codon = UAA; UAG; UGADegeneracy – More than on codon for an amino acidPROTEIN STRUCTUREPROTEIN STRUCTUREChemical BondsChemical BondsHydrogen BondingHydrophobic Interaction- Hydrophobic – “afraid of water”; Hydrophilic – “water friendly”Secondary StructureSecondary Structure--Structural MotifsStructural Motifsα-Helix β-SheetQuaternary StructureQuaternary StructureTertiary StructureTertiary StructureBIG PICTURESBIG PICTURESDNA molecule is a marvelous storehouse of complicated informatioDNA molecule is a marvelous storehouse of complicated information:n:––BlueprintsBlueprints for the amino acid sequences of every protein an organism makes.––Traffic signalsTraffic signals that direct the cell to interpret the information properly.CENTRAL DOGMACENTRAL DOGMAProkaryotesProkaryotesEukaryotesEukaryotesMisunderstandings About GenesMisunderstandings About Genes• “Genes make proteins”Genes contain information for making proteins. However, proteins are made by other proteins that use the gene as a manufacturing guide. Proteins cannot manufacture proteins without guide, but the guide alone is not sufficient for protein production.• “Genes are on chromosomes”Genes are not “on” chromosomes. A chromosome is composed of a very long molecule of DNA that isbound to proteins named histones. A gene is a given length of DNA that is translated into a chain of amino acids. The genes plus the bound proteins are the chromosome.• “Genes replicate themselves”Genes do not replicate themselves. Proteins replicate genes using the gene as a guide.• “DNA is like a blue print”DNA is much more than architectural blueprints. DNA is like a blueprint because it contains information for building proteins just as architectural blueprints contain information for building a structure. However, DNA not only has information for building the structure of an organism but it also contains information for making enzymes, hormones, receptor molecules, transport proteins, and antibodies.• “Genes determine who we are”Genes do not determine who we are. Genes ‘influence’ who we are. Genes are only one factor that contribute to a trait (phenotype), many genes influence a single trait, and any one gene affects many traits.Next Class:Next Class:Molecular Biology ToolsMolecular Biology