Bioinformatics

1
Bioinformatics

• Student host
• Chris Johnston
• Speaker
• Dr Kate McCain

2
Molecular Biology and Biological Chemistry

• Genetic Material
• DNA organize inanimate molecules into functioning
  living cells

• Nucleotides
• Four bases in DNA molecule
• GATC
• Genes are many thousand nucleotides long

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Central Dogma

• Transcription Translation
• DNA RNA Protein
• RNA polymerase Ribosome
• Proteins do all the work
• Catalysts called Enzymes

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Gene Structure and Information content

• DNA has been the same for billions of years

• Use of Energy is important
• Promoter Sequence
• Positive regulation
• Allow transcription
• Negative regulation
• Prevent transcription

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The Genetic Code

• Nucleotides information storage and transfer (DNA
  RNA)
• Amino Acids Make proteins that do work
• Degeneracy genetic code robust hard for
  nucleotide to change function of protein it
  encodes

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Protein Structure and Function

• 20 amino acids
• Protein Chain
• Starts at Amino group amino terminus
• Ends at Carboxylic acid group carboxy terminus
• Native Structure complex globular structure
• Amino acids determine shape
• Shape helps perform role

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Molecular Biology Tools

• Restriction Enzyme Digest
• Enzymes that break double strands used like
  scissors later pasted to DNA to isolate given
  nucleotides
• Restriction mapping
• Cloning
• insert DNA into vectors and replicate to get
  large numbers

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Molecular Biology Tools

• Gel electrophoresis
• Uses electrodes to separate molecules by size.

• Blotting and Hybridization
• Looking for one or more fragments
• Probes used to find unique piece

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Genomics and Impact

• Genome Organisms complete set of DNA
• Chromosomes
• 24
• Genes made up of 50 to 250 million base pairs
• Proteins perform the work
• 20 amino acids
• 3D structure defines function in cell

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Human Genome Project

• DNA sequence consists of 3 billion base pairs
• Will guide research and discovery for years
• Find out how cells-genes-proteins work to create
  living organisms

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Medicine and the New Genetics

• Genetic Testing
• Confirm or predict risk of disease
• Prognosticate disease path
• Detecting mutations

• Pharmacogenomics
• Drugs for a genotype
• Minimal side effects
• Work faster
• Cheaper cost to develop
• Faster to develop

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Other Benefits

• Molecular Medicine
• Microbial Genomics
• Risk assessment
• Bioarchaeology, Anthropology, Evolution, and
  Human migration
• DNA identification
• Agriculture, Livestock breeding, and
  Bioprocessing

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Resources form the NCBI

• National Center for Biotechnology Information
• Infrastructure for Molecular Biology research
• Diverse Data a challenge
• Sequence Data needs to be used for analysis and
  retrieval

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GenBank

• DNA sequence Database
• 133,000 sequences form species other than human
• Protein sequence

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GenBank

• Building GenBank
• DNA sequence given unique corresponding Accession
  number
• When sequence changed gi number given to new
  sequence
• BLAST algorithms screen for contaminated unwanted
  erroneous sequence data

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GenBank

• BankIt and Sequin
• Submission tools to build GenBank

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RefSeq

• Reference Sequence
• Aims to nonredundant source of sequence data
• Gene characterization
• Mutation analysis
• Expression studies
• Polymorphism discovery
• Submitted data gets organized

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Entrez

• Integrated access and retrieval system
• Links many resources to help Scientists find what
  they need
• Significant innovation for Bioinformatics

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BLAST

• Family of sequence comparisons algorithms
• Nucleotides and protein sequences understood by
  comparison to one another
• Type in sequence and BLAST finds similar in the
  Entrez system