Intro to Protein Structure Flashcards
define protein
group of organic compounds composed of 1 or more A.A chains and form essential part of all living life
what is the simplest A.A and what is its R group?
glycine-R group is H
What are lysine and arginine at physiological pH?
protonated and basic
When is histidine protonated?
below pH 6
What are glutamic acid and aspartic acid at physiological pH?
negatively charged
What chiral form are all A.A in?
L-form
Peptide bond characteristics
no rotation round bond, C=O and N-H in same plane, other 2 bonds can rotate, side chains can’t clash with main chain (steric hindrance)
What is the strongest bond in a protein?
covalent
What type of bond is disulphide bridges?
covalent
What are ionic interactions?
electrostatic attractions between charged side chains
When are ionic interactions especially strong?
when ion pairs are in protein interior and excluded from water
Where are the majority of charged groups on a protein and what happens to them?
surface of protein and they get neutralised
What are hydrophobic interactions?
hydrophobic core and hydrophilic surface as hydrophobic side chains packed into centre of protein
Why do Van der Waals still have an effect on protein conformation if they’re so weak?
large number of them
What is the alpha helix stabilised by?
H bonds between C=O and N-H
Which handed helices are favoured and why?
Right handed because A.A are L-form.
How many A.A along the helix stabilise the structure?
4
What bond hold 2 or more beta stands together to form a beta pleated sheet?
hydrogen between N-H and C=O
What are the 2 forms of beta pleated sheet and what do they allow for?
parallel and antiparallel and allow for best h bond group alignment
Which A.A is know as the “kinky” A.A and why?
Proline - loses NH group when joins polypeptide chain, no h bond with C=O of another residue, distorts helix
What conformation are proteins folded into?
single of lowest energy
What are the 2 ways folding can occur?
spontaneous or with chaperones
What do chaperones do?
Bind to partly folded polypeptide, ensuring folding goes along most energetically favourable route
Name 2 common denaturants and what they break
urea (H bonds) and 2-mercaptoethanol (breaks disulphide)
Define secondary structure, give examples
local structural motifs within a protein, alpha helix or beta pleated sheet
Define tertiary structure
arrangement of secondary structure motifs into compact globular structures called domains
Define quaternary structure
3 dimensional structure of a multimeric protein composed of several sub units
What does post-translational modifications allow?
A.A to be modified to novel A.A to enhance capabilities of protein
