Current Topics in Computer Science: Computational GenomicsTemporary course websiteMolecular Biology PrimerReview of molecular biology for computer scientistsAll Life depends on 3 critical moleculesAll 3 are specified linearlyCentral Dogma of Biology: DNA, RNA, and the Flow of InformationDNADNARNA (ribonucleic acid)Types of RNATranscriptionMore complex genesTerminologyRNA secondary structuresGene expressionProteins: Workhorses of the CellThe genetic code: RNA→proteinSlide 19Protein FoldingSlide 21Experimental methodsAnalyzing a Genome: 3 stepsPolymerase Chain Reaction (PCR)Copying DNA: CloningCutting DNA: Restriction EnzymesSlide 27Measuring DNA: ElectrophoresisReading/Sequencing DNA: ElectrophoresisReading/Sequencing DNA: Gene chipsComputational GenomicsWhat is Bioinformatics?What is computational biology?Why computational biology?Biological DatabasesProblems in computational biologyData storageAssembling genomesAssembling genomes: ComplexitiesPattern matching / discoveryPattern matching / discovery (cont’d)Sequence similarity searchesSequence similarity searches IIGene chip analysisStructure to FunctionComparative genomicsNetwork determinationPredict protein functionModelingThe future…Current Topics in Computer Science: Computational Genomics CSCI 7000-005Debra [email protected] course websitehttp://llama.med.harvard.edu/~goldberg/cuMolecular Biology PrimerAngela Brooks, Raymond Brown, Calvin Chen, Mike Daly, Hoa Dinh, Erinn Hama, Robert Hinman, Julio Ng, Michael Sneddon, Hoa Troung, Jerry Wang, Che Fung Yungwww.bioalgorithms.infoAn Introduction to Bioinformatics AlgorithmsReview of molecular biology for computer scientistsAll Life depends on 3 critical molecules•DNA•RNA•ProteinAll 3 are specified linearly•DNA and RNA are constructed from nucleic acids (nucleotides) •Can be considered to be a string written in a four-letter alphabet (A C G T/U) •Proteins are constructed from amino acids •Strings in a twenty-letter alphabet of amino acidsCentral Dogma of Biology: DNA, RNA, and the Flow of Information TranslationTranscriptionReplicationDNA•DNA provides a code, consisting of 4 letters.•Each nucleic acid (or base) is always paired with it’s designated complement on the other strand of the double helix:•A and T are complementary•C and G are complementaryDNA•DNA has a double helix structure. •It is not symmetric. It has a “forward” and “backward” direction. The ends are labeled 5’ and 3’. •DNA always reads 5’ to 3’ for transcription replicationACTTCGCAACAGTGAAGCGTTGTC5’3’3’5’RNA (ribonucleic acid)•Similar to DNA chemically •Usually only a single strand•Built from nucleotides A,U,G, and C with ribose (ribonucleotides) •T(hyamine) is replaced by U(racil)Types of RNA•mRNA – carries a gene’s message out of the nucleus. •The type “RNA” most often refers to.•tRNA – transfers genetic information from mRNA to an amino acid sequence•rRNA – ribosomal RNA. Part of the ribosome. •involved in translation.•siRNA – small i nterfering RNA. Interferes with transcription or translation. Recent discovery.Transcription•The process of making RNA from DNA•Needs a promoter region to begin transcription.More complex genesExonsControl regionsSplicingTranscriptionTerminology•Exon: A portion of the gene that appears in both the primary and the mature mRNA transcripts.•Intron: A portion of the gene that is transcribed but excised prior to translation. •Junk DNA: Any DNA not contained in exons.•NOT junk•Many functions, some known, some unknownRNA secondary structures •Some forms of RNA can form secondary structures by “pairing up” with itself. This can change its properties dramatically.http://www.cgl.ucsf.edu/home/glasfeld/tutorial/trna/trna.giftRNA linear and 3D view:Gene expression•Human genome is ~ 3 billions base pair long•Almost every cell in human body contains same set of genes•But not all genes are used or expressed by those cells•Different cell types•Different conditionsProteins: Workhorses of the Cell•20 different amino acids •Proteins do essential work for the cell•cellular structures•enzymes•transmit information•Proteins work together with other proteins or nucleic acids as "molecular machines" •structures that fit together and function in highly specific, lock-and-key ways.The genetic code: RNA→protein•Three bases of RNA (called a codon) correspond to one amino acid. •Degenerate: several codons for one AA•Always starts with Methionine and ends with a stop codonTerminology•Codon: The sequence of 3 nucleotides in DNA/RNA that encodes for a specific amino acid. •mRNA (messenger RNA): A ribonucleic acid whose sequence is complementary to that of a protein-coding gene in DNA.Protein Folding•Proteins are not linear, they fold into 3D structures•A protein’s structure determines how the protein can functionProtein Folding•Proteins fold predominantly into •α-helices, •β-sheets, and •turnsUbiquitinImage from wisc.eduExperimental methodsAnalyzing a Genome: 3 steps•Copy DNA many times • make it easier to see and detect•Cut it into small fragments •Read small fragmentsPolymerase Chain Reaction (PCR)•Problem: Cannot easily detect single molecules of DNA •Solution: PCR massively replicates DNA sequences•Doubles the number of DNA fragments at every iteration 1… 2… 4… 8…Copying DNA: Cloning•DNA Cloning•Insert DNA fragment into the genome of a living organism and watch it multiply.•Once you have enough, remove the DNA.Vector DNACutting DNA: Restriction Enzymes•Restriction Enzymes cut DNA•Only cut at special sequencesBal I ---TGGCCA--- ---ACCGGT--- ---TGG CCA--- ---ACC GGT---EcoR I ---GAATTC--- ---CTTAAG--- ---G AATTC--- ---CTTAA G---Blunt ends Staggered (“sticky”) endsCutting DNA: Restriction Enzymes•DNA contains thousands of these sites.•Applying different Restriction Enzymes creates fragments of varying size.Restriction Enzyme “A” Cutting SitesRestriction Enzyme “A” & Restriction Enzyme “B” Cutting SitesRestriction Enzyme “B” Cutting Sites“A” and “B” fragments overlapMeasuring DNA: Electrophoresis•A gel•Backbone of DNA is highly negatively charged•DNA will migrate in electric field•Determine DNA fragment sizes •Compare their migration in the gel to known size standards•Use 2D gel to separate