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BIOCHEMISTRY > ME02 - ENZYMES : Introduction > Flashcards

ME02 - ENZYMES : Introduction Flashcards

1
Q

Energy required in order for reaction to occur

A

Activation Energy

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2
Q

Determine the direction and equilibrium states of the reaction

A

Free energy changes

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3
Q

Catalysts

A

Enzymes

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4
Q

Properties of Enzymes

A

Reaction-specific
Substrate-specific
Stereo-specific

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5
Q

Description for Enzymes

A

Increase reaction rates without being consumed or permanently altered
D sugars & L-amino acids
Typically proteins but can also be nucleotides
Affected by pH and temp

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6
Q

Non-protein catalysts with ribonuclease & peptidyl transferase activity

A

Ribozymes

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7
Q

What kind of gene is present in Ribozymes and its function

A

It contains autocatalytic RNA molecules that can adopt complex structures like proteins

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8
Q

Involved in Gene Therapy

A

Intron and tRNA processing

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9
Q 
Enzymes classified by reaction. Complete table
Class                                   Type of Reaction                Example
Hydrolase
Isomerase
Ligase/Polymerase
Lyase
Oxidoreductase
Transferase
A

Class Type of Reaction Example
Hydrolase Hydrolysis Lipase

Isomerase Rearrangement of atom Phosphoglucoisomerase
within a molecule

Ligase/Polymerase Joining two or more Acetyl-CoA synthetase
chemicals together

Lyase Splitting a chemical into Fructose 1,6-BP Aldolase
smaller parts w/o using water

Oxidoreductase Transfer of electrons or Lactic acid
H atoms from one molecule dehydrogenase
group to another

Transferase Moving a functional group Hexokinase
from one molecule group to another

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10
Q 
IUBMB Number corresponds to
1st number
2nd number
3rd number
4th number
A

1st number - Major class: Enzymes
2nd number - Subclass: Mechanism
3rd number - Sub-Subclass: Substrate Clase
4th number - Specific Substrate

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11
Q

Catalyze the oxidation of a substrate with simultaneous reduction of another substrate or coenzyme
Transfer of electrons or H atoms from one molecule to another

A

Oxidoreductases

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12
Q

Example of Oxidoreductase

A

Lactic acid-dehydrogenase - oxidizes lactic acid to form pyruvic acid during FERMENTATION

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13
Q

Moving a functional group from one substrate/molecule to another
(may be anabolic)

A

Transferase

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14
Q

Example of Transferase

A

Hexokinase - transfers phosphate from ATP to glucose in the first step of glycolysis

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15
Q

Break single bonds (ester, ether, peptide or glycosidic) by the addition of water
This is Catabolic

A

Hydrolysis

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16
Q

Example of Hydrolysis

A

Lipase - breaks down lipid molecules

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17
Q

Form or cleave bonds with group elimination non hydrolytically
Splitting a chemical into smaller parts without using water

A

Lyase

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18
Q

How does LYASE catalyze cleavage of C-C, C-O, C-N, and other covalent bonds

A

By atom elimination and generating double bonds

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19
Q

Example of Lyase

A

Fructose 1,6-bisphosphate aldolase - splits fructos into G3P and DHAP

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20
Q

Carry out intramolecular rearrangements
Catalyze geometric or structural changes within a molecule
(Neither catabolic or anabolic)

A

Isomerase

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21
Q

Example of Isomerase

A

Phosphoglucoisomerase - converts glucose 6 phosphate into fructose 6 phosphate during glycolysis

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22
Q

Link two substrates together usually with the Hydrolysis of ATP
Joining two or more chemicals together coupled with ATP hydrolysis

A

Ligase or Polymerase

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23
Q

Example of Ligase/Phosphorylase

A

Acetyl-CoA synthetase - combines acetate and coenzyme A to form acetyl-CoA for the Krebs Cycle

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24
Q

ENZYMES THAT HAS Catabolic Reactions

A

Hydrolases - Lipase

Lyase - Fructose 1,6-Bisphosphate aldolase

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25
Q

ENZYMES THAT HAS Anabolic Reactions

A

Transferase - Hexokinase

Ligase/Polymerase - AcetylCoA synthetase

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26
Q

ENZYMES THAT HAS Neither Catabolic and Anabolic Reactions

A

Isomerase - Phosphoglucoisomerase

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27
Q

Where does Catalysis occur

The site on the enzyme where the substrate binds to

A

at the ACTIVE site

Active Site - cleft or pocket on the enzyme

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28
Q

Events happening on the Active Site of Enzyme

A

Desolvation effects
Binds substrates properly for transition state formation
Binds cofactors & prosthetic groups

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29
Q

Factors for substrates’ transition state formation properly

A

Geometric & Electronic complementarity

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30
Q

Substrate-binding sites are largely preformed but some degree of induced-fit usually occurs on

A

Lock & Key model by Emil Fischer

Induced Fit model by Daniel Koshland

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31
Q

Reciprocal changes in both substrate & enzyme structure binding
Hand glove fitting

A

Induced-fit model by Daniel Koshland

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32
Q

What happens to the concentration rate in Induced Fit Model

A

Interactions that preferentially bind the transition state increase its concentration and therefore proportionally increase the reaction rate

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33
Q

What happens in the “glove-fitting” in Induced-Fit Model

A

The enzyme in turn induces a reciprocal changes in substrates, harnessing the energy of binding to facilitate the transformation of substrates into products

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34
Q

Components of active holoenzyme

A

Inactive apoenzyme & the non-protein cofactor

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35
Q

Participate in substrate binding or in catalysis

Molecules that are required by certain enzymes to carry out analysis

A

Co-factors

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36
Q

Binds to the active site of enzyme and participate in catalysis but are not considered substrates of the reaction

A

Co-factors

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37
Q 
Vitamin B as precursors its coenzymes and Reaction Type
Vitamin B                           CoEnzyme                            Reaction Type
B1 Thiamine
B2 Riboflavin
B3 Panthotenate
B6 Pyridoxine
B12 Cobalamin
Niacin
Folic Acid
Biotin
A

Vitamin B CoEnzyme Reaction Type
B1 Thiamine TPP Oxidative phosphorylation
of alphaketo acids
B2 Riboflavin FMN, FAD Oxidoreduction
B3 Panthotenate CoA Acyl group transfer
B6 Pyridoxine PLP AA transamination & decarboxylation
B12 Cobalamin Methylcobalamin Isomerization (1C transfer)
Niacin NADP Oxidoreduction
Folic Acid Tetrahydrofolate 1 C group transfer
Biotin Biocytin Carboxylation

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38
Q

Co-enzymes that participate in oxidation-reduction reaction

A

Nicotinamide
Flavin
Non-Vitamins are Tetrahydrobiopterin & Ubiquinone

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39
Q

Needed in Kinase-Catalyzed reactions

Presents “Charge shielding”

A

Nucleoside triphosphates

Mg2+

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40
Q

Involved in electron-transfer reactions

A

Iron in heme

Iron-sulfur bridges

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41
Q

How does enzymes form transition states at a lower activation energy

A

Through strategic binding & Catalytic Residues/Cofactors

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42
Q

Factors in which enzymes bind substrates in a manner that favors bond formation

A

Proximity & Orientation

    - High substrate concentration
    - Proper alignment, low entropy

Catalysis by Strain
-Bonds become distorted, weak & prone to cleavage

43
Q

Promotes catalysis through charge stabilization and water ionization, acting as Lewis “super” acids

A

Metal Ion Catalysis

44
Q

How does proteases work in forming an unstable tetrahedral intermediate

A

Covalent

Acid-base Catalysis

45
Q

What is the similarity in covalent and non covalent (acid base catalysis) processes for proteases

A

Stabilization of the tetrahedral intermediate

46
Q

Nucleophiles that participate in covalent catalysis

A

Serine, Cysteine or Threonine

Base is usually Histidine

47
Q

Acids and Bases involved in General Acid-Base Catalysis

A

Side chains of aspartic residues or glutamic residues

Zinc in case of metalloproteinases

48
Q

Fundamental Distinction between the covalent catalysis and general acid-base catalysis

A

Evolution of natural inhibitors, chemistries available for design of small molecule inactivators

49
Q

What is the Catalytic Triad

A

Catalytic Triad: Charge Relay Network
Serine - strong nucleophile that could attack carbonyl C
Histidine - accepts proton from Serine
Aspartate - stabilizes protonated Histidine

50
Q

How does serine proteases display bond specificity

A

Through their active site pockets

51
Q

How are serine proteases synthesized and activated

A

They are synthesized as zymogens.

They are activated via proteolysis by another serine protease or by autolysis

52
Q

Pockets of Serine Proteases

A

Trypsin - deep narrow pocket with Asp
Chymotrypsin - wide hydrophobic pocket
Elastase - very shallow, narrow pocket

53
Q

Serine proteases that are degradative proteases of Digestive System

A

Trypsin, Chymotrypsin, Elastase

54
Q

Serine proteases that are regulatory proteases found in amplification cascades associated with blood clotting (thrombogenesis) or the dissolving of blood clots (thrombolysis) - opposing processes that regulate hemostasis

A

Plasmin, Tissue plasminogen activator, Thrombin

55
Q

Serine proteases that are regulatory proteases that funcitn to activate peptide pro-hormones and growth factors by cleaving prosequences from the zymogen forms of such peptides

A

Kallikreins

56
Q

Serine proteases that are degradative bacterial protease, sometimes added to laundry detergents to break down protein-pigment complexed in blood and grass stains

A

Substillin

57
Q

What part does deprotonated serine side chain attack to produce tetrahedral oxyanion intermediate

A

Carbonyl Carbon

Involves stabilization of tetrahedral intermediate states through hydrogen bonds

58
Q

What is donated by the protonated histidine, acting as a general acid, to generate quaternary amine

A

Donating a proton to the amino group

59
Q

What results in Proteolysis

A

Quaternary amine & Tetrahedral oxyanion collapse

60
Q

What deprotonates Histidine then attacks the carbonyl carbon for the formation of another oxyanion intermediate

A

Histidine deprotonates H2O

61
Q

When tetrahedral oxyanion collapses, what happens.

A

It liberates the peptide & regenerating serine

62
Q

SUMMARY SUMMARY SUMMARY

A

ENZYMES - Highly efficient & specific catalysts
Ribozymes - catalytic RNA molecules
Enzymes are classified based on 6 reaction types
Active site - binds/shields substrates & cofactors
Cofactors include co-enzymes, derived mostly from Vit B, metal ions and co-substrates
Enzymes catalyze reactions by proximity & strain and metal ion catalysis, acid-base catalysis and covalent catalysis

63
Q

Rate of enzyme-catalyzed reactions in humans generally doubles with every ______________

A

increase of 10˚C until 45-55˚C

64
Q

All enzyme-catalyzed reactions depend on ___________

A

Optimal Hydrogen Ion reaction

65
Q

Factors affecting reaction rates

A

Temperature
pH (Hydrogen Ion Concentration)
Substrate concentration

66
Q

Related to the ionization of specific amino acid residues that constitute the substrate binding site

A

Optimum pH

67
Q

What kind of graph is produced in substrate concentration vs reaction rate

A

Rectangular Hyperbolic curve

68
Q

Rectangular Hyperbolic Curve represents _________

A

Plateauing towards enzyme saturation

69
Q

What happens to the rate of the enzyme at zero-order kinetics

A

The rate depends on how fast the product dissociates from the enzyme so that the latter may combine with more substrate

70
Q

The substrate concentration at half the maximal velocity

A

Michaelis contant Km

71
Q

In Michaelis Menten Plot, when is Vmax approached

A

Vmax is approached when [S] is close to 20 km

72
Q

What does the Michaelis constant approximate

A

Binding constant

73
Q

When [S] is less than, equal to or greater than Km, what is the effect on V?

A

At [S] > Km, V ≈ Vmax

74
Q

What is the effect of decreasing the enzyme concentration

A

A large Km may result either from
K2 Product is formed rapidly
K1 Enzyme-substrate complex dissociates rapidly, suggesting low substrate affinity

75
Q

Allows precise determination of Km & Vmax at less than saturating concentrations

A

Double reciprocal or Lineweaver-Burk plot

76
Q

Alternative single-reciprocal plots

A

Eadie-Hofstee

Hanes-Woolf plots

77
Q 
Parameters          Eadie-Hofstee                 Hanes Woolf
x-axis                             
y-axis                           
slope                            
x-intercept                   
y-intercept
A

Parameters Eadie-Hofstee Hanes Woolf
x-axis V [S]
y-axis V/[S] [S]/V
slope -1/Km 1/Vmax
x-intercept Vmax -Km
y-intercept Km/Vmax

78
Q

Compares the relative activity of enzymes

A

Specificity Activity
Turnover Number
Catalytic Constant

79
Q

Compares impure preparations of the same enzyme

Measures enzyme homogeneity and purity in body tissues and fluids: Maximal when all protein present is enzyme protein

A

Specificity Activity

Vmax/Protein

80
Q

To compare across homogenous enzymes

A

Turnover Number
Vmax/mol(enzyme)
Larger the turnover number = faster reaction

81
Q

S(t) = number of active sites
Unit = s-1
Best expressed in the ratio kcat/km

A

Catalytic Constant (Km)

82
Q

Describes the behavior of enzymes exhibiting cooperativity

A

Hill equation

83
Q

Depicts cooperativity in multimeric enzymes

A

Hill Plots

84
Q

Sequential reactions

Any of the substrates may combine first followed by the other substrate before catalysis can begin

A

Random sequential reactions

85
Q

Sequential reactions
One substrate must bind first with the enzyme to form a complex before the other substrate can bind and catalysis can begin

A

Ordered sequential reactions

86
Q

One or more products are released before all substrates are added

A

Double displacement reactions

87
Q

Kind of Lineweaver Burk plots displacement reactions produce

A

Single Displacement Reaction - Intersecting Lineweaver Burk plot
Double Displacement Reaction - Parallel Lineweaver Burk plot

88
Q

All substrates must combine with the enzymes before a reaction can occur & products can be released.

A

Single Displacement Reactions

89
Q 
SUMMARY ON ENZYME KINETICS
Temperature
Michaelis-Menten equation
Lineweaver - Burk
Kcat/Km
Hill plots
Cooperative Binding
A

Temperature, pH & [Substrate] AFFECT reaction rates.
Michaelis-Menten equation GIVES the reaction rate
Lineweaver - Burk plots clearly SHOW THE VMAX AND KM
Kcat/Km - is the best measure of CATALYTIC EFFICIENCY
Hill plots - depict cooperativity in multimeric enzyme
Cooperative Binding -appears to be sequential (KNF)
Most enzymatic reactions are of the Bi-Bi type

90
Q

Alters the structure of an enzyme and thus also change its function

A

Inhibitors

91
Q

Type of Inhibitor
Denaturation
Examples are Acids & Bases, Temperature, Alcohol, Heavy Metals, Reducing Agents

A

Non-Specific

92
Q

Type of Inhibitor
Irreversible
Reversible - Competitive
- Non competitive, allosteric, feedback

A

Specific

93
Q

Potent inhibitors

Compounds with a structure that resemble the transition state of a substrate

A

Transition State Analogs

94
Q

Enzymes that interact with a substrate by means of ______________, moving the substrate towards the transition stte

A

By means of strains or distortions

95
Q

Enzymes inhibitors which resemble the transition state structure would ______

A

Bind more tightly to the enzyme than the actual substrate

96
Q

How can transition state analogs be able to be used as inhibitors

A

By blocking the active site of the enzyme

97
Q

Substrate analogs transformed by the catalytic machinery of the enzyme into a product that blocks the function of the same catalytic subunit

A

Suicide or mechanism based inhibitors

98
Q

Substrate analogs that bind to the active site, preventing enzyme-substrate complex formation

A

Competitive inhibitors

99
Q

Bind to the free enzyme & enzyme substrate complex at the allosteric site and lower the cat efficiency of the enzyme

A

Simple noncompetitive

100
Q

Bind to the enzyme-substrate complex rather tan to the free enzyme and lower both Vmax and Km

A

Uncompetitive inhibitors

101
Q

Lower concentration of S is required to form half of the ____________

A

Maximal concentration of ES, resulting in a reduction of the apparent value of KM

102
Q

Facilitates the evaluation of inhibitors

A

Double reciprocal plots

103
Q 
Summary
Inhibitors
Transition state analogs
Enzyme
Competitive inhibitors
Uncompetitive inhibitors
A

Inhibitors alter the enzyme structure & thus funciton
Transition state analogs are potent inhibitors
Enzymes commit suicide through mechanism based inhibitors
Competitive inhibitors block active sites & increase Km
Noncompetitive inhibitors bind at allosteric sites & lower the Vmax
Uncompetitive inhibitors bind ES complexes and lower both Km and Vmax

104
Q

Endergonic vs Exergonic Reaction

A

Endergonic Exergonic
non-spontaneous spontaneous
energy is required energy is required
activation energy is higher

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