Download Notes from Lecture 1 - Tufts Computer Science

Comp 150-05: Computational Biology Challenges
Prof. Lenore Cowen
Tufts University, Fall 2016
Scribe: Rebecca Newman
Lecture 1: Biology Review
1
Metaphor: The Cell = Factory Floor
Proteins are the machines, DNA is the blueprint set
2
Metaphor: Proteins = Beads on a String
20 types of ”beads” called amino acids. Amino acids differ from eachother
based on what ”hangs off” the standard chemical backbone. We use letters
represent the alphabet of all amino acids.
3
The Central Dogma
There exists a direct correspondance between the 4-letter DNA alphabet and
the 20-letter protein alphabet.
DNA
Alphabet
4
DNAalphabet
triple
Protein
Alphabet
Genes
Genes are the parts of the DNA that code for proteins. You can get different
proteins from the same portion of DNA via splicing.
1
5
Available Data
Linear
Sequence
on Chromosome
RNA:
Transcription
Expression
Levels,
Abundance
Ribosomes:
Translation
Protein
sequence,
structure
Protein
Function
Amino
Acid Chain
Phenotypes
Information Inferred
Variations,
annotations
Alt.
Splicing,
Non-coding
RNA
There is a huge knowledge gap between data collection and understanding
of the data. It’s publicly available, we just need to process and interpret it!
How is this data organized? Either by organism or across-organisms.
Which models do we want to look at? Yeast, worm, fly, mouse, rat,
plants, human.
2
6
Yeast
Baker’s yeast is a simple single-cell Eukaryote: 12 million base pairs, 32
chromosomes, 6000 genes.
Yeast Genome Database: www.yeastgenome.org
ORF (Open Reading Frame): The exact codon letters for this gene is known.
Sequence Section: tells you exactly where on the chromosome the gene is
located.
Essential Gene: If you inactivate the gene, the organism dies.
3