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CHM040: Biomolecules > Enzymes > Flashcards

Enzymes Flashcards

1
Q

_ _ is a rod-shaped bacterium originally discovered in a hot spring in Yellowstone National Park

A

Thermus aquaticus

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2
Q

is a laboratory technique for rapidly producing (amplifying) millions to billions of copies of a specific segment of DNA, which can then be studied in greater detail.

A

Polymerase Chain Reaction (PCR)

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3
Q

Steps in PCR:

A

• Denaturation of helical DNA (94-96 ̊C)
• Annealing (68 ̊C)
• Elongation (72 ̊)

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4
Q

from T. aquaticus can withstand the temperature constraints of PCR

A

Taq polymerase

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5
Q

was first recognized and described in the late 1700s

A

Biological catalysis

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6
Q

What did they study in 1700s when recognizing biological catalysis?

A

digestion of meat by secretions of the stomach

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7
Q

Continued studying in 1800s

A

conversion of starch to sugar by saliva and
various plant extracts

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8
Q

he concluded that fermentation of sugar into alcohol by yeast is catalyzed by
“ferments”

A

Louis Pasteur (1850)

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9
Q

In __, he discovered that yeast extracts could ferment sugar to alcohol, proving that fermentation was promoted by molecules that continued to function when removed from cells.

A

in 1897 Eduard Buchner

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10
Q

What did buchner discovered in yeast extracts could ferment sugar to alcohol?

A

fermentation was promoted by molecules that continued to function when removed from cells.

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11
Q

He later gave the name enzymes (from the Greek “en” = inside and “zymos” = yeast) to the molecules detected by Buchner.

A

Frederick W. Kühne

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12
Q

Made the isolation and crystallization of urease; it was a breakthrough in early enzyme studies

A

James Sumner in 1926

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13
Q

postulate of Sumner

A

he postulated that all enzymes are proteins

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14
Q

(2) They crystallized pepsin, trypsin, and other digestive enzymes and found them also to be proteins.

A

1930s John Northrop and Moses Kunitz

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15
Q

Who wrote treatise titled Enzymes?

A

J. B. S. Haldane

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16
Q

He made the remarkable suggestion
that weak bonding interactions between an enzyme and its substrate might be used to
catalyze a reaction.

A

J. B. S. Haldane

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17
Q

Living organisms seethe with _ _

A

metabolic activity

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18
Q

Virtually all of these transformations are mediated by _

A

enzymes

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19
Q

proteins (and occasionally RNA; ribozymes) specialized to catalyze metabolic
reactions.

A

enzymes

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20
Q

it catalyze the reactions that break down food molecules to allow the cell to harvest energy

A

enzymes

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21
Q

They also catalyze the biosynthetic reactions that
produce the great variety of molecules required for cellular life.

A

enzymes

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22
Q

Enzymes also catalyze the biosynthetic reactions that produce the great variety of _ _ _ _ _

A

molecules required for cellular life.

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23
Q

Enzymes are highly effective catalysts for an enormous diversity of chemical reactions because of their _ _ _ _ _ _ _ _ _ _

A

capacity to specifically bind a very wide range of molecules.

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24
Q

Enzymes _ _ _ _ _ _ _ the prelude to making and
breaking chemical bonds.

A

bring substrates together in an
optimal orientation,

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25
Q

Enzymes catalyze reactions by _ _ states, the highest-energy species in reaction pathways.

A

stabilizing transition

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25
Q

3 mechanism of enzyme catalysis

A
  1. enzyme + substrate
  2. enzyme-substrate complex
  3. enzyme + product
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26
Q

An additional chemical component either one or more inorganic ions, such as Fe2+, Mg2+, Mn2+, or Zn2+

A

cofactor

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26
Q

By selectively stabilizing a transition state,

A

an enzyme determines which one of several potential chemical reactions actually
takes place.

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27
Q

complex organic or metalloorganic molecule

A

coenzyme.

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28
Q

how are metal ions taken?

A

Almost any type of diet will provide adequate amounts of needed metallic cofactors because they are needed in very small (trace) amounts.

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28
Q

5 parts of holoenzyme

A
  1. cofactor (tung bilog)
  2. catalytic site (space)
  3. coenzyme (katung sa sulod)
  4. apoenzyme (kanang pinakadako)
  5. holoenzyme (overall)
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29
Q

hala ka maam, Why do apoenzymes need cofactors?

A

Cofactors provide additional chemically reactive functional groups besides those present in the amino acid side chains of apoenzymes.

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30
Q

how are coenzymes taken?

A

synthesized within the human body using building blocks obtained from other nutrients.

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31
Q

A complete, catalytically active enzyme together with its bound coenzyme and/or metal ions is called a

A

holoenzyme

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31
Q

coenzyme or metal ion that is very tightly or even covalently bound to the enzyme protein is called a

A

prosthetic group

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32
Q

The protein part of such an enzyme is called the

A

apoenzyme or apoprotein

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33
Q

Once the cofactor binds to the apoenzyme (b), the _ _ _ _ _ _ _ , the enzyme-substrate complex forms, and the reaction occurs.

A

active site takes on the correct configuration

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34
Q

NAD+ to NADP+

A

huhu how

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35
Q

alternate name name for all cofactor

A

coenzyme

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36
Q

conjugates enzyme always contains a

A

nonprotein part

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37
Q

what is the interaction of cofactors with apoenzymes?

A

they can, but do not have to be, covalently bonded to the apoenzyme

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38
Q

a sugar that can be stored indefinitely on
the shelf with no deterioration

A

glucose

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39
Q

Its reaction with oxygen is strongly exergonic (can release energy), but it doesn’t occur under normal
conditions

A

thermodynamic potentiality

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40
Q

, enzymes can catalyze such _ _ _, causing them to proceed at extraordinarily rapid rates.

A

thermodynamically favorable reactions

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41
Q

6 MAJOR CLASSES ON THE TYPES OF REACTIONS AND ENZYMES

A

oxidoreductase
Transferase
Hydrolase
Lyase
Isomerase
ligase

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42
Q

catalyzes an oxidation–reduction reaction.

A

Oxidoreductase

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43
Q

why is oxidoreductase requires a coenzyme that is oxidized or reduced as the substrate is reduced or oxidized?

A

Because oxidation and reduction are NOT independent processes but linked processes that must occur together,

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44
Q

An organic oxidation reaction is an oxidation that: (2)

A

increases the number of C—O bonds and/or
decreases the number of C—H bonds

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45
Q

An organic reduction reaction is a reduction that:

A

decreases the number of C—O bonds and/or
increases the number of C—H bonds

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46
Q

Example of enzyme oxidoreductase

A

Phenolase and enzymatic browning

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47
Q

How is enzymatic browning be preventetd?

A
  1. immersion in cold water
  2. refrigeration
  3. boiing temperature
  4. lemon juice
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48
Q

catalyzes the transfer of a functional group from one molecule to another

A

Transferase

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49
Q

Transferase two major subtypes:

A
  1. transaminase
  2. Kinases
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50
Q

transfer of an amino group from one molecule to
another.

A

transaminase

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51
Q
  • transfer of a phosphate group from adenosine
    triphosphate (ATP) to give adenosine diphosphate (ADP) and a phosphorylated product
A

Kinases

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52
Q

enzyme that transfers amino group from one to another functional group

A

Transaminase

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53
Q

makes glucose + atp to ADP + glucose 6-phosphate

A

hexokinase

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54
Q

catalyze a reaction between a
glutamine residue in a protein and a lysine residue in the same or another protein, resulting to the formation of large polymers of protein that are very tightly linked to one another.

A

Transglutaminases

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55
Q

can be used to make consistent, uniform
portions of meat or fish from smaller scraps.

A

meat glue

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56
Q

catalyzes a hydrolysis reaction in which the addition of a water molecule to a bond causes the bond to break.

A

hydrolase

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57
Q

Examples of hydrolase:

A

maltase
lipase
protease

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58
Q

What does maltase break?

A

maltose into 2 glucose

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59
Q

What does lipase break?

A

triglyceride to glycerol and fatty acids

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60
Q

What does protease break?

A

fruit hydrolyses peptide linkage in gelatin, preventing the hydrogel from forming

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61
Q

catalyzes the addition of a group to a double bond or the removal of a
group (H2O, CO2
, NH3) to form a double bond in a manner that does not involve hydrolysis or oxidation

A

Lyase

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62
Q

Lyase example:

A

fumarase adding H20 in from fumarate to L-Malate

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62
Q

Example of isomerase:

A

Phosphoglyceromutase — from 3-Phosphoglycerate to 2-Phosphoglycerate

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62
Q

catalyzes the isomerization (rearrangement of atoms) of a
substrate in a reaction, converting it into a molecule isomeric with itself

A

isomerase

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63
Q

Pyruvate carboxylase :

A

pyruvate = oxaloacetate + ADP + P + H+

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63
Q

catalyzes the bonding together of two molecules into one with the
participation of ATP

A

Ligase

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64
Q

DNA Ligase

A

glues OH in phosphate group of DNA strands

64
Q

What does the AMP nucleotide worked?

A

which is
attached to a lysine residue in the
enzyme’s active site, is transferred to
the 5′-phosphate.

65
Q

How does the AMP—phosphate bond carried?

A

attacked by the 3′-OH, forming the covalent bond and releasing AMP.

66
Q

To allow the enzyme to carry out further
reactions in AMP nucleotides,

A

ATP must replenish the AMP in the enzyme’s active site.

67
Q

Subclasses of oxidoreductases (3)

A

oxidases
reductases
dehydrogenases

68
Q

Subclasses of transferases (2)

A

Transaminases
kinases

69
Q

Subclasses of hydrolases (5)

A

lipases
proteases
nucleases
carbohydrases
phosphatases

70
Q

Subclasses of lyases (4)

A

dehydratases
decarboxylases
deaminases
hydratases

71
Q

Subclasses of isomerases (2)

A

racemases
mutases

72
Q

Subclasses of ligases (2)

A

synthetases
carboxylases

73
Q

Which of the following statements concerning an enzyme substrate is incorrect?
a. substance upon which the enzyme “acts”
b. reactant in an enzyme-catalyzed reax
c. product in enzyme-catalyzed reaction

A

c

74
Q

most enzymes end with suffix -ase, but few names end in:
a. ose
b. ine
c. in

A

c

75
Q

A thermodynamic property that is a measure of useful
energy, or the energy that is capable of doing work.

A

Gibbs Free Energy (G)

76
Q

two thermodynamic properties of the reaction:

A

(1) the free-energy difference (∆G) between the products and reactants
(2) the energy required to initiate the conversion of reactants into products (Ea).

77
Q

The free-energy change provides information about the _ but OT the _ _ _

A

spontaneity but NOT the rate of a reaction

78
Q

A reaction can take place spontaneously only if ∆G is negative (∆G<0). Such reactions are said to be

A

exergonic

79
Q

no net change can take place if ∆G is zero:

A

A system is at equilibrium (∆G=0)

80
Q

A reaction cannot take place spontaneously if ∆G is positive (∆G>0). An
input of free energy is required to drive such a reaction

A

endergonic

80
Q

The ∆G of a reaction
is _ _ _ _ of the transformation.

A

independent of the molecular mechanism

80
Q

The rate of a reaction depends on the ?

A

free energy of activation (∆G‡
)

81
Q

How does an enzyme speed up a chemical reaction?

A

providing a lower energy route for
the conversion of the substrate into the
product(s).

81
Q

Thus, enzymes speed up reactions by _ _ _ of the
reaction.

A

lowering the activation energy

81
Q

Spontaneity (5)

A

> exergonic
equilibrium
endergonic
independent of the molecular mechanism
The rate of a reaction depends on the free energy of activation (∆G‡)

82
Q

In the graph, what is changed and not changed?

A

The energy difference between reactant (substrate) and product is not
changed. It is only the activation energy that
is reduced.

83
Q

transitory molecular structure that is no
longer the substrate but is not yet the
product

A

transition state X‡

84
Q

The difference in free energy between the transition
state and the substrate is called _ _ of activation or simply the

A

Gibbs free
energy; activation energy
(∆G‡).

85
Q

Enzymes bind to and then alter the structure of the substrate to ?

A

promote the formation of the
transition state.

86
Q

Evidence 1: At constant concentration
of enzyme, ?

A

the reaction rate
increases with increasing
substrate concentration
until a maximal velocity is
reached

87
Q

The spectroscopic characteristics of many enzymes and substrates change on the?

A

formation of an ES complex.

88
Q

These changes are particularly striking if the enzyme
contains a

A

colored prosthetic group

89
Q

Sequence of Crystallography:

A

crystal
diffraction pattern
electron density map
protein model

89
Q

provided high-resolution images of substrates and
substrate analogs bound to the active sites of many enzymes

A

X -ray crystallography

90
Q

The active sites of enzymes have some common features (5):

A
  1. 3D cleft or crevice
  2. small part of total volume
  3. unique microenvironments
  4. bounded by multiple weak attractions
  5. specificity
91
Q

formed by groups that come from different parts of the amino acid
sequence

A

3D cleft; crevice

92
Q

an enzyme that
degrades the cell walls of some bacteria

A

lysozyme

93
Q

protein structure:

A

scaffold to support and position active site

94
Q

bind and orient substrate

A

binding site

95
Q

reduce chemical activation energy

A

catalytic site

96
Q

Experiments show that the minimum size requires about 100 amino acid and that all amino acids in the protein

A

The active site takes up a small part of the
total volume of an enzyme.

97
Q

the
cleft may also contain polar residues, some of which may acquire special properties
essential for substrate binding or catalysis. Why?

A

Active sites are unique microenvironments

98
Q

Substrates are bound to enzymes by:

A

multiple weak attractions

99
Q

3 weak attractions:

A

electrostatic interactions, hydrogen bonds, and van der Waals forces.

100
Q

become significant in binding only
when numerous substrate atoms simultaneously come close to many enzyme atoms through the hydrophobic effect.

A

Van der Waals forces

101
Q

Hence, the enzyme and substrate should have

A

complementary shapes

102
Q

The directional character of hydrogen bonds between
enzyme and substrate often enforces a ?

A

high degree of
specificity

103
Q

3 types of R groups:

A
  1. bind the substrate to enzyme active site
  2. maintain 3D structure of enzyme
  3. noninteracting groups helping determine the solubility of enzyme
104
Q

The specificity of binding depends on the ?

A

precisely defined arrangement of atoms in an active site

105
Q

explains the action of numerous
enzymes. It is, however, too restrictive for the action of many other enzymes.

A

The lock-and-key model (1890)

106
Q

the substrate may bind to only certain conformations of the enzyme

A

conformation selection

107
Q

the intermediate
reaction species that is formed
when a substrate binds to the
active site of an enzyme.

A

enzyme–substrate (ES) complex

108
Q

released by the formation of a large number of weak interactions between a complementary enzyme and its substrate

A

free energy; binding energy

109
Q

the free energy that is released by the formation of a large number of weak
interactions between a complementary enzyme and its substrate

A

Binding energy

110
Q

Only the _ can participate in most or all of the interactions with the enzyme and
thus maximize binding energy

A

correct substrate

111
Q
  • a state in which the substrate is in an energetically unstable
    intermediate form, having features of both the substrate and the product
A

transition state

112
Q

What kinds of transition state changes might occur in the substrate that would make a reaction
proceed more rapidly?

A
  1. stress
  2. facilitating
  3. modify the pH of microenvironment
113
Q

the extent to which an enzyme’s activity is restricted to a specific substrate, a specific group of substrates, a specific type of chemical bond, or a specific type of chemical reaction.

A

enzyme specificity

114
Q

the extent to which an enzyme’s activity is restricted to (3)?

A
  1. a specific substrate, a specific group of substrates
  2. a specific type of chemical bond
  3. a specific type of chemical reaction.
114
Q

Types of Specificity

A
  1. Absolute specificity
  2. Group specificity
  3. Linkage specificity
  4. Stereochemical specificity
115
Q

the enzyme will catalyze only one reaction. This most restrictive of all
specificities is not common

A

Absolute specificity

116
Q

Aminoacyl tRNA synthetases absolute specificity:

A

correct amino acid has the highest binding affinity for
the binding pocket of the catalytic site;

116
Q

what affects more in absolute specificity?

A

differences in size and chemistry among amino acids suffice for effective discrimination.

117
Q

catalyzes the conversion of hydrogen peroxide (H2O2
) to O2 and H2O.
Hydrogen peroxide is the only substrate it will accept.

A

catalase

118
Q

examples of enzymes in group specificity:

A

carboxypeptidase
hexokinase

119
Q

the enzyme will act only on molecules that have a specific functional
group, such as hydroxyl, amino, or phosphate groups.

A

group specificity

120
Q

the enzyme will act on a particular type of chemical bond, irrespective
of the rest of the molecular structure.

A

linkage specificity

121
Q

examples of linkage specificity:

A

Phosphatases hydrolyze phosphate-ester bonds; proteases hydrolyze peptide bonds

122
Q

—the enzyme will act on a particular stereoisomer. Chirality is
inherent in an enzyme active site because amino acids are chiral compounds.

A

stereochemical specificity

123
Q

Factors that affect enzyme activity:

A

(1) Temperature
(2) pH
(3) substrate concentration, and
(4) enzyme concentration

124
Q

is a measure of the rate at which an enzyme converts substrate to
products in a biochemical reaction

A

enzyme activity

125
Q

How does temperature affect?

A

As the temperature of an enzymatically catalyzed reaction increases, so does the
rate (velocity) of the reaction

126
Q

Examples of temperature as a factor:

A
  1. fever
  2. autoclaves
  3. sterilization
127
Q

is the pH at which an enzyme exhibits maximum activity.

A

optimum pH

128
Q

clinical pathologist who had examined many stomach biopsy specimens
noticed a parallel between the severity of the inflammation and the number of bacteria present.

A

J. Robin Warren

129
Q

optimum pH range:

A

pH range of 7.0–7.5

130
Q

optimum pH of pepsin

A

2.0

131
Q

optimum pH of trypsin

A

8.0

132
Q

stomach and duodenal ulcers were thought to be due to:

A

excess stomach acid,
emotional stress and spicy food, among others.

133
Q

looking for a research topic
and learned that Warren had a list of patients whose gastric biopsies showed “curved” bacteria.

A

Barry James Marshall

134
Q

absence of
hydrochloric acid in the gastric secretions.

A

achlorhydria

135
Q

Why does Marshall and Warren awarded nobel prize in medicine in 2005?

A

discovery of “the bacterium
Helicobacter pylori and its role in gastritis
and peptic ulcer disease.”

135
Q

How do the enzymes present in the H. pylori bacterium can function in the acidic environment of the stomach?

A

The urease itself
is protected from denaturation
by its complex quaternary
structure.

136
Q

Enzyme-catalyzed reaction must occur in two stages:

A
  1. formation of an enzyme-substrate complex
  2. Conversion of substrate into product and release of the product and enzyme.
137
Q

the number of substrate molecules transformed per minute by
one molecule of enzyme under optimum conditions of temperature, pH, and saturation.

A

turnover number

137
Q

the active sites of all the enzyme molecules are occupied by a substrate
molecule.

A

at maximum rate of substrate concentration

138
Q

enzyme concentration

A

The concentration of substrate in a reaction is much higher than that of the enzyme.

139
Q

mechanism of enzyme action

A

Formation of an enzyme-substrate complex as an intermediate species provides an alternative pathway, with lower activation energy, through which a reaction can occur.

140
Q

active site has a fixed geometric shape. only a substrate with a matching shape can fit into it

A

lock-and-key model

141
Q

active site has a flexible shape that can change to accept a variety of related substrates. enzymes vary in their degree of specificity for substrates

A

induced-fit model

142
Q

FACTORS THAT AFFECT THE RATE OF ENZYME ACTIVITY: TEMPERATURE

A

reaction rate increases; activity drops sharply as proteins are denatured

143
Q

FACTORS THAT AFFECT THE RATE OF ENZYME ACTIVITY: PH

A

max enzymatic activity is possible only within a narrow pH range; outside range, the proteins are denatured and activity drops sharply

144
Q

FACTORS THAT AFFECT THE RATE OF ENZYME ACTIVITY: SUBSTRATE CONCENTRATION

A

reaction rate increases with substrate concentration until full saturation occurs; then rate levels off

144
Q

FACTORS THAT AFFECT THE RATE OF ENZYME ACTIVITY: ENZYME CONCENTRATION

A

reaction rate increases with increasing enzyme concentration; assuming enzyme concentration is much lower than that of substrate

145
Q

microorganism
that thrives in extreme environments

A

extremophile

146
Q

(optimal growth at pH levels of 3.0 or below

A

acidophiles

147
Q

optimal growth at pH levels of 9.0 or
above

A

alkaliphiles

148
Q

high salinity, a salinity that exceeds 0.2 M NaCl needed for growth

A

halophiles

149
Q

a temperature between 80°C and 121°C needed to thrive

A

hyperthermophiles

150
Q

a high hydrostatic pressure needed for growth

A

piezophiles

151
Q

extremely dry conditions needed for growth

A

xerophiles

152
Q

temperature of 15°C or lower needed for growth

A

cryophiles

153
Q

enzymes present in extremophiles; microbial enzyme
active at conditions that would inactivate human enzymes
as well as enzymes present in other types of higher
organisms.

A

extremozymes

154
Q
A
154
Q
A
154
Q
A
154
Q
A
155
Q
A
156
Q
A

CHM040: Biomolecules (3 decks)

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