Class Note for ADSC 730 at KU
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Date Created: 02/06/15
EECS 730 Introduction to Bioinformatics Luke Huan Electrical Engineering and Computer Science httppeopleeecskuedujhuan Administrative 3 0 Take home background survey is due next Monday 0 The background survey is online 2009826 EECS 730 2 Cell structure and function I The nature of cells A Basic cell features 1 cell membrane 2 DNA RNA ribosomes 3 cytoplasm B Cell theory II Prokaryote cells III Eukaryotic cells V Molecular Biology explains life with chemistry 2009826 EECS 730 I Organization of Life A The hierarchy of life Chemical Emanu nmm Ecosystem Biotic and abiotic cycling of chemical A Human Comm r Ecosystem Community gnaw S ecies definition Population am wum P Org1mm amp Organism spinning Electron 23mquot Organ systems 1 fit quot9quot Iain mu Tissue quot animus c m a Atom ell avoch W 39 A 2009826 9 Organelle quotm may Molecule Subatomic particles TABLE MEAS MENT EQUIVALENTS 1 meter m 10 rn 3937 inches 1 centlmetercm 10 2 m 1100 rn 04 inch 1 millimeter mm 1r3 m 1 1 000 m 11 0 cm 1 micrometer pm 7 10 5 rn 1 14000000 m 1 nanometer nm 0 9 rn 11ooooooooo rn lmeter102cm103mm105um109nm um um um mml u l Mudv um 3mm Mllochondllon znnararze EECS 73m l he nature of cells w Cell life requirement EECS 730 B Cell theory well documented explanatory principle 1 All living systems are made of cells Induc l39ive reasoning ZEIEIBVEVZE B Cell theory 2 All cells come from preexis n 2009826 EECS 730 9 cells B Cell theory Cell 0 The basic unit of life Every living thing is made of cells Every cell comes from a preexisting cell All of life s functions are cellular Smooth A Rough endoglasmic PM endaElasmic reticulum reticulum Not In most plant cells UM Cenlrinle Ribnsumes Peraxlsome Golgl Micrulubule aQQaratus Intermediate quotlament 2m Microviiamem quot 39 Mitochondrion Cytoskeleton Plasma membrane Composition of Cells an 0 Cell membrane o Boundary between cell and outside world 0 Cell membranes consist of two layers of lipid molecules with hydrophobic ends facing in keeps water out o Nuclei 0 Contain genetic material 0 Separated from the rest of the cell by a nuclear membrane 2009826 EECS 730 11 Cell Membrane 39 Extracellular Glycoprotein Flmd 39 Chuleslerol l Carbohydrate 39 I f hw ail39hophobic Peripheral prutein if Filaments of cytnskeletnn Integral prc te39n Cytoplasm 2009826 EECS 730 12 B The nucleus 1 nuclear envelope 2 nucleolus 3 chromosomes Rlbasumes Eenlnule Nam Lysnsomajrmnsn plain Flagnllum calls Mlcmlilamem WWW Mlcmmhule Plasma membrane Milochondvmn Rnugh endnplzs mm rellculum endnplzsmlc mmmnm Gulglapparams lal An animal cell cwgm a 20m 4 52mm Cummlngi n mm M Mm new chromosomes 2009826 Svnlhasrs of mHNA in the nucleus mHNA inm cyloynlasm via nuclear pure 9 Synthesis of protein in the cytoplasm Outer membrane Inner membrane Nucleoplasm Nucleolus Chromatin Nuclear envelope Pore in nuclear envelope DNA homologies Carnals Plgs AA EPHARE prnARE A inuAREZ Peccaries A Chevratal ns lno ARE aaa792BovRA FasBovCA H YV A A c21352CHR1 PghaCHH1 A A A A aaaZZNCHFl aaa792CHH 1 Gm5CHR1 HlP5CHR1 Pecorans Hippapnmmuses m Toolhed whales whm Q A HIP5CHFI2 A A A A HIP24CHR 1 KMMtCHR1 A A A HIP4CHR1 Pm52CHFI2 AFCHFI1 Pm72CHFI 2 M11CHR2 aaa792tcHR2 14 IV Eukaryote cells Organelles B The nucleus 1 nuclear envelope 2 Nucleolus 3 Chromosomes C Endoplasmic reticulum and ribosomes D Golgi bodies E Lysosomes F Mitochondria and The endosymbiom Theory 6 H I Plant cell components chloroplasts and cell walls The cy139oskele139on Flogello and cilia Prokaryote cells I l 2 I 322 nun 9 a 4 921 quot9amp1 I I I I 1 5 I a 9 3 are 38 39II 1 II 139 139 139 or s an an 339 I 139 I II II I 391 3 730 Molecular Biology Studying life at the molecular level 339 0 DNA 0 Protein 0 RNA 0 mRNA 0 rRNA tRNA 0 Protein synthesis 0 Protein transcription 0 Protein translation 2009826 EECS 730 17 Central dogma of molecular biology RNA protein phenotype 2009826 EECS 730 18 DNA fascinating fact quot Each cell has 2m of DNA Average person has 75 trillion cells 75 1012 Length of DNA in a person 150 1012 m Each person has enough DNA to go to the sun and back 500 times 2009826 EECS 730 19 IV Organionion of DNA in chromosomes i is l39one proteins 3 bases amino acid 27000 bases protein 1 gene L 3000000000 base pairs genome 20000 genes genome 33 1 zoom homologous m K m 1333 5 nal saga H059 xqg ta 39 B N u Bo atquot e a 6 I Genome 0 Gene Contiguous sub arts of single strand DNA that are templates for producing proteins 0 Chromosomes compact chains of coiled DNA 0 Genome The set of all wwrgenes in a given organism o Noncoding part The function of DNA material between genes is largely unknown znnararze EECS 73m 21 Source WWW mBll39ial on CadegGenetlcsbaslc htm Exons regions of genes coding or protein RNA ur IRNA 15 DNA sequences in The human genome Repeli ve may Inlmns and regulatory Innapusnhla sequences elemems 24 and relnlsd sequences M94 Alu elements 1 0 mama simple sequence Largesegmem DNA 3 duplications 54 DNA sTr39ucTur39e Rlbbon modal Fanlnl chamlcal immune The Two jobs of DNA 355 Self replication and genetic code H Transiatimn Repimatmn DNA prCiteizn synthesis Transcr ipticsn RNA synthesis Protein 0 A sequence from 20 amino acids Lys H Lys H Gly H Gly H Leu H Val H Ala H His o Adopts a stable 3D structure that can be measured experimentally 2009826 EECS 730 25 Polypeptide gggz Nterminal H3N CDCquot C terminal 2009826 EECS 730 26 The 20 amino acids Each amino acid contains an quotaminequot group NHS and a quotcarboxyquot group COOH shown in black in the diagram The amino acids vary in their side chains indicated in blue in the diagram may a za Emma 27 Primary Structure o Primary structure is described by the sequence of Amino Acids in the chain 5 s A n nn ue Val Gm liln By Bus Tm Ser Ile Ev Sm len Tyv an LEu an An In an Asn GN s s s s B H th Val Am Gln Nix Len Cys Giv SIr His Lian Val Glu Ali lau Tyr Lau Vui Cvs By Bill Am Ely PM Pquot TM 7hr Pm Ly Ala UH 1114 5 6 7 G 10 Hi1 3i41 1517151920111113 152617131930 FIG 2 The amino acid sequence of pig insulin Each molcqulc cnnlnins two polypcplidc chains A and i3 disui dc bridgcsjmn the A and E chains Iogcthzr and a third one connects differcnl pans ofthc A chain zuuararza EECS 73m 28 Secondary Structure o fSedcondary structure describes the way the chain 0 s 0 Local structure of consecutive amino acids 0 Common regular secondary structures o a Helix w c b Sheet o b turn 2009 8 26 EECS 730 29 Tertiary Structure of protein o Tertiary Structure describes the shapes which form when the secondary spirals of the protein chain further fold up on themselves 2009826 EECS 730 30 Quaternary structure 0 Quaternary structure describes any final adjustments to the molecule before it can become active For example pairs of chains may bind together or other inorganic substances may be incorporated into the molecule 20098726 Bl http www nigms nih govpsl 32 2009826 RNA E mm n E H N M W KNRN w u N mm unackgune EB 3 Types v RNA DNA Nllrugenuus Nlmgenuus Eases thonudenc acvd Deoxynbonuo ewc and Eases zanaarze EECS 73m 33 Messenger RNA DNA TAC CAT GAG ACT ATC mRNA AUG GUA CUC UGA UAG Ribosomal RNA and ribosomes 4980 RNA bases 49 proteins 1900 RNA bases 33 proteins 2mm Transfer RNA Amino acid attaches here znnararze 36 H Anllcodon Protein synthesis Protein synthesis A Transcription C Translation 1 The genetic code 2 Translation the final steps ii 1 I 3 I Overview of pr39o l39ein syn l39hesis Transcripfion same language Translafion differenf language 2mm Overview of protein sym hesis Tmscmmou TRANSLATION i a Prokaryolln cell zuuara b Eukaryotlc cell Blg mnnwmev Win it Ribosome I 7 I fPulypepIide No Thymine ins l39 A TPOHSCPIPTIOH UracI FINA nucleotides RNA polymerase Puff gt Direction of transcription Template ZEIEIBVEVZE strand 01 DNA 4D Newly made RNA 2 Transla rion The final s reps Elongation translation 200982 Rules the secret of life 0 Transcription A U c G gtC T A o C gtG 0 Translation 2ndbaseincndon U c A G Pm su M Q N12 5 n cys m Sir sin smP m Szr smp rm Lnu Pm His Am Leu Pm His m9 Len Pm Gln Ar Leu Pm Gin An n m Arr 5w uapoo u vsaq p1 1slbast In codon gt O C quot9 TM kn Szr Ila Thy HPl 1quot M m Lys Am var AI Asp Gly G v1 u As any an Au am Gly v N an my mm26 The Genetic Code u mgtncngtocngtocmgtnc Codons and an ricodons DNA TAC CAT GAG ACT mRNA AUG GUA CUC UGA I39RNA UAC CAU GAG ACU G U G w m w my an Ala Glu The Genetic Code 2009826 43 0 0 Protein 3 Gene expression structure 3 database databases quot transcrip 39on translation Protein CDNA sequence Genomic ESTS databases DNA UnIGene Databases 2009826 EECS 730 44 T end
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