Course information

• To reach me:Barry Cohen

• bcohen@cs.njit.eduGITC 3800T 4:00-5:30 Th 3:00-4:30www.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 BioinformaticsArthur Lesk

• Recommended:Current Topics in Computational Molecular BiologyTao 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