Enzyme Mechanisms

Front 1

Why are enzymes powerful catalysts ? ( 2 reasons)

Back 1

1: They have a very high specificity for its substrate binding

2: They induce optimal arrangement of catalytic groups in the active sites

Front 2

What two characteristic thing does an enzyme do in a reaction?

Back 2

1: Enzymes are unchanged at the end of the reaction

2: Enzymes do not affect the equilibrium constant.

Front 3

Are enzyme's effects unidirectional?

Back 3

No they affect both the forward and reverse reaction.

Front 4

What is the difference between enzymes and chemical catalysts ? (2)

Back 4

1: Enzymes are proteins ( much larger than the substrate).

2: Display structural and stereo specificity.

Front 5

From where does the specificity of the enzymes comes from ?

Back 5

The structure of the active site.

Front 6

What is a characteristic of the active site in terms of amino acids?

Back 6

They are from different parts of the sequence and only a few will actually bind the substrate.

Front 7

What is the (general) function of the amino acids that are not part of the active site for an enzyme ?

Back 7

serve as a scafforld for the 3D structure of the active site

Front 8

What can the amino acids that are not part of the active site be involved with (4 things)?

Back 8

1: Regulatory sites

2: Interaction with other proteins

3: Channels to bring substrate to active site

4: Cellular localization

Front 9

What complex is indicative of the enzymatic activity on a reaction?

Back 9

The enzyme-substrate complex

Front 10

What are the two factors that creates the specificty of the formation of the enzyme-substrate complex?

Back 10

1: Required complimental charges to bind

2: Structure of the active site that is specific

Front 11

What are the four interactions that are usually involved in a substrate binding on an enzyme?

Back 11

1: Hydrogen bond

2: Van der waals interactions

3: electrostatic interactions

4: Hydrophobic interactions

Front 12

What is the Van der waals interaction?

Back 12

Interaction between two compounds through their dipole moments created according to the electrostatic properties and arrangement of the elements composing the compound.

Front 13

What are the 6 possible catalytic mechanisms?

Back 13

1: Acid-Base catalysis

2: Covalent catalysis

3: Metal ion catalysis

4: Electrostatic catalysis

5: catalysis through proximity and orientation effects

6: Preferential binding of transition state

Front 14

What is a simplistic way to explain the pK of a molecule?

Back 14

The pK is the pH at which the molecule has a 50% protonated and 50% deprotonated states.

Front 15

What is the characteristic of a acid-base catalysis enzyme?

Back 15

One of the amino acids of the side chain in the active site will act as an acid or a base to render "base like" or "acid like" conditions to a reaction in a cell with a neutral pH.

Front 16

How is the acceleration of the reaction achieved in an acid-base catalysis ?

Back 16

It is achieved through a catalytic transfer of a proton.

Front 17

If a compound has a pK of 3, what form this compound will most likely be at a neutral pH ?

Back 17

It will most likely be deprotonated (wanting to acidify the pH)

Front 18

What is a synonym for covalent catalysis ? What is the menaing of that synonym?

Back 18

Nucleophilic catalysis ( "nucleus lover" which means that the compound is electron rich).

Front 19

What are the two condition for an effective covalent catalytic enzymes?

Back 19

1: nucleophilic ( acts like it)

2: forms a good leaving group

Front 20

What transient bond is formed in a covalent catalysis?

Back 20

a trasient covalent bond.

Front 21

How are nucleophiles usually activated?

Back 21

through the deprotonation by a general base.

Front 22

What is the target of a nucleophile ( type of molecule) /

Back 22

An electrophile since they are proton defficient.

Front 23

What are two examples of enzymes that usually involve covalent catalysis?

Back 23

Pyruvate dehydrogenase complex reactions and proteolytic enzymes.

Front 24

What proportion of enzymes require a metal ion for proper functionning ?

Back 24

1/3 of the enzymes

Front 25

What is the difference between a metaloenzyme and a metal activated enzyme? what are a few examples of typical metal ions for each type?

Back 25

Metaloenzyme has a tightly bound metal ion to it while the metal activated enzyme is loosely bound.

eg metaloenzyme ion: Fe (2 or 3+) Zn2+, Cu2+, Mn2+,Ca2+

eg metal activated enzyme ions: Na+, K+, Mg+, Ca+

Front 26

What is the primary relevance of metal ion enzymes in metabolic chemistry?

Back 26

It is heavily involved in the electron transport chain.

Front 27

Why is water usually excluded from the active site of a electrostatic catalytic enzyme during a reaction?

Back 27

This lowers the dielectric constant resulting in more reactive substrates as their charde is not "diluted" by the dipole moments of water.

Front 28

What is the dielectric constant of a solvant? What does a low dielectric constant favors?

Back 28

Ability of a solvent to keep opposit charges appart. A low dielectric constant favours electrostatic interactions.

Front 29

How does a catalysis through proximity and orientation effects work?

Back 29

By binding the substrates on a single binding surface, hence orienting then for the reaction and optimizing its rate.

Front 30

What is an equivalant analogy of having reactants being in proximity and correct orientation to one another?

Back 30

It is similar to increasing the concentration of each reactant.

Front 31

What could explain why an enzyme would preferentially bind the transition state of a substrate?

Back 31

The increase of covalent bonds between the active site and the substrate when the substrate reaches the transition state.

Front 32

What is the most probable mechanism behind a preferential binding of the transition state complex?

Back 32

Substrate binding to the enzyme's active site can cause a confirmationnal change in the active site which in turn deforms the substrate putting it in a transition like state. The released energy induced by this change can be used for the reaction to occur. The strained substrate fits better the enzyme than the normal substrate.

Front 33

What are potential inhibitors of an enzyme that preferentially binds the transition state of a substrate?

Back 33

Analogues of the enzyme's substrate's transition state structure. They will tightly bind the enzyme, but they will not be catalysed.

Front 34

What is the presumed origin of the mitocondria?

Back 34

Through a symbiotic relationship between eukariotic cell that relied on glycolysis as energy and an oxidative bacterium.

Front 35

What modulates the efficency of the mitochondrias in a cell?

Back 35

their flexible variation in their shape and also of fusion/seperation.

Front 36

What are the main functions of the mitocondria? (5)

Back 36

Mediates the citric acid cycle, the pyruvate dehydrogenase complex, fatty acid oxidation, electron transport and oxidative phosphorilation.

Front 37

Why are there numerous folds in the inner mitochondrial membrane?

Back 37

A lot of the enzymes are membrane bound in the IMM. increasing the surface of the IMM with fold will increase the number of membrane bound enzymes such as the electron chain complex.

Front 38

Why does the outer mitochondrial membrane let any molecule of 10kDa and less diffuse freely? Name the molecule involved.

Back 38

It contains porins, a protein that forms a large aqueous channel through the lipid bilayer

Front 39

How do compounds get into the inner membrane space ?

Back 39

Specific transport mechanisms on the inner mitochondrial membrane.

Front 40

What is the percentage of protein content by weight of the Inner mitochondrial membrane?

Back 40

80%

Front 41

What does the high content of cardiolipin give as an attribute to the inner mitochondrial membrane?

Back 41

Very impermeable to ions.

Front 42

What is the name of the inner folds of the inner mitochondrial membrane ?

Back 42

Cristae