Lecture 15 - Quarternary Structure

Question 1

secondary structure:

Answer 1

interactions that occur between the C=O & N—H groups on amino acids

Question 2

super secondary structure:

Answer 2

structural motifs made up of more than one element of secondary structure

Question 3

tertiary structure:

Answer 3

organisation in three dimensions of all the atoms in the polypeptide

Question 4

quaternary structure:

Answer 4

conformation assumed by a multimetric protein

Question 5

non bonded interactions:

Answer 5

atoms that are not linked by covalent bonds: electrostatic attractions, hydrogen bonds, hydrophobic interactions & Van de Walls forces

Question 6

what does polymerisation lead to?

Answer 6

polymerisation leads to an electrically neutral backbone

Question 7

basic and acidic R-groups are affected by the pH of the environment:

Answer 7

• charged amino acids have an acid dissociation constant - pH at which molecule carries no net charge

Question 8

salt bridge:

Answer 8

at a neutral pH, when most charged side chain R-groups are ionised electrostatic interactions occur between a positive and negative side chain (if they are closely arranged in space

salt bridge - electrostatic interaction between three GLU (-1) & ARG (+1)

charge is then spread across the whole residue

Question 9

hydrophobic effect:

Answer 9

• a polar (non-polar) molecules aggregate in the presence of water
• hydrophobic residues usually are found in the centre of a folded molecule

Question 10

where are hydrophobic residues found in a protein molecule?

Answer 10

hydrophobic residues are usually found in the centre of a folded protein molecule

Question 11

Van de Walls:

Answer 11

• weak electrostatic attractions between atoms in close proximity, generated by dipoles from the electron cloud
• the atoms cannot become too close, as the negatively charged electrons will repel
• each atom has a specific van de waals radii

Question 12

what is a homotetramer?

Answer 12

a protein what is composed of four identical subunit molecules

Question 13

multimeric protein terminology:

Answer 13

identical chains: homo-
different chains: hetero-

2 chains: dimer
3 chains: trimer
4 chains: tetrameter
12 chains: dodecameter

Question 14

fibrous proteins:

Answer 14

play a structural role in organisms: providing support, shape or protection

elongated with a specific and usually repetitive structure

some examples are collagen, keratin and silk

Question 15

case study - collagen:

Answer 15

found in connective tissue (tendons, cartilage, organic matrix of bones, cornea)

consists of three polypeptide chains that each form left-handed helices (polyproline helix)

humans have 16 distinct versions of collagen that differ in their primary sequence

collagen has three intertwined polypeptide chains that form a triple helix

Question 16

globular proteins:

Answer 16

have a spherical blob-like shape and are far more numerous than fibrous proteins and they exist as an enormous variety of three dimensional structures

Question 17

protein to protein interfaces:

Answer 17

interface atoms are coloured

bright colours indicate hydrophilic interactions

pale colours indicate hydrophobic interactions

interface waters - green spheres

Question 18

how can you classify protein to protein interactions?

Answer 18

protein to protein interactions can either be permanent or transient

Question 19

characteristics of protein to protein interactions:

Answer 19

• hydrophobic
• surface accessible
• protruding
• planar
• specific residue propensities

Question 20

Membrane proteins interact with ______ and have very specific ________ __________ and ___________

Answer 20

(1) lipids

(2) primary sequences

(3) structures

Question 21

protein toxin examples:

Answer 21

Gramicidin A in DMPC lipid bilayer and water

•Antibiotic peptide

Forms a pore in the cell wall of a bacteria and lets out monovalent cations (K+, Na+).

[Membrane potential disappears and bacteria dies!]

• 15 amino acids, helical
• channel is formed by a head-to-head dimer

Question 22

types of typical ion channels and their examples:

Answer 22

• Simple pores (GA, GAP junctions)
• Substrate gated channels (Nicotinic receptor)
• Voltage-gated channels (K-channels)
• Pumps (ATP-synthase, K+,Na+-ATPase)

Question 23

how to proteins bind to other proteins?

Answer 23

proteins bind to other proteins via ‘interfaces’

Question 24

Drugs can be designed to bind
specifically in binding or active sites:

Answer 24

•Drugs can be designed to inhibit or enhance a proteins function

•The drug should be the correct size and have the right chemical properties to fit in the active site and compete with substrate