Lesson 4: Protein Function and Regulation

Question 1

What is protein conformation?

Answer 1

Another word for the SHAPE of the protein. The arrangements of the atoms in space.

Question 2

What does the activity of a protein depend on?

Answer 2

Depends on its ability to bind specifically to other molecules

Question 3

What is a ligand?

Answer 3

Aka the substrate, is the molecule that a protein can bind (can be an ion, small molecule, or macromolecule)

Question 4

What is the binding site?

Answer 4

The part of a protein that interacts with the ligand (consists of a cavity formed by a specific arrangement of amino acids)
- Note: It forms when amino acids within the protein come together (the remaining sequences may play a role in regulating the protein’s activity)

Question 5

What type of interactions allow proteins to bind to one another?

Answer 5

The formation of WEAK, noncovalent interactions
- Hydrogen bonds
- Van der Waals (hydrophobic/hydrophilic interactions)
- Ionic interactions (electrostatic interactions)

Question 6

What are the different levels of protein association?

Answer 6

1) “Few” interactions: molecules will disassociate quickly
2) “Some” interactions: there is productive interaction but association will not persist (ex: enzyme reactions with reactant)
3) “Many” interactions: molecules will remain associated for a long time (ex: ribosome)

Question 7

How are protein-ligand interactions used in antibodies?

Answer 7

Each antibody had a distinct antigen-binding site, allowing it to recognize its antigen with great specificity.
- Binding to another molecules is an antibody’s main function.

Question 8

How are protein-ligand interactions used in enzymes?

Answer 8

• In enzymes, the binding of the ligand (substrate) is just the first step.
• Enzymes bind to one or more substrates and convert them into chemically modified products.
• Enzymes are very specific and only catalyze one reaction.

Question 9

What are cofactors?

Answer 9

Small molecules that help proteins perform their specific activity. These molecules may be covalently or non-covalently linked to the protein.

ex: Heme and iron

Question 10

How are heme and iron an example of a cofactor?

Answer 10

• Hemoglobin is dependent on heme and iron to carry out its function.
• A molecule of Heme is noncovalently bonded to each of the four polypeptides in hemoglobin. Heme binds reversibly to dissolved oxygen gas through its iron atom.
• Note: Heme and iron ARE NOT coenzymes

Question 11

What are coenzymes?

Answer 11

Different from cofactors!

• Small molecules that help ENZYMES carry out their function.

Question 12

Why does protein activity need to be controlled?

Answer 12

• Proteins have different functions and we do not always need them at work. This allows us to CONSERVE ENERGY!
• Protein regulation helps maintain a cell in its optimal state

Question 13

How can we control protein activity?

Answer 13

1. Cell controls the amount of protein it makes
2. Cell regulates the rate the protein is degraded
3. Cell regulates the location of the protein in the cell (location can control function or prevent it from interfering with other pathways)
4. The activity of a protein can be regulated at the level of the protein itself.

Question 14

How are enzymes regulated?

Answer 14

Through feedback inhibition!

• Multiple enzymes are often involved in a mechanistic pathway where the product of one enzyme becomes the substrate for the next.
• In feedback inhibition, an enzyme acting early in a reaction pathway is INHIBITED by a product produced by an enzyme at the end of the pathway

Question 15

What are some characteristics of feedback inhibitors?

Answer 15

1) Allows recognition when there is “enough” product
2) Conserves cellular energy
3) Reversible when product level fall (not as much product to bind to and inhibit enzyme)
4) NEGATIVE REGULATION: turning off the activity of enzyme/protein (very common and not only in enzymes)

Question 16

What are regulatory binding sites?

Answer 16

Enzymes often have TWO or MORE binding sites - one that binds to the substrate and one or more regulatory binding sites

Question 17

What are allosteric enzymes?

Answer 17

They have two or more binding sites. One that binds to the substrate and ore or more regulatory binding sites (allosteric sites)

Question 18

What is an allosteric inhibitor?

Answer 18

The allosteric inhibitor binds to the regulatory binding site. It changes the shape of the enzyme so that it can no longer to bind to its reactant. Thus, the enzyme becomes inactive (conserves energy).

Question 19

How is there conformational coupling between the two binding sites?

Answer 19

• Binding of the allosteric inhibitor to the allosteric site causes a change in conformation/shape of the enzyme. Therefore, the enzyme becomes inactive.
• Enzyme cannot perform its function until the allosteric inhibitor is no longer bound.
• When the allosteric inhibitor is no longer bound, enzyme changes conformation back to its active state.

Question 20

What is allosteric positive regulation?

Answer 20

Binding to the allosteric site TURNS ON an enzyme

Question 21

How can phosphorylation regulate an enzyme/protein?

Answer 21

1) The addition of a phosphate group can change a protein’s conformation. Thus changing its activity.

2) Phosphorylation of one protein can allow it to bind to another protein or molecule and promote an interaction

• NOTE: It is reversible!

Question 22

What are kinases?

Answer 22

Enzymes that ADD phosphate groups

• Note: phosphorylation modifications are a COVALENT MODIFICATION

Question 23

What are phosphatases?

Answer 23

Enzymes that REMOVE phosphate groups

• Note: phosphorylation modifications are a COVALENT MODIFICATION

Question 24

Does phosphorylation do positive or negative regulation?

Answer 24

IT DEPENDS!

• Phosphorylation can turn proteins on or off (positive or negative). This is specific to the individual protein.