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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
• 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)
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