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Course information • To reach me: Barry Cohen • [email protected] GITC 3800 T 4:00-5:30 Th 3:00-4:30 www.cs.njit.edu/~bcohen Projects • • • • • • Team projects (3 person) One hour presentations Literature review / algorithms / programs Sample applications Open problems 6 Homeworks Texts • Introduction to Bioinformatics Arthur Lesk • Recommended: Current Topics in Computational Molecular Biology Tao Jiang, Ying Xu, Michael Zhang Watson & Crick, 1953 http://www.nature.com/genomics/human/watson-crick/ Stylized double helix Replication • ‘It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.’ Sequence to structure The information cycle The triplet code In the beginning … • Life began when the earth was young • Life arose from simple chemistry (most life still is relatively simple) • Universal common ancestor • Common molecular machinery (oldest fossils are living fossils) What is life? • Information and metabolism • RNA world hypothesis • DNA as program file (information coding for activity) • Replication (information which codes for itself) • Variation, evolution (life adapts to its environment) DNA • DNA is a polymer (sequence, string) • DNA is composed of just four kinds of chemical units (A, C, G, T) • DNA is redundant (double helix); A’s pair with T’s, G’s pair with C’s • Some DNA codes for RNA, proteins (exons – expressed regions) • Some DNA is noncoding (introns – intervening regions) • Coherent sets of DNA are genes RNA • RNA is a also polymer (sequence, string) • RNA is composed of just four kinds of chemical units (A, C, G, U) • RNA is single stranded • Some RNA codes for proteins, some is functional (e.g., tRNA) Proteins • Proteins account for most life activity and structure • A protein is a polymer (sequence, string) • Proteins are composed of 20 kinds of chemical units (amino acids) • Proteins fold into a specific shape, which determines their function • Proteins are made from genetic templates (they don’t code) Evolution • Darwin – evolution is adaption • Nature has no aim, it is a result of random events • Most events are DNA string edits (indels, substititions) • Some events are on ‘higher level’ structures (e.g., chromosomes) The ‘tree of life’ • Some errors is replication divide gene pools into two (speciation). (Or vice versa.) • These bifurcations give the history of life a tree-like structure rRNA universal tree of life