Basic Molecular Biology for CS374OverviewBioinformatics schematic of a cellSlide 4Slide 5Watson and CrickSlide 7Nucleic acids (DNA and RNA)NucleotidesMonomers of DNAMonomers of RNASlide 12Slide 13Slide 14Slide 15ProteinsSlide 17DipeptideProtein structureDNA in actionThe need for an intermediaryThe IntermediaryNext question…The Genetic CodeSlide 25TranslationtRNASlide 28Slide 29The gene and the genomeMore complexitySplicingCentral Dogma of Molecular BiologyCentral dogmaTranscription – key stepsSlide 36Slide 37Slide 38Slide 39PromotersSlide 41Computer Scientists vs Biologists (courtesy Steven Skiena, SUNY Stony Brook)Computer scientists vs BiologistsSlide 44Slide 45Slide 46Slide 47Slide 48Computer Science is to Biology what Mathematics is to PhysicsBasic Molecular Biology for CS374Scientific Method: The widely held philosophy that a theory can never be proved, only disproved, and that all attempts to explain anything are therefore futile.OverviewStructures of biomoleculesHow does DNA function?What is a gene?Computer scientists vs BiologistsBioinformatics schematic of a cellMacromolecule (Polymer)MonomerDNA Deoxyribonucleotides (dNTP)RNA Ribonucleotides (NTP)Protein or Polypeptide Amino AcidWatson and CrickNucleic acids (DNA and RNA)Form the genetic material of all living organisms.Found mainly in the nucleus of a cell (hence “nucleic”)Contain phosphoric acid as a component (hence “acid”)They are made up of nucleotides.NucleotidesA nucleotide has 3 componentsSugar (ribose in RNA, deoxyribose in DNA)Phosphoric acidNitrogen base Adenine (A)Guanine (G)Cytosine (C)Thymine (T) or Uracil (U)Monomers of DNAA deoxyribonucleotide has 3 componentsSugar - DeoxyribosePhosphoric acidNitrogen base Adenine (A)Guanine (G)Cytosine (C)Thymine (T)Monomers of RNAA ribonucleotide has 3 componentsSugar - RibosePhosphoric acidNitrogen base Adenine (A)Guanine (G)Cytosine (C)Uracil (U)NucleotidesPhosphate GroupSugarNitrogenousBasePhosphate GroupSugarNitrogenousBaseTCACTGGCGAGTCAGCGAGUCAGCDNA RNAA = TG = CT UComposed of a chain of amino acids. R | H2N--C--COOH | HProteins20 possible groupsR R | | H2N--C--COOH H2N--C--COOH | | H H ProteinsDipeptide R O R | II | H2N--C--C--NH--C--COOH | | H H This is a peptide bondProtein structureLinear sequence of amino acids folds to form a complex 3-D structure.The structure of a protein is intimately connected to its function.DNA in actionQuestions about DNA as the carrier of genetic information:How is the information stored in DNA?How is the stored information used ?Answers:Information is stored as nucleotide sequences... and used in protein synthesis.The need for an intermediaryFact 1 : Ribosomes are the sites of protein synthesis.Fact 2 : Ribosomes are found in the cytoplasm.Question : How does information ‘flow’ from DNA to protein?The IntermediaryRibonucleic acid (RNA) is the “messenger”.The “messenger RNA” (mRNA) can be synthesized on a DNA template.Information is copied (transcribed) from DNA to mRNA. (TRANSCRIPTION)Next question…How do I interpret the information carried by mRNA?Think of the sequence as a sequence of “triplets”.Think of AUGCCGGGAGUAUAG as AUG-CCG-GGA-GUA-UAG.Each triplet (codon) maps to an amino acid.The Genetic Codef : codon amino acid1968 Nobel Prize in medicine – Nirenberg and KhoranaImportant – The genetic code is universal!It is also redundant / degenerate.The Genetic CodeTranslationThe sequence of codons is translated to a sequence of amino acids.Transfer RNA (tRNA) – a different type of RNA.Freely float in the cytoplasm.Every amino acid has its own type of tRNA that binds to it alone.Anti-codon – codon binding crucial.Show animationtRNAtRNAtRNAThe gene and the genomeA sequence of nucleotides on the DNA that encodes a polypeptide is called a gene.Genome = Set of all genes in the organism.More complexityThe RNA message is sometimes “edited”.Exons are nucleotide segments whose codons will be expressed.Introns are intervening segments (genetic gibberish) that are snipped out.Exons are spliced together to form mRNA.SplicingfrgjjthissentencehjfmkcontainsjunkelmthissentencecontainsjunkCentral Dogma of Molecular BiologyDNA RNA Protein Phenotype Transcription : DNA RNATranslation : RNA ProteinCentral dogmaDNAtRNArRNAsnRNAmRNAtranscriptiontranslationPOLYPEPTIDEZOOM INTranscription – key stepsInitiationElongationTermination+DNARNADNATranscription – key stepsInitiationElongationTerminationDNATranscription – key stepsInitiationElongationTerminationDNATranscription – key stepsInitiationElongationTerminationDNATranscription – key stepsInitiationElongationTermination+DNARNADNAPromotersPromoters are sequences in the DNA just upstream of transcripts that define the sites of initiation.The role of the promoter is to attract RNA polymerase to the correct start site so transcription can be initiated.5’Promoter3’PromotersPromoters are sequences in the DNA just upstream of transcripts that define the sites of initiation.The role of the promoter is to attract RNA polymerase to the correct start site so transcription can be initiated.5’Promoter3’Computer Scientists vs Biologists(courtesy Steven Skiena, SUNY Stony Brook)Computer scientists vs Biologists(Almost) Nothing is ever completely true or false in Biology.Everything is either true or false in computer science.Computer scientists vs BiologistsBiologists strive to understand the very complicated, very messy natural world.Computer scientists seek to build their own clean and organized virtual worlds.Computer scientists vs BiologistsBiologists are more data driven.Computer scientists are more algorithm driven.One consequence is CS www pages have fancier graphics while Biology www pages have more content.Computer scientists vs BiologistsBiologists are obsessed with being the first to discover something.Computer scientists are obsessed with being the first to invent or prove something.Computer scientists vs BiologistsBiologists are comfortable with the idea that all data has
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