Chapter 5 Enzymes

Question 1

page 53.

Overview

1. define what an enzyme is ?
2. define what a substrate is ?

Answer 1

1. are protein catalysts that speed up rxns with out being changed in the overall process.
2. reactants that are selectively chanelled by enzymes

Question 2

page 53.

NOMENCLATURE

1. Each enzyme are assigned how many names ?
2. Common enzyme name have a suffix attached to the
3. the suffix attached is spelled as ?
4. give an example of question # 2. ?
5. give two examples of suffix exceptions in nomenclature ?

Answer 2

1. each enzyme are assigned two names
2. substrate of the reaction
3. “-ase”
4. Glucosid-ASE
5. Trypsin and pepsin

Question 3

page 53.

Systematic name

1. In systematic naming how many major classes are enzymes divided into ?
2. the suffix -ase is attached to a complete description of what ?
3. give an example of question two?

Answer 3

1. six classes
2. of the chemical reaction
3. Lactate: (nicotinamide adenine dinucleotide) NAD+

Question 4

page 54.

III. Properties of Enzymes

Answer 4

1. Active Site
2. Efficiency
3. specificity
4. with non-protein component/without non- protein component

(holoenzymes, apoenzymes, cofactors and coenzymes)

5. regulation
6. location with in the cell

Question 5

page 54.

Active Site

1. what is that “special pocket/cleft” called on an enzyme?
2. how is an active site formed in an enzyme ?
3. how do substrate stick with enzymes (bond w/enzymes)
4. when a substrate and enzyme sticks together it forms ?
5. EP is derived from
6. EP dissociates to

Answer 5

1. Active site
2. by folding
3. non-covalently
4. ES complex
5. ES complex converting into EP enzyme-product comp.
6. enzyme and product

Question 6

page 54.

Efficiency

1. enzyme -catalyzed rxns proceed from 10³ to how much more?
2. define what a turnover number is ?
3. another meaning for turnover number is ?
4. Kcat is the rate constant for the conversion of ES to ?

Answer 6

1. 10⁸ times faster than uncatalyzed reactions
2. the number of substrate molecules converted to PRODUCT/enzyme molecule/sec.
3. K_{<strong>cat</strong>}
4. E + P

Question 7

Specificity

Answer 7

• lock and key mechanism

Question 8

Define each term :

1. Holoenzyme
2. Apoenzyme (inactive)
3. Cofactor
4. Coenzyme
5. Cosubstrates
6. what actually dissociates from the enzyme in an altered state ?
7. NAD is an example of what ?
8. where do coenzymes commonly derive from ?
9. Example of derivation NAD⁺ contains what vit ?
10. FAD contains what vit ?

Answer 8

1. an active enzyme WITH its non-protein component
2. enzyme WITHOUT its non-protein component
3. if the non-protein is a METAL ION (Fe²⁺) or (Zn²⁺)
4. SMALL organic molecule
5. coenzymes that transiently associate with enzymes
6. cosubstrates
7. cosubstrate
8. vitamins
9. Niacin
10. Riboflavin

Question 9

Answer the following questions:

Concept: Mechanism of Enzyme Rxns

1. In a chemical reaction, the important thing needed to “overcome” the energy barrier ?
2. The rate of reaction is determined by ?
3. When the activation energy is low; (complete this sentence)
4. Low Activation Energy (E_a) will have a faster or slower rate of reaction ?

Answer 9

1. they must contain sufficient amount of energy “overcome” the energy barrier
2. The number of ENERGIZED molecules
3. the more molecules have sufficient energy to pass through the TRANSITION state.
4. FASTER

Question 10

Enzyme Inhibition

1. Any substance that can decrease the velocity of an enzyme-catalyzed reaction ?
2. What are the two kinds of enzyme inhibitor
3. A type of enzyme inhibitor that are converted by the enzyme itself to a form that covalently links to enzymes ?
4. mechanism-based inhibitors are also referred to as ?
5. what type of inhibitor enzyme binds to enzymes via NONCOVALENT bonds ?
6. what type of enzyme inhibitor results in the dissociation of the reversible bound inhibitor and recovery of enzyme activity ?

Answer 10

1. INHIBITOR
2. reversible and irreversible
3. mechanism-based inhibitors
4. suicide inhibitors
5. Reversible inhibitors
6. Reversible enzyme inhibitors

Question 11

1. When the substrate is lesser than K_m the reaction rate is proportional to what ?
2. when [S] is <<< K_m; what order is it referring to ?

Answer 11

1. [S]
2. FIRST ORDER

Question 12

1. Regulated molecules called EFFECTORS ?
2. Where do effectors bind to ?
3. Allosteric enzymes are composed of
4. When [S] is greater than K_m** the reaction rate is independent of [S]; so **what order does this refer to ?
5. The rates of most enzymes are responsive due to what changes ?

Answer 12

1. ALLOSTERIC enzymes
2. to sites other than than the active site
3. multiple subunits
4. ZERO order
5. substrate concentration

Question 13

HOMOTROPIC AND HETEROTROPIC EFFECTORS

1. define “homotropic” effectors in three points ?
2. define “heterotropic” effectors in three points ?

Answer 13

• substrate itself serves as an effector
• presence of a substrate at one site; enhances cooperativity
• sigmoidal shape (curve)
• effector maybe different from the substrate
• has an allosteric site that binds the end product
• involves feedback inhibition (regulation flow of substrate)

Question 14

Competitive Inhibition

Answer 14

inhibitor binds reversibly to the same site that the substrate would normally occupy, competes with the substrate for that site

Question 15

Statin Drugs as examples of competitive inhibitors

Lipitor

Pravastatin

Answer 15

inhibits the rate limiting step in cholesterol synthesis

limits the new cholesterol synthesis thereby lowering cholesterol levels

Question 16

Binding of Substrate to Enzyme

1. how do substrates bind to the enzyme’s active site ?
2. what are some examples of these non-covalent binding interactions between substrate and active site of enzymes ?

Answer 16

1. through non-covalent bonds
2. Vander-walls, electrostatic hydrogen and hydrophobic bonds

Question 17

1. the smallest energy required to activate substrate so they can react ?
2. Transition state: ( S* or ES*) define the concept ?
3. which state has the highest energy along the reaction coordinate ?

Answer 17

1. Activation energy E_a
2. Transition state is unstable because they are NOT YET products BUT also NO LONGER just substrates. It is referred to as one which is ES complex.
3. the transition state

Question 18

enzymes in regards to Equilibrium constant, Gibbs Free energy and time

Answer 18

• does not change the Keq of the reaction
• does not change the Gibbs free energy of the reaction
• Decreases the time needed/required for the reaction to reach equilibrium

Question 19

Do enzymes decrease or increase the Activation Energy ?

Answer 19

Decrease, they make it easier for things to work

Question 20

what are the types of catalytic mechanisms

there are 5 of them

Answer 20

1. acid base
2. covalent
3. metal-ion
4. preferential
5. proximity

Question 21

define the mechanisms of each type of catalysis

acid-base catalysis

metal-ion catalysis

proximal catalysis

preferential catalysis

covalent catalysis

Answer 21

1. donation or accepting hydrogen ion
2. used by kinases; redox reactions, stabilize ions like Fe+3
3. immobilize substrate close and in proper orientation
4. during the reaction enzymes convert substrates to the transition state that have energy LOWER than the energy of the intermediates created during the time with out the enzymes.
5. nucleophilic groups are introduced to active sites of enzymes by coenzymes as PLP, TPP

Question 22

1. enzyme without a coenzyme is called ?
2. an enzyme with a coenzyme is called ?

Answer 22

1. apoenzyme and is inactive
2. holoenzyme and is active

Question 23

Activated Groups

1. Groups which have energy high enough to used by enzymes in synthetic reactions

Answer 23

• SAMe- provides methyl groups for methylation reactions
• PAPS - provides sulfate groups for sulfonation reactions
• UDP glucose- provides glucose for glycosylation
• CDP choline- provides choline
• Acteyl-CoA- provides acetyl groups (anabolic and catabolic)
• Acyl-CoA- provides groups oxidized in B-oxidation

Question 24

Give some enzymes used by Oxidoreductases

Answer 24

1. NAD- TCA , PDC dehydrogenases
2. NADP- dehydrogase - pentose phosph, reductase fatty acid
3. FMN- transfer of 2 electrons FMNH2 complex I ETC & NOS
4. FAD- TCA cycle, PDC, TCA used by acyl-coa dehydrogenase
5. Heme- transfer of electrons Fe+2 to Fe+3 in cytochromes complex III (cytochrome b and c1)
6. CoQ- transfer of two electrons and two hydrogen cations