Biology Overview

1. Biology Overview Microarray Database Systems 9/18/2002

2. Additional Information • Review papers on microarray • Genomics, gene expression and DNA arrays (Nature, June 2000) • Microarray - technology review (Natural Cell Biology, Aug. 2001) • Magic of Microarrays (Scientific American, Feb. 2002) • Molecular biology tutorial • http://www.lsic.ucla.edu/ls3/tutorials/

3. References • Class materials are based on • Introduction to Computational Molecular Biology, Setubal and J. Meidanis, PWS Pub. Company, 1997 • Illustrations (http://www.nhgri.nih.gov/DIR/VIP/Learning_Tools/genetic_illustrations.html) (http://www.accessexcellence.org/AB/GG/

4. Central Dogma of Molecular Biology replication transcription translation DNA RNA Protein reverse transcription • understanding the structure and function of proteins and nucleic acids

6. DNA replication transcription translation DNA RNA Protein

7. DNA • The double helix • stable • Nucleotide • A, T, G, C • Base pair • A – T • G – C • Oligonucleotide • short DNA (tens of nucleotides, or bps) (http://www.nhgri.nih.gov/)

8. DNA (Nucleotide)

9. DNA (Detailed) Nucleotide 5’ 3’ 5’ Base 3’ (http://www.nhgri.nih.gov/)

10. DNA Strand • DNA has canonical orientation • read from 5’ to 3’ • antiparallel: one strand has direction opposite to its complement’s 5’ … TACTGAA … 3’ 3’ … ATGACTT … 5’

11. RNA replication transcription translation DNA RNA Protein

12. RNA • Types • messenger RNA • ribosomal RNA (rRNA) • transfer RNA (tRNA)

13. RNA • Differences from DNA • ribose instead of 2’-deoxyribose • U (Uracil) instead of T (Thymine) • single strand • may bind to other DNA • may bind to itself • various forms • relatively unstable

14. RNA (Detailed) (http://www.nhgri.nih.gov/)

15. Protein replication transcription translation DNA RNA Protein

16. Proteins • Types • Structural proteins • tissue building • Enzymes • catalysts, enabling otherwise slow biochemical reactions • Others • specific functions such as oxygen transport, antibody defense • chain of amino acids

17. Amino Acids • Amino acid • Ca • hydrogen • amino group • carboxy group • side chain • what distinguishes amino acids • 20 common amino acids found in nature H H2N Ca COOH R • R = CH3 : alanine • R = H : glycine

18. Common Amino Acids

19. Peptide bond R1 H H2N Ca COOH H2N Ca COOH H R2 H H R1 H2O N Ca COOH H2N Ca C H O R2

20. Proteins as Chains of Amino Acids • The backbone: polypeptide chain • unidirectional: – N – Ca – (CO) – • f and y determine the folding (3-D structure) R1 H O R3 H N Ca C C Ca Ca N f y O R2 H

21. Primary Structure (http://www.nhgri.nih.gov/)

22. Folding: Higher-Order Structure (http://www.nhgri.nih.gov/)

23. DNA Replication replication transcription translation DNA RNA Protein

24. DNA Replication DNA Helicase The enzyme that unwinds the DNA strand. DNA Polymerase The enzyme that bonds nucleotides to the DNA strand during replication. (http://www.nhgri.nih.gov/)

25. Transcription replication transcription translation DNA mRNA Protein

26. Gene Structure Gene A region in a DNA molecule that contains information necessary for building a protein or an RNA molecule Promoter a region before a gene that serves as an indication to the cellular mechanism that a gene is ahead Transcription Unit the region that is copied into RNA

27. Gene Structure Upstream regulatory region Downstream regulatory region Coding sequence Tc TL tL tc 3’ 5’ Promoter Transcription unit

28. Transcription • Exon the “coding” region • Intron the “skipped” region • Genomic DNA the full gene • Complementary DNA (cDNA) exon only • RNA Polymerase the enzyme that unzips DNA and make a complimentary RNA strand. (http://www.nhgri.nih.gov/)

29. Message RNA (mRNA) • the product of transcription • complement to the template strand • template strand is read from 3’ • similar to the coding strand (T becomes U) coding strand 5’ TGCGCTATC 3’ template strand 3’ ACGCGATAG 5’ mRNA 5’ UGCGCUAUC 3’

30. Altrnative Splicing • the same genomic DNA can give rise to two or more different mRNA molecules by choosing the introns and extrons in different ways

31. Translation replication transcription translation DNA RNA Protein

32. Codon • a group of three bases (nucleotide triplets) in an RNA strand • each codon stands for a certain amino acid • except for some codons which code for STOP and do not correspond to amino acids (http://www.nhgri.nih.gov/)

33. Translation: Protein Synthesis • mRNA • leaves the nucleus • Ribosome • assembly line for protein synthesis • contains rRNA • Transfer RNA (tRNA) • builds protein chain from mRNA codons • anti-codon

34. Genetic Code

35. Genome • The complete set of DNA contained in an organism’s cell • Complexity (in million bps) • Escherichia coli (backterium): 4.6 • Saccharomyces cerevisiae (yeast): 12.1 • Drosophila melanogaster (fruit fly): 150 • Homo sapiens (man): 3000 • Mus musculus (mouse): 3300

36. Gene Expression • All the processes involved in converting genetic information from DNA sequence into proteins. • all cells contains the same genome, but the set of genes expressed are different • in prokaryotes, no splicing (intron skipping) is needed

37. Housekeeping Genes • Genes which encode proteins or RNAs whose function is required by all cell types in a multicellular organism • e.g. RNA polymerase, ribosomal protein • constitutively expressed

38. More Terms Eukaryotic Cell with a nucleus Prokaryotic Cell without a nucleus Open reading frame (ORF) A contiguous stretch of a given DNA sequence that is • beginning at the start codon, • multiple of three • contains no STOP

39. Laboratory Methods: Next • Genome Sequencing • Human Genome Project • DNA Cutting • DNA Cloning • Polymerase Chain Reaction (PCR)