Lec5/6 - Proteins: Types, Shape and Function

Question 1

Define “Native Conformation”

Answer 1

The single, stable shape that a polypeptide chain folds into under physiological conditions (determined by primary structure)

Question 2

What two key factors contribute to protein shape?

Answer 2

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)

Question 3

Are cis or trans conformations more common?

Answer 3

Trans!
(Cis conformations are less favourable due to steric interference of alpha-carbon side chains)

Question 4

Which bonds in proteins are known as phi and psi?

Answer 4

N-C(a) is Phi
C(a)-C is Psi

Question 5

Which direction does the alpha helix turn?

Answer 5

It is right handed (i.e., it turns clockwise when viewed from the N terminus)

Question 6

What are the rise and pitch distance in a protein (and what do these mean) - hence, how many amino acids are there per turn?

Answer 6

Rise = 0.15 nm per residue
Pitch = 0.54 nm per turn
Therefore 3.6 Amino Acids per turn

Question 7

What stabilises ß-sheets?

Answer 7

Hydrogen bonding between C=O and N-H groups on adjacent strands

Question 8

What are the two types of ß-sheets, and which is more stable?

Answer 8

Parallel and antiparallel - antiparallel is more stable as the H bonds are mostly perpendicular to the strands and less distorted

Question 9

Why are ß-sheets described as pleated?

Answer 9

Because side chains project alternately above and below the plane of the ß-sheet

Question 10

What do loops and turns do in proteins and what is the difference between them?

Answer 10

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)

Question 11

What is the tertiary structure of a protein and how is it stabilised?

Answer 11

It is the closely packed 3D form of a protein, stabilised mainly by non-covalent interactions and disulfide bridges

Question 12

What are motifs?

Answer 12

Motifs (or Super-Secondary Structures) are recurring folding patterns found in many proteins, which contain at least 2 connected secondary structure elements

Question 13

Name the most common motifs (8 total - just need to recognise)

Answer 13

Helix-loop-helix, coiled coil, helix bundle (antiparallel a-helices), ß-a-ß, hairpin, ß-meander, Greek Key, ß-sandwich

Question 14

What are domains?

Answer 14

Compact, independently folded units in proteins (consisting of 25-300 residues) that often have standalone functions

Question 15

How are domains connected to each other?

Answer 15

They are connected by LOOPS, and associate with each other via non-covalent interactions between side chains

Question 16

Name 4 examples of common domain folds

Answer 16

Parallel twisted sheet, ß-barrel, a-ß barrel, ß-helix

Question 17

What are the 4 broad categories of proteins in terms of the alpha and beta structures they contain?

Answer 17

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

Question 18

In quarternary structure, how do different subunits interact with each other?

Answer 18

By weak, non-covalent interactions and (more rarely) by disulfide bridges

Question 19

What kinds of proteins are most likely to have quarternary structure?

Answer 19

Regulated proteins, and large membrane proteins