2. COT 6930 HPC and Bioinformatics Introduction to Molecular Biology Xingquan Zhu Dept. of Computer Science and Engineering

3. Outline Cell DNA DNA Structure DNA Sequencing RNA (DNA-> RNA) Protein Protein structure Protein synthesis

4. Central Dogma of Biology: DNA, RNA, and the Flow of Information TranslationTranscription Replication

5. A sequence from 20 amino acids Adopts a stable 3D structure that can be measured experimentally Ribbon Space filling Cartoon Surface Oxygen Nitrogen Carbon Sulfur Protein Lys Gly LeuValAlaHis

6. X-ray Crystallography

9. The 20 amino acids Each amino acid contains an "amine" group (NH3) and a "carboxy" group (COOH) (shown in black in the diagram). The amino acids vary in their side chains (indicated in blue in the diagram).

10. Protein Structure Primary structure (amino acid sequence) Secondary structure (local folding) Tertiary Structure (global folding) Quaternary structure (multiple-chain) Protein Structure Animation https://mywebspace.wisc.edu/jonovic/web/protein s.html https://mywebspace.wisc.edu/jonovic/web/protein s.html

11. Primary Structure Primary structure is described by the sequence of Amino Acids in the chain

12. C- terminal N-terminal Polypeptide One end of every polypeptide, called the amino terminal or N-terminal, has a free amino group. The other end, with its free carboxyl group, is called the carboxyl terminal or C-terminal. Peptide: 50 amino acids or less Polypeptide: 50-100 amino acids Protein: over 100 amino acids

13. Polypeptide The amino acids are linked covalently by peptide bonds. The image shows how three amino acids linked by peptide bonds into a tripeptide.

14. Secondary Structure Secondary structure describes the way the chain folds Local structure of consecutive amino acids Common regular secondary structures  Helix  Sheet b turn

15. Secondary Structure Alpha helix Beta strand / pleated sheet Coil

16. Tertiary Structure of protein Tertiary Structure describes the shapes which form when the secondary spirals of the protein chain further fold up on themselves.

17. Quaternary structure (multi-chain structures) 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.

18. Protein Structure Space http://www.nigms.nih.gov/psi/ Protein folding taxonomy : all alpha all beta alpha/beta alpha+beta others

19. Geometry of Protein Structure rotatable Total number of degree is 2*(n-1) where n is the length of the protein

20. The Leventhal Paradox Given a small protein (100aa) assume 3 possible conformations/peptide bond 3 100 = 5 × 10 47 conformations Fastest motions 10- 15 sec so sampling all conformations would take 5 × 10 32 sec 60 × 60 × 24 × 365 = 31536000 seconds in a year Sampling all conformations will take 1.6 × 10 25 years Proteins do not have problem in folding, we have! ­ the Leventhal paradox

21. Outline Cell DNA DNA Structure DNA Sequencing RNA (DNA-> RNA) Protein Protein structure Protein synthesis

22. 3 types of RNA RNA

23. Messenger RNA DNA: TAC CAT GAG ACT … ATC mRNA: AUG GUA CUC UGA … UAG

24. Ribosomal RNA and ribosomes

25. Transfer RNA

26. Overview of protein synthesis Transcription: same language Translation: different language

27. Overview of protein synthesis

28. A. Transcription No Thymine, instead has Uracil

29. 2. Translation, the final steps

30. Rules (the secret of life) Transcription: A →U T →A Translation G →C C →G AUG: Methionine (Met)

31. Codons and anticodons DNA: TAC CAT GAG ACT … ATC mRNA: AUG GUA CUC UGA … UAG tRNA: UAC CAU GAG ACU … AUC

32. DNARNA cDNA ESTs UniGene phenotype Genomic DNA Databases Protein sequence databases protein Protein structure databases transcriptiontranslation Gene expression database

33. List of Amino Acids (1)

34. List of Amino Acids (2)

35. Transcription & Open Reading Frame (ORF) Open Reading Frame (ORF) Where to start reading codons (ATG) 6 possible reading frames (3 forward, 3 backward) Gene is usually longest ORF found Forward reading frame example

36. Complication – Non-coding Regions Non-coding regions Very little genomic DNA produce proteins Exon – DNA expressed in protein (2–3% of human genome) Intron – DNA transcribed into mRNA but later removed Untranslated region (UTR) – DNA not expressed UTRs may affect gene regulation & expression Biological processes Remove introns from mRNA, splice exons together Transition between intron / exon = splice site Splicing can be inconsistent Some exons may be skipped Result = splice-variant gene / isoform Estimated 30% of human proteins from splice-variant genes

37. Non-coding regions

38. Transcription The process of making RNA from DNA Needs a promoter region to begin transcription. Exons Control regions Splicing Transcription Introns

39. Alternative Splicing One single gene produce different forms of a protein A single gene can contain numerous exons and introns, and the exons can be spliced together in different ways

40. Complication: Mutations Mutations Modifications during DNA replication Possible changes Point mutation / single nucleotide polymorphism (SNP) 5’ A T A C G T A … 5’ A T G C G T A … Occur every 100 to 300 bases along the 3-billion-base human genome Duplicate sequence Inverted sequence Insert / delete sequence ( indel )

41. Mutations

43. Outline Cell DNA DNA Structure DNA Sequencing RNA (DNA-> RNA) Protein Protein structure Protein synthesis

44. Excellent Animation Cell http://www.youtube.com/watch?v=UB6G9GD2KF k http://www.youtube.com/watch?v=UB6G9GD2KF k Central Dogma http://www.youtube.com/watch?v=GkdRdik73kU