2.4 - Quaternary Structure

Question 1

non-bonded interactions (4)

Answer 1

1. electrostatic interactions
2. hydrogen bonds
3. hydrophobic interactions
4. van der waals forces

Question 2

acid dissociation constant

Answer 2

pH at which charged amino acids carry no net charge

Question 3

+ve charged R group amino acids (3)

Answer 3

1. lysine (Lys, K)
2. arginine (Arg, R)
3. Histidine (His, H)

Question 4

what affects basic and acidic amino acid R groups?

Answer 4

pH of the environment

Question 5

-ve charged R group amino acids (2)

Answer 5

1. glutamic acid (Glu, E)
2. aspartic acid (Asp, D)

Question 6

when do salt bridges form?

Answer 6

at neutral pH, when most charged side chain R groups are ionised

Question 7

how do salt bridges form?

Answer 7

electrostatic interaction occurs between a +ve and -ve side chain (if they are closely arranged in space)

Question 8

effect of salt bridge formation

Answer 8

charge spread across whole residue

Question 9

where do H-bonds form between amino acids?

Answer 9

between R groups (as well as main chain)

Question 10

hydrophobic effect

Answer 10

apolar (non-polar) molecules aggregate in presence of water

Question 11

where are hydrophobic residues usually found in molecule?

Answer 11

in the centre of the folded molecule

Question 12

van der waals

Answer 12

weak electrostatic interaction between atoms in close proximity, generated by dipoles from the electron cloud

Question 13

why cant atoms interacting via van der waals come too close?

Answer 13

-vely charged e- will repel (van der waals radius)

Question 14

multimeric protein nomenclature: identical chains

Answer 14

homo-

Question 15

multimeric protein nomenclature: different chains

Answer 15

hetero-

Question 16

multimeric protein nomenclature: 2 chains

Answer 16

dimer

Question 17

multimeric protein nomenclature: 3 chains

Answer 17

trimer

Question 18

multimeric protein nomenclature: 4 chains

Answer 18

tetramer

Question 19

fibrous proteins

Answer 19

elongated and structural role in nature - provide support, shape or protection

Question 20

examples of fibrous proteins (3)

Answer 20

1. collagen
2. keratin
3. silk

Question 21

collagen role

Answer 21

connective tissue

Question 22

examples of collagen (4)

Answer 22

1. tendons
2. cartilage
3. organic matrix of bone
4. cornea

Question 23

collagen structure

Answer 23

3 intertwined polypeptide chains that form triple helix

Question 24

how many distinct versions of collagen do humans have?

Answer 24

16 - differ in primary sequence

Question 25

globular protein structure (2)

Answer 25

1. spherical shape 2. exist in enormous variety of 3D structures

Question 26

globular protein frequency vs fibrous proteins

Answer 26

globular much more numerous

Question 27

classifications of protein interactions (2)

Answer 27

1. permanent 2. transient

Question 28

characteristics of permanent protein interactions

Answer 28

tight binding with strong affinities

Question 29

characteristics of transient protein interactions

Answer 29

weaker and more dynamic

Question 30

characteristics of protein-protein interaction sites (5)

Answer 30

1. hydrophobic 2. surface accesible 3. protruding 4. planar 5. specific residue propensities

Question 31

membrane proteins

Answer 31

interact with lipids and have very specific primary sequences and structures

Question 32

what is gramicidin A

Answer 32

antibiotic peptide

Question 33

where is gramicidin found?

Answer 33

DMPC lipid bilayer and water

Question 34

gramicidin A action (2)

Answer 34

1. forms pore in cell wall of bacteria letting out monovalent cations (K+/Na+) 2. membrane potential disappears and bacteria dies

Question 35

gramicidin structure (2)

Answer 35

1. 15 amino acids 2. helical

Question 36

how does gramicidin form a channel

Answer 36

head-to-head dimer

Question 37

types of ion channels (4)

Answer 37

1. simple pores 2. substrate gated channels 3. voltage-gated channels 4. pumps

Question 38

example of simple pore ion channels

Answer 38

GAP junctions

Question 39

example of substrate gated ion channel

Answer 39

nicotinic receptor

Question 40

example of voltage-gated ion channel

Answer 40

K+ channel

Question 41

examples of pump ion channels (2)

Answer 41

1. ATP-synthase 2. K+/Na+-ATPase

Question 42

requirements for drug to interact with protein to inhibit/enhance function (3)

Answer 42

1. correct size 2. right chemical properties to fit active site 3. compete with substrate