Directed Reading in Design
Directed Reading in Design ADSC 730
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Date Created: 09/07/15
EECS 730 Introduction to Bioinformatics Luke Hua E Ecmca Engmeerwg and Cumputer Smence mm NpEup E 22 w gnumuan Administrative 0 Take home background survey is due next Monda The background suweyws onhne Cell structure and function I The mm of cells A Basic cell feamms 1 cell membmne 2 DNA RNA ribosomes a cytoplasm I Organiza rion of Life A The hierarchy of life mm Lammum were mm 0mm ow yvem Am LeH o e m g Ma ezu e 39 Subrqwm Wm The nature of cells Cell life requirem em 39 B Cell theory well documented explanatory principle 1 All living sysfems are made of cells Inductive reasoning llllmlllllllll B Cell theory quot5 2 All cells come from pre exisfi t39tlls t 39 H T n B Cell theory 3 All of life39s functions are cell I39u39F ell a The baslc unllulllle MllmmlsmMamas Mllcellmesm apwalngcel All a less Dells mam mm M Com position of Cells 0 Cell membrane Boundary between cell and oulslde World Cell membranes conslsl oflwo layers Ofllpld molecules Wlm nydropnoblc ends facan m keeps Water out o Nuclei Conlaln genellc malenal Separated from membrane Cell Membrane Trunnnme um WW Mam B The nucleus 1 Wquot DNA homologies Prokaryote cells Molecular Biology Studying life at the molecular level 0 DNA 0 Protein 0 mRNA o rRNA 0 Protein synthesis o Protein transcription Proteiritrarislatiori Central dngma of mulecular binlogy E i NA RNA protein phenotype DNA fascinating fact Each cell has 2m of DNA Average person has 75 trillion cells 75 10iZ Length of DNA in a person 150 quotml2 m Each person has enough DNA to go to the sun and back 500 times zapsza ms nu IV Organization of DNA in chromosomes 3 bases amino acid 27000 bases protein 1 gene 3000000000 base pairs genome 20000 genes genome N M n 3 CS 394 TI 7539 391 r 1 zupaza homologous a 3 n w a m 1 21 n 2 v Genome O I 39imm Null Gene Contiguous sub arts W V V of single strand DNA that are A A templates for producing 5 proteins 7 quot quotVquot Chromosomes compact tax chains of coiled DNA M Genome The set of all 7 genes in a given organism Noncoding part The function of DNA material between genes is largely unknown zapsza ms m mm mm mum 4 DNA sequences in The human genome Mm mm Wm 1 i m Mumq may Simph Muenw Large ern DNA s rr39uc rur e The Two jobs of DNA Self replication and genetic code Translation Rephcat39on mRN protein synthesis DNA mam mom quotofPA jwm A W 11 er x Transcription Ribosome RNA synthesis Protein GIMP W Protein o Adopts a stable 3D structure that can be measured experimentally if d II L a 3 c o v mm m zzcsm 2 Polypeptide N eterminal C7 terminal mm m EEcs m m The 20 ainoacids blue in the diagram mm m EEcs m 21 Primary Structure Ammo Actds m the charm t 4 x z t 1 trmmtrrtptum m A um I hammsdlnw m mm wnmzhmrm mm lm A err Secondary Structure regutar secondary 5 met a erx e rotds tocat structure or consecutwe arhrho actds orhrho t urea H t 7 n bShEEt ur Tertiary Structure of protein Ternary Structure descrrbes the shapes whrch form when the seconda y sprrats orthe proterh charh rurther tore up ch therhsehes Quaternary structure me mu ecme befure rt ean became actwe Fur ex pars er thaws may bmd tugether ur emer murga r substances may be mcurpurated mm the mu ecme were me Protein Structure Space in Messenger RNA DNA TAC CAT GAG ACT ATC mRNA AUG GUA CUC UGA UAG 1 x A m Ribosomal RNA and ribosomes 4930 mm bases 49 prolains 1900 RNA bases gt33 praieins Transfer RNA 7min lcld anaches here 7 Amieodon Pr39o rein synthesis Protein synthesis A Transa iption C Translation 1 The genetic code 2 Translation the final steps Translation different languag Overview of pro rein syn lhesis rr A me39 quot4 L W I 4 warrude ul 2m lb Sum all 13 No Thymine ins A Transcrlp rlon Uracil RNA nuzlmlldon ANA pawnmu Puff YCCAA I IA a r a I u 1 6 a c 0 V 4 Y A a a Y 1 a mum Immu lan quotmm mammal n mwivmnm 2 Transla rion The final s reps Elongation translation Anticodon Incoming 99 tRNA Rules the secret of life Transcription o G TaA CG Translation m K 3 x 5 J 7 E 5 E 3 i 37 E g E E 3 mm The Genetic Code Codons and an ricodons DNA TAC CAT GAG ACT mRNA AUG GUA CUC UGA UAG fRNA UAC CAU GAG ACU AUC J JL mnsmn n mnslamn NA RNA prmein phenotype 1 Protein DNA sequence Genomic E575 databases DNA UnIGene Dakabases Th end EECS 730 Background Survey Open book open notes open to intemet resources but NO copy and paste Develop your own solutions NO discussion among classmates treat this as a take home exam Total point 100 Assigned Aug 24th Due Aug 31th before class meeting time Problem 1 25 points Given the following graph show the result of different graph search 1 Starting at node 2 show the sequence of Visited nodes using breadth rst search 2 Starting at node 2 show the sequence of Visited nodes using depth rst search 3 What is the shortest distance between node 2 and node 6 4 Draw a spanning tree of the graph 5 Outline two data structures that you may use to implement a tree Problem 2 25 points A string T is a subsequence of a string S if T can be obtained by removing characters from S without changing the order of remaining characters For example a string T ABC is a subsequence ofthe string S ADBBCD since we could obtain ABC by removing the second D the fourth B and the last character D of S without changing the order of the remaining characters in S As another example T ABC is not a subsequence of the string S ACBD since there is no way that we can obtain T from S by removing characters from S alone With the above de nition answer the following questions Justify your answer 1 Whether the string T CCAGT is a subsequence ofthe string S ACGCTATGT If yes specify how to obtain T from S If no state your reason 2 Giving two string S1 ACGGACT S2 GTCGTTCGGGATGC find a common subsequence where a string T is a common subsequence to two string S1 and S2 if T is a subsequence to both S1 and S2 3 Identify the longest common subsequence the common subsequence with the maximal number of characters among all common subsequences of S1 and S2 from above 4 Discuss how to develop an algorithm to solve the longest common subsequence problem in general The input to the algorithm is a set of two sequences and the output from the algorithm is the common longest subsequence Write down your pseudo code and explain how it works 5 Apply your algorithm to solve question 3 Problem 3 25 points A biomedical company is evaluating a new diagnostic tool kit Scientists established that the probability that a single diagnostic kit works is p and hence the probability that a single diagnostic kit fails is lp Scientists also established that if atool kit works it produces correct diagnostic results and when it fails it produces no results 1 Suppose a technician is using the diagnostic kit to perform lab test where she use one kit for one lab test The procedure she follows is that she will stop once she obtains correct diagnostic results Otherwise she will repeat the lab test once more until she obtains the correct results Following the procedure please compute the probability that she uses exactly two tool kits to obtain correct diagnostic results 2 Following the same procedure please compute the probability that she uses exactly ktool kits to obtain correct diagnostic results where k is a positive integer 3 Compute the expected number and the variance of the number of tool kits that the technician uses to obtain correct diagnostic results Problem 4 25 points Explain the following biological terms in a concise way 13 sentences in most cases 1 Chromosome 2 DNA 3 Gene 4 Protein 5 Transcription 6 Translation in terms of protein synthesis 7 Microarray 8 Proteinprotein interaction 9 extra credit write down your comments about the class so far too fast too slow too much biology too little biology whether it is easy to nd reference 5 points EECS 730 Introduction to Bioinformatics Luke Huan Electrical Engineering and Computer Science httppeopleeecskuedujhuan Administrative 3 0 Take home background survey is due next Monday o 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 7110 5 Biosphere 1391 W3 Ecosystem Biotic and abiotic M nulrlenla Ecosystem Community Population aw Species definition 333 Organism am i quotEmma Organ systems m1 MM m m Organ Tissue Cell manual Ml Alum 2009826 Ovalulu Organelle um um I I Molecule Subatomic particles TABLE 4 MEASUREMENT EQUIVALENTS 1 meter m 10 rn 3937 inches 1 centimeter an 10 2 m 1100 rn 04 inch 1 millimeter mm r3 m 1 1 000 m 110 cm 1 micrometer pm 7 10 5 rn 11ooooop rn 1 nanometer nm rn 11ooooooooo rn o 1meter102cm103mm105um109nm znnararze EECS 73m The nature of cells 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 0 cells B Cell theory 3 All of life39s functions are cell for 20098 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 Rough endoglasmic endogiasmic reticulum reticulum Notinmnst Lsosume piamneiis 1 Centrinle I V Ribnsumes Golgl Micrulubule agparalus ln ermed39a e Plasma membrane lilament Microviiamem Cytoskeleton 2mm Mitochcndrion Composition of Cells an 0 Cell membrane a Boundary between cell and outside world a Cell membranes consist of two layers of lipid molecules with hydrophobic ends facing in keeps water out o Nuclei 0 Contain genetic material a Separated from the rest of the cell by a nuclear membrane 2009826 EECS 730 11 Cell Membrane Extracellular Fluid Carbohydrate i 2009826 Irrte ral pratein Glycopratein Glycullpld 1 39 Peripheral protein EECS 730 Chulee teml r Ex I Filaments of ey39teskeletun Cytoplasm B The nucleus 1 nuclear envelope 2 nucleolus 3 chromosomes Rlbasumes Eenmule Nam Lysnsnmajrmoslplam nagnllum cells Mlcmlilamanl CV 5kElE quot Mlcmluhule Plasma membrane Synthesis of protein in the cytoplasm Mlmchondrlnn Rough endnplas mm rellculum Smnmh endnplasmlc Gulgl apparams rellculum la An animal cell CupyngM 0 20m by 55mm cum n mm m Addlxm Wesley Outer membrane Inner membrane Nucleoplasm Nucleolus chromosomes Chromatin Nuclear envelope Pore in nuclear envelope 2009826 DNA homologies Carnals AAAA A Pigs 1 inoAREZ QPKARE Peccanes prnAHE A Chevratalns noARE aaa792BovIA A A Faggotm t c21352CHR1 A A A A anatc q Pecorans aaa223CHR1 aaanz crmd A Hippopotamuses Gm5ICHR1 HIP5CH nz HlP5CHR1 Toolhed whales Hlpzucnm KMMtCHR1 quotmucus1 Ancnm Balean whaias Pm52CHH2 Pm72CHFI2 M1 1CHR2 A aaa752tcHR2 IV Eukaryote cells Organelles B The nucleus 1 nuclear envelope 2 Nucleolus 3 Chromosomes Endoplasmic reticulum and ribosomes Golgi bodies Lysosomes Mitochondria and The endosymbiom Theory Plant cell components chloroplasts and cell walls The cy139oskele139on Flogello and cilia Plam s HIm39nrnon mmagripiclurecom1ll4985 F im 7 Animals Prokaryote cells i w 39a 39 2393 quot Molecular Biology Studying life at the molecular level 0 DNA 0 Protein 0 RNA mRNA rRNA o tRNA 0 Protein synthesis 0 Protein transcription 0 Protein translation 2009826 EECS 730 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 3 boses amino acid 27000 boses protein 1 gene E 3000000000 base pairs genome 3 75 43 20000 genes genome 2009826 homologous G c f 7 a II 5 Na 15 33 1o 11 12 393 17 18 an 93910 I 22 X Y O 0 Gene Contiguous sub arts of single strand DNA that are templates for producing proteins a Chromosomes compact chains of coiled DNA 0 Genome The set of all w genes in a given organism o Noncoding part The function of DNA material between genes is largely unknown znnararze EECS 73m mow M l Source WWW mBll39ial on CaDdrngGenetlcsbaslc htrn DNA sequences in The human genome Exuns regions or genes coding or prokmn RNA ur cam 15 Hepexiuve nun mat Includes anspu enhla elemems a Inlrans and r ulam sequences 41 sequences 24 zuuaaezs Alu elements 1 0 Simple sequence DNA 3 Largesegmem duplications 545 DNA sTr39ucTur39e r v Rlbban modal lenl enamlcal structure Computer modal The Two jobs of DNA Self replication and genetic code Transiation Finv Iaa quottn i aptl a Ion DNA mami pmtern synthems W Transcripticn Ribosmiie a RNA synthesis Miateam DNA Protein 0 A sequence from 20 amino acids o Adopts a stable 3D structure that can be measured experimentally nun ramc 2009826 EECS 730 Polypeptide an Nterminal CDCquot C terminal 2009826 EECS 730 26 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 Primary Structure o Primary structure is described by the sequence of Amino Acids in the chain 5 S A H nn lle Val cm liln By Bus Tm Ser lb on Sun EH Tyv Gln Lau an lkn Ivi Ev Asn un S S S S B H Phu Val Am Gin Nix Lian Cys Giv SIr His Lian Val Glu All lau Tyr Lau iai Cvs y Giu Am Ely PM PM TVi 1hr Pm Ly Ala UH 1214 5 6 7 E 910 ililiiidii39l quot15192021221324 152617281930 FIG 2 The nmina acid sequence of mg insulin Each rnolcqulc cnnlains two polypcpiidc chains A and i3 disui dc bridgesjmn the A and E chains logemzr and a third one connects differcnl pans ofthe A chain zuuararza EECS 73m 28 0 O 0 O 0 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 Hl39 m 332 a c b turn quot a a gt 9 a 39 2 2009 8 26 EECS 730 r i P 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 55 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 B4 g http www mng mh govpsl 2009826 D 3 D2 D 1 32 RNA Wm N 2 cl mc W MC V r o H N u H c N M mm Bases Base paw E s m 3 es of A M L Wm Ty D o P NcI NK V MC cCxNH H I c g 940 u L H DNA Numgenuus Nllmgenuus Eases Ribonucleic and Deoxynbonuc ewc and QUEBEVZE EECS 73D Eases 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 83 proteins 2mm Transfer RNA Amino acid attaches here znnararze Amman Protein synthesis Protein synthesis A Transcription C Translation 1 The genetic code 2 Translation the final steps Overview of pr39o l39ein syn l39hesis Transcripfion same language Translafion differenf language 2mm Overview of protein sym hesis a Prokaryolln cell znnara WWWDMW harmn u Tnmscnlnmu I RNA PROCESSING TnAMsLAnuN i WSZIypemide Hibosome b Eukaryotlc cell No Thymine ins l39 A TPOHSCPIPTIOH Uracul FINA nucleotides RNA polymerase Puff Direction of transcription Template ZEIEIBVEVZE strand 51 DNA Newly made RNA 2 Transla rion The final s reps Elongation translation 200982 Rules the secret of life 0 Transcription o A u G gtC o T gtA C gtG 0 Translation 1slbast In codon 0 mm The Genetic Code uapoo u vsaq p1 Codons and an ricodons DNA TAC CAT GAG ACT A C mRNA AUG GUA CUC UGA UAG I39RNA UAC CAU GAG ACU AUC The Genetic Code Protein Gene expression structure database databases transcrip39on translation RNA protein phenotype 1 Protein CDNA sequence Genomic ESTS databases DNA UnIGene Databases 2009826 EECS 730 44 T end
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