Proteins Determine Function • Proteins make us tick • Problems occur when – Proteins are missing – Proteins are malfunctioning – Proteins are present that should not be there • Controlling disease – Understanding protein function – Stopping protein function – Supplying missing/desired protein function 06/27/22 1 Sequence Alignment
Proteins Determine Function. Proteins make us tick Problems occur when Proteins are missing Proteins are malfunctioning Proteins are present that should not be there Controlling disease Understanding protein function Stopping protein function Supplying missing/desired protein function. - PowerPoint PPT Presentation
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Proteins Determine Function• Proteins make us tick• Problems occur when
– Proteins are missing– Proteins are malfunctioning– Proteins are present that
should not be there• Controlling disease
– Understanding protein function
– Stopping protein function– Supplying missing/desired
protein function
04/21/23 1Sequence Alignment
The Central Dogma
04/21/23 2Sequence Alignment
The Human Genome
• The entire collection of our DNA– Consists of about
3.5x109 base pairs
• Our genome is split across chromosomes– Makes packaging
easier/more efficient
04/21/23 3Sequence Alignment
Human Genome Project• Began in 1990, a 13-year effort coordinated by the
DOE and the NIH. Project goals included:– identify all the approximately 30,000 genes in human DNA,– determine the sequences of the 3 billion chemical base
pairs that make up human DNA,– store this information in databases,– improve tools for data analysis,– transfer related technologies to the private sector, and.– address the ethical, legal, and social issues.
• The Human Genome Project ended in 2003 with the completion of the human genetic sequence.
04/21/23 4Sequence Alignment
DNA Sequencing
• Determining the sequence of nucleotides in a strand of DNA– 1978 Sanger
• Determined the DNA sequence for phi-x 174• 3.5x103 base pairs• Took about 2 years to sequence
– 2001 Venter/Celera• Sequenced the human genome• 3x109 base pairs• Took about 9 months to sequence
04/21/23 5Sequence Alignment
Sequence DataTCTAGGAGGGAAGCACCCACCTCCCCTAAGCTCCATCTCCCTGAGCACTCATTTCCCAATGACCATACCAGGTTTTGGCCCTAGAGAGTTTATTACAAAATAAGAAAGAGAAGTCTGGGGAAGGTTCACTCATCATAGAATTTTGGCAGTTCATTGCCCAAGATGACTCGATGGTCCACACCGGCAGCTGTAATAGTGACCAGGTAGATGACACCCCCGCTTGAGCCATCCCGGCTCATGGCCAGAGCAATAGCTGCAGAGGGTTTCAAGTTGGAGAGAGGGAGAGAGAGGATGGCTTAGCTTCAAAAATCTTTTTACTCCCCCTCCATCCATATGCCTACTACCACTTTCACCTCAAAACTCATCTTCCAGGAAGGCATATTTAGTGGTGTGCTGGTAAATCAGTTTTTTTACAAAAAGGCTTCCATATGTGGCATCTGCTGATGTCCGTGGTGTAAATGCTCCCGCTATGATGAATTGCAAGTTACAAATAGCTAAGCAGTTCACAAATCCTTGACTATTTAACAGTCCGCTCTCATGAGTGGTCCCAAGCCAGCCTCAGCACACCTCAGCACACCACTGGTTCTTTTTTTTTTTTTTTTTCTCCAGACAGGGTCTCTCTCTGTCACCTAGGCTGCAGCGCAGTGGTGCAATCACCGCTCACTACAGCCTTGATCTCCCCGGCTCAGATGATCTTTCCACCTCAGCCTCCTGAGTAGCTGGGACTACAGGTGTGCACCACTATGCCCAGTTCATTTTTTTTTTTACTTTTTTTTATTGTTTTTTGTGGAGACAGGGTTTCACCATCTTGCCTAGGCTGGCCTCAAACTCCTGGGCTCAAGTAATCCTCCTGCCTCAGCCTCCCAAATTGTTGGCATTACAGGTGTGAGCCACTGTGCTTAGCACACCACTGGTTCTCACAGTGACTGTGTATCCTCATTTGATTTACTCAGAACAGCCCTGGTTTATCCGTATTGCCCAAGAACCCCATTGAGCTTTGCATTTGTCCTGCCCCTTTTCACTCTTAAAAGTGTACCAGGCCCGGCATTAACTTAAATGGCCACCCCTGTATTTCTCTTCCTGTTCCTCATAATCTACTTCCTTCCCATGTTTCAAAGCCCTCCCCAGGTACCCTTCCACTTGGCTGGTTACCGTCTGTGGTGAAGCGCCTGCACTCCTCGGGAGACATGCCTGGCTTATATGCTGCATCCACATAACCATAGATAAAGGTGCTGCCGGAGCCACCAATGGCAAAAGGCTGTCGAGTCAGCATTCCTCCCAGGGTTCCATATACCTGGGAAAGGGATCCTCAGGTTAAAGAATCATCAAGCCCTTCCTTCCCACTGAGACATTAAGTGGTCTCTGCACCCTGCAATGAAGCCCTGGTATCTCATATCCCCAAAGTACTATGCTTTCAGAGGTAGTGTCCTTGGAACTCATTGCTAGAATGACATAGGACTTCCATCTTCCTCTGCAGGAGAGTGGGGAAGCCCAGAGGAGAGAGTGCTTTGGGAGAAACTCACCTGACCTCCTTCACGTTGGTCCCAGCCAGCTACCATGAGATGTGCAGACAAGTCCTCTCGATATTTATAGCTGATATTTCTCACCACATTTGCAGCAGCCAAAACAAGTGGAGGTTCCTCCAGTTCTATCCTGAGGGAAATATTAGGAATAAAGGTTGATAGAATTTTAAGTCTCATTCTCCTATACTGTTACCATCATCCCTGCTAAACGACCCCTGAAAACTGTAACTGCAATAGCTCAAACTGCAGCCTCCCTCCCACATGTACAGGGGAACCAGAGTCCCACACCACCAACTGGTAAGAAGCTTTCAATTGCTCACTCTTTTGCTCAGCCCCACCCACATAACTTTCTTTTGGCTGCAAGGACCCTGCTCTTATGGGGAAAAGCAGATAAGGTTCACTCGGTTCACCACCGCCTCGCTGTCAGGAGGGAGTCAACAGTCACCAAGTTAAAACTCAGGTTTTTTTTTTTTTTTTTTTTTTTTGAGACAGTCTCACTCTGTCACCCAGGCTGGAGTGCAGTGGATCAATCTTGGGCTCACTGCAAACTTCGCCTCCCTGGTTCAAGTGATTCTCCTGCCTCAGCCTCCCGAATAGCTGGGATTACAGGCACCCACCACCAAGCCCAGCTAATGTTTGTATTTTCAGTAGAGACAAGGTCCCAACATGTTGGCCAGGCTGGTCTCAAACTCCTGACCTCAAATATCTGCCCACCTCGGCATCCCAAAGTGCTGAGATTATAGATGTGAGCCACTGCACCCAACCAGAACTCAGGAATTTTTGAGGGTGATCATTCAATGTCTCTCAAATTTCTTTGACAAGAGAATAGCATGAAGTTTAATGCTTGGATTAAAGCAGGAGGCAAATAATCATCTCAGATATTATTAATCACTGCAGATGTTAATCAAAATTAGGCTTATTTTTCAGGCTTAGATTTTATAACAAAGCAAAAAATGCTAAGGTAAGAAAAATATGCCTCATCAATTTTCTTTGCTATTAACAATCTTGAGAGAGTTATGTTCTATGGAACATAATGTCAGTAATATTGACCTAACCCCATATACTCATTTTGCATGTGAGGAAATTGGTTAGGAGTGGGAGAAGAGACAAAATAGTTCAATATATGGTAAATGAGAAACCAGGTATCTGCTTGACAGAATCATCTTTTTGATCCCTAAGCACAGATGGAAAGAAGACCCTCAAAAATCTATCTCCTGTCCCCCTCTCAGACCCTATTCCTTTACTCATCCCTGTACACTACTGGGACAGGTCACATACACATTCAGACCCCAGATCCTCCTCCACAAATTCAGAGACCCAAGCACCCACCAAATAGCTTATCATAGTGGCTTTTGGGGAAGGTCAACTCCATTCCTCCAAGGCTCCAGTTTGCCAGTCTTTTCATGAATGGGTAAGGAAAGTGTGTATTTGAGGCCATTAGCTTCTTTCCAAATGCATACATCTTCACTTTTACTCACCCTGCAGACACTCGGGAATCAGAACCCATCACAACGCCCCCGTCAAACTCCACTGCCATGATGGTGGTCTGCAGAGACACAGAATATGGAATGTCAGGGCAAGAACAGCCTTGATGCCCTCATGTTAGAGAAGAAGAAACATTCCCAGAGAGGCGAAGTGACTGGCTCAAAGATTACACAGTAACAGGCCAGAGCTGACTGTCAGTACAGGCTTTTTTTCCCTTCATCTTTCCACTTTCTCTATTGCTTCATCCGGCTGCAGGGGAATGCCACAGCCCAGCTGTGATACAACACAGAAAGAACTGTGTCCCTAAGTTCCAACTTGCCTAGTGGAATCCTCTCCACTGTAGAGAGGTGGAG…….. 19,000 base pairs omitted!!!
04/21/23 6Sequence Alignment
Genes
• Definition varies– To a geneticist a gene is the region of a
chromosome that confers a particular trait– To a molecular biologist a gene is a sequence of
DNA which encode a protein or RNA and includes all of the relevant regulatory sequences• Genes can be turned on/off, up/down
• Not all parts of the DNA sequence are involved with the production of proteins
Predict Protein Sequence>18:21:37|GENSCAN_predicted_peptide_2|966_aaMASSRCPAPRGCRCLPGASLAWLGTVLLLLADWVLLRTALPRIFSLLVPTALPLLRVWAVGLSRWAVLWLGACGVLRATVGSKSENAGAQGWLAALKPLAAALGLALPGLALFRELISWGAPGSADSTRLLHWGSHPTAFVVSYAAALPAAALWHKLGSLWVPGGQGGSGNPVRRLLGCLGSETRRLSLFLVLVVLSSLGEMAIPFFTGRLTDWILQDGSADTFTRNLTLMSILTIASAVLEFVGDGIYNNTMGHVHSHLQGEVFGAVLRQETEFFQQNQTGNIMSRVTEDTSTLSDSLSENLSLFLWYLVRGLCLLGIMLWGSVSLTMVTLITLPLLFLLPKKVGKWYQLLEVQVRESLAKSSQVAIEALSAMPTVRSFANEEGEAQKFREKLQEIKTLNQKEAVAYAVNSWTTSISGMLLKVGILYIGGQLVTSGAVSSGNLVTFVLYQMQFTQAVEVLLSIYPRVQKAVGSSEKIFEYLDRTPRCPPSGLLTPLHLEGLVQFQDVSFAYPNRPDVLVLQGLTFTLRPGEVTALVGPNGSGKSTVAALLQNLYQPTGGQLLLDGKPLPQYEHRYLHRQVAAVGQEPQVFGRSLQENIAYGLTQKPTMEEITAAAVKSGAHSFISGLPQGYDTEVDEAGSQLSGGQRQAVALARALIRKPCVLILDDATSALDANSQLQVEQLLYESPERYSRSVLLITQHLSLVEQADHILFLEGGAIREGGTHQQLMEKKGCYWAMPTEFFQSLGGDGERNVQIEMAHGTTTLAFKFQHGVIAAVDSRASAGSYISALRVNKVIEINPYLLGTMSGCAADCQYWERLLAKECRLYYLRNGERISVSAASKLLSNMMCQYRGMGLSMGSMICGWDKKGPGLYYVDEHGTRLSGNMFSTGSGNTYAYGVMDSGYRPNLSPEEAYDLGRRAIAYATHRDSYSGGVVNMYHMKEDGWVKVESTDVSDLLHQYREANQ