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

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

Bioinformatics is Multidisciplinary

ComputerScience

Math

Statistics

StructuralBiology

Phylogenetics

Drug Design

Genomics

MolecularLife Sciences

Textbook

Bioinformatics and FunctionalGenomicsby Jonathan PevsnerISBN: 0471210048

• Genome sequence acquisition and analysis. • Basic and applied research with DNA microarrays. • Proteomics.

History of the Human Genome Project

1953

Watson,CrickDNAstructure

1972

Berg,1st recombinantDNA

1977

Maxam,Gilbert,SangersequenceDNA

1980

Botstein,Davis,SkolnickWhitepropose to map humangenome withRFLPs

1982

Wadaproposes tobuild automated sequencingrobots

1984

MRCpublishesfirst largegenomeEpstein-Barrvirus (170 kb)

1985

Sinsheimer hosts meeting to discuss HGP at UCSantaCruz;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)

History of the Human Genome Project (continued)

1987 (cont)

Hood producesfirst 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 sequence20 Mb in model organism by 2005;Lipman, Myers publish the BLAST algorithm

1991

Venter announces strategy to sequence ESTs. He plans to patentpartial cDNAs;Uberbacher develops GRAIL, a gene finding program

1992

Simon develops BACs; US and French teams publish first physical maps of chromosomes; 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)

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 Microbial18 Eukaryotes1275 Viruses

Basis of molecular biology Hierarchy of relationships (some exceptions):

Genome

Gene 1 Gene 3Gene 2 Gene X

Protein 1 Protein 2 Protein 3 Protein X

Function 1 Function 2 Function 3 Function X

How can one use bioinformatics to link diseases to genes?

Positional cloning of genes1. 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 abnormality5. Predict gene function

from sequence information

Disease

Map

Gene

Function

Unknown Function

How much of the genome is defined?

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

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

Amino acid characteristics

Website for Amino acid interactive Workshop Amino acids

1 2

DNA sequenceWrite the primary sequence of the DNA displayed in 3Bhttp://www.blc.arizona.edu/Molecular_Graphics/DNA_Structure/DNA_Tutorial.HTML

http://www.rothamsted.bbsrc.ac.uk/notebook/courses/guide/dnast.htm

Website for interactive workshop for DNA analysis

Interactive display of amino acids and codons

Translation exercise

Translate the following sequence using the codontable:

ATGGUGCACCUGACUCCUGAGGAGAAG

Perform same procedure using a software program:

http://us.expasy.org/tools/dna.html

Central Dogma

DNA

RNA

Protein

DNA

RNA (with ribosomes)

*

>gi|1244762|gb|AAA98563.1| p53 tumor suppressor homolog

MSQGTSPNSQETFNLLWDSLEQVTANEYTQIHERGVGYEYHEAEPDQTSLEISAYRIAQPDPYGRSESYD

LLNPIINQIPAPMPIADTQNNPLVNHCPYEDMPVSSTPYSPHDHVQSPQPSVPSNIKYPGEYVFEMSFAQ

PSKETKSTTWTYSEKLDKLYVRMATTCPVRFKTARPPPSGCQIRAMPIYMKPEHVQEVVKRCPNHATAKE

HNEKHPAPLHIVRCEHKLAKYHEDKYSGRQSVLIPHEMPQAGSEWVVNLYQFMCLGSCVGGPNRRPIQLV

FTLEKDNQVLGRRAVEVRICACPGRDRKADEKASLVSKPPSPKKNGFPQRSLVLTNDITKITPKKRKIDD

ECFTLKVRGRENYEILCKLRDIMELAARIPEAERLLYKQERQAPIGRLTSLPSSSSNGSQDGSRSSTAFS

TSDSSQVNSSQNNTQMVNGQVPHEEETPVTKCEPTENTIAQWLTKLGLQAYIDNFQQKGLHNMFQLDEFT

LEDLQSMRIGTGHRNKIWKSLLDYRRLLSSGTESQALQHAASNASTLSVGSQNSYCPGFYEVTRYTYKHT

ISYL

FASTA format

Multiple sequence alignment Human-locus number AAA35732 Dog-locus number CCDG Yeast-locus number from structure

database 1YCC

CLUSTAL PROGRAM

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)