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Biochemistry Broyles > Enzymatic Catalysis > Flashcards

Enzymatic Catalysis Flashcards

1
Q

The unique physical and chemical properties of the active site limit what?

A

an enzyme’s activity to specific substrates and reactions.

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2
Q

What may require metal ions or organic co factors?

A

some enzymes

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3
Q

What occurs when enzymatic reactions take the slowest steps?

A

Will exert the most control.

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4
Q

What is an enzyme?

A

a protein

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5
Q

RNA models can function as what?

A

catalyst

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6
Q

Most chemical reactions are driven by what?

A

catalyzed by an enzyme.

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7
Q

What makes reaction rates go faster?

A

enzymes

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8
Q

Why are enzymes useful to living things under mild reaction conditions?

A

Reactions will occur under conditions not optimal for reaction rates….. different temperatures.

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9
Q

With an enzyme, what type of side reactions are avoided?

A

ones that may have deleterious effects are usually avoided.

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10
Q

Enzymes have what type of specificity?

A

greater reaction specificity

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11
Q

What has the capacity of regulation?

A

an enzyme; we may not want this reaction to occur all the time.

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12
Q

What is the main thing that an enzyme is known for?

A

make a chemical reaction proceed faster than normal.

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13
Q

How much faster can en enzyme make a reaction go?

A

million folds faster.

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14
Q

What does oxidoreductases catalyze?

A

Oxidation-reduction reactions

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15
Q

What type of reaction does transferases catalyze?

A

Transfer of function groups.

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16
Q

Oxidoreductases takes off what to form energy?

A

Hydrogen

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17
Q

What enzymes breaks bonds by water addition?

A

hydrolases

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18
Q

What type of chemical reaction is catalyzed by hydrolases?

A

hydrolysis reactions.

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19
Q

What type of chemical reaction is catalyzed by the enzyme lyases?

A

group elimination to form double bonds.

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20
Q

What type of enzyme is needed to catalyze an isomerization?

A

Isomerases

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21
Q

What does the enzyme isomerase do in the catalysis of the reaction?

A

rearrange molecules.

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22
Q

What type of enzyme is used for the bond formation coupled with ATP hydrolysis?

A

ligases

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23
Q

In the bond formation coupled with ATP hydrolysis, Ligase does what?

A

tries to conserve energy.

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24
Q

In enzymes, the exact fir may not be as obvious from their independent structures, why?

A

binding may require an adjustment on the part of the enzyme.

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25
Q

What is it called when an adjustment on the part of the enzyme is done?

A

induced fit.

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26
Q

Enzymes encounter substrates as 3 dimensional objects much like what?

A

antibody

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27
Q

In stereospecifc enzymes-substrate interaction may require what?

A

stereospecificity on the part of the enzyme.

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28
Q

What does Chymotrypsin do?

A

cleaves polypeptide bonds.

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29
Q

Is chymotrypsin specific?

A

no, not completely specific for a peptide bond but can catalyze the same hydrolysis with esters.

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30
Q

What enzyme can catalyze same hydrolysis with esters?

A

Chymotrypsin.

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31
Q

What do many enzymes require?

A

auxiliary molecules, or cofactors to help them with chemistry.

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32
Q

Cofactors expand the range of enzymatic reactions. What can cofactors be broken down to?

A

metal ions and coenzymes.

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33
Q

Where are co-enzymes typically derived from?

A

Vitamins

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34
Q

What can coenzymes can be subdivided into?

A

cosubstrates and prosthetic groups.

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35
Q

What are cosubstrates?

A

they are dissociable

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36
Q

What are prosthetic groups?

A

They are permanently bound once bound.

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37
Q

Hemoglobin is an example of what group and why?

A

a prosthetic group because the heme molecule is stuck on the protein and can’t dissociate once it is bound.

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38
Q

What does an enzyme provide in terms of a reaction other than speed?

A

a lower-energy pathway from substrate to product.

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39
Q

What does not affect the overall free energy change for reactions?

A

Enzyme

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40
Q

Describe the relationship between equilibrium reaction and an enzyme?

A

it will not disrupt the equilibrium of any reaction.

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41
Q

The higher the transition rate what occurs?

A

The slower the reaction will occur.

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42
Q

The higher the change of G (Gibbs Free Energy) What occurs?

A

The slower the reaction.

43
Q

When a step is slow what can be determined?

A

It is rate limiting

44
Q

What can lower free energy?

A

Enzymes will lower the free energy of the transition state.

45
Q

If a reaction goes faster due to an enzyme what will it not effect?

A

the change of G of the overall reaction nor its equilibrium.

46
Q

What are curved arrows used for in drawing chemical reaction mechanisms?

A

shows movement of electrons vs old and new chemical bonds.

47
Q

What can be commonly said about the transition state?

A

Something you will never see in life.

48
Q

What can be seen when a general acid is catalyzed?

A

A proton is donated.

49
Q

What be said was catalyzed when a proton is extracted?

A

base was catalyzed.

50
Q

Acid-Base catalysis involves what?

A

a proton transfer

51
Q

What occurs when a proton is donated by an acid?

A

Acid is catalyzed.

52
Q

What occurs when a proton is extracted by a base?

A

Base is catalyzed.

53
Q

What does the structure of the bovine pancreatic RNAse S do?

A

hydrolyzes RNA…..adds water across a phosphodiester bond.

54
Q

In the RNAse A reaction His- 12 acts as what?

A

a general base.

55
Q

In an RNase A mechanism what does His-119 act as?

A

a general acid

56
Q

Why is it important that His-12 acts as a general base and His-119 act as a general acid?

A

to promote nucleophilic attack and bond cleavage.

57
Q

In the RNase A mechanism His-12 acts as a general acid in step 2 and His-119 acts as a general base, why?

A

to promote hydrolysis.

58
Q

What is an important feature of the bovine pancreatic RNase S enzyme?

A

the original enzyme is restored intact and unmodified.

59
Q

Does an enzyme turn off when it is over?

A

no an enzyme doesn’t, if it does then it is not an enzyme. It can do more than one reaction. It doesn’t just simply do one reaction.

60
Q

What does covalent catalysis usually involve?

A

a nucleophile

61
Q

The catalyst is the nucleophile and does what to the substrate?

A

attack the substrate to form a covalent bond.

62
Q

When covalent catalysis occurs what happens to electrons?

A

the electrons of the reaction center withdraw.

63
Q

What is step 3 of covalent catalysis?

A

the catalyst leaves in a reversal of step 1

64
Q

Why must step 3 need to be as efficient as step1?

A

the amino acid of the enzyme needs to be a good leaving group.

65
Q

What are examples of unprotonated groups?

A

Lys, His, Cys, Asp, and Ser

66
Q

What do biologically important nucleophilic groups do?

A

donate an electron pair to an electrophile to form a chemical bond.

67
Q

What are the 4 groups that are good nucleophiles?

A

hydroxyl, sulfhydryl, amino, and imidazole.

68
Q

When metal ions act as enzyme cofactors, what orients a proper reaction?

A

binding substrates

69
Q

What mediates oxidation-reduction reactions?

A

Metal ions oxidation states

70
Q

Metal ions are responsible mainly for what?

A

electronic stabilizing or shielding negative charges.

71
Q

What are biologically important electrophilic groups?

A

protons, metal ions, carbonyl carbon atom, and cationic imine.

72
Q

What is a schiff base?

A

a cationic imine

73
Q

What is the definition of an electrophile?

A

positively charged or neutral groups attracted to electron.

74
Q

What is the role of Zn 2+ in carbonic anhydrase?

A

3 His residues will chelate the zinc.

75
Q

Zn 2+ in carbonic anhydrase will use CO2 why?

A

as a catalyze in blood stream.

76
Q

What is a transition state?

A

an intermediate in a chemical reaction that shares structure with both the substrate and the product.

77
Q

An enzyme can have higher affinity for what?

A

the transition state than for either the substrate or the product of the reaction.

78
Q

The greater the affinity for the transition state what occurs to the reaction?

A

the faster the reaction will be catalyzed.

79
Q

What is an example of inhibition by transition state analogs?

A

enzyme proline isomerase and it can interconvert proline into a D isomer from an L isomer.

80
Q

These analogs are potent inhibitors that demonstrate what?

A

their affinity for the enzyme

81
Q

What will lysozyme cleave?

A

bacterial cell wall and the polysaccharide part of the cell wall.

82
Q

In a lysozyme-substrate interaction what occurs to the 6 sugar residues around the substrate cleavage?

A

site are contacted by hydrogen bonds with amino acid R groups of the enzyme.

83
Q

In the lysozyme-substrate interactions how many amino acids are directly involved in catalysis?

A

2

84
Q

What is step 1 in the lysozyme reaction mechanism?

A

Polysaccharide substrate binds enzyme and distorts the D residue

85
Q

Why in the lysozyme reaction mechanism does Glu-35 protonated at neutral pH?

A

The environment is very hydrophobic and this shifts its pKa

86
Q

What occurs once step 1 in the lysozyme reaction mechanism reaction to Glu-35?

A

Donates its proton to initiate cleavage site.

87
Q

What occurs in lysozyme reaction mechanism in step two?

A

general acid catalysis. Asp 52 nucleophyllically attacks the electron poor C1 to form a substrate-enzyme covalent intermediate.

88
Q

What occurs in the lysozyme reaction mechanism in step 3?

A

covalent catalysis and then onward to the covalent intermediate.

89
Q

What is step 4 of the lysozyme reaction mechanism?

A

water binding, water replaces the E residue in the active site.

90
Q

What occurs in step 5 of the lysozyme reaction mechanism?

A

General base catalysis occurs and Glu 35 assists with the addition.

91
Q

What is there to note on the lyzsozyme: transition state analog inhibitor?

A

the rings are planar supporting the half chair conformation of reisdue D

92
Q

What were identified by chemical labeling and structural analysis?

A

catalytically active Ser, His, and Asp residues of Serine proteases.

93
Q

What does a binding pocket determine?

A

the substrate specificity of the various proteases.

94
Q

What does the Serine Protease catalyze?

A

peptide bond hydrolysis

95
Q

How does the Serine proteases catalyze the peptide bond hydrolysis? (5 ways)

A

proximity and orientation effects, acid base catalysis,covalent catalysis, electrostatic catalysis, and transition state stabilization.

96
Q

What are Zymogens?

A

inactive precursors of enzymes

97
Q

What is the specificity of chymotrypsin?

A

Cleavage specificity on the carboxyl side of large aromatic R groups.

98
Q

What is chymotrypsin?

A

a protease

99
Q

What does chymotrypsin do?

A

breaks peptide bonds.

100
Q

Chymotrypsin is the reverse of what?

A

the synthesis of bond and all have amino acid side chains specificity.

101
Q

Describe chymotrypsin?

A

Red is active site and next to that little cleft that is coated with hydrophobic residues.

102
Q

What type of adduct does chymotrypsin have?

A

Covalent peptide adduct.

103
Q

What do enzymes form?

A

covalent intermediates with their substrates.

104
Q

How do enzymes differ from ordinary chemical catalyst?

A

in reaction rate, reaction conditions, reaction specificity, and control.

Biochemistry Broyles (3 decks)

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