ECE 501 Introduction to BME

ECE 501 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.

Introduction to Molecular Biology - Genome

Genome: The entire genetic information of an individual organism

Gene: The basic unit of genetic information

Introduction to Molecular Biology - Genome

Introduction to Molecular Biology - Genome

Nuclear genome and mitochondrial genome

Introduction to Molecular Biology - DNA

Genes are made of deoxyribonucleic acid (DNA)

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.

Introduction to Molecular Biology - DNA

Sugar is deoxyribose

Pyramidine: C, T; Purine: A, G

Introduction to Molecular Biology - DNA

A short DNA polynucleotide

Introduction to Molecular Biology - DNA

Double Helix

Introduction to Molecular Biology - DNA

(a) B (b) A (c) Z

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.

Introduction to Molecular Biology – Central Dogma

DNA RNA Protein

Introduction to Molecular Biology – Human Genome

The length of human genome: 5000km (2.6 billion base pairs)

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

Introduction to Molecular Biology – Genome Anatomy

A segment of human genome (on chromosome 7)

• 1 Gene: TRY4

• 2 Gene Segments: V28 & V29-1

• 1 Pseudogene: TRY5

• 52 genome wide repeat sequences:

LINE, SINE, LTR, & DNA transposon.

• Two Microsatellites

Introduction to Molecular Biology – Human Genome

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