a super quick introduction to molecular biology and genomics · 2018-01-31 · a super quick...
TRANSCRIPT
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A super quick introduction to molecular biology and
genomics
Héctor Corrada Bravo Dept. of Computer Science
Center for Bioinformatics and Computational BiologyUniversity of Maryland
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Keyterms• Genotype/Phenotype• Cell• Proteins• Evolu6on:inheritance,selec6on,varia6on• DNA/RNA• Chromosome• Gene• Genome• Replica6on• Transcrip6on• Exon/Intron• Transla6on• Codon• CentralDogma• GeneExpression• Regula6on• Epigene6cs
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Whyaremychildrensuchpigs?
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WhyamIsuchapig?
Phenotype,cells,metabolism,protein
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Proteins• phenotype:characteris6cs(traits)ofanorganism• characteris6csduetocellularstructuresandac6vi6es–mostlycarriedoutbyproteins
• Examples:
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alpha-kera7n componentofhair
insulin regulatesbloodglucoselevel
ac7n&myosin musclecontrac7on
hemoglobin oxygentransport
DNApolymerase synthesisofDNA
DNAglycosylases DNArepair
matrixmetalloproteinase extra-cellularmatrixdegrada7on
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Gene6cs
• gene:inclassicalgene6csitwasanabstractconcept– aunitofinheritancepassedfromparenttooffspring– specifyproteins
• genomereferstothecompletesetofgenes• genotype:gene6ccharacteris6csofanindividual
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Hector Corrada Bravo
What is Genomics?
• Study the molecular basis of variation in development and disease
• Using high-throughput experimental methods
• algorithms
• ML
• data management
• modeling
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cancer
healthy
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WhatisGenomics?• Eachcellcontainsacompletecopyofanorganism’sgenome,orblueprintforallcellularstructuresandac6vi6es.
• Thegenomeisdistributedalongchromosomes,whicharemadeofcompressedandentwinedDNA.
• Cellsareofmanydifferenttypes(e.g.blood,skin,nervecells),butallcanbetracedbacktoasinglecell,thefer6lizedegg.
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Chromosomes
Theseareactuallyhuman.Andforadownsyndromepa6ent
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DNA
WatsonandCrick1953
DNAs(Deoxyribonucleicacids)aremoleculestostoregene6cinforma6onofalivingorganism.
DNAconsistsoftwopolymersmadefromfourtypesofnucleo6des:adenine(A)guanine(G),cytosine(C)andthymine(T).
Purines:A,G;Pyrimidines:C,T
Twopolymersarecomplementarytoeachotherandfromadouble-helixstructure
5’-ACCGTTCGACGGTAA-3’ ||||||||||||||| 3’-TGGCAAGCTGCCATT-5’
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chromatin
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Measurement
• Forasmallenoughpiece,wecanmeasurethesequenceofbases,referredtoassequencing
• HumanGenomeProject
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GenomeTCAGTTGGAGCTGCTCCCCCACGGCCTCTCCTCACATTCCACGTCCTGTAGCTCTATGACCTCCACCTTTGAGTCCCTCCTCTCACACCTGACATGAAAAGGCACATGAGGATCCTCAAATACCCCGTGATCAGTCTCAGGGTAGCTCTCATAGCCTGGACAGGGCCCCCCTCGGGGGTTGCGCCCAGGTCCAGGCGGGGGATGCACAGCAACAGTCACCGAAGCAGAAGCCGTCACAGTGGTGATGGGCTGGCAGTAGCTGGGCACAGAGCTGCCCATGGCGGTGGACGTTGGGTTCCGAGGGTTGTGAGAACGGGCCCCACGGGGCCCTGAGCGGTCCCTATTGCTAGGGCCAGAATGCCCTTCAGTAGAAATTTCAAAAGCGTCTCTGCGCGGTCTGTAGGGGGGTGGCCGCAAGCCTTCTCTAGGGGGATCCCTTCGAGGCTGCTGGCCTTGCCGTCCAGGGGACAAGGAGCCAGAGTCCAGGTGGGGCTGTTGCCGAGGGGTCAAGGGAGGCTGATGTCTGGAGTCCGGATGGACCACCTGCAGAGGAGAGACATAGGTCAACACAGGGAGGTAGGATGGTGGTGATGTTCCACCCACAAAAGAAAACCTATTCCTTTAGAAACCTCCAGGATGTGAATCCTGCCTGCACCTGCACAGCTGGCTGGAGGCATATAGCCACTGCCCATAGATCTCAACTTACCCTCACAACCAACTGCCCCCAGGCCTAAGTTCTCTGCCTCAAAACTGCCAAGGCCTGGATAGCCAAGAGCCTGGGTGTCTTGGAAATATGCAACCATAAATAGTAGCTTTTAGAAGTATAAGGCTCCTGTTTCTGGGTCATATTAGTGTTGTTTTCACCTGTCCCCAGCCCTAAGCCAGGTGTGGCCAGAAGCAAATGTACTGTAAGAGCAGAGCAAAAACTTCCACACAGATAGTTCTGTTAGGCAATACATCTCTGCCTGACTATTAGGAATCTGGTTTCTGGGTCCTCTGTACAAAGCTCGGAGCAACACAGTGGCCACATCAATCAAAAGGACCGTGACCAACTTCAAAGTCGGTGAGCTTGTACCTATTTTTAGGCTCCTGCTGAACAGAACCAGATTCACACTACAGCTCAGCAGGGCATCGTCACGGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTGGGGGGGGGGGGTGGACAGAGGACGGGGACACAATTCACTGGCCAGCCCTTCTCTCCTTCAAGGAAGGCTGCTCTAGCCTGGGACTGGAATACACATTTCCTGTAAACATGGTGGGGGCCTCAGGCAAGCCAGAGTTTTGGAGCCTTCCTTAACTCTTCAAGGTGAGCATCTTGACTTGGAGGGTGGGGGTGCGGGTAAGGAAGGAACCTGTGGACTCCTCCCTACAAGACAGAAAAGGAATAAGCCACGAAGACAATAACGATTTTTGTATCAAGCGTCCTCTCCCATTTCAGCTTACCTGACAATGAAATCAAATTCGGACCCTGCAAGCATCAGTACACCCAGCAGAGTGGACACAGCACCGTCCAGAACGGGAGCAAACATGTGCTCCAGAGCGAGCATAGCCCTGTGGTTCTTGTCCCCAATGGCTGTCAGAAAGGCCTGAACAAAGGAGAAAATTGACACGGTCACATTCTGGGTGTGGTAAAGTGCTCAGCTGTGTCTATACTTGGGTTTTGTAT…
TotalamountofDNAinhumangenome:3*109basepairs(bp)
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Replica6on
TTCGATTACGA
AAGCTAATGCT
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TTCGATTACGA
AAGCTAATGCT
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TTCGATTACGA
AAGCTAATGCT
CCCGTAAGTATTTG
TTGGGTAATGC
ATGGGTCAATTA
TTTAGTAG
AATGTCnucleo6desavailableincells
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TTCGATTACGA
AAGCTAATGCT
TTCGATTACGA
AAGCTAATGCT
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TTCGATTACGA
AAGCTAATGCT
TTCGATTACGA
AAGCTAATGCT
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Genes
Gene Gene Gene Gene Gene
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CentralDogma
DNA RNA Proteins
GenesencodeproteinswhicharetranscribedintomRNAandtranslatedintoproteins.
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Transcrip6on
C T A G C G C T C
| | | | | | | | | G A T C G C G A G
DNA
C U A G C G
RNApolymerase
mRNA
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Transla6on
h\p://gel.ym.edu.tw/~ycl6/sc2005/images/transla6on.gif
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The genetic code
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gene regulation
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gene regulation
http://string-db.org/version_9_0/newstring_cgi/show_network_section.pl?identifier=9606.ENSP00000279441&all_channels_on=1&network_flavor=evidence&targetmode=proteins
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Whatmakesthemdifferent?
Muchhumanvaria6onisduetodifferencein~6millionbasepairs(0.1%ofgenome)referredtoasSNPs
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TACATAGCCATCGGTANGTACTCAATGATGATAGenomicDNA: A SNP
G
SingleNucleo6dePolymorphism(SNP)
Threegenotypes
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TACATAGCCATCGGTAAGTACTCAATGATGATA
AA
ATGTATCGGTAGCCATTCATGAGTTACTACTAT
TACATAGCCATCGGTAAGTACTCAATGATGATAATGTATCGGTAGCCATTCATGAGTTACTACTAT
Mother
Father
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TACATAGCCATCGGTAAGTACTCAATGATGATA
AG
ATGTATCGGTAGCCATTCATGAGTTACTACTAT
TACATAGCCATCGGTAGGTACTCAATGATGATAATGTATCGGTAGCCATCCATGAGTTACTACTAT
Mother
Father
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TACATAGCCATCGGTAGGTACTCAATGATGATA
GG
ATGTATCGGTAGCCATCCATGAGTTACTACTAT
TACATAGCCATCGGTAGGTACTCAATGATGATAATGTATCGGTAGCCATCCATGAGTTACTACTAT
Mother
Father
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