1. ECE 501 Introduction to BME
Dr. Hang

2. Part VII Bioinformatics
ECE 501
Dr. Hang

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.
Gregor Mendor realized that inheritance was decided by discrete units we call genes today by studying pea plants

4. Introduction to Molecular Biology - Genome
Genome: The entire genetic information of an individual organism
Gene: The basic unit of genetic information
Gregor Mendor realized that inheritance was decided by discrete units we call genes today by studying pea plants

5. Introduction to Molecular Biology - Genome
Gregor Mendor realized that inheritance was decided by discrete units we call genes today by studying pea plants

6. Introduction to Molecular Biology - Genome
Gregor Mendor realized that inheritance was decided by discrete units we call genes today by studying pea plants
Nuclear genome and mitochondrial genome

7. Introduction to Molecular Biology - DNA
Genes are made of deoxyribonucleic acid (DNA)
Gregor Mendor realized that inheritance was decided by discrete units we call genes today by studying pea plants

8. Introduction to Molecular Biology - DNA
DNA is a linear polymer in which the monomeric subunits are
four chemically distinct nucleotides that can be linked together
in any order in chains hundreds, thousands or even millions of
units in length.
Gregor Mendor realized that inheritance was decided by discrete units we call genes today by studying pea plants

9. Introduction to Molecular Biology - DNA
H atom is linked to 2’carbon instead of hydroxyl group OH-
Sugar is deoxyribose
Pyramidine: C, T; Purine: A, G

10. Introduction to Molecular Biology - DNA
Gregor Mendor realized that inheritance was decided by discrete units we call genes today by studying pea plants
A short DNA polynucleotide

11. Introduction to Molecular Biology - DNA
Double Helix
Gregor Mendor realized that inheritance was decided by discrete units we call genes today by studying pea plants

12. Introduction to Molecular Biology - DNA
Gregor Mendor realized that inheritance was decided by discrete units we call genes today by studying pea plants
(a) B (b) A (c) Z

13. Introduction to Molecular Biology - RNA
Sugar is ribose
Thymine is replaced by Uracil (U)
Gregor Mendor realized that inheritance was decided by discrete units we call genes today by studying pea plants
RNA is a linear polynucleotide containing A, U, C, and G.

14. Introduction to Molecular Biology – Central Dogma
Gregor Mendor realized that inheritance was decided by discrete units we call genes today by studying pea plants
DNA RNA Protein

15. Introduction to Molecular Biology – Human Genome
Gregor Mendor realized that inheritance was decided by discrete units we call genes today by studying pea plants
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
Gregor Mendor realized that inheritance was decided by discrete units we call genes today by studying pea plants
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
Gregor Mendor realized that inheritance was decided by discrete units we call genes today by studying pea plants
A segment of human genome (on chromosome 7)

18. Introduction to Molecular Biology – Human Genome
Gregor Mendor realized that inheritance was decided by discrete units we call genes today by studying pea plants
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. Introduction to Molecular Biology – Genome Anatomy
tandem repeats :
Satellite:
Microsatellite: fewer copies