CO457 - Bioinformatics

Basavaraj TalawarCSE, NITK

bt.nitk.2014@gmail.com

About the Course● Molecular Biology, Genomics, Proteins, RNA

structure prediction, Proteomics● Data searches, Pairwise alignments, Distance

and Character based Phylogenetics● Programming assignments from

http://rosalind.info (30% credit)● Quizzes (10%), Mid-Sem (20%), Final (40%)● Krane & Raymer, Fundamentals of

Bioinformatics, Pearson.● Attwood, Introduction to Bioinformatics,

Pearson.

Miller-UreyExperiment

● Emergence– Self replication

● Natural selection– Brains

● Human intelligence● Recursively self-improving AI

DNA Double Helix

Nucleotides

Ribose and Dexyoribose Sugars

http://www.mun.ca/biology/scarr/Ribose_sugar.html

Phosphate Group

DNA

Hydrogen Bonds

The Central Dogma of Molecular Biology

The Central Dogma of Molecular Biology

Gene Structure and Content● Gene expression

– Promoter sequences

● RNA Polymerase● Regulatory proteins● Positive and negative regulation● Jacob and Monod (Nobel 1965)

DNA Codon Table

Proteins – Functions and Structure● Proteins do most of the work

– Structural proteins (collagen), Enzymes (pepsin), hemoglobin, insulin, rhodopsin, etc.

● Linear polymers of amino acids– backbone and side chain (R)

● Primary Structure (sequence)

– NH2 → COOH

● Native structure

φ

ψ

Proteins – Native Structure

φ

ψ

It is not sci-fi, it is φ-ψ – T-Shirt Slogan, Molecular Biophysics Unit, IISc.

http://isite.lps.org/sputnam/AdvancedChem/Ch%2018%20Notes_files/primary_bondangles.jpg

Protein – Secondary Structure● α – helix and β – sheet

φ-ψ ≈ -60

Φ ≈ -135ψ ≈ 135

Protein Structure

● Secondary, Tertiary, Quaternary Structures

α-helix

β-sheet

Covalent Bond

Covalent Bond

http://whatanart.com/2013/06/24/fun-chemistry-inspired-art/

Polar Covalent Bond

http://chemwiki.ucdavis.edu

Hydrophilicity and Hydrophobicity● Hydrophilicity

– Molecules with polar bonds

– Hydrogen bonds with water

● Hydrophobicity

That is why Polar bears are found in the Arctic!

LinusPauling (1953, 1962)

Molecular Biology Tools● Restriction enzyme digests● Gel electrophoresis● Blotting and Hybridization● Cloning● PCR● DNA sequencing

Restriction Enzyme Digests● Restriction enzymes

– EcoRI from Escherichia Coli

● Ligase– Sticky ends and Blunt ends

Gel Electrophoresis● Separate DNA fragments● Sugar-phosphate backbone is negatively

charged● Agarose

or Acrylamidegel

Blotting and Hybridization

Blotting and Hybridization

Cloning

CLONING

Cloning● Vectors● Genetic Library● Genomic equivalent● Inefficiency of cloning● cDNA Library

– mRNA

– reverse transcriptase

PolymeraseChainReaction

DNA Sequencing● Generate subfragments

– Lengths differ by single nucleotide

● Labeling each fragment● Separation of fragments by size to read the

order of different tags● Sanger's Chain-termination method

Reassociation Kinetics● C-Value: Total DNA in a cell of an organism● C-value paradox● cot equation

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