L1+L2 Flashcards
How may the pI of an amino acid be determined?
½(pk1 + pK2)
How do you find the Pk?
Flattest part of the curve (buffered by equilibrium)
how do ionisable side groups affect the pI?
Acidic groups have lower pI, alkaline have higher pI
Draw the structure of Arginine
(see)
Draw the structure of lysine
(see)
What is chymotrypsin specific to? Trypsin?
Aromatic amino acids, positively charged (Lys arg)
Draw asparagine and glutamine
(see)
Draw methionine
(see)
Draw histidine
(see)
What are the stats of an alpha helix?
3.6aa
5.4A
n and n+4
right handed
What is an ampholyte?
Can act as acid and base
what is a psi angle? What is a thi angle? draw a ramachandran plot
psi - carbon alpha carbon
thi - carbon nitrogen
thi in x, psi in y
What are the angles of Beta sheets and aloha helices?
50-60 degree turn for alpha helices, 180 for beta sheets
what forces stabilise alpha helices?
hydrophobic effect, intrahelical hydrogen bonding
what forces stabilise beta sheets?
interstrand hydrogen bonds, van der waals between stacked sheets
Define the van der waals contact distance and minimum distance allowed with a graph
See notes
what is a helix-loop helix?
protein domain - helix loop helix, fits in major groove of DNA
Give an example of a helix loop helix motif
EF hand motif, Central loop binds and coordinates calcium ion
What is a beta alpha beta helix?
joined by alpha helix, more energetically favourable to form an alpha helix than long unstructured region
give an example of a beta alpha beta
Central subunit of pyruvate kinase formed from beta alpha barrel, and leucine rich repeat alpha beta alpha forms horseshoe fold
What does rcsb stand for and what is it used for?
research collabaratory for structural bioinformatics
grab pdb files of crystal structures
