Lec5/6 - Proteins: Types, Shape and Function Flashcards
Define “Native Conformation”
The single, stable shape that a polypeptide chain folds into under physiological conditions (determined by primary structure)
What two key factors contribute to protein shape?
Allowable bond rotation (determines the possible conformations of the polypeptide chain)
Weak non-covalent interactions between backbone and side-chain groups (e.g., H bonding, electrostatic, hydrophobic effect)
Are cis or trans conformations more common?
Trans!
(Cis conformations are less favourable due to steric interference of alpha-carbon side chains)
Which bonds in proteins are known as phi and psi?
N-C(a) is Phi
C(a)-C is Psi
Which direction does the alpha helix turn?
It is right handed (i.e., it turns clockwise when viewed from the N terminus)
What are the rise and pitch distance in a protein (and what do these mean) - hence, how many amino acids are there per turn?
Rise = 0.15 nm per residue
Pitch = 0.54 nm per turn
Therefore 3.6 Amino Acids per turn
What stabilises ß-sheets?
Hydrogen bonding between C=O and N-H groups on adjacent strands
What are the two types of ß-sheets, and which is more stable?
Parallel and antiparallel - antiparallel is more stable as the H bonds are mostly perpendicular to the strands and less distorted
Why are ß-sheets described as pleated?
Because side chains project alternately above and below the plane of the ß-sheet
What do loops and turns do in proteins and what is the difference between them?
They connect a-helices and ß-sheets to allow a polypeptide chain to fold back on itself and make a compact structure
(Turns are loops which contain 5 resides or less - shorter)
What is the tertiary structure of a protein and how is it stabilised?
It is the closely packed 3D form of a protein, stabilised mainly by non-covalent interactions and disulfide bridges
What are motifs?
Motifs (or Super-Secondary Structures) are recurring folding patterns found in many proteins, which contain at least 2 connected secondary structure elements
Name the most common motifs (8 total - just need to recognise)
Helix-loop-helix, coiled coil, helix bundle (antiparallel a-helices), ß-a-ß, hairpin, ß-meander, Greek Key, ß-sandwich
What are domains?
Compact, independently folded units in proteins (consisting of 25-300 residues) that often have standalone functions
How are domains connected to each other?
They are connected by LOOPS, and associate with each other via non-covalent interactions between side chains
Name 4 examples of common domain folds
Parallel twisted sheet, ß-barrel, a-ß barrel, ß-helix
What are the 4 broad categories of proteins in terms of the alpha and beta structures they contain?
All alpha - only a-helices and connecting loops
All ß - only ß-sheets and connecting loops
Mixed alpha/ß - regions of a/ß are alternating or inter-dispersed
a + ß - local clusters of a-helices and ß-sheets in clearly distinc regions
In quarternary structure, how do different subunits interact with each other?
By weak, non-covalent interactions and (more rarely) by disulfide bridges
What kinds of proteins are most likely to have quarternary structure?
Regulated proteins, and large membrane proteins
