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CHEM 441A+B > Chapter 7: Enzyme Mechanisms > Flashcards

Chapter 7: Enzyme Mechanisms Flashcards

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1
Q

What are enzymes and what do they do?

A
  • Often proteins
  • Enhance reaction rate
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2
Q

What is an enzyme made of RNA called

A

Ribozyme

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3
Q

What are the two models of enzymes and how do they differ?

A

Lock and key:
- Substrate binds to enzyme perfectly
- This means that the substrate will be unable to be released because of a tight fit
Induced fit:
- Enzyme is flexible
- Substrate will change conformation during catalysis
- Allows for larger number of weaker interactions between substrates and enzymes

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4
Q

What happens when a substrate binds to an enzyme in the induced fit model (Hexokinase example)

A
  • Glucose binds to active site
  • Conformational change blocking water from active site
  • Phosphorylation is promoted
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5
Q

Enzymes usually bind to substrates with ____________ and ________. They also promote __________ reactions.

A

High Affinity
Specificity
Catalytic

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6
Q

Substrates binding to the active site induces _________ in the enzyme.

A

Changes

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7
Q

How is enzyme activity regulated in cells?

A
  • Bioavalibility
  • Catalytic efficiency
    • Activity enzymes regulate covalent modification
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8
Q

How do enzymes affect the reaction rate, ratio of substrate to product, and ΔG?

A
  • Speed up reaction rate
  • Ratio of substrates and products remains at equilibrium (undisturbed)
  • No Change in ΔG
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9
Q

How do enzymes speed up the rate of reaction?

A
  • Decrease Activation energy
  • Change ΔG‡
    • Decrease of ΔG‡ by 5.7 kJ/mol results in 10-fold increase in reaction rate
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10
Q

How can the reaction 2H2O2 ⇋ 2H2O + O2 be sped up?

A
  • Reaction normally takes 1 year for one mol
  • Adding Fe2+/Fe3+ speeds time up to 12 minutes
  • Adding catalase speeds up to 10^-7 seconds (10^15 rate increase)
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11
Q

How can X be transferred from A to B, what factors influence the reaction?

A
  • Orientation must be right
  • Energy must be sufficient enough for X to be transferred
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12
Q

How do enzymes influence the activation energy and ΔG‡ of a reaction?

A
  • Decrease activation energy
  • Decrease ΔG‡ resulting in increase of reaction rate
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13
Q

What are cofactors and what do they do?

A
  • Small molecules that aid in catalytic reaction within active site
    • Ex. Fe2+, Cu2+, Mg2+
  • Help in catalysis when amino acid side chains are insufficient
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14
Q

What are coenzymes and what do they do?

A
  • Enzyme cofactors that require organic component
  • Include vitamin derivative species such as NAD+ and FAD+
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15
Q

What are prosthetic groups?

A

Coenzymes that are permanently associated with enzymes

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16
Q

Fill in the blanks with the following word bank: Cofactors, Coenzymes, Cosubstrates, Metal ions, Prosthetic groups

A
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17
Q

What is NADH and what does it do?

A
  • Nicotinamide adenine dinucleotide (NAD+/NADH)
  • Common coenzyme in oxidation/reduction reactions
    • Carrier of electrons
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18
Q

What is Lipoamide and what does it do?

A
  • Temporary carrier of acetyl group in reaction catalyzed by pyruvate dehydrogenase
  • Permanently attached to enzyme
    • Pyruvate + CoA + NAD+ → acetyl-CoA + CO2 + NADH
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19
Q

What two things are included in most enzyme names?

A
  • Most enzymes end in -ase
  • Substrate usually included in name
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20
Q

How does an enzyme’s structure increase the reaction rate?

A
  • Lower activation energy by stabilizing transition state
  • Provide alternate path for product formation
  • Reduce entropy by orienting the substrates appropriately for reaction to occur
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21
Q

How do enzymes create products?

A
  • Enzymes bring substrates together
  • Geometric and chemical complimentarity
    • High local concentration
    • Optimal orientation
  • Bind via non-covalent interactions
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22
Q

How do active sites contribute to catalytic properties?

A
  • Sequester microenvironment of active site
    • Provide optimal orientation and exclude excess solvents such as H2O
  • Binding between substrate and enzyme create a transition state
  • Presence of catalytic function groups
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23
Q

How does orientation influence the formation of Fructose 1,6 bisphosphate? (list steps)

A
  1. Dihydroxyacetone phosphate forms intermediate with Lys229 in enzyme with active site
  2. Glyceraldehyde-3-phosphate binds to active site
  3. Adol addition takes place in the active site forming 1,6 bisphosphate
  • Because of the orientation when the substrates bind to the active site the formation of a product is possible.
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24
Q

How is water excluded in the phosphorylation of glucose in hexokinase? Fatty acid Isomerase?

A
  • Water is excluded via conformational change
  • This way phosphate is transferred to glucose instead of H2O
  • Fatty acid isomerase creates a hydrophobic channel
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25
Q

What facilitates transition states?

A

Binding energy such as Van der Waals interactions, Ionic interactions, and H-bonds

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26
Q

What are powerful inhibitors of enzymes?

A
  • Transition state Analogs
  • Stable molecules that mimic the transition state
  • Bind tightly to active site
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27
Q

How can you determine if an amino acid is in its acid or base form?

A
  • Acid will be protenated or have a (+) charge
  • Base will be deprotenated or have a (-) charge
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28
Q

How do amino acids participate in acid-base catalysis?

A

Function groups can act as acids or bases

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29
Q

How does covalent catalysis occur?

A
  • Nucleophile group on enzyme attacks electrophile center on substrate making a covalent enzyme-substrate intermediate
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30
Q

How does metal ion catalysis occur?

A
  • Metals used to promote proper orentation of bound substrates to aid in redox reactions
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31
Q

What is a coenzyme-dependent redox reaction?

A
  • Energy conversion redox reaction such as CAC, ETC, or photosynthesis
  • Include dehydrogenases
  • Involve NAD+/NADH, NADP+/NADPH, FAD+/FADH2, and FMN/FMNH2
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32
Q

What is a Metabolic transformation reaction?

A
  • Involve isomerizations, condensations, and dehydrations (hydrolysis) reactions
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33
Q

The transformation from 2-phosphoglycerate to phosphoenolpyruvate and the splitting of a polypeptide chair with chymotrypsin require _______

A

H2O

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34
Q

What is reversible covalent modification?

A
  • Act as molecular switches that turn on and off cell signaling and gene expression
  • Include kinases and phosphotases
  • ATP is commonly used as a phosphoryl group source
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35
Q

What does chymotripsin do?

A

Hydrolyze peptide bonds

36
Q

What do proteases do?

A

Cleave peptide bonds
- Peptide + H2O ⇋ Peptide 1 (COO-) + Peptide 2 (NH3+)

37
Q

Why is a peptide bond more stable (than cleaved peptides)?

A
  • Resonance structure provides partial double bond character
  • Carbonyl carbon is less electrophilic and resistance to hydrolysis
38
Q

What is the role of proteases in the stomach?

A
  • pH 1-2
  • kills bacteria
  • unfold proteins
  • pepsin
39
Q

What is role of proteases in the pancreas?

A
  • Bicarbonate secretion bring pH back to 7
  • trypsinogen - converted to trypsin then breaks down proteins
    -chymotripsinogen - precursor of chymotripsin which breaks down proteins into smaller peptides
    -procarboxypeptidases - enzyme that hydrolyzes peptide bond at C-terminal
40
Q

What is the role of proteases in the small intestine?

A

Zymogens convert to trypsin, chymotripsin, and carboxypeptidase

41
Q

Where are zymogens produced?

A

The pancreas

42
Q

What is a zymogen?

A

Precursor of an enzyme such as trypsinogen, chymotripsin,proelastase,procarboxy-peptidase, and prolipase

43
Q

Describe the structure of chymotripsin.

A
  • 245 amino acids
  • Synthesized as chymotripsinogen (single chain)
  • Activated by removal of 4 aminoacids at the boundaries of the chains
    • 3 chains
  • Chains held by disulfide bond
  • Three critical residues for catalysis: His 57, Asp 102, Ser 195
44
Q

How does chymotripsin catalysis work?

A
  • General acid-base catalysis
    • proton transfer by groups other than water
  • Covalent catalysis
  • Formation of powerful nucleophile
  • Rate of hydrolysis increase by 10^9
45
Q

Why is chymotripsin considered a serine protease?

A

It makes Serine a highly reactive nucleophile which is used to cleave proteins

46
Q

What is the catalytic triad and what do they do?

A
  • His 57, Asp 102, Ser 195
  • Asp oreints His residue
  • His positions and polarizes -OH of Ser
  • His acts as a base catalyst (H+ acceptor)
  • Ser wants to deprotenate
47
Q

What is step 1 and 2 of chymotripsin cleaving?

A
  1. Polypeptide binds to active site
  2. His57 removes proton form Ser195 allowing nucleophilic attack by Ser O- on carbonyl carbon of the peptide
48
Q

What is step 3 of chymotripsin cleaving?

A
  1. His57 donates a proton to amino group of substrate resulting in peptide bond cleavage
    • carbonyl-terminal fragment released as first product
49
Q

What is step 4 of chymotripsin cleaving?

A
  1. H2O (reactive) enters active site and His57 acts as base and deprotenates water, resulting -OH acts as nucleophile and attacks carbonyl carbon of covalent acyl-enzyme intemediate
50
Q

What is step 5 and 6 of chymotripsin cleaving?

A
  1. His 57 donates proton to Ser 195 causing cleavage of acyl-enzyme resulting in the release of amino-terminal fragment
  2. Product 2 is released and catalytic triad is regenerated
51
Q

Outline the major points in the catalytic mechanism for chymotripsin

A
  • 2 nucleophilic attacks
    • Ser and H2O attack carbonyl group
  • Peptide bond cleavage
  • Carboxy-terminal fragment released as 1st product
  • N terminal fragment released
  • Protein cleaves into 2 fragments
52
Q

What are two other examples of enzymes with the same catalytic strategy (binding pocket)?

A

Chymotripsin, Trypsin, Elastase

53
Q

What do statins do?

A

Inhibit cholesterol sythesis

54
Q

What is the reaction rate of a first order reaction?

A

v = k [S]
k = rate constant
First order: one substrate and one product

55
Q

What is the reaction rate of a second order reaction?

A

k = kBT/h e^(-ΔG‡/RT)
kB = Bolzman constant
h = Planck’s constant

56
Q

How are enzyme kinetics measured?

A

Rate of substrate disappearance/ product formation as a function of time = velocity of reaction

57
Q

How does [S] affect reaction rate in Michaelis-Menten Kinetics?

A

v0(initial velocity) = Reaction rate
v0 varies with [S]

58
Q

What happens when [S] reaches a high concentration?

A

Eventually if the [S] is high enough vmax will be reached and enzyme activity plateaus

59
Q

What is the equation for finding v0?

A
60
Q

What is the Michaelis-Menten Constant?

A
61
Q

What does v0 equal when in Steady-State conditions?

A
62
Q

______ varies with [E]
Km is ______________ [E]

A
  • Vmax
  • independent of
63
Q

What does the Lineweaver-Burk equation do

A

Plot Km/Vmax to get quantitative information

64
Q

What is the Lineweaver-Burk Equation?

A
65
Q

What is the v0 equation accounting for catalytic efficiency (Kcat)?

A
66
Q

How efficient is enzyme activity at varrying pH for pepsin, Glucose-6-phosphotase, and Arginase?

A
  • Pepsin 1.6
  • Glucose-6-Phosphatase 7.8
  • Arginase 9.7
67
Q

How is DNA poly efficiency effected by temperature when using E. coli vs Taq?

A
  • E. coli 37C
  • Taq 80C
68
Q

What two factors mediate enzyme activity?

A
  • Bioavailibility (amount of enzyme in tissues)
  • Control of Catalytic efficiency through
    • Proteolytic modification
    • Covalent modification
    • binding of regulatory molecules
69
Q

Compare reversible and irreversible enzyme inhibition

A

Reversible
- Noncovalent binding of small biomolecule/protein to enzyme subunit
- Competitive
- Uncompetitive
- Mixed

Irreversible
- Inhibitory molecule forms covalent or strong noncovalent bond with catalytic group in enzyme active site
- Kills enzyme through tight binding
- enzyme will never function again

70
Q

What type of inhibitor is DFP (Diisopropylfluorophosphate) and what does it do?

A
  • Irreversibly enzyme inhibitor
  • DFP blocks protease and phospholipase enzymes
  • Forms covalent bond with (specific) reactive serine in active site
  • Kills enzyme
71
Q

What type of inhibitor is Malonate and how does it work?

A
  • Competes with succinate to bind to active site
  • Competition often in cells
72
Q

Diagram competitive inhibition, uncompetitive inhibition, and mixed inhibition

A
73
Q

How can competitive inhibition be overcome?

A

Increase [S]

74
Q

What type of inhibitor is Saquinavir and what does it do?

A
  • An HIV protease inhibitor (competitive)
  • Mimics Phe-Pro substrate
  • Binds tightly to active site
75
Q

What type of inhibitor is methanol and what does it do?

A
  • Methanol(competitive) binds to dehydrogenase in the liver and is converted to formaldehyde
  • Extremely harmful to tissue can result in blindness and death
  • Therapy involves slow intravenous infusion of ethanol as a competitor to methanol resulting in the filtering out of methanol
76
Q

How does uncompetitive inhibition work?

A
  • Inhibitor binds to enzyme-substrate complex resulting in a conformation change of the active site
77
Q

How does uncompetitive inhibition affect Vmax and Km-app?

A
  • Decrease in Vmax and Km-app
78
Q

How does competitive inhibition affect Vmax and Km-app

A

Vmax will be unchanged but Km-app will change

79
Q

How does mixed inhibition work?

A
  • Binding to site different to active site
  • Can be a mix of competitive and uncompetitive inhibitors
80
Q

How does mixed inhibition affect Vmax and Km?

A
  • Decrease Vmax
  • Increase or decrease in Km
81
Q

Why are metabolic pathways controlled by a regulated enzyme?

A
  • To maximize the efficiency of metabolic intermediates
82
Q

What is feedback inhibition?

A
  • End product of a pathway functions as an inhibitor in a prior enzyme in the pathway

Example: ATCase (aspartate transcarbamoylase)

83
Q

What type of curve do regulatory enzymes exhibit?

A
  • Sigmoidal curve (allostery)
  • Sigmoidal is s shaped
84
Q

How does ATCase work?

A
  • Feedback inhibition
  • CTP and ATP are allosteric regulators
85
Q

Diagram and outline the steps in Allosteric regulation

A
86
Q

Describe the ACTase organization

A
  • C6R6
  • 2 trimers C3R3
  • R = regulatory subunit
  • C = catalytic subunit

CHEM 441A+B (22 decks)

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