lecture 11

Question 1

what are enzymes?

Answer 1

Catalysts that carry out biochemical reactions

Question 2

what is a catalyst?

Answer 2

a substance that changes the rate of a chemical reaction without affecting the position of the equilibrium or being changed during the course of the reaction.

Question 3

*how do enzymes work as biological catalysts?

Answer 3

keep in mind that most biochemical reactions will not proceed at any rate in the absence of an enzyme; they can increase the rates of biochemical reactions by 10^4 to 10^10; generally no side reactions; chemical catalysts catalyze a number of unwanted side reactions.

Question 4

are enzyme catalyzed reactions fully reversible?

Answer 4

yes, most of them

Question 5

do enzymes have an active site?

Answer 5

yes

Question 6

where do substrates bind in relation to the enzyme?

Answer 6

the binding site, a cleft of the protein, also known as the catalytic or active site of the enzyme

Question 7

does catalysis involve amino acids? if so which are the common amino acids used?

Answer 7

yes; catalysis involves the actions of one or more amino acid residues with reactive side chains like ser, cys, his, glu, asp specifically located near the substrate binding site

Question 8

enzymes are not highly specific, T/F?

Answer 8

F, they are highly specific; they often react with only a single molecule and even its stereoisomers are ignored to give stereo specific products, a chemical catalyst usually causes a loss of stereochemistry

Question 9

what is catalytic activity dependent on?

Answer 9

the tertiary structure of the enzyme, one enzyme one function

Question 10

*what are the factors that affect enzyme activity?

Answer 10

substrate concentration, temperature and pH

Question 11

*how does substrate concentration affect enzyme activity?

Answer 11

the rate of an enzyme-catalyzed reaction increases with substrate concentration until a maximal velocity is achieved (Vmax); leveling off indicates saturation of all binding sites

Question 12

*how does temperature affect enzyme activity?

Answer 12

reaction velocity will increase with temperature until a peak velocity is reached (more molecules have inc. energy to pass over barrier); further elevation of temperature causes a decrease in reaction velocity due to denaturation of enzyme; so in short physiological temperature does not vary significantly so this is not a viable means to control enzyme activity

Question 13

*how does pH affect enzyme activity?

Answer 13

it effects ionization state of the active site, extreme pH leads to denaturation of the enzyme though pH at which maximal enzyme activity is achieved is different for each enzyme and reflects the (H^+) at which the enzyme functions; pH can affect protein folding and 3D structure but also specific amino acid side chains located inside the active site

Question 14

*what are the different types of enzyme classes?

Answer 14

oxidoreductases, transferases, hydrolases, lyases, isomerases, ligases, isozymes

Question 15

*what is an oxidoreductase?

Answer 15

add or remove one or more electrons from or to substrates and are sometimes called dehydrogenases because their oxidation reactions often remove two electrons and a proton from the oxidized substrate

Question 16

*what is a transferase?

Answer 16

transfer a group from one substrate to another

Question 17

*name an example of a transferase?

Answer 17

kinase, transfer phosphate groups from ATP to substrate

Question 18

*what are hydrolases?

Answer 18

carry out the hydrolysis of substrates

Question 19

*name an example of hydrolase?

Answer 19

phosphatase which remove phosphate groups from substrates

Question 20

*what is a lyase?

Answer 20

carry out the cleavage of a molecule into parts

Question 21

*what is an isomerase?

Answer 21

rearrange a substrate into an isomeric form (i.e., D to L form)

Question 22

*what is a ligase?

Answer 22

join molecules together by condensation, usu. eliminating water.

Question 23

what is an isozyme?

Answer 23

different enzyme that carry out the same reaction but with different regulatory properties or in different locations within the organism (liver vs. heart, etc)

Question 24

what is the free energy change for a chemical reaction?

Answer 24

it determines the spontaneity of a reaction like which direction a reaction is likely to proceed

Question 25

*what is the change in Gibbs free energy (ΔGo’) for a reaction?

Answer 25

it is the difference in energy between the products and the substrate or the free energy change under biological conditions

Question 26

*what happens if the ΔG is negative?

Answer 26

the reaction will proceed spontaneously with the release of energy

Question 27

*what happens if the ΔG is positive?

Answer 27

the reaction will not proceed spontaneously

Question 28

*what happens if the ΔG = 0?

Answer 28

the reaction is at equilibrium and although the substrates react to form products and products react to form substrates there is not net change in concentrations

Question 29

*enzyme catalysis can change both the rate at which the equilibrium in the reaction is achieved and position of the equilibrium (thermodynamics), T/F?

Answer 29

false, the position or thermodynamics of the reaction cannot be changed

Question 30

*explain what happens in an energy coordinate diagram for an enzyme catalyzed reaction, because you will have to know how to interpret it?

Answer 30

in an energy coordinate diagram, in order to proceed with a chemical reaction you have to change the electronic structure of the bond in the substrate (enzyme binding with substrate to illicit a change in structure) to raise it to a transition state. Once there, a decision has to be made if the molecule wants to go back to its initial state or move forward breaking bonds producing a carboxylic acid and a free amino group. The forward reaction is favored because the final energy is much lowered and also energy is given away, producing a negative delta G or being spontaneous

Question 31

enzymes act on substrates changing it from the initial form to the final form, T/F?

Answer 31

false, enzymes increase the rate of a reaction by decreasing the reaction activation energy

Question 32

what is the rate of the reaction dependent on?

Answer 32

the magnitude of the activation energy, E sub A.

Question 33

what does K sub eq (equilibrium constant) tell you?

Answer 33

how much product and reactant there is and is written product/reactant and so if we relate this back to ΔGo’ it tells us something about the equilibrium and vice versa

Question 34

the binding of the enzyme to substrate forms weak interactions and energy is liberated used to decrease the activation energy to achieve lower state, T/F?

Answer 34

T

Question 35

what are the four ways enzymes increase the rate of a reaction?

Answer 35

binding energy, proximity, induced fit, orientation

Question 36

what is binding energy?

Answer 36

interaction of S with enzyme active site providing binding energy, bringing S closer in structure to the transition state. This lowers the activation energy and increases the reaction rate

Question 37

what is proximity?

Answer 37

Binding substrates increases their effective concentration within the active site, thereby increasing the reaction rate.

Question 38

what is induced fit?

Answer 38

Binding of S induces changes in the tertiary structure of E (conformational changes) that in turn distort S toward the transition state.

Question 39

what is orientation?

Answer 39

geometry of S binding the active site will allow the reacting molecules to be in the perfect orientation for reaction, thus increasing the reaction rate.

Question 40

Recall the terms “binding energy,” “proximity effect” and “induced fit” and relate these terms to an enzyme’s ability to lower the activation energy of a reaction.

Answer 40

so enzyme recognizes substrate and they are brought together in a proximity effect so they are one bond distance apart and can react. Keep in mind too about orientation so that the atoms of each substrate and enzyme are right by each other and of course you also have induced fit once you have substrate enzyme binding and conformation change occurs

Question 41

what is also known as the catalytic triad?

Answer 41

histdine, serine and aspartate

Question 42

what does serine protease do?

Answer 42

a family of enzymes that hydrolyze specific peptide bonds in proteins (i.e., splits the protein into smaller polypeptides) and these enzymes hydrolyze amide bonds adjacent to specific amino acid residues. The main area is digestion and these are synthesized in the pancreas as pro-enzymes or zymogens that are initially inactive and become active after they are released from the pancreas

Question 43

how do these proteases work?

Answer 43

so these proteases or enzymes recognize a specific amino acid and so if you take chymotrypsin for example, it will break a peptide bond beside an aromatic amino acid and so you see a hydrophobic binding pocket favoring the aromatic residues and large nonpolar residues and so in short the process is used for identification purposes other examples include trypsin and elastase

The purpose of the pocket is to bind the substrate protein side chain and hold it in place, so that the active site of the protease can cut the peptide bond on the substrate protein

Question 44

what type of reaction mechanism does serine protease perform?

Answer 44

This is a great example of the proximity effect and also orientation: the individual amino acids that make up the catalytic triad are far apart in the primary sequence, but are right next to each other in the tertiary fold. Thus they can interact to provide an activated oxygen atom on the serine. Plus, the specificity pocket that binds the Tyr residue positions the substrate peptide perfectly in the active site so that the target peptide bond is right beside the activated serine oxygen. Together, this facilitates a highly specific and rapid reaction.

Question 45

how does the catalytic triad tie into the serine protease reaction mechanism?

Answer 45

The “catalytic triad” of residues cooperate to make the Ser-OH a strong nucleophile, which attacks the peptide carbonyl bond allowing for proper orientation and proximity effect (for both enzyme and substrate and amino acids with it) for reaction to take place and transition state to provide for stabilization, though it can go forward weak interactions are holding the substrate in such a way compelling the reaction to move forward and so once formed, the transition state breaks down to more stable products and the target peptide bond is cleaved. The first product (a peptide piece) is released, whereas a fragment remains bound to the enzyme. The enzyme-substrate bond is broken by hydrolysis. The enzyme interacts with water, making it a stronger nucleophile, which attacks the carbonyl carbon.
Think proximity and orientation

Question 46

why don’t proteins break down spontaneously in the cell?

Answer 46

the serine is in position to bind with carbon that allows that decision to be made to move forward and isn’t bound to a carboxyl group

Question 47

how does aspartyl protease work?

Answer 47

activation of water for nucleophilic attack, no enzyme-bound intermediates, rearrangement of tetrahedral carbon intermediate leads to cleavage of peptide bond. This is what we would see with viral proteases and they use this enzyme to carry out their function, HIV for example

Question 48

what is the binding pocket like for chymotrypsin?

Answer 48

a hydrophobic binding pocket that favors aromatic residues and large non-polar residues

Question 49

what is the binding pocket like for trypsin?

Answer 49

a deep binding pocket with a negatively charged residue (glu) at the bottom that favors the binding of lys and arg

Question 50

what is the binding pocket like elastase?

Answer 50

a very small binding pocket that favors binding of ala or gly residues.

Question 51

what is the purpose of the binding pocket?

Answer 51

The purpose of the pocket is to bind the substrate protein side chain and hold it in place, so that the active site of the protease can cut the peptide bond on the substrate protein

Question 52

so we know that enzymes decrease the activation energy of a reaction and that weak interactions are formed with substrate, liberating energy used to lower the activation energy, how?

Answer 52

Any time a weak interaction is formed (H-bond, ionic interaction, hydrophobic interaction, van der Waals), a tiny bit of energy is released. The enzyme will capture the sum of all these small energy changes and use this energy to lower the energy required to reach the transition state.

Question 53

how is the equilibrium position determined?

Answer 53

the free energies of substrate and product

Question 54

explain the principles of catalysis?

Answer 54

1) substrate binding
2) histidine activates serine for nucleophilic attack
3) the oxyanion tetrahedral intermediate is stabilized by hydrogen bonds
4) cleavage of the peptide bond
5) the covalent acyl-enzyme intermediate
6) water attacks the carbonyl carbon
7) second oxyanion tetrahedral intermediate
8) acid catalysis breaks the acyl enzyme covalent bond
9) product is free to dissociate