ECE 501 Introduction to BME

1. ECE 501 Introduction to BME Dr. Hang ECE501

2. Part VII Bioinformatics Dr. Hang ECE 501

3. What is Bioinformatics Bioinformatics describes any use of computers to handle biological information. In practice it is treated as a synonym for "computational molecular biology“ ----- the use of computers to characterize the molecular components of living things.

4. Introduction to Molecular Biology - Genome Genome: The entire genetic information of an individual organism Gene: The basic unit of genetic information

5. Introduction to Molecular Biology - Genome

6. Introduction to Molecular Biology - Genome Nuclear genome and mitochondrial genome

7. Introduction to Molecular Biology - DNA Genes are made of deoxyribonucleic acid (DNA)

8. Introduction to Molecular Biology - DNA DNA is a linear polymer in which the monomeric subunits are four chemically distinct nucleotidesthat can be linked together in any order in chains hundreds, thousands or even millions of units in length.

9. Introduction to Molecular Biology - DNA Sugar is deoxyribose Pyramidine: C, T; Purine: A, G

10. Introduction to Molecular Biology - DNA A short DNA polynucleotide

11. Introduction to Molecular Biology - DNA Double Helix

12. Introduction to Molecular Biology - DNA (a) B (b) A (c) Z

13. Introduction to Molecular Biology - RNA • Sugar is ribose • Thymine is replaced by Uracil (U) RNA is a linear polynucleotide containing A, U, C, and G.

14. Introduction to Molecular Biology – Central Dogma DNA RNA Protein

15. Introduction to Molecular Biology – Human Genome The length of human genome: 5000km (2.6 billion base pairs)

16. Introduction to Molecular Biology – Human Genome The structure of a protein-coding gene Exon: A coding region within a discontinuous gene. Intron: A non-coding region within a discontinuous gene

17. Introduction to Molecular Biology – Genome Anatomy • 1 Gene: TRY4 • 2 Gene Segments: V28 & V29-1 • 1 Pseudogene: TRY5 • 52 genome wide repeat sequences: • LINE, SINE, LTR, & DNA transposon. • Two Microsatellites A segment of human genome (on chromosome 7)

18. Introduction to Molecular Biology – Human Genome Mitochondrial Genome

19. Introduction to Molecular Biology – Genome Anatomy Comparison of the genomes of humans, yeast, fruit flies, maize and Escherichia coli.

20. Introduction to Molecular Biology – Genome Anatomy Genome = non-coding DNA + coding DNA

21. Introduction to Molecular Biology – Genome Anatomy • Prokaryotic Genome: • More compact • No introns • Gene=coding DNA • Infrequency of repetitive sequences

22. Introduction to Molecular Biology – Genome Anatomy • Eukaryotic Genome: • Non-coding DNA including introns, • Exon=coding DNA • Gene=Exons+Introns • More advanced species, more repetitive sequences

23. Introduction to Molecular Biology – Genome Anatomy Eukaryotic Gene

24. Introduction to Molecular Biology – Genome Anatomy Protein-coding Genes

25. Introduction to Molecular Biology – Genome Anatomy Protein – coding Genes: Alternative Splicing

26. Introduction to Molecular Biology – Genome Anatomy Reading frame: A series of triplet codons in a DNA sequence. Six reading frames

27. Introduction to Molecular Biology – Genome Anatomy • Open reading frames (ORFs) • a series of codons in DNA/RNA that specify the amino acid • sequence of the protein that the gene codes for • begins with an initiation codon - usually (but not always) ATG • ends with a termination codon: TAA, TAG or TGA

28. Introduction to Molecular Biology – Genome Anatomy Example of ORF

29. Introduction to Molecular Biology – Genome Anatomy Genetic code (RNA)

30. Introduction to Molecular Biology – Genome Anatomy • Non-coding genes: Encode RNAs • Ribosomal RNAs(rRNAs) • Transfer RNAs(tRNAs) • Small nuclear RNA(snRNA ): mRNA processing • Small nucleolar RNA(snoRNA): rRNA processing • Small cytoplasmic RNA(scRNA): ?

31. Introduction to Molecular Biology – Genome Anatomy • Gene segment: • only segments of a gene • must be linked to other gene segments from elsewhere in the locus before being expressed

32. Introduction to Molecular Biology – Genome Anatomy • Pseudogene: non-functional copy of a gene • Conventional: caused by mutation (deletion, insertion etc.) • Processed:

33. Introduction to Molecular Biology – Genome Anatomy • Repetitive DNA: • interspersed repeats: distributed at random • tandemly repeated DNA : placed next to each other

34. Introduction to Molecular Biology – Genome Anatomy • interspersed repeats: • SINE: Short interspersed element • LTR: Long terminal repeat • LINE: Long interspersed element • DNA transposon: Mobile DNA segment

35. Introductionto Molecular Biology – Genome Anatomy • tandem repeats : • Satellite: • Microsatellite: fewer copies