Transcript Announcements - Hiram College

Bioinformatics
Why Can’t It Tell Us Everything?
Bioinformatics
What are our Data Sets?
• Interested in information flow with cells
• Currently, the key information is mostly a
matter of biological macromolecules
• Eventually, information of interest will also
include flow of nutrients, energy, and impact
of small molecules on macromolecular
function
Bioinformatics
What are our Questions?
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What is in there?
What does it do?
How similar is it to something else?
How does it fold?
Where does it go in a cell?
What does it interact with?
How it is regulated?
Level of confidence?
Bioinformatics
Logical Reasoning Behind Data Sets
* Function of organism is determined by function
of its cells
* Function of cells determined by chemical
reactions that take place within them
* Chemical reactions occur or not according to
presence and activity of enzymes
* Enzymes are proteins
* Proteins are determined by genes
* Therefore, genes determine organismal function
Genomics
Proteomics
Central Dogma
Flow of Information
Central Dogma
DNA as the Blueprint for Life?
Central Dogma
DNA as the Blueprint for Life?
Central Dogma
DNA
RNA
Protein
Genes & proteins are different molecular languages,
but they are colinear
DNA
Basic Unit (alphabet): Nucleotide (base)
Only 4: A, T, G, and C
Double-stranded: A<>T and G<>C
5’..AGCTGCATGCTAGCTGACGTCA….3’
3’..TCGACGTACGATCGACTGCAGT….5’
“Words” (genes) to encode proteins, RNA
Double helical
DNA
Structure Connected to Information
DNA Tower in Perth, AUS
DNA
Replication & Transcription as Algorithms
• With rare exceptions, all
DNA is replicated
• Crucial tool is ability to go
from one strand to another
• Transcription uses same
base-pairing rules with U
instead of T, but occurs in
packets
Transcription = DNA to RNA
Where to Start is a Big Question
Protein
Alphabet: amino acids
There are 20 amino acids
Met Cys Ser Leu
Ala
Ala
Val
Proteins
Number of Possible
100-mer Peptides?
20 possible residues at each
position
For 2-mers, 20 possible at
position 1 and 20 possible
at position 2, so 20 x 20 =
202 = 400
Same logic for 100-mers,
20100 = 2100 x 10100 =
(210) 10 x 10100 =
~ (103) 10 x 10100 = 10130
beta-pleated sheet
Proteins
Folding Starts Local
alpha-helix
Proteins
Folding Goes Global
Proteins
Predictive Protein Folding as Holy Grail
Protein
Alphabet: amino acids
There are 20 amino acids
Encoded by codons (triplets of nucleotides)
ATG TGCAGCCTAGCTGCCGTC
CTAGCTGCCGTC
Met Cys Ser Leu
Ala
Ala
Val
Genetic Code Found on Earth:
How Does It Work?
5’-UCGACCAUGGUUGACCAUUGAUUACCACG-3’
Genetic Code
• Triplet
• Nonoverlapping
• Comma-less
• Redundant
Bioinformatics:
Mining a Mountain of Data
Where are the
putative genes?