Chapter 6

Question 1

Enzymes

Answer 1

• are proteins
• act as a protein catalyst for biochemical reactions (have catalytic properties)
• accelerate the rate of a reaction
• decrease activation energy for a reaction to proceed
• enzymes will not change the equilibrium of a reaction
• highly specific for substrates
• will facilitate conversion of a substrate (reactants) into products
• are not degraded or destroyed during a reaction
• activity is measured in umol/min/mg protein

Question 2

Specificity

Answer 2

For reactions to take place in physiological useful way, must occur at a rate that meets cell’s needs and must display specificity

Enzymes w/ similar functions may use different substrates

specificity = a particular reactant should always yield a particular product

Specificity of enzyme is due to the precise interaction of the substrate with the enzymes

Question 3

Proteolysis Enzymes

Answer 3

• show the range of enzyme specificity
• catalyze the hydrolysis of peptide bonds

Question 4

Substrate

Answer 4

reactants in enzyme-catalyzed reactions

Question 5

6 Major Classes of Enzymes

Answer 5

1. Oxidoreductases - transfer electrons between molecules (catalyze oxidation-reduction reactions)
2. Transferases - transfer functional groups between molecules
3. Hydrolyases - cleaves molecule by the addition of water
4. Lyases – remove or add atoms to form double bonds
5. Isomerases - move functional groups within a molecule
6. Ligases - join two molecules in a reaction through the power of ATP hydrolysis

Question 6

Enzyme Nomenclature

Answer 6

• Enzyme names have suffix (end) “ase”
• Enzyme naming is based on substrates and/or reactions

Ex. lactase – splits lactose into glucose and galactose
Ex. alcohol dehydrogenase – oxidizes or dehydrogenates ethanol

Question 7

Cofactors

Answer 7

The catalytic activity of an enzyme may depend on Cofactors, which are small molecules (two types). Some enzymes require cofactors for optimal enzymatic activity

1. Coenzymes
   - Small organic molecule required for the activity of many enzymes
   - derived from vitamins
   - are typically loosely bound to the enzyme
   - Tightly bound coenzymes are called prosthetic (helper) group
2. Metals

Question 8

Apoenzyme

Answer 8

an enzyme w/o its cofactor (inactive)

Question 9

Holoenzyme

Answer 9

an enzyme associated w/ its cofactor

will be in a configuration with a fully functional active site

catalytically active enzymes, consist of the protein components that form the main body of an enzyme (apoenzyme) and any other small cofactors

Question 10

🔺G

Answer 10

difference between the reactants and the products

Question 11

positive🔺G

Answer 11

endergonic reaction (requires energy, reaction won’t occur spontaneously)

Question 12

negative 🔺G

Answer 12

exergonic reaction (releases energy, reaction will occur spontaneously)

Question 13

When 🔺G = 0

Answer 13

at equilibrium

Question 14

🔺G =🔺H - T🔺S where….

Answer 14

🔺G = gibbs free energy; change in free energy when a reaction proceeds

G = free energy: amount of energy available to do work

🔺 = change

🔺H = enthalpy or total energy

T = temperature in K (kelvins)

🔺S = entropy or unusable energy

Question 15

It’s often difficult to determine the “true” 🔺G value. This can depend on….

Answer 15

• Temp
• pressure
• pH
• concentrations of products and reactants

Question 16

Standard free energy change: 🔺G^o

What are the standard conditions?

Answer 16

• 298 K (25 C)
• products/reactants all at 1 M (molar concentration)
• pressures at 1 atmosphere
• to quantify standard free energy changes at pH 7, use 🔺G^o’ –> simple way to find this is to measure the concentrations of reactants and products when reaction has reached equilibrium

Question 17

Equilibrium constant under standard conditions is:

Answer 17

K’eq = [C][D] / [A][B] where products are over reactants

🔺G^o’ = -RT ln K’eq

can be rearranged to:

K’eq = e^-🔺G^o’ /RT

K’eq = e^-🔺G^o’ /2.47

R is the gas constant (8.32J/mol K or 8.315 x 10 ^-3), T is 298 kelvins

Question 18

Hydrolysis of ATP steps

Answer 18

There an ATP molecule. Water is added. This gives you ADP + pi (additional phosphate group)

ATP + H2O = ADP + Pi

The delta G naught prime for this reaction is -7.3 Kcal/mol mole or -30.5 kJ/mol. This is an exergonic reaction

Question 19

Spontaneity rules

Answer 19

1. A reaction can take place spontaneously only if 🔺G is negative
2. A reaction cannot take place spontaneously if 🔺G is positive
3. In a system at equilibrium, there is no net change in the concentrations of the products and the reactants and 🔺G is zero
4. 🔺G of reaction depends only on the free energy of the products (the final state) minus free energy of reactants (initial state)

• The 🔺G of a reaction is independent of the path of the transformation

5. 🔺G provides no information about the rate of a reaction

Question 20

Enzyme reaction rates

Answer 20

enzyme can’t alter law of thermodynamics and can’t alter the equilibrium of a chemical reaction

reaction equilibrium is determined only by the free energy difference

reaction rate will be faster w/ enzyme

Enzymes facilitate the formation of the transition state

Enzymes lower transition states

Question 21

ΔG‡ or activation energy

Answer 21

energy required to get to transition state

ΔG‡ = Gx^‡ - Gs

Question 22

Transition state

Answer 22

molecule is no longer the substrate, but not yet the product

Question 23

FACT: Chemical species that have the highest free energy and lowest concentration are those on the pathway from substrate to product

Question 24

Enzyme Substrate Complex

Answer 24

The product of specific binding between the active site of an enzymes and its substrate

Question 25

Active Site

Answer 25

A specific region of an enzyme that binds the enzyme’s substrate and carries out catalysis

Question 26

Enzymatic Catalysis

Answer 26

• Begins w/ formation of an enzyme substrate complex. Enzymes bring substrates together to form an enzyme substrate complex on a particular region of the enzyme (active site)
• Interaction of enzyme and substrate promotes formation of the transition state

1. The active site is a three-dimensional cleft or crevice created by amino acids from different parts of the primary structure of the protein
2. The active site constitutes a small portion of the total enzyme volume or mass
3. The active site creates a unique pocket or micro environment to facilitate the reaction
4. The interaction of the enzyme and substrate at the active site involve multiple weak interactions
5. Enzyme specificity depends on the molecular architecture at the active site

Question 27

Enzyme Binding Energy

Answer 27

• Binding energy is the free energy released upon interaction of the enzyme and substrate
• Binding energy is greatest when the enzyme interacts w/ the transition state, thus facilitating the formation of the transition state

Question 28

Enzyme Inhibitors

Answer 28

Enzyme inhibitors mimic the transition state; these can be called transition state analogs, which are potent inhibitors of enzymes