The languages of signal transduction- conformational change

Question 1

What is a hallmark of many signalling proteins, such as kinases and G proteins

Answer 1

1. Their ability to convert conformational changes into catalytic activity changes, or vice versa.
2. This means that many signalling proteins are enzymes.

Question 2

What do enzymes do

Answer 2

1. Enzymes are biological macromolecules that catalyse chemical reactions in living systems.
2. They can greatly increase the rates of reactions that occur spontaneously but slowly.
3. In addition, they can promote unfavourable reactions that would not occur spontaneously by coupling them to energetically more favourable reactions (such as ATP or GTP hydrolysis).

Question 3

What does the rate of reaction depend on

Answer 3

1. Reaction rate depends on kcat and [ES].
2. kcat tells you how many substrate molecules per second per enzyme are converted to product.
3. Km (Michaelis Menten constant): measure of how tightly the substrate is bound (large Km value = weak binding)
4. Vmax: maximum rate at which a product is formed

Question 4

Define allostery

Answer 4

1. Allostery: a change in the shape and activity of a protein (such as an enzyme) that results from binding to another molecule at a point other than the chemically active site (comformational coupling).

Question 5

What is the basis of allosteric control

Answer 5

1. Signalling proteins often exist as an equilibrium of different conformations.
2. Stabilising one conformation over another is the basis of allosteric control

Question 6

Describe positive regulation by conformational coupling

Answer 6

1. Positive regulation caused by conformational coupling between two separate binding sites.
2. In this example, both glucose and molecule X bind best to the closed conformation of a protein with two domains.
3. Because both glucose and molecule X drive the protein toward its closed conformation, each ligand helps the other to bind.
4. Glucose and molecule X are therefore said to bind cooperatively to the protein.

Question 7

Describe negative regulation by conformational coupling

Answer 7

1. Negative regulation caused by conformational coupling between two separate binding sites.
2. here molecule X prefers the open conformation, while glucose prefers the closed conformation.
3. Because glucose and molecule X drive the protein toward opposite conformations (closed and open, respectively), the presence of either ligand interferes with the binding of the other.

Question 8

What are two types of intracellular signaling proteins that act as molecular switches.

Answer 8

1. A protein kinase

2. A GTP-binding protein

Question 9

Describe how a protein kinase acts as a molecular switch

Answer 9

1. covalently adds a phosphate from ATP to the signalling protein, and a protein phosphatase removes the phosphate.
2. Many signaling proteins are activated by dephosphorylation rather than by phosphorylation.

Question 10

Describe how a GTP-binding protein acts as a molecular switch

Answer 10

1. is induced to exchange its bound GDP for GTP, which activates the protein;
2. the protein then inactivates itself by hydrolyzing its bound GTP to GDP

Question 11

Describe action of protein kinase

Answer 11

1. Rely on conformational change to relay signals
2. Transfer terminal phosphate residue from atp to substrates
3. Often arranged in kinase cascades
   - Input kinase
   - Main kinase
   - Output kinase
4. Effector proteins which leads to change in activity or change in gene expression if transcription factors
5. Scaffold proteins- Facilitate the formation of signalling cascade by bringing individual kinases into close proximity

Question 12

Describe the signal cascade

Answer 12

1. Signal IN causes the protein kinase to phosphorylate the target protein.
2. Phosphorylation changes the conformation of the target protein, making the “ON” conformation more stable than “OFF”
3. Signalling occurs (signal OUT)
4. De-phosphorylation changes the equilibrium again, making the OFF conformation more stable.

Question 13

What are G proteins controlled by

Answer 13

1. G proteins are controlled by GAPs and GEFs:
2. Signal IN causes GEF (guanine exchange factor) to swap GDP for GTP
3. GTP binding changes the conformation of the target protein, making the “ON” conformation more stable than “OFF
4. Signalling occurs (signal OUT)
5. GAP (GTPase-activator proteins) catalyse hydrolysis of GTP to GDP – this changes the equilibrium again, making the OFF conformation more stable.

Question 14

Two classes of cell-surface receptors.

Answer 14

1. Ion-channel-coupled receptors (also called transmitter-gated ion channels)
2. G-protein-coupled receptors.

Question 15

Describe Ion-channel-coupled receptors (also called transmitter-gated ion channels)

Answer 15

1. Don’t have enzymatic activity
2. Form gated pores through plasma membrane
3. Signal molecule binds
4. The structure changes to allow ions to pass

Question 16

Describe G-protein-coupled receptors.

Answer 16

1. Signal binds to g-protein coupled receptor

2. Conformational change allows it to bind to cytoplasmic domain which triggers the activation of G protein