2. Overview of Bioinformatics and Molecular Biology June 13, 2005 History of Genome Sequencing Project Learning objectives- What is sickle cell anemia? Increased knowledge of the structure of atoms, molecules, and biomolecules Central Dogma How DNA mutations result in abnormal proteins Protein structure classifications How to perform comparisons of protein sequences Workshop-Import cytochrome C protein sequences from different species. Perform Clustal W comparison Homework-Use the internet or written text sources

3. Definition of Bioinformatics Many definitions at the moment: Use of computers to catalog and organize biological information into meaningful entities. Conceptualization of biology in terms of molecules and the application of “informatics” techniques (from disciplines such as applied math, computer science and statistics) to understand and organize the information associated with these molecules

4. Bioinformatics is Multidisciplinary Computer Science Math Statistics Structural Biology Phylogenetics Drug Design Genomics Molecular Life Sciences

5. Textbook Bioinformatics and Functional Genomics by Jonathan PevsnerJonathan Pevsner ISBN: 0471210048 Genome sequence acquisition and analysis. Basic and applied research with DNA microarrays. Proteomics.

6. History of the Human Genome Project 1953 Watson, Crick DNA structure 1972 Berg, 1st recombinant DNA 1977 Maxam, Gilbert, Sanger sequence DNA 1980 Botstein, Davis, Skolnick White propose to map human genome with RFLPs 1982 Wada proposes to build automated sequencing robots 1984 MRC publishes first large genome Epstein-Barr virus (170 kb) 1985 Sinsheimer hosts meeting to discuss HGP at UCSanta Cruz; Kary Mullis develops PCR 1986 DOE begins genome studies with $5.3 million 1987 Gilbert announces plans to start company to sequence and copyright DNA; Burke, Olson, Carle develop YACs; Donis- Keller publish first map (403 markers)

7. History of the Human Genome Project (continued) 1987 (cont) Hood produces first automated sequencer; Dupont devolops fluorescent dideoxy- nucleotides 1988 NIH supports the HGP; Watson heads the project and allocates part of the budget to study social and ethical issues 1989 Hood, Olson, Botstein Cantor propose using STS’s to map the human genome 1990 Proposal to sequence 20 Mb in model organism by 2005; Lipman, Myers publish the BLAST algorithm 1991 Venter announces strategy to sequence ESTs. He plans to patent partial cDNAs; Uberbacher develops GRAIL, a gene finding program 1992 Simon develops BACs; US and French teams publish first physical maps of chromosome s; first genetic maps of mouse and human genome published 1993 Collins is named director of NCHGR; revise plan to complete seq of human genome by 2005 1995 Venter publishes first sequence of free-living organism: H. influenzae (1.8 Mb); Brown publishes on DNA arrays 1996 Yeast genome is sequenced (S. cerevisiae)

8. History of the Human Genome Project (continued) 1997 Blattner, Plunket complete E. coli sequence; a capillary sequencing machine is introduced. 1998 SNP project is initiated; rice genome project is started; Venter creates new company called Celera and proposes to sequence HG within 3 years; C. elegans genome completed 1999 NIH proposes to sequence mouse genome in 3 years; first sequence of chromosome 22 is announced 2000 Celera and others publish Drosphila sequence (180 Mb); human chromosome 21 is completely sequenced; proposal to sequence puffer fish; Arabadopsis sequence is completed 2001 Celera publishes human sequence in Science; the HGP consortium publishes the human sequence in Nature 2003 Completed genomes: 112 Microbial 18 Eukaryotes 1275 Viruses

9. Basis of molecular biology Hierarchy of relationships (some exceptions): Genome Gene 1Gene 3Gene 2Gene X Protein 1Protein 2Protein 3Protein X Function 1Function 2Function 3Function X

10. How can one use bioinformatics to link diseases to genes? Positional cloning of genes 1. Find genetic markers associated with disease 2. Sequence DNA next to the markers 3. Compare DNA from afflicted individuals to DNA of normal individuals (database) 4. Find abnormality 5. Predict gene function from sequence information Disease Map Gene Function

11. Unknown Function How much of the genome is defined?

12. How is Bioinformatics Used? Experimental proof is still the “Gold Standard”. Bioinformatics isn’t going to replace lab work anytime soon Bioinformatics is often used to help “focus” the experiments of the benchtop scientist

13. Symptoms of Sickle Cell Anemia pain episodes strokes increased infections leg ulcers bone damage yellow eyes or jaundice early gallstones lung blockage kidney damage and loss of body water in urine painful erections in men (priapism) blood blockage in the spleen or liver (sequestration) eye damage low red blood cell counts (anemia) delayed growth

21. Amino acid characteristics

22. Website for Amino acid interactive Workshop Amino acids 1 2

25. DNA sequence Write the primary sequence of the DNA displayed in 3B http://www.blc.arizona.edu/ Molecular_Graphics/DNA_Str ucture/DNA_Tutorial.HTML http://www.blc.arizona.edu/ Molecular_Graphics/DNA_Str ucture/DNA_Tutorial.HTML http://www.rothamsted.bbs rc.ac.uk/notebook/courses/g uide/dnast.htm http://www.rothamsted.bbs rc.ac.uk/notebook/courses/g uide/dnast.htm Website for interactive workshop for DNA analysis

26. Interactive display of amino acids and codons

27. Translation exercise Translate the following sequence using the codon table: ATGGUGCACCUGACUCCUGAGGAGAAG Perform same procedure using a software program: http://us.expasy.org/tools/dna.html

28. Central Dogma DNA RNA Protein

29. DNA RNA (with ribosomes)

30. *

32. >gi|1244762|gb|AAA98563.1| p53 tumor suppressor homolog MSQGTSPNSQETFNLLWDSLEQVTANEYTQIHERGVGYEYHEAEPDQTSLEISAYRIAQPDPYGRSESYD LLNPIINQIPAPMPIADTQNNPLVNHCPYEDMPVSSTPYSPHDHVQSPQPSVPSNIKYPGEYVFEMSFAQ PSKETKSTTWTYSEKLDKLYVRMATTCPVRFKTARPPPSGCQIRAMPIYMKPEHVQEVVKRCPNHATAKE HNEKHPAPLHIVRCEHKLAKYHEDKYSGRQSVLIPHEMPQAGSEWVVNLYQFMCLGSCVGGPNRRPIQLV FTLEKDNQVLGRRAVEVRICACPGRDRKADEKASLVSKPPSPKKNGFPQRSLVLTNDITKITPKKRKIDD ECFTLKVRGRENYEILCKLRDIMELAARIPEAERLLYKQERQAPIGRLTSLPSSSSNGSQDGSRSSTAFS TSDSSQVNSSQNNTQMVNGQVPHEEETPVTKCEPTENTIAQWLTKLGLQAYIDNFQQKGLHNMFQLDEFT LEDLQSMRIGTGHRNKIWKSLLDYRRLLSSGTESQALQHAASNASTLSVGSQNSYCPGFYEVTRYTYKHT ISYL FASTA format

33. Multiple sequence alignment Human-locus number AAA35732 Dog-locus number CCDG Yeast-locus number from structure database 1YCC CLUSTAL PROGRAM

34. Workshop due on Tuesday Find out the chromosomal location of the gene that causes sickle cell anemia. Give the name of the gene. Find out the nucleotide change and amino acid change that leads to sickle cell anemia (there may be more than one change that gives rise to the disease) If sickle cell anemia is so devastating, why has it lasted in the population for such a long time? Give a molecular explanation (you may have to do a little research to get this)