Transcript ppt - NJIT.edu

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
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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