1. Course information To reach me: Barry Cohen bcohen@cs.njit.edu GITC 3800 T 4:00-5:30 Th 3:00-4:30 www.cs.njit.edu/~bcohenbcohen@cs.njit.edu

2. Projects Team projects (3 person) One hour presentations Literature review / algorithms / programs Sample applications Open problems 6 Homeworks

3. Texts Introduction to Bioinformatics Arthur Lesk Recommended: Current Topics in Computational Molecular Biology Tao Jiang, Ying Xu, Michael Zhang

4. Watson & Crick, 1953 http://www.nature.com/genomics/human/watson-crick/

5. Stylized double helix

6. Replication ‘It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.’

7. Sequence to structure

8. The information cycle

9. The triplet code

10. 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)

11. 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)

12. 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

13. 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)

14. 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)

15. 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)

16. 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

17. rRNA universal tree of life