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Biochemistry > Enzymology > Flashcards

Enzymology Flashcards

1
Q

The molecules that enzymes act upon

A

Substrate

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2
Q

Enzymes convert substrates into

A

Products

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3
Q

______ depend upon enzymes to catalyze individual steps

A

Metabolic Pathways

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4
Q

Almost all enzymes are

A

Proteins

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5
Q

Enzymes follow the physical and chemical reactions of proteins. Notable exceptions include

A

Ribosomal RNAs and a handful of RNA molecules (Ribozymes)

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5
Q

Enzymes are

A

Heat-labile and Water-soluble

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6
Q

Enzymes can be precipitated by

A

Protein Precipitating Reagent

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7
Q

Enzymes contain how much percent of nitrogen?

A

16%

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8
Q

Enzymes that uses its first description in the earliest days of Biochemistry

A

Pepsin, Trypsin, Amylase

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9
Q

Enzymes that remove hydrogen atoms

A

Dehydrogenases

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10
Q

Enzymes that hydrolyze proteins

A

Proteases

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11
Q

Enzymes that catalyze the rearrangements in configuration

A

Isomerases

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12
Q

6 classes of enzymes according to IUBMB

A

Oxidoreductases, Transferases, Isomerases, Hydrolases, Lyases, Ligases

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13
Q

Classification of enzyme that transfers hydrogen or adds oxygen

A

Oxidoreductases

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14
Q

Oxidoreductases catalyze oxidation of one substrate while

A

Simultaneously reduces another substrate or Co-enzyme

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15
Q

Examples of oxidoreductases

A

Lactate dehydrogenase, Glucose-6-phosphate dehydrogenase, Succinate dehydrogenase

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16
Q

Classification of enzyme that transfers groups other than hydrogen

A

Transferases

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17
Q

Examples of transferases

A

Hexokinase, Aminotransferases

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18
Q

This type of enzymes can hydrolyze ester, ether, peptide, or glycosidic bonds by adding water and then breaking the bond

A

Hydrolases

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19
Q

Examples of Hydrolases

A

Amylase, Maltase, Lactase, Lipase, Sucrose, Proteases, Acetyl Choline Esterase, Trypsin

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20
Q

All digestive enzymes are

A

Hydrolases

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21
Q

Classification of enzymes that cleaves without adding water

A

Lyases

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22
Q

These enzymes can remove groups from substrates or break bonds by mechanisms other than hydrolases

A

Lyases

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23
Q

Examples of lyases

A

Aldolase, HMG CoA lyase, ATP citrate lyase

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24
Q

Compound with same number of atoms rearranged

A

Isomers

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25
Q

Intramolecular transfers

A

Isomerases

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26
Q

The enzymes can produce optical, geometric or positional isomers of substrates

A

Isomerases

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27
Q

Examples of isomerases

A

Racemases, Epimerases, cis-trans isomerases

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28
Q

Classification of ATP dependent condensation of molecules

A

Ligases

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29
Q

These enzymes link 2 substrates together, usually with the simultaneous hydrolysis of ATP

A

Ligases

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30
Q

Meaning of the latin word Ligare

A

To bind

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31
Q

Examples of ligases

A

Acetyl CoA Carboxylase, Glutamine synthetase, PRPP synthetase

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32
Q

These types of enzymes are ATP-dependent which belong to ligases

A

Synthetase

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33
Q

Examples of Synthetase

A

Carbamoyl phosphate synthetase, Arginine succinate synthetase, PRPP Synthetase, Glutamine synthetase

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34
Q

Enzyme that do not require ATP directly

A

Synthase

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35
Q

Enzymes that belong to other classes other than ligase

A

Synthase

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36
Q

Examples of synthase

A

Glycogen synthase, ALA synthase

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37
Q

The deficient enzyme in Phenylketonuria

A

Phenylalanine hydroxylase

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38
Q

Phenylalanine is converted into _______ without phenylalanine hydroxylases, this accumulates that results to metabolic derangement

A

Tyrosine

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39
Q

Lactose is not digested at a normal rate and accumulates in the gut where it is metabolized by bacteria

A

Lactase deficiency

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40
Q

Emphysema results from an inherited deficiency of _____ an enzyme that inhibits elastase action in the lungs

A

a1-antitrypsin

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41
Q

____ is a serine protease found in neutrophils that utilize the enzyme to destroy inhaled organisms in the air

A

Elastase

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42
Q

At times, elastase may escape from the _____ and then the protease beings to destroy the lung cells

A

Neutrophil

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43
Q

The circulating ______ blocks the action of elastases and protects the lung from damage

A

protein cx1-antitrypsin

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44
Q

Cigarette smoke contains ____that will destroy a key ____ residue in a1-antitrypsin and destroy a1-antitrypsin activity

A

oxidizing agents, methionine

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45
Q

Complex enzymes contain a non-protein part called the

A

Prosthetic group

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46
Q

The prosthetic group is also called the

A

Co-enzyme

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47
Q

The co-enzyme is

A

heat stable

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48
Q

The apoenzyme is

A

heat-labile

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48
Q

The protein part of the enzyme is called the

A

Apozyme

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49
Q

The apoenzyme and co-factor combined together is called the

A

Holo-enzyme

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50
Q

This is essential for the biological activity of the enzyme

A

Co-enzyme

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51
Q

Co-enzyme is a ______ organic substance

A

low molecular weight

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52
Q

Generally, co-enzymes combine loosely with the

A

Enzyme molecule

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53
Q

The enzyme and co-enzyme can easily be separated by

A

Dialysis

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54
Q

Inside the body, when the reaction is completed, the co-enzyme is ________ from the apo-enzyme and can bind to another enzyme molecule

A

Released

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55
Q

One molecule of the co-enzyme is able to convert a large number of

A

Substrate molecules

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56
Q

Most of the co-enzymes are derivatives of

A

Vitamin B complex group of substances

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57
Q

2 groups of co-enzymes

A

(1) 1st group - donates and accepts Hydrogen atoms/electrons, (2) 2nd group - transfers groups other than Hydrogen

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58
Q

Group of co-enzymes that take part in reactions catalyzed by oxidoreductases by donating or accepting H atoms/electrons

A

First group

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59
Q

In the first group of co-enzymes, the change occurring in the substrate is ______ by the co-enzymes

A

counter-balanced

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60
Q

Where counter balancing by co-enzyme occurs it can be considered as

A

Co-substrates or secondary substrates

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61
Q

Examples of 1st group co-enzymes

A

NADP-NADPH; FAD-FADH2, FMN-FMNH2

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62
Q

These group of co-enzymes take part in reactions transferring groups other than hydrogen

A

2nd group of co-enzymes

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63
Q

In 2nd group of co-enzymes, a particular group or radical is ______ from the substrate to another substrate

A

transferred

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64
Q

(2nd group of co-enzyme) what group is transferred in the co enzyme thiamine pyrophosphate (TPP)?

A

hydroxy ethyl

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65
Q

(2nd group of co-enzyme) what group is transferred in the co enzyme pyridoxal phosphate (PLP)

A

amino group

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66
Q

(2nd group of co-enzyme) what group is transferred in the co enzyme biotin?

A

carbon dioxide

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67
Q

(2nd group of co-enzyme) what group is transferred in the co enzyme coenzyme-A (Co-A)

A

acyl groups

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68
Q

(2nd group of co-enzyme) what group is transferred in the co enzyme tetra hydrofolate (Fh4)

A

one carbon group

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69
Q

(2nd group of co-enzyme) what group is transferred in the co enzyme adenosine triphosphate (ATP)

A

phosphate

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70
Q

Considered as the energy currency in the body

A

ATP

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71
Q

in the ATP molecule, the ___ and ___ bonds are ‘high energy’ bonds

A

2nd; 3rd

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72
Q

During oxidation of food stuff, energy is released, a part of which is stored as ________ in the form ATP

A

chemical energy

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73
Q

These are enzymes which require certain metal ions for their activity

A

metallo-enzymes

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74
Q

What metal is contained in carbonic anhydrase, carboxy peptidase, alcohol dehydrogenase?

A

zinc

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75
Q

What metal is contained in hexokinase, phospho fructo kinase, enolase, glucose-6-phosphatase?

A

magnesium

76
Q

What metal is contained in phospho gluco mutase, hexokinase, enolase, glycosyl transferases?

A

manganese

77
Q

What metal is contained in tyrosinase, cytochrome oxidase, lysyl oxidase, superoxide dismutase?

A

copper

78
Q

What metal is contained in cytochrome oxidase, catalase, peroxidase, xanthine oxidase?

A

iron

79
Q

What metal is contained in lecithinase and lipase?

A

calcium

80
Q

What metal is contained in xanthine oxidase?

A

molybdenum

81
Q

Metal presence in enzymes can _____ activity

A

enhance

82
Q

What do you call the enzymes that have enhanced activity when metal ions are added?

A

ion-activated enzymes

83
Q

What are the mode of actions of enzymes?

A

lowering of activation energy, acid base catalysis, substrate strain, serine proteases, covalent catalysis, entropy effect

84
Q

Enzymes lowers the

A

energy of activation

85
Q

This is defined as the energy required to convert all molecules of a reacting substance from the ground state to the transition state

A

activation energy

86
Q

Many acid-base catalysis reactions involve

A

histidine

87
Q

why is histidine usually involved in acid-base catalysis?

A

because it’s pH is close to 7

88
Q

Having a pH of almost 7 allow for

A

acting as both acid and base

89
Q

this helps histidine in acting as either an acid or base

A

ribonuclease

90
Q

Binding of a substrate to a performed site on the enzyme can induce ____ in the substrate

A

strain

91
Q

in the presence of substrate strain, the energy level of the substrate is

A

raised

92
Q

A combination of substrate strain and acid base catalysis is seen in the action of

A

lysozome

93
Q

enzymes that cleave peptide bonds in proteins

A

serine proteases

94
Q

examples of serine proteases

A

chymotrypsin, trypsin, clotting factors

95
Q

in this mode of action, this involves the substrate forming a transient covalent bond with residues in the enzyme active site or with a cofactor.

A

covalent catalysis

96
Q

An additional covalent intermediate to the reaction in covalent catalysis helps to _____ the energy of later transition states of the reaction

A

reduce

97
Q

in this mode of action, enzymes enhance reaction rates by decreasing entropy

A

entropy effect

98
Q

In entropy effect, this reduces disorder by ______ substrates for reaction

A

orienting

99
Q

a product substrate orientation theory that is also the enzyme-substrate complex theory

A

michaelis-menten theory

100
Q

in michaelis-menten theory, the enzyme and substrate combine to form the

A

enzyme-substrate (ES) complex

101
Q

in michaelis-menten theory, the ES complex breaks down to enzyme and

A

product

102
Q

This theory states that the 3D of the active site of the enzyme is complementary to the substrate. Thus, substrate and enzyme fit together, similar to a lock and key.

A

fisher’s template theory

103
Q

the fisher’s template theory cannot explain

A

the flexibility shown by enzymes

104
Q

this theory states that conformational changes are occurring at the active site of enzymes concomitant with the combination of enzyme with the substrate

A

koshland’s induced fit theory

105
Q

this is the region of an enzyme where substrate molecules bind and undergo a chemical reaction

A

active site

106
Q

the active site consists of amino acids residues that form ___ with the substrate (binding site) and residues (catalytic site) that catalyze a reaction of that substrate

A

temporary bonds

107
Q

catalytic triad of amino acids in the catalytic site

A

his (57), asp (102), ser (195)

108
Q

important amino acid at the catalytic site of chymotrypsin

A

his (57), asp (102), ser (195)

109
Q

important amino acid at the catalytic site of trypsin

A

ser, his

110
Q

important amino acid at the catalytic site of thrombin

A

ser, his

111
Q

important amino acid at the catalytic site of phosphoglucomutase

A

ser

112
Q

important amino acid at the catalytic site of alkaline phosphatase

A

ser

113
Q

important amino acid at the catalytic site of acetyl cholinesterase

A

ser

114
Q

important amino acid at the catalytic site of carbonic anhydrase

A

cysteine

115
Q

important amino acid at the catalytic site of hexokinase

A

his

116
Q

important amino acid at the catalytic site of carboxy peptidase

A

his, arginine, tyr

117
Q

from the standpoint of energy, the enzymatic reactions are divided into 3 types:

A

exothermic/exergonic, isothermic, endothermic/endergonic

117
Q

important amino acid at the catalytic site of aldolase

A

lysine

118
Q

here energy is released from the reaction, and therefore reaction essentially goes to completion

A

evergonic/exothermic

119
Q

examples of exergonic

A

urease enzyme

120
Q

at equilibrium of exergonic reactions the substrate will be at ___ and the product will be at ___

A

0.5%; 99.5%

121
Q

reactions for this type are generally invisible

A

exergonic

122
Q

type of reaction where energy exchange is negligible and the reaction is easily reversible

A

isothermic

123
Q

type of reaction where energy is consumed and external energy is to be supplied for these reactions

A

endergonic

124
Q

in the body, this is usually accomplished by coupling the endergonic reaction with an exergonic reaction

A

endergonic

125
Q

factors influencing enzyme activity

A

enzyme concentration, effect of substrate concentration, effect of concentration of products, effect of temperature, effect of hydrogen ion concentration (pH), presence of activators, presence of inhibitors, feedback inhibition and repression, stabilization and compartmentalization

126
Q

rate of a reaction or velocity is directly proportional to the enzyme concentration , when sufficient substrate is present

A

enzyme concentration

127
Q

as substrate concentration is increased, the velocity is also correspondingly increased in the initial phases, but the curve flattens afterwards

A

effect of substrate concentration

128
Q

this represents the maximum reaction rate attainable in presence of excess substrate

A

Vmax

129
Q

this is the concentration of substrate which permits the enzyme to achieve half Vmax

A

Km (Michaelis constant)

130
Q

this is also the signature of the enzyme

A

Km

131
Q

this value is a constant for an enzyme

A

Km value

132
Q

It is the characteristic feature of a particular enzyme for a specific substrate

A

Km value

133
Q

Type of factor where in a reversible reaction, S ↔ P, when equilibrium is reached, as per the law of mass action, the
reaction rate is slowed down. So, when product concentration is increased, the reaction is
slowed, stopped or even reversed.

A

Effect of Concentration of Products

134
Q

In effect of concentration of products, in inborn errors of metabolism, one enzyme of a metabolic pathway is

A

blocked

135
Q

Type of factor where the velocity of enzyme reaction increases when
temperature of the medium is increased; reaches
a maximum and then falls (Bell shaped curve).

A

Effect of Temperature

136
Q

The temperature at which maximum amount of
the substrate is converted to the product per unit
time is called the

A

optimum temperature

137
Q

Most human enzymes have the optimum
temperature around

A

37°C

138
Q

Factor where each enzyme has an optimum pH, on both sides of which the velocity will be drastically reduced.

A

Effect of Hydrogen ion concentration (pH)

139
Q

Optimum pH may vary depending on the
temperature, concentration of substrate, presence
of ions etc. Usually, enzymes have the optimum
pH _______. Some important exceptions
are ______

A

between 6 and 8, pepsin (with optimum pH 1-2); alkaline
phosphatase (optimum pH 9-10) and acid
phosphatase (4-5)

140
Q

Factor where in presence of certain inorganic ions, some enzymes show higher activity. Thus, chloride ions
activate salivary amylase and calcium activate lipases.

A

Presence of Activators

141
Q

Another type of activation is the ______ of an inactive pro-enzyme or zymogen to the active
enzyme.

A

conversion

142
Q

BY splitting a single peptide bond, and removal of a small polypeptide from trypsinogen, the _______ is formed

A

active trypsin

143
Q

types of inhibition

A

competitive, non-competitive, uncompetitive inhibition, allosteric regulation

144
Q

Here inhibitor molecules are competing with the normal substrate molecules for binding to the active site of the enzyme

A

competitive inhibition

145
Q

In competitive inhibition, the inhibitor is a ______ of the substrate

A

structural analog

146
Q

type of inhibition which is usually reversible

A

competitive inhibition

147
Q

In competitive inhibition, the excess substrate _____ the inhibition

A

abolishes

148
Q

In competitive inhibition, _____ is increased in presence of competitive inhibitor but Vmax is not changed

A

Km

149
Q

E + S -><- E-S ——-> E + P

A

Competitive inhibition

150
Q

Example of medication that exhibits competitive inhibition

A

metotrexate

151
Q

type of inhibition that is usually irreversible

A

non-competitive inhibition

152
Q

poisons such as ____, ____, & _____ act as irreversible non-competitive inhibitors

A

lead, cyanide, mercury

153
Q

In non-competitive inhibition, substrates can bind but the reaction is

A

blocked

154
Q

The Vmax is reduced but the ___ is not

A

Km value

155
Q

type of inhibition that does not have any affinity for free enzyme

A

uncompetitive inhibition

156
Q

this may be reversible or irreversible

A
157
Q

in uncompetitive inhibition, inhibitors bind to the ____ but not the free enzyme

A

enzyme-substrate complex

158
Q

in uncompetitive inhibition, both Vmax and Km are

A

decreased

159
Q

Example of uncompetitive inhibition

A

finasteride in benign prostatic hyperplasia

160
Q

______ has one catalytic site where the substrate binds and another separate allosteric site where the modifier binds

A

allosteric enzyme

161
Q

in allosteric regulation, the binding of the regulatory molecule enhances the activity of the enzyme, this is known as

A

allosteric activation

162
Q

in allosteric activation, the regulatory molecule is known as the

A

positive modifier

163
Q

in allosteric regulation, the binding of the regulatory molecule inhibits the activity of the enzyme, this is known as

A

allosteric inhibition

164
Q

in allosteric inihibition, the regulatory molecule is known as the

A

negative modifier

165
Q

what does the body use allosteric enzymes for?

A

regulating metabolic pathways

166
Q

the regulatory enzyme in a particular pathway is called the

A

key enzyme/rate limiting enzyme

167
Q

The allosteric inhibitor is most effective when substrate concentration is

A

low

168
Q

in allosteric regulation, when more substrate molecules are available, there is less necessity for

A

stringent regulation

169
Q

in heme biosynthesis what is the end product?

A

heme

170
Q

heme will allosterically inhibit the

A

ALA synthase

171
Q

this is the key enzyme in heme synthesis

A

ALA synthase

172
Q

another factor influencing enzyme activity, where for its mechanism, the accumulated end products binds with the enzyme and inhibits the enzyme activity

A

feedback inhibition

173
Q

another factor influencing enzyme activity, where for its mechanism, the accumulated end products works as a repressor and inhibits the enzyme synthesis at a genetic level

A

feedback repression

174
Q

in feedback inhibition, end products binds with the ____

A

active site of the enzyme

175
Q

in feedback repression, end products binds with the _____ that encode the enzyme and prevent its synthesis

A

DNA of the gene

176
Q

in this factor influencing enzyme activity, the enzyme molecules undergo usual wear and tear and finally get degraded. such degradation if prevented can lead to increased overall enzyme activity

A

stabilization of enzyme

177
Q

degradation of tryptophan pyrrolase is retarded by

A

tryptophan

178
Q

what stabilizes phospho fructo kinase

A

growth hormone

179
Q

SH groups

A

papain, urease, succinate dehydrogenase

180
Q

what stabilizes enzymes with SH groups?

A

glutathione

181
Q

this is used to inhibit the enzyme thymidylate synthase

A

5-fluorouracil (5-FU)

181
Q

this factor influencing enzyme activity is exhibited by certain enzyme pathways being located in mitochondria whereas others of the same pathway cytoplasmic

A

compartmentalization

182
Q

this enzyme converts deoxyuridine monophosphate (dUMP) to deoxy-thymidine monophosphate (dTMP) which provides the thymine for DNA synthesis

A

thymidylate synthetase

183
Q

this drug irreversibly inhibits the enzyme cyclooxygenase and interferes with the generation of prostaglandins and thromboxanes

A

aspirin

184
Q

this is the secondary mediator of pain signaling

A

thromboxane

185
Q

this drug is a suicide inhibitor of xanthine oxidase and is used in the treatment of gout

A

allopurinol

186
Q

xanthine oxidase will recognize allopurinol as a substrate and oxidize it to create _____, which binds so tightly to the active site that it is not released and then inhibits further reactions by the enzyme

A

oxypurinol

187
Q

this is a drug that is used to treat alcoholism irreversibly inhibits the enzyme aldehyde dehydrogenase leading to an accumulation of acetaldehyde whenever alcohol is ingested

A

disulfiram

188
Q

acetaldehyde leads to ____ and may deter the patient from drinking alcohol

A

hangover symptoms

Biochemistry (5 decks)

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