2.2 ENZYMES

Question 1

activation energy (Ea)

Answer 1

he energy barrier that blocks the tendency for a chemical reaction to occur.

Question 2

active site

Answer 2

The region on the surface of an enzyme or ribozyme where the substrate binds, and where catalysis occurs.

Question 3

allosteric activation

Answer 3

when the binding of one ligand enhances the attraction between substrate molecules and other binding sites

Question 4

allosteric inhibition

Answer 4

a form of noncompetitive inhibition: a molecule that binds to the enzyme at an allosteric site. This site is not at the same location as the active site. Upon binding with the inhibitor, the enzyme changes its 3D shape.

Question 5

chemical change

Answer 5

a process that leads to the chemical transformation of one set of chemical substances to another

Question 6

catalyze

Answer 6

to increase, the rate of (a chemical reaction) by catalysis

Question 7

chemical change

Answer 7

the process that causes products to have different properties than reactants because their atoms and molecules are arranged differently.

Question 8

chemical kinetics

Answer 8

chemical kinetics – an area of chemistry dealing with speeds/rates of reactions

1) rates of reactions affected by four factors
2) concentrations of reactants
3) temperature at which reaction occurs
presence of a catalyst
4) surface area of solid or liquid reactants and/or catalysts

Question 9

conenzyme

Answer 9

a subset of cofactors that are organic (carbon-based) molecules.

Question 10

cofactor

Answer 10

non-protein helper molecules

Question 11

catalyze

Answer 11

means to increase the reaction rate by using an enzyme that’ll reduce the activation energy

Question 12

confirmations change

Answer 12

a change in the shape of a macromolecule, often induced by environmental factors such as:

• temp
• pH
• enzyme concentration
• substrate concentration

Question 13

catalysis

Answer 13

The process by which a substance speeds up a chemical reaction without being consumed or altered in the process

Question 14

covalent modification

Answer 14

enzyme-catalyzed alterations of synthesized proteins and include the addition or removal of chemical groups

Question 15

enzyme

Answer 15

biological catalyst: proteins and RNA (ribozymes)

Question 16

enzyme activation

Answer 16

the process of the increasing rate of the enzyme reaction

Question 17

enzyme inhibition

Answer 17

a molecule that disrupts the normal reaction pathway between an enzyme and a substrate

Enzyme inhibitors can be either competitive or non-competitive depending on their mechanism of action
prevent the formation of an enzyme-substrate complex and hence prevent the formation of product

Inhibition of enzymes may be either reversible or irreversible depending on the specific effect of the inhibitor is used

Question 18

enzyme-catalyzed reaction

Answer 18

a reaction that occurs converting the substrate into products and forming an enzyme products complex once an enzyme will grab on (bind) to one or more reactant molecules

Question 19

enzyme-substrate complex

Answer 19

the structure formed when the substrate is held within the active site of the enzyme; initiates chemical reaction

Question 20

feedback inhibition

Answer 20

The end product of a metabolic pathway acts on the key enzyme regulating entry to that pathway, keeping more of the end product from being produced.

Question 21

induced fit

Answer 21

a continuous change in the conformation and shape of an enzyme in response to substrate binding. This makes the enzyme catalytic which results in the lowering of the activation energy barrier causing an increase in the overall rate of the reaction.

Question 22

irreversible modification

Answer 22

involves the addition or removal of some type of group, most commonly the phosphoryl group, onto or from the enzyme. The addition of phosphoryl groups involves the use of ATP (energy source) and requires a protein called protein kinase. On the other hand, proteins that can remove phosphoryl groups from enzymes are called protein phosphatases. Unlike proteolytic cleavage, the addition or removal of phosphoryl groups is reversible.

Question 23

kinase

Answer 23

an enzyme that adds phosphate groups (PO43−) to other molecules

Question 24

maximum velocity

Answer 24

rate attained when the enzyme sites are saturated with substrate, i.e. when the substrate concentration is much higher than the KM.

Question 25

metabolic pathway

Answer 25

series of chemical reactions in a cell that build and breakdown molecules for cellular processes

Question 26

Michaelis constant (KM)

Answer 26

the substrate concentration at which the reaction rate is half of its maximal value (or in other words, it defines the substrate concentration at which half of the active sites are occupied). It indicates the affinity of an enzyme for a given substrate: the lower the KM value, the higher the affinity of the enzyme for the substrate.

Question 27

non-covalent modifications

Answer 27

a type of reversible protein modification that allows enzymes to be turned on or off when special molecules bind noncovalently to the enzyme

Question 28

noncompetitive inhibitor

Answer 28

an inhibitor that binds to an allosteric site resulting in decreased efficacy of the enzyme

Question 29

orientation

Answer 29

the exact way that reactant molecules must make direct contact with each other in order to form a bond

Question 30

phosphatase

Answer 30

an enzyme that removes a phosphate group from a protein

Question 31

physical strain

Answer 31

this occurs when a molecule has an additional amount of internal energy which an unstrained molecule does not

Question 32

protein-protein interaction

Answer 32

are physical contacts of high specificity established between two or more protein molecules as a result of biochemical events steered by interactions that include electrostatic forces, hydrogen bonding, and the hydrophobic effect

Question 33

reversible modification

Answer 33

is the making and breaking of a covalent bond between a non-protein group and an enzyme molecule. The most common reversible modification is the addition and removal of phosphate groups through the processes of phosphorylation and dephosphorylation

Question 34

saturable

Answer 34

capable of being saturated.

Question 35

substrate

Answer 35

a molecule upon which an enzyme acts, in order to catalyze chemical reactions

Question 36

thermodynamics

Answer 36

a branch of science dealing with the transfer of energy from one place to another and from one form to another

Question 37

transition state

Answer 37

an enzyme-catalyzed reaction, the reactive condition of the substrate after there has been sufficient input of energy (activation energy) to initiate the reaction.

Question 38

uncatalyzed reaction

Answer 38

reaction proceeds via a one-step mechanism (one transition state-observed)

Question 39

Explain why spontaneous reactions often proceed very slowly.

Answer 39

these type of reaction often proceed very slowly because they require extra energy in order to reach the necessary activation energy for the reactants to overcome the transition state, and become lower energy
products

Question 40

Describe what an enzyme is, why it is needed, and how they help chemical reactions proceed in living cells.

Answer 40

what: these proteins act as catalysts in reactions
why: they stabilize the structure of the transitions state by binding substrates to their active sites. This in turn lowers the free energy of the transition state, which in turn decreases the rate of the chemical reaction. Enzymes do not however change the Gibbs free energy of the chemical reaction.
how:

Question 41

Explain the role of the active site.

Answer 41

The active site of an enzyme is the region that binds the substrates(and cofactor if any) The interaction of the enzyme and substrate at the active site promotes the formation of the transition state. the enzyme changes shape on substrate binding.

Question 42

Describe the process of enzyme action, including how they increase the rate of chemical
reactions.

Answer 42

Enzymes are proteins that act as catalysts within living cells. Catalysts increase the rate of chemical reactions occurs without being consumed or permanently altered themselves.
The basic mechanism by which enzymes catalyze chemical reactions begins with the binding of the substrate to the active site on the enzyme. The active site is the specific region of the enzyme which combines with the substrate. Mechanism of enzyme action is well explained in terms of lock and key model of enzyme action.
The active site was thought to have a fixed structure (the lock), which exactly matched the structure of a specific substrate (the key). Thus the enzyme and substrate interact to form an enzyme-substrate complex. The substrate is converted to products that no longer fit the active site and are therefore released, liberating the enzyme.

Question 43

Explain each component of a free energy diagram for an uncatalyzed vs. enzyme-catalyze
reaction.

Answer 43

The addition of a catalyst to a reaction lowers the activation energy, increasing the rate of the reaction. The activation energy of the uncatalyzed reaction is shown by Ea, while the catalyzed reaction is shown by Ea’. The heat of reaction (ΔH) is unchanged by the presence of the catalyst.

Question 44

Explain each element of an enzyme kinetics curve.

Answer 44

The rate of reaction when the enzyme is saturated with substrate is the maximum rate of reaction, Vmax.
The relationship between rate of reaction and concentration of substrate depends on the affinity of the enzyme for its substrate. This is usually expressed as the Km (Michaelis constant) of the enzyme, an inverse measure of affinity.

For practical purposes, Km is the concentration of substrate which permits the enzyme to achieve half Vmax. An enzyme with a high Km has a low affinity for its substrate, and requires a greater concentration of substrate to achieve Vmax.”

Question 45

Describe how reaction rates change with differences in substrate concentration

Answer 45

The rate of a chemical reaction increases as the substrate concentration increases. Enzymes can greatly speed up the rate of a reaction. However, enzymes become saturated when the substrate concentration is high.

Question 46

Explain why enzymes are sensitive to environmental conditions.

Answer 46

they’re sensitive to environment conditions such as:

1) Temperature: Raising temperature generally speeds up a reaction, and lowering temperature slows down a reaction. However, extremely high temperatures can cause an enzyme to lose its shape (denature) and stop working.
2) pH: Each enzyme has an optimum pH range. Changing the pH outside of this range will slow enzyme activity. Extreme pH values can cause enzymes to denature.
3) Enzyme concentration: Increasing enzyme concentration will speed up the reaction, as long as there is substrate available to bind to. Once all of the substrates is bound, the reaction will no longer speed up, since there will be nothing for additional enzymes to bind to.
4) Substrate concentration: Increasing substrate concentration also increases the rate of reaction to a certain point. Once all of the enzymes have bound, any substrate increase will have no effect on the rate of reaction, as the available enzymes will be saturated and working at their maximum rate.

Question 47

Contrast the different mechanisms used by cells to regulate enzyme activity

Answer 47

Enzymes can be regulated by other molecules that either increase or reduce their activity. Molecules that increase the activity of an enzyme are called activators, while molecules that decrease the activity of an enzyme are called inhibitors.

feedback inhibition, reversible covalent modification of enzymes, proteolytic activation of the enzyme, feedback regulation, and regulation of isozymes.

Question 48

Distinguish between different types of reversible inhibitors.

Answer 48

Irreversible: permanently change enzymes conformations by covalent modification (binding)

ex: allosteric inhibition
reversible: cause temporary changes in the enzyme confirmation via non-covalent modification (binding) when they undergo the process of induced fit
ex: competitive, uncompetitive, and noncompetitive

Question 49

Describe how enzymes work together in metabolic pathways that can be regulated by feedback
inhibition.

Answer 49

Metabolic pathways are a series of reactions that multiple enzymes catalyze. Feedback inhibition, where the pathway’s end product inhibits an upstream step, is an important regulatory mechanism in cells.