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BIOCHEM LEC > ENZYMES > Flashcards

ENZYMES Flashcards

1
Q

all reactions in our body are mediated by

A

ENZYMES

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2
Q

are protein that catalyzes and increases reactions without being changed in the overall process

A

ENZYMES

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3
Q

among the many biological reactions that are energetically possible, enzyme selectively channel ____

A

REACTANTS which are referred to as SUBSTRATES

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4
Q

direct all metabolic events

A

ENZYMES

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5
Q

concluded that fermentation was catalyzed by a vital force contained within the yeast cells called “ferments”, which were thought to function only within living organisms.

A

LOUIS PASTEUR

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6
Q

according to him, alcoholic fermentation is an act correlated with the life and organization of yeast cells not with the death or putrefaction of the cell

A

LOUIS PASTEUR

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7
Q

GLUCOSE molecular formula

A

C6H12O6

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8
Q

an enzyme found on yeast that is capable of converting carbohydrates (glucose) into two molecules of ethyl alcohol and two molecules of carbon dioxide

A

ZYMASE

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9
Q

first used the term enzyme, which literally means “in yeast”

1878, GERMAN PHYSIOLOGIST

A

WILHELM KUHNE

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10
Q

the word enzyme literally means

A

“IN YEAST”

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11
Q
  • began to study the ability of yeast extracts that lacked any living yeast cells to ferment sugar.
  • He also found that the sugar was fermented even when there were no living yeast cells in the mixture.
  • He named the enzyme that brought about the fermentation of sucrose as zymase

1897

A

EDUARD BUCHNER

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12
Q

when did Eduard Buchner received a nobel prize in biochemical research & his discovery of cell free fermentation

A

1907

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13
Q

Essential for breakdown of nutrients that are used to supply energy and chemical building blocks.

A

ENZYMES

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14
Q

TRUE OR FALSE

most enzymes are proteins

A

TRUE

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15
Q

one of the most important role of an enzyme

A

CATALYSIS

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16
Q

most enzymes are proteins except

A

RIBOZYMES

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17
Q

are nucleic acids but act as enzymes

A

RIBOZYMES

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18
Q

structurally, most of the enzymes are

A

GLOBULAR

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19
Q

considered as the most efficient catalyst known

A

ENZYMES

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20
Q

enzymes can speed the rate of reaction by a factor up to

A

10, 20

more than a thousand folds

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21
Q

non enzymatic catalyst typically enhance the rate of the reaction by factors of

A

10, 10

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22
Q

the substance wherein the enzymes act upon

A

SUBSTRATE

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23
Q

has a specific geometric shape wherein specific substrate would fit in

A

ACTIVE SITE

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24
Q

The basic function of an enzyme

A

INCREASE THE RATE OF A REACTION

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25
Q

Most enzymes act specifically with how many reactant (called a substrate) to produce products

A

ONLY ONE

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26
Q

enzymes are regulated from a state of what activities

A

low to high and vice versa

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27
Q

the minimum energy needed to start a chemical reaction

A

ACTIVATION ENERGY

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28
Q

WITH OR WITHOUT ENZYME

higher activation energy is needed

A

WITHOUT ENZYME

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29
Q

WITH OR WITHOUT ENZYME

lower activation energy is need

A

WITH ENZYME

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30
Q

Enzyme that is capable of hydrolyzing or breaking down lactose to form glucose & galactose

A

LACTASE

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31
Q

Most genetic disorders are due to a deficiency in

A

ENZYME FUNCTION

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32
Q

a hereditary disease that is caused by the lack of a liver enzyme phenylalanine hydroxylase.

A

PHENYLKETONURIA
pku

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33
Q

Phenylektonuria is caused by the lack of what enzyme

A

PHENYLALANINE HYDROXYLASE

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34
Q

if nawala si phenylalanine hydroxylase, what set of enzyme would take effect

A

TRANSAMINASE

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35
Q

transaminase will lead to the accumulation of a substance known as

A

PHENYLPYRUVIC ACID

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36
Q

an amino acid that is most commonly found in protein-containing foods such as meat, cow’s milk, over the counter infant formulas (both regular and soy) and breast milk.

A

PHENYLALANINE

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37
Q

ratio of the case of pku

A

1:150,000

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38
Q
  • common disease, 1:150,000
  • an inborn error of metabolism
  • can be found in the recessive genes that are found on the both sides of the parents
  • probability of getting is 1 in 4 (high, 25% chance)
A

PHENYLKETONURIA

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39
Q

CAN CAUSE
* mental retardation
* convulsions
* behavior problems
* skin rash
* musty body odor

BABIES ARE TESTED USING
* formula fed
* breast fed
* reaction is needed to be checked within 24 hours after taking milk
* to confirm, retest in 7-10 days

IF POSITIVE, DIET RESTRICTIONS ARE:
NO
* meat
* dairy products
* dry beans
* nuts
* eggs

A

PHENYLKETONURIA

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40
Q

in testing pku, reaction is needed to be checked within how many hours after taking the milk

A

24 hours

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41
Q

to ensure the test for pku, how many days should the baby be retested to catch earlier false negatives

A

7 - 10 days

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42
Q

long term effect of pku

A

irreversible brain damage & mental retardation

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43
Q

treatment of pku

A

elimination of phenylalanine from the diet

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44
Q

RA about newborn screening

A

RA 9288

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45
Q

Enzymes may require a non-peptide (non-protein) component as a

A

COFACTOR

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46
Q

The peptide component is called

A

APOENZYME

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47
Q

cofactor is called

A

COENZYME

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48
Q

combined functional unit of apoenzyme + coenzyme is called

A

HOLOENZYME

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49
Q

Cofactors that are tightly bound to the polypeptide are called

A

PROSTHETIC GROUPS

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50
Q

an enzyme has what structure

A

complex 3D structure

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51
Q
  • Important part of an enzyme.
  • The shape and the chemical environment inside this permits a chemical reaction to proceed more easily.
A

ACTIVE SITE

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52
Q

are the reactants that are activated by the enzyme.

A

SUBSTRATE

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53
Q
  • May be inactive in its original synthesized structure;
  • a protein that forms an active enzyme system by combination with a coenzyme and determines the specificity of this system for a substrate.
A

APOENZYME

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54
Q

inactive protein

A

APOENZYME

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55
Q
  • nonprotein portion
  • activates enzyme
  • cofactor
  • binds specifically to apoenzyme to complete the shape of the active site
A

COENZYME

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56
Q
  • active protein
  • capable of performing its job by catalysis
  • product of apoenzyme + coenzyme
A

HOLOENZYME

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57
Q
  • The inactive form of the apoenzyme
  • May contain several extra amino acids in the protein which are removed, and allows the final specific tertiary structure to be formed before it is activated as an apoenzyme.
A

PROENZYME OR ZYMOGEN

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58
Q

proenzyme is also known as

A

ZYMOGEN

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59
Q

either one or more inorganic ions or metal ion activator

A

COFACTOR

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60
Q

complex organic or metalloorganic molecule

A

COENZYME

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61
Q

the site other than the active site

A

ALLOSTERIC SITE

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62
Q
  • acts as transient carriers of specific functional groups
  • Derived from vitamins, organic nutrients
A

COSUBSTRATE

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63
Q
  • If a coenzyme or a cofactor is very tightly or even covalently bound to the enzyme protein
  • Examples include derivatives of B vitamins: pyridoxal phosphate, FMN, FAD, thiamine pyrophosphate, biotin and METAL IONS of Co, Cu, Mg, Mn, and Zn.
A

PROSTHETIC GROUPS

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64
Q

FMN

A

Flavin mononucleotide

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65
Q

FAD

A

Flavin adenine dinucleotide

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66
Q

enzymes that contain tightly bound metal ions

A

METALLOENZYMES

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67
Q

common suffix for enzymes

A

-ase

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68
Q

hydrolyze proteins

A

PROTEASES

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69
Q

remove hydrogen atoms

A

DEHYDROGENASE

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70
Q

catalyze rearrangement in configuration

A

ISOMERASE

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71
Q

may be added to identify multiple forms of an enzyme

A

ALPHANUMERIC DESIGNATORS

72
Q

NOMENCLATURE

MODIFIERS used to indicate

A
  • substrate
  • source
  • regulation
  • MOA (mechanism of action)
73
Q

names that do not end with -ase

A

TRIVIAL NAMES

74
Q

MAJOR CLASSES OF ENZYMES

6

A

Oxidoreductases
Transferases
Hydrolases
Lyases
Isomerases
Ligases

OTHILL

75
Q

7th class of enzyme

A

TRANSLOCASES

76
Q
  • Catalyze a variety of oxidation-reduction reactions
  • Common names include dehydrogenase, oxidase, reductase and catalase
A

OXIDOREDUCTASE

77
Q
  • Catalyze transfers of groups (acetyl, methyl, phosphate(kinases), etc.).
  • The first three subclasses play major roles in the regulation of cellular processes.
  • The polymerase is essential for the synthesis of DNA and RNA (polynucleotides)
A

TRANSFERASE

78
Q

essential for the synthesis of DNA and RNA (polynucleotides)

A

POLYMERASE

79
Q
  • Catalyze hydrolysis reactions where a molecule is split into two or more smaller molecules by the addition of water
A

HYDROLASES

80
Q

split protein molecules

A

PROTEASES

81
Q

essential for HIV replication

A

HIV PROTEASE

82
Q

plays a major role in apoptosis

A

CASPASE

83
Q

splits nucleic acids (DNA & RNA)

A

NUCLEASES

84
Q

Nucleases can be divided into

A

EXOnuclease
ENDOnuclease

85
Q

progressively splits off single nucleotides from one end of DNA or RNA.

A

EXONUCLEASE

86
Q

splits DNA or RNA at internal sites

A

ENDONUCLEASE

87
Q
  • catalyzes dephosphorylation (removal of phosphate groups).
  • Example: calcineurin (aka protein phosphatase 3)
  • Tacrolimus, Sirolimus, Everolimus and Cyclosporin A are the calcineurin inhibitors
A

PHOSPHATASE

88
Q
  • Catalyze the cleavage of C-C, C-O, C-S and C-N bonds by means other than hydrolysis or oxidation.
  • Common names include decarboxylase and aldolase.
A

LYASES

89
Q
  • Catalyze atomic rearrangements within a molecule.
  • Examples include rotamase, protein disulfide isomerase (PDI), epimerase and racemase
A

ISOMERASES

90
Q
  • Catalyze the reaction which joins two molecules
  • Examples include peptide synthase, aminoacyl-tRNA synthetase, DNA ligase and RNA ligase
A

LIGASES

91
Q

means that there is no net change in the concentrations of the reactants and products

A

REACTION EQUILIBRIA

92
Q

Rate enhancements that enzymes bring about are in the range of ____ orders of magnitude (MO)

A

5 - 17

93
Q
  • Formation of transient (temporary) covalent bond with a substrate
  • Transient transferring of chemical group from the substrate to the enzyme
  • Usually happens in the active site
A

REARRANGEMENT OF COVALENT BONDS

94
Q

Much of the energy required to lower activation energies is derived from ____ interactions between the enzyme and substrate mediated by the same forces that stabilize protein structure.

A

WEAK, NONCOVALENT

95
Q
  • the energy derived from enzyme-substrate interaction
  • energy released that stabilizes the interaction
  • major source of free energy used by enzymes to lower the activation energies of reactions
  • contributes to specificity as well as to catalysis
A

BINDING ENERGY

96
Q
  • first postulated in 1894 by Emil Fischer;
  • The lock is the enzyme and the key is the substrate;
  • Only the correctly sized key (substrate) fits into the keyhole (active site) of the lock (enzyme).
A

LOCK AND KEY THEORY

97
Q

Lock & key theory is first postulated by

A

EMIL FISCHER

98
Q
  • Enzymes were structurally complementary to their substrates - perfect fit
  • May be misleading when applied to enzyme catalysis
  • “An enzyme completely complementary to its substrate would be a very poor enzyme.”
A

LOCK & KEY HYPOTHESIS

99
Q

An enzyme must be complementary to the

A

REACTION TRANSITION STATE

100
Q

optimal interactions (weak interactions) between the enzyme and substrate occur only in the

A

TRANSITION STATE

101
Q
  • Postulated by Daniel Koshland
  • It states that, when substrates approach and bind to an enzyme they induce a conformational change
  • This change is analogous to placing a hand (substrate) into a glove (enzyme).
A

INDUCED FIT THEORY

102
Q

Induced fit theory is postulated by

A

DANIEL KOSHLAND

103
Q

In induced fit theory:
enzymes are

A

REUSABLE

104
Q

In induced fit theory:
active site changes

A

SHAPE

105
Q

This explains the enzymes that can react with a range of substrates of similar types.

A

INDUCED FIT THEORY

106
Q

MECHANISMS TO FACILITATE CATALYSIS

  • For molecules to react, they must come within bond-forming distance of one another
  • The higher the concentration, the more frequently they will encounter one another and the greater will be their rate of interaction aka entropy reduction
A

CATALYSIS BY PROXIMITY

107
Q

MECHANISMS TO FACILITATE CATALYSIS

  • Refers to proton transfers mediated by other classes of molecules
  • General or Specific
  • The active sites of some enzymes contain amino acid functional groups that can participate in catalysis as proton donors or acceptors
A

ACID-BASE CATALYSIS

108
Q

MECHANISMS TO FACILITATE CATALYSIS

Reaction between bound molecules doesn’t require an improbable collision of 2 molecules – they’re already in “contact” (increases the local concentration of reactants).

A

PROXIMITY

109
Q

MECHANISMS TO FACILITATE CATALYSIS

Reactants are not only near each other on enzyme, they’re oriented in optimal position to react, so the improbability of colliding in correct orientation is taken care of.

A

ORIENTATION

110
Q

MECHANISMS TO FACILITATE CATALYSIS

  • Involves the formation of a transient covalent bond between the enzyme and one or more substrates
  • Common among enzymes that catalyze group transfer reactions
A

COVALENT CATALYSIS

111
Q

MECHANISMS TO FACILITATE CATALYSIS

  • Ionic interactions between an enzyme-bound metal and a substrate can help orient the substrate for reaction or stabilize charged reaction states
  • Metals can also mediate oxidation-reduction reaction by reversible changes in the metal ion oxidation state
A

METAL ION CATALYSIS

112
Q

MECHANISMS TO FACILITATE CATALYSIS

  • When substrate binds to enzyme, water is usually excluded from active site
  • causes local dielectric constant to be lower, which enhances electrostatic interactions in the active site, and also
  • results in protection of reactive groups from water, so water doesn’t react to form unwanted by-products.
A

DESOLVATION

113
Q

MECHANISMS TO FACILITATE CATALYSIS

Involvement of charged enzyme functional groups in stabilizing otherwise unstable intermediates in the chemical mechanism can also correctly be called

A

ELECTROSTATIC CATALYSIS

114
Q

MECHANISMS TO FACILITATE CATALYSIS

  • Strain is created by binding to substrates in a conformation slightly unfavorable for the bond to undergo cleavage
  • The strain stretches or distorts the targeted bond, weakening it and making it more vulnerable to cleavage
A

CATALYSIS BY STRAIN

115
Q

MECHANISMS TO FACILITATE CATALYSIS

the most important rate enhancing mechanism available to enzymes

A

CATALYSIS BY STRAIN

116
Q

MECHANISMS TO FACILITATE CATALYSIS

a more modern concept: it is not the substrate that is distorted but rather that the transition state makes better contacts with the enzyme than the substrate does, so the full binding energy is not achieved until the transition state is reached.

A

TRANSITION STATE STABILIZATION

117
Q

MECHANISMS TO FACILITATE CATALYSIS

assumes that the active site of an enzyme is not complementary to that of the transition state in the absence of the substrate. Such enzymes will have a lower value of kcat/Km, because some of the binding energy must be used to support the conformational change in the enzyme. Induced fit increases Km without increasing kcat.

A

INDUCED FIT

118
Q

The field of biochemistry concerned with the quantitative measurement of the rates of enzyme-catalyzed reactions and the systematic study of factors that affect these rates.

A

ENZYME KINETICS

119
Q

Describes how reaction velocity varies with substrate concentration

A

MICHAELIS MENTEN EQUATION

120
Q

k1, k-1, and k2

A

RATE CONSTANTS

121
Q

Michaelis constant

A

(k-1 + k2) / k1

122
Q

ASSUMPTIONS

[S] >[E], so [ES] at any time is small

A

RELATIVE CONCENTRATIONS OF E & S

123
Q

ASSUMPTIONS

  • [ES] does not change in time
  • E + S = ES = E + P, the rate of formation of ES is equal to that of the breakdown of ES
A

STEADY STATE ASSUMPTION

124
Q

ASSUMPTIONS

  • Used in the analysis of enzyme reactions
  • Rate of reaction is measured as soon as E and S are mixed
  • [P] is very small, the rate of back reaction from P to S can be ignored
A

INITIAL VELOCITY

125
Q

CHARACTERISTICS OF Km

reflects high affinity of the E for S because a low concentration of S is needed to half-saturate the enzyme – that is, reach a velocity that is 1⁄2 Vmax

A

small Km

126
Q

CHARACTERISTICS OF Km

Reflects low affinity of E for S because a high concentration of S is needed to half-saturate the enzyme

A

Large Km

127
Q

The rate of reaction is ____ to the enzyme concentration at all substrate concentrations

A

DIRECTLY PROPORTIONAL

128
Q

ORDER OF REACTION

[S] < Km, the velocity of reaction is roughly proportional to the enzyme concentration

A

FIRST ORDER

129
Q

ORDER OF REACTION

[S] > Km, the velocity is constant and equal to Vmax; the rate of reaction is then independent of substrate concentration

A

ZERO ORDER

130
Q
  • Also called a double-reciprocal plot
  • If 1/v0 is plotted VS 1/[S], a straight line is obtained
  • The intercept on the x-axis is equal to -1/Km
  • The intercept on the y-axis is equal to 1/Vmax
  • Can be used to calculate Km and Vmax as well as to determine the mechanism of enzyme inhibitors
A

LINEWEAVER-BURK PLOT

131
Q

lineweaver-burk plot is also called

A

DOUBLE-RECIPROCAL PLOT

132
Q

substance that can diminish the velocity of an enzyme catalyzed reaction

A

INHIBITOR

133
Q
  • tend to compete with the substrate to the active site
  • Inhibitors tend to resemble the structures of a substrate, and thus are termed as substrate analogs
A

COMPETITIVE INHIBITION

134
Q

competitive inhibitors are also termed as

A

SUBSTRATE ANALOGS

135
Q
  • Malonate ( ̄O−CO−CH2−COO ̄) competes with Succinate ( ̄OOC−CH2−CH2−COO ̄) for the active site of succinate dehydrogenase (SDH)
  • SDH catalyze the removal of one H atom from each of the 2 methylene C’s of succinate
A

COMPETITIVE INHIBITION

136
Q

CONSEQUENCES OF COMPETITIVE INHIBITION

At high levels of substrate all of the inhibitor is displaced by substrate.

A

Vmax is unchanged

137
Q

CONSEQUENCES OF COMPETITIVE INHIBITION

Higher substrate concentrations are required to reach the maximal velocity.

A

Km is increased

138
Q

NONCOMPETITIVE INHIBITION

At high levels of substrate the inhibitor is still bound.

A

Vmax is decreased

139
Q

NONCOMPETITIVE INHIBITION

Noncompetitive inhibitors do not interfere the binding of substrate to enzyme

A

Km is not changed

140
Q

FACTORS AFFECTING ENZYME REACTIONS

The rate of enzyme catalyzed reaction ____ with substrate concentration until a maximal velocity (Vmax) is reached

A

INCREASES

141
Q

FACTORS AFFECTING ENZYME REACTIONS

The rate of enzyme-catalysed reactions increases as the temperature rises to the ____

A

OPTIMUM TEMPERATURE

142
Q

FACTORS AFFECTING ENZYME REACTIONS

Above a certain temperature, activity begins to decline because the enzyme begins to ____

A

DENATURE

143
Q

Enzymes are usually damaged above about what temperature

A

45C

144
Q

example of enzyme that work best at a pH of about 2.0

A

GASTRIC PROTEASE

145
Q

molecules that regulate allosteric enzymes that bind noncovalently at a site other than the active site

A

EFFECTORS

146
Q

EFFECTORS

inhibit enzyme activity

A

NEGATIVE EFFECTORS

147
Q

EFFECTORS

increases enzyme activity

A

POSITIVE EFFECTORS

148
Q
  • Substrate itself serves as an effector
  • Most often a positive effector
  • The presence of a substrate molecules at one site on the enzyme enhances the catalytic properties of the other substrate-binding sites ⎯ (their sites exhibit cooperativity)
A

HOMOTROPIC EFFECTORS

149
Q

The effector may be different from the substrate

A

HETEROTROPIC EFFECTORS

150
Q

A form that may be more or **less active **than the unphosphorylated enzyme

A

PHOSPHORYLATED FORM

151
Q

(degrades glycogen)

A

Glycogen phosphorylase

152
Q

(synthesize glycogen)

A

Glycogen synthase

153
Q

Alter the total population of active sites rather than influencing the efficiency of existing enzyme molecules

A

INDUCTION & REPRESSION OF ENZYME SYNTHESIS

154
Q

Enzymes that are needed at only one stage of development or under selected physiologic conditions are subject to

A

REGULATION OF SYNTHESIS

155
Q

Enzymes that are in constant use are NOT regulated by

A

ALTERING THE RATE OF ENZYME SYNTHESIS

156
Q

a common form of enzyme regulation in which the product inhibits the enzyme

A

FEEDBACK INHIBITION

157
Q

enzymes are most active at what temperature

A

OPTIMUM TEMPERATURE

usually 37C in humans

158
Q

enzymes show little activity at what temperature

A

LOW TEMPERATURES

159
Q

enzymes lose activity at what temperature as denaturation occurs

A

HIGH TEMPERATURES

160
Q

what is disrupted in the structure of enzymes at high or low pH

A

TERTIARY STRUCTURE

161
Q
  • HMG Coenzyme A reductase inhibitors
  • lower serum lipid concentration
A

STATINS

162
Q
  • inhibitors of viral reverse transcriptase
  • block replication of HIV
A

EMTRICITABINE and TENOFOVIR DISOPROXIL FUMARATE

163
Q

antihypertensive agents

A

ACE inhibitors

164
Q

inhibitors of alanyl alanine carboxypeptidase-transpeptidase, thus blocking cell wall synthesis

A

Lactam Antibiotics (Penicillin and Amoxicillin)

165
Q

may indicate tissue damage accompanied by increased release of intracellular enzymes, thus useful as a diagnostic tool

A

ELEVATED ENZYME ACTIVITY

166
Q

aminotransferase is also called

A

GLUTAMATE

167
Q
  • Enzymes that catalyze the same reaction but differ in their physical properties because of genetically determined differences in amino acid sequence
  • Different organs frequently contain characteristic proportions of different isoenzymes
A

ISOENZYMES

168
Q

isoenzymes are also called

A

ISOZYMES

169
Q

present in more than 5% in myocardial muscles

A

CK2 (MB)

170
Q

Creatine kinase is also called

A

CREATININE PHOSPHOKINASE (CPK)

171
Q

each isoenzyme is a ____ composed of 2 polypeptides

A

DIMER

172
Q
  • Appears approximately 4 to 8 hours following onset of chest pain, and reaches a peak in activity at approximately 24 hours
A

CK, CREATININE KINASE

173
Q
  • Elevated following an infarction peaking 3 to 6 days after the onset of symptoms
  • Of diagnostic value in patients admitted more than 48 hours after the infarction
A

LACTATE DEHYDROGENASE

174
Q

ENZYME INDUCER

A

Phenobarbital
Rifampicin
Carbamazepine
Phenytoin
Griseofulvin
Smoking
Chronic addiction

REMEMBER: PRC

175
Q

ENZYME INHIBITOR

A

Cimetidine
Ketoconazole
Fluconazole
Miconazole

BIOCHEM LEC (29 decks)

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