BIO/CSC295 2011F, Class 08: Protein Alignments (1)

Overview:
* Overview of Chapter 4.
* Bio-Concept Questions from Chapter 4.
* From Aligning Nucleotides to Aligning Amino Acids.
* Building PAM Matrices.
* Lab.

Admin:
* Due Thursday: Response paper on the HIV paper.
* Due Thursday: HIV assignment.
* EC for Men's Soccer at Simpson Tuesday at 7 p.m.
* EC for Tutorial Debate Wednesday at 7:45 p.m.
* EC for Kington's Town Hall Meeting on Wednesday.  (You shouldn't need extra cr
edit to go - it's interesting and important, but we're giving it anyway.)
* EC for Volleyball Thursday at 7:00 p.m.
* EC for Family Weekend Poster Session (9:00-11:00 Saturday), provided you visit
your classmates' posters.
* EC for Volleyball Saturday at 11 a.m.
* EC Friday for Bio students talking at noon! Bring your own lunch.  
* EC for CS Thursday Extra about CS Grad School. Thursday 4:15PM. Bio majors can come too.
* Bake sale for ISO. CUPCAKES from an unknown source -- buy at your own risk!

Up until now: scoring mismatches! BLAST! 
Let's look at Protein alignments.

Review Central Dogma. Euk's make things interesting - they have noncoding bits which
aren't always conserved. 

Prok: bacteria! Single, circular chromosome.
YOU are Eukar: other alive things -- multicell (plants, animals, Prof Rebelsky)

Some Prok codes are synonymous (produce same code even if the exact sequence is different ), which is why we should compare amino acids instead.
FtsZ & Tubulin

We are about to do Bio 251 in 1 hour!


Protein: a chain of amino acids (varying in length) 
Amino acids: Amino group, central cardon, COOH, plus the side chain.
Side chains: 
  Affect Shape: hydrophobic (cluster in middle) /hyrdophilic (cluster outside) 
         Folds: charged  
Tertiary struct: combination of these.
Quad struct: 

Common folds: secondary structure (alpha helix [twist/corkscrew] & beta sheet [beta strands which loop/fold around]).

Open question: What is final fold of protein? 
(possible final project!!)
 We can find out Crystal structure. (Defraction pattern -> molecule.)


These primary sequences allow us to predict structure & find homologs.


Euk proteins fold the same way in Pro.

But some need context: Chaperon Proteins



Mutations:
-new stop codon. Could partially work, not at all.
-change shape (with only one amino acid change)
-Hyrdophobic->philic. 

could do nothing!
eg. switching from a positive charge to something else positively charged might not effect structure.