Introduction to Bioinformatics Algorithms Algorithms for Molecular Biology CSCI Elizabeth White

CSCI 4314/5314, Algorithms for Molecular Biology DNA revisited Double helix A, C, G, T “letters” A::T = 1 G::C = 1 Image from

CSCI 4314/5314, Algorithms for Molecular Biology Why these ratios? Same size pairs Matching shapes Matching charges Image from

CSCI 4314/5314, Algorithms for Molecular Biology Base pairs bond to give double helix Image from

CSCI 4314/5314, Algorithms for Molecular Biology DNA is designed to be replicated Each of the 2 strands can specify the other one Result is 2 helices, each with one old strand and one new Image from

CSCI 4314/5314, Algorithms for Molecular Biology Replication bubbles (made of 2 forks) Image from

CSCI 4314/5314, Algorithms for Molecular Biology DNA is designed to be transcribed Similar mechanism to replication Result is original helix + RNA strand Image from

CSCI 4314/5314, Algorithms for Molecular Biology DNA transcription to RNA Image from

CSCI 4314/5314, Algorithms for Molecular Biology RNA molecule is processed further Except in bacteria, RNA molecule contains Introns: do not code for protein Exons: protein-coding regions Introns are spliced out of the RNA transcript Result is “messenger RNA”, mRNA Image from

CSCI 4314/5314, Algorithms for Molecular Biology RNA splicing can give many variants Image from

CSCI 4314/5314, Algorithms for Molecular Biology RNA specifies 3-base codons Image from

CSCI 4314/5314, Algorithms for Molecular Biology 3-letter codons map to amino acids Image from

CSCI 4314/5314, Algorithms for Molecular Biology Transfer RNAs do the mapping Image from

CSCI 4314/5314, Algorithms for Molecular Biology Translation: RNA to protein Messenger RNA is “read” by a ribosome Ribosome connects amino acids to build new protein strand as it reads Image from

CSCI 4314/5314, Algorithms for Molecular Biology Ribosomes at work Image from

CSCI 4314/5314, Algorithms for Molecular Biology Overview: transcription/translation Image from

CSCI 4314/5314, Algorithms for Molecular Biology Protein structure Primary: amino acid sequence Secondary: short regions of protein form Alpha-helix Beta-sheet Tertiary: helices and sheets nestle together to make a 3 dimensional shape Quaternary: 2 or more proteins associate together

CSCI 4314/5314, Algorithms for Molecular Biology Primary structure: amino acid sequence Top image from Bottom image from

CSCI 4314/5314, Algorithms for Molecular Biology Left image from Bottom image from Secondary structure: alpha-helix

CSCI 4314/5314, Algorithms for Molecular Biology Secondary structure: beta-sheet Left image from Right image from

CSCI 4314/5314, Algorithms for Molecular Biology Tertiary structure: 3D shape Image from

CSCI 4314/5314, Algorithms for Molecular Biology Quaternary structure: assembly Image from

CSCI 4314/5314, Algorithms for Molecular Biology Structural proteins Image from

CSCI 4314/5314, Algorithms for Molecular Biology DNA-binding proteins Recognize particular DNA sequences Regulate which genes are transcribed into RNA Often act in pairs Image from

CSCI 4314/5314, Algorithms for Molecular Biology Enzymatic proteins Catalyze chemical reactions Beta-lactamase enzyme inactivates penicillin Image from

CSCI 4314/5314, Algorithms for Molecular Biology Open problem: protein folding Amino acid sequence of protein determines its shape Proteins seem to “fall” into correct shape In theory, we should be able to look at a protein’s sequence and deduce its shape Unfortunately, this is not computationally possible In practice, we deduce shapes by similarity Proteins with similar amino acid sequences tend to take similar shapes