L5 - Protein Interactions

Question 1

What forms the binding site in a protein?

Answer 1

The folding of the protein

Hydrogen bonds form between side chains

Question 2

How do enzymes work?

Answer 2

Lower the activation energy of the reaction - catalyst

• Bring substrate into close proximity
• Bending substrate
• Providing electron donor/acceptors

Question 3

Hydrolases

Answer 3

Catalyse a hydrolytic cleavage reaction

Question 4

Nucleases

Answer 4

Break down nucleic acids by hydrolysing bonds

Question 5

Proteases

Answer 5

Break down proteins by hydrolysing bonds

Question 6

Synthases

Answer 6

Synthesis molecules in anabolic reactions

Question 7

Isomerases

Answer 7

Catalyse the rearrangement of bonds within a single molecule

Question 8

Polymerases

Answer 8

Catalyse polymerisation reactions

Question 9

Kinases

Answer 9

Catalyse the addition of a phosphate group to a molecule

Question 10

Phosphatases

Answer 10

Catalyse the hydrolytic removal of a phosphate group

Question 11

Oxido-reductases

Answer 11

Catalyse reactions in which one molecule is oxidised and one is reduced

Question 12

ATPases

Answer 12

Hydrolyse ATP

Question 13

Kinetics of protein interactions for not covalent interactions

Answer 13

Dissociation rate = dissociation rate constant x concentration of AB
Association rate = association rate constant x concentration A x concentration B
At equilibrium association rate = dissociation rate

Question 14

Equilibrium constant

Answer 14

[AB]/[A]x[B]

Question 15

Protein-protein interactions require complementary surfaces

Answer 15

Surface-string
Helix-helix
Surface-surface

Question 16

Protein-protein binding enables

Answer 16

The formation of enough weak bonds to withstand thermal jolting.
Enables formation of protein complexes
Often causes a conformational change

Question 17

Activation of GTP

Answer 17

EF-Tu binds to GTP to become activated

GTP hydrolyses to GDP resulting in inactivation of EF-Tu

Question 18

SH2 domain

Answer 18

Binds phosphorylated tyrosine

Question 19

SH3 domain

Answer 19

Binds proline rich motifs

Question 20

PH domain

Answer 20

Binds phospholipids

Question 21

EF hand domain

Answer 21

Binds calcium/magnesium in structural or signalling mode

Question 22

Zinc finger domain

Answer 22

Bind zinc in structural mode

Question 23

Leucine zipper domain

Answer 23

Protein-protein or protein-DNA binding

Question 24

SH2 domain role

Answer 24

Formation of signalling complexes
Kinases and phosphatases modulate the level of tyrosine phosphorylation
- Helps regulate binding

Question 25

Specificity between the phosphate of the protein tyrosine - SH2 domain

Answer 25

Ionic interactions between - phosphate and + amino acids | Some hydrogen bonds

Question 26

SH3 domain role

Answer 26

Linking signalling components | Structural role in maintaining multiprotein complexes

Question 27

Minimum consensus sequence for SH3 binding is

Answer 27

P-x-x-P | 2 amino acids

Question 28

SH3 domain contains

Answer 28

Several aromatic residues - interdigitate between prolines of PxxP - Stabilised by aromatic stacking - Electrostatic interactions due to aromatic stacking of proline and tyrosine

Question 29

PH domain role

Answer 29

Lipid binding Signalling Anchoring proteins to membrane Kinases modify phospholipids to create binding sites for proteins containing PH domains

Question 30

Spectrin

Answer 30

Structural protein | Combination of hydrophobic and charged interactions bind phospholipid an drive association with membrane surface

Question 31

Metal ion binding domain role

Answer 31

Structural - Zn Regulatory - Ca Catalytic - iron and copper

Question 32

Size and valencies of metal ion

Answer 32

These are liganded by different numbers of amino acid | Have different structural requisites

Question 33

EF hand binding domain role

Answer 33

Regulatory - binding Ca | Structural - binding Ca/Mg

Question 34

How do they accommodate tight turn in EF hands?

Answer 34

Octadentate - 7 oxygen containing side chains | Invariant glycine chains

Question 35

Calmodium structure and regulation

Answer 35

Ca binding exposes hydrophobic patch which enables binding to amphipathic alpha helix

Question 36

Protein DNA binding domain classes

Answer 36

Zinc fingers Leucine zipper motifs - dimers of short coiled sequence and a specific DNA recognition helix Basic helix-loop-helix - charged residues in the helix interact with charged groups on DNA Beta sheet

Question 37

Protein DNA binding domain role

Answer 37

Basic charge to mediate interaction with acidic DNA strand through interactions with major groove

Question 38

Zinc fingers role

Answer 38

Structural function in protein-DNA or protein-protein interactions Zn is coordinated tetrahedrally by cysteine or histidine residues

Question 39

Protein DNA binding domain often form

Answer 39

Homo or hetero dimers increasing the repertoire of available DNA binding proteins