ECE 501 Introduction to BME Dr. Hang

Part VII Bioinformatics ECE 501 Dr. Hang

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

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

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

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

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

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

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

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

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

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

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.

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

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)

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

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)

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

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

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

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

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

Introduction to Molecular Biology – Genome Anatomy Eukaryotic Gene

Introduction to Molecular Biology – Genome Anatomy Protein-coding Genes

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

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

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

Introduction to Molecular Biology – Genome Anatomy Example of ORF

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

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): ?

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

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

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

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

Introduction to Molecular Biology – Genome Anatomy tandem repeats : Satellite: Microsatellite: fewer copies