Chapter 4: Enzymes Flashcards
(149 cards)
1
Q
- a rod-shaped bacterium originally discovered in a hot spring in Yellowstone National Park
- Can survive at temperatures between 50°C and 80°
A
Thermus aquaticus
2
Q
proteins that catalyze the biochemical reactions.
A
enzymes
3
Q
How do Thermus aquatics survive at extreme temperatures that would cook the life forms with which we are more familiar?
A
the structure of the enzymes is held together
by many more attractive forces than the structure of the low-temperature version of the same enzyme. Thus, these proteins are stable and functional even at temperatures above the boiling point of water.
4
Q
Why was Thermus aquatica’s discovery important?
A
The thermostability of one of the enzymes of T. aquaticus, its DNA polymerase, revolutionized molecular biology by allowing the development of polymerase chain reaction (PCR)
5
Q
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)
6
Q
Steps in PCR:
A
- Denaturation of helical DNA (94-96˚C)
- Annealing (68˚C)
- Elongation (72˚)
7
Q
__ from T. aquaticus can withstand the temperature constraints of PCR.
A
Taq polymerase
8
Q
- Biological catalysis was first recognized and described in the late 1700s, in studies on the __.
- Research continued in the 1800s with examinations of the __and various plant extracts.
A
- digestion of meat by secretions of the stomach
- conversion of starch to sugar by saliva
9
Q
- In the 1850s, __ concluded that fermentation of sugar into alcohol by yeast is catalyzed by “__.” He postulated that these were inseparable from the structure of living yeast cells; this view, called __, prevailed for decades.
A
- Louis Pasteur
- ferments
- vitalism
10
Q
- In 1897 __ discovered that __ could ferment sugar to alcohol, proving that fermentation was promoted by __ that continued to function when removed from cells.
A
- Eduard Buchner
- yeast extracts
- molecules
11
Q
- __ later gave the name enzymes (from the Greek “en” = inside and “zymos” = yeast) to the molecules detected by Buchner.
A
- Frederick W. Kühne
12
Q
The isolation and crystallization of urease by __ in 1926 was a breakthrough in early enzyme studies. He found that urease crystals consisted entirely of __, and he postulated that __. In the absence of other examples, this idea remained controversial for some time.
A
- James Sumner
- protein
- all enzymes are proteins
13
Q
- In 1930s __ and __ crystallized pepsin, trypsin, and other digestive enzymes and found them also to be __.
A
- John Northrop
- Moses Kunitz
- proteins
14
Q
- During the 1930s, __ wrote a treatise titled Enzymes. Although the molecular nature of enzymes was not yet fully appreciated, he made the remarkable suggestion that __. This insight lies at the heart of our current understanding of enzymatic catalysis.
A
- J. B. S. Haldane
- weak bonding interactions between an enzyme and its substrate might be used to catalyze a reaction
15
Q
- Living organisms are filled with ____________.
- Thousands of ____________ occur rapidly within all living cells.
- Virtually all these transformations are mediated by ____________.
- ____________ are proteins specialized for catalyzing metabolic reactions.
- Enzymes catalyze reactions breaking down ____________.
- This breakdown allows cells to harvest ____________ for various cellular processes.
A
- metabolic activity
- chemical reactions
- enzymes; enzymes
- food molecules
- food molecules
16
Q
Why are proteins, specifically enzymes, highly effective catalysts for a wide range of chemical reactions?
A
due to their capacity to specifically bind a very wide range of molecules.
17
Q
How do enzymes bring substrates together for chemical reactions?
A
Enzymes bring substrates together in an optimal orientation by utilizing the full repertoire of intermolecular forces.
18
Q
What is the role of enzymes in making and breaking chemical bonds?
A
bringing substrates together in an optimal orientation.
19
Q
How do enzymes catalyze reactions?
A
by stabilizing transition states, which are the highest-energy species in reaction pathways.
20
Q
What determines which chemical reaction takes place among several potential reactions?
A
by selectively stabilizing a transition state.
21
Q
What are the two types of enzymes based on their requirement for chemical groups?
A
- those that require no chemical groups other than their amino acid residues for activity
- those that require an additional chemical component called a cofactor.
22
Q
What is a cofactor, and what are the two main types of cofactors mentioned?
A
A cofactor is an additional chemical component required by some enzymes.
There are two main types of cofactors:
- inorganic ions (such as Fe2+, Mg2+, Mn2+, or Zn2+)
- complex organic or metalloorganic molecules called coenzymes.
23
Q
What is a coenzyme, and what distinguishes it from inorganic ions in enzyme activity?
A
A coenzyme is a complex organic or metalloorganic molecule that serves as a cofactor for some enzymes. It differs from inorganic ions as it is a more complex, often organic molecule.
24
Q
Why do apoenzymes require cofactors?
A
cofactors provide additional chemically reactive functional groups beyond those present in the amino acid side chains of apoenzymes.
25
How are metal ions, essential as cofactors, supplied to the human body?
26
* All metal ions must be supplied to the __ through __. Almost any type of diet will provide adequate amounts of needed __ because they are needed in __ amounts.
* Coenzymes are synthesized within the human body using __. Most often, one of these building blocks is a __. Vitamins must be obtained through __.
- human body
- dietary mineral intake
- metallic cofactors
- very small (trace)
- building blocks obtained from other nutrients
- B vitamin or B vitamin derivative
- dietary intake
27
A coenzyme or metal ion that is very tightly or even covalently bound to the enzyme protein is called a
prosthetic group
28
A complete, catalytically active enzyme together with its bound coenzyme and/or metal ions is called a
holoenzyme
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The protein part of such an enzyme is called the
apoenzyme or apoprotein
30
apoenzyme + substrate =
- no enzyme-substrate complex
- no reaction
31
cofactor + apoenzyme + substrate =
- enzyme-substrate complex forms
- reaction occurs
32
* __ is NOT an absolute requirement for a coenzyme to be an active part of an enzyme. Sometimes a coenzyme __ to the amino acid portion of an enzyme at the time it is needed and then it is __ after the reaction has occurred. The coenzyme __ provides an
example of such coenzyme behavior.
- Permanent attachment
- temporarily binds
- released
- NAD+
33
some enzyme proteins are modified covalently by __, __, and other processes. Many of these alterations are involved in the __.
- phosphorylation
- glycosylation
- regulation of enzyme activity
34
Glucose represents __: Its reaction with oxygen is strongly __ (can release energy), but it doesn’t occur under normal conditions. On the other hand, enzymes can catalyze such __, causing them to proceed at extraordinarily __.
- thermodynamic potentiality
- exergonic
- rapid rates
- thermodynamically favorable reactions
35
Three important aspects of the enzyme-naming process:
1) suffix -ase identifies a substance as an enzyme.
2) type of reaction catalyzed by an enzyme is often noted with a prefix.
3) The identity of the substrate is often noted in addition to the type of reaction
36
Give examples of enzyme designations with the suffix -ase.
- urease
- sucrase
- lipase
37
Provide examples of enzymes with prefixes indicating the type of reaction.
- glucose oxidase (oxidation of glucose)
- pyruvate carboxylase (carboxylation of pyruvate)
- succinate dehydrogenase (dehydrogenation of succinate)
38
Provide examples of enzymes where only the substrate, and not the type of reaction, is given.
- urease (hydrolysis of urea)
- lactase (hydrolysis of lactose)
39
six major classes of enzymes on the basis of the types of reactions they catalyze
1. Oxidoreductase
2. Transferase
3. Hydrolase
4. Lyase
5. Isomerase
6. Ligase
40
__ catalyzes an oxidation–reduction reaction. Because these reactions are NOT independent processes but linked processes that must occur together, an __ requires a __ that is oxidized or reduced as the __ is reduced or oxidized
- Oxidoreductase
- oxidoreductase
- coenzyme
- substrate
41
* An organic oxidation reaction is an oxidation that:
__ the number of C—O bonds and/or
__ the number of C—H bonds
* An organic reduction reaction is a reduction that:
__ the number of C—O bonds and/or
__ the number of C—H bonds.
- increases
- decreases
- decrease
- increases
42
Prevent phenolase and enzymatic browning
1. cold water slows the browning process. The lower temperature decreases enzyme activity, and the water limits the enzyme’s access to oxygen.
2. Refrigeration slows enzyme activity even more
3. boiling temperatures destroy (denature) the enzyme.
4. Phenolase works very slowly in the acidic
environment created by the lemon juice. In
addition, the vitamin C (ascorbic acid)
present in lemon juice functions as an
antioxidant. It is more easily oxidized than
the phenolic-derived compounds, and its
oxidation products are colorless.
43
catalyzes the transfer of a functional group from one molecule to another. What are its two major subtypes?
- transferase
- transaminase
- Kinases
44
transfer of an amino group from one molecule to another.
transaminase
45
- transfer of a phosphate group from adenosine
triphosphate (ATP) to give adenosine diphosphate (ADP) and a phosphorylated product (a product containing an additional phosphate group);
- play a major role in energy-harvesting
processes involving ATP
Kinases
46
__ catalyze a reaction between a glutamine residue in a protein and a lysine residue in the same or another protein, resulting in the formation of large polymers of protein that are very tightly linked to one another
Transglutaminases
47
catalyzes a hydrolysis reaction in which the addition of a water molecule to a bond causes the bond to break.
Hydrolase
48
example of hydrolase
- maltose + h20 -> glucose + glucose
- triglyceride + 3h20 -> glycerol + 3 fatty acids
49
Why do fresh pineapple, kiwi, or papaya prevent gelatin from gelling?
These fruits contain a protease (hydrolase) that catalyzes the hydrolysis of peptide (amide) linkages in gelatin, preventing the formation of a hydrogel.
50
What distinguishes canned pineapple from fresh pineapple in relation to gelatin gelling?
Gelatin will gel in the presence of canned pineapple because the protease is deactivated during the cooking process prior to packaging.
51
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. example in lyase
Lyase
- fumarate + h2o -> L-Malate
52
catalyzes the isomerization (rearrangement of atoms) of a substrate in a reaction, converting it into a molecule isomeric with itself. give example
Isomerase
- 3-phosphoglycerate <=> (phosphoglyceromutase) 2-phosphoglycerate
53
catalyzes the bonding together of two molecules into one with the participation of ATP. give example.
ligase
- pyruvate + ATP --pyruvate carboxylate--> oxaloacetate + ADP + Phosphate + H+
54
Ligase
1) The __ (AMP) nucleotide, which is attached to a __ in the enzyme’s active site, is transferred to the __.
2) The AMP—phosphate bond is attacked by the __, forming the covalent bond and releasing AMP. To allow the enzyme to carry out further reactions, ATP must replenish the AMP in the enzyme’s active site.
- Adenosine monophosphate
- lysine residue
- 5′-phosphate
- 3′-OH
55
– A thermodynamic property that is a measure of useful energy, or the energy that is capable of doing work.
Gibbs Free Energy (G)
56
To understand how enzymes operate, we need to consider only two thermodynamic properties of the reaction:
(1) the free-energy difference (∆G) between the products and reactants
(2) the energy required to initiate the conversion of reactants into products (Ea).
57
The free-energy change provides information about the __ but NOT the __ of a reaction
- spontaneity
- rate
58
The free-energy change of a reaction (∆G) tells us if the reaction can take place spontaneously:
1. A reaction can take place spontaneously only if ∆G is __. Such reactions are said to be __.
2. A system is at equilibrium and no net change can take place if ∆G is zero (∆G=0).
3. A reaction cannot take place spontaneously if ∆G is __. An input of free energy is required to drive such a reaction. These reactions are termed __.
- negative (∆G<0)
- exergonic
(the reactants will tend to move toward the products without requiring external energy input; The reactants have more energy stored in their chemical bonds than the products.)
- positive (∆G>0)
- endergonic
(external energy input is required to drive the reaction forward; products have more energy stored in their chemical bonds than the reactants)
59
4. The ∆G of a reaction depends only on the free energy of the __ minus the free energy of the __. The ∆G of a reaction is independent of the molecular mechanism of the transformation. For example, the ∆G for the oxidation of glucose to CO2 and H2O is the __ whether it takes place by combustion or by a series of enzyme-catalyzed steps in a cell.
- products (the final state)
- reactants (the initial state).
- same
60
The ∆G provides no information about the rate of a reaction. A negative ∆G indicates that a reaction can take place spontaneously, but it does not signify whether it will proceed at a __. The rate of a reaction depends on the __ (∆G‡), which is largely unrelated to the ∆G of the reaction.
- perceptible rate
- free energy of activation
61
the minimum amount of energy required for a reaction to proceed.
Activation Energy
62
How does an enzyme speed up a chemical
reaction?
It __ by which the reaction occurs, providing a __ for the conversion of the substrate into the product(s).
Thus, enzymes speed up reactions by __ of the reaction. The energy difference between the reactant (substrate) and the product is not changed. It is only the __ that is reduced.
Enzymes alter only the __ and
not the __.
- changes the path
- lower energy route
- lowering the activation energy
- activation energy
- reaction rate
- reaction equilibrium
63
- a state in which the rates of the forward and reverse reactions are equal, resulting in no net change in the concentrations of reactants and products.
- Enzymes do not alter the position of __. They do not change the __.
- Reaction equilibrium
- equilibrium
- final concentrations of reactants and products at equilibrium
64
X‡ denotes
transition state
65
▪ transitory molecular structure that is no longer the substrate but is __.
▪ the least-stable and most-seldom occupied
species along the reaction pathway because it
is the one with the __.
transition state
- not yet the product
- highest free energy
66
The difference in free energy between the transition state and the substrate is called the __ or simply __.
- Gibbs free energy of activation
- the activation energy (∆G‡).
67
The formation of an enzyme-substrate complex is the first step in __
- enzymatic catalysis
68
Enzymes bind to and then __ the structure of the substrate to promote the formation of the __
- alter
- transition state
69
What is the evidence for the existence of an enzyme–substrate complex?
1) At a constant concentration of enzyme, the reaction rate increases with increasing substrate concentration __; further increases in substrate concentration have __ on the rate of the reaction
- until a maximal velocity is reached
- no effect
70
What is the evidence for the existence of an enzyme–substrate complex?
2) The __ of many enzymes and substrates change in the formation of an ES complex. These changes are particularly striking if the enzyme contains a __
3) __ has provided high-resolution images of substrates and substrate analogs bound to the active sites of many enzymes
- spectroscopic characteristics
- colored prosthetic group
- X-ray crystallography
71
The active sites of enzymes have some common features
1. The active site is a __, or __, formed by groups that come from different parts of the amino acid sequence: indeed, residues far apart in the amino acid sequence may interact more strongly than adjacent residues in the sequence, which may be __ from interacting with one another. In __, an enzyme that degrades the cell walls of some bacteria, the important groups in the active site are contributed by residues numbered 35, 52, 62, 63, 101, and 108 in the sequence of 129 amino acids.
- three-dimensional cleft; crevice
- sterically constrained
- lysozyme
72
The active sites of enzymes have some common features
2. The active site takes up a __ of the total volume of an enzyme. Experiments show that the minimum size requires about __ and that all amino acids in the protein, not just those at the active site, are ultimately required to form a functional enzyme
- small part
- 100 amino acid
73
scaffold to support and position active site
protein structure
74
a specific region on an enzyme where the substrate (reactant) binds and undergoes a chemical reaction.
active site
75
a broader term that encompasses regions on the enzyme where various molecules, including substrates, cofactors, or inhibitors, can bind.
binding site
76
- a subset of the active site that directly participates in the chemical reaction.
- portion of the active site where catalysis occurs, involving interactions with the substrate and facilitating the conversion of substrate molecules into products.
- crucial for the enzyme's ability to lower the activation energy of the reaction and accelerate the rate of the chemical transformation.
catalytic site
77
The active sites of enzymes have some common features
3. Active sites are __. Water is usually excluded unless it is a reactant. The __ of the cleft enhances the binding of substrates as well as catalysis. Nevertheless, the cleft may also contain __, some of which may acquire special properties essential for substrate binding or catalysis
- unique microenvironments
- nonpolar microenvironment
- polar residues
78
The active sites of enzymes have some common features
4. Substrates are bound to enzymes by __. These weak reversible contacts are mediated by __, __, and __.
multiple weak attractions
- electrostatic interactions
- hydrogen bonds
- van der Waals forces
79
__ become significant in binding only when numerous substrate atoms simultaneously come close to many enzyme atoms through the hydrophobic effect. Hence, the enzyme and substrate should have __.
The directional character of hydrogen bonds between enzyme and substrate often enforces a __, as seen in the RNA-degrading enzyme ribonuclease
- Van der Waals forces
- complementary shapes
- high degree of specificity
80
The active sites of enzymes have some common features
5. The specificity of binding depends on the precisely __ in an active site. Because the enzyme and the substrate interact by means of short-range forces that require close contact, a substrate must have a matching shape to fit into the site.
* __ (1890); explains the action of numerous enzymes. It is, however, too restrictive for the action of many other enzymes.
* __ - , it is a flexible pocket that approximates the shape of the substrate. When
the substrate enters the pocket, the active site “molds” itself around the substrate. This
produces the perfect enzyme-substrate “fit.”
Moreover, the substrate may bind to only certain conformations of the enzyme, in what is
called __.
- defined arrangement of atoms
- lock-and-key model
- induced fit model
- conformation selection
81
the intermediate reaction species that is formed
when a substrate binds to the active site of an enzyme.
enzyme–substrate (ES) complex
82
Enzymes lower the activation energy, but where does the energy to lower the activation energy come from?
- The energy required to lower the activation energy comes from the thermal energy present in the environment, typically in the form of heat.
- The reactant molecules absorb energy from their surroundings, leading to increased molecular motion.
83
Free energy is released by the formation of a large number of weak interactions between a complementary enzyme and its substrate. The free energy released on binding is called the __
binding energy
84
Only the correct substrate can participate in most or all of the interactions with the enzyme and thus __-, accounting for the exquisite substrate specificity exhibited by many enzymes. Furthermore, the full complement of such interactions is formed only when the substrate is converted into the __. Thus, the __ is released when the enzyme facilitates the formation of the __. The energy released by the interaction between the enzyme and the substrate can be thought of as __.
- maximize binding energy
- transition state
- maximal binding energy
- transition state
- lowering the activation energy
85
a state in which the substrate is in an energetically unstable intermediate form, having features of both the substrate and the product
transition state
86
What kinds of transition state changes might occur in the substrate that would make a reaction proceed more rapidly?
1) The enzyme might put “stress” on a bond and thereby promote bond breakage
2) An enzyme may facilitate a reaction by bringing two reactants close to one another and in the proper orientation for the reaction to occur.
3) The active site of an enzyme may modify the pH of the microenvironment surrounding the substrate.
For instance, it may serve as a donor or an acceptor of H+. This would cause a change in the pH in the vicinity of the substrate without disturbing the normal pH elsewhere in the cell.
87
- an enzyme essential for the final stages of viral replication.
- The enzyme cleaves large viral polyproteins into functional components, facilitating the assembly of new virus particles.
HIV protease
88
__ of the normal HIV protease
substrate can be designed and used as candidates as HIV protease inhibitors
structural analogs
89
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. The degree of this is determined by the __.
Enzyme specificity
- active site
90
Types of specificity
- Absolute specificity
- Group specificity
- Linkage specificity
91
the enzyme will catalyze only one reaction. This most restrictive of all specificities is not common. Give examples.
Absolute specificity
- Aminoacyl tRNA synthetases
- Catalase - catalyzes the conversion of hydrogen peroxide (H2O2) to O2 and H2O. Hydrogen peroxide is the only substrate it will accept.
92
the enzyme will act only on molecules that have a specific functional group, such as hydroxyl, amino, or phosphate groups. Give examples.
Group specificity
- Carboxypeptidase is group-specific; it cleaves amino acids, one at a time, from the carboxyl end of a peptide chain.
- Hexokinase catalyzes the addition of a phosphoryl group to the hexose sugar glucose in the first step of glycolysis. Hexokinase can also add a phosphoryl group to several other six-carbon sugars
93
the enzyme will act on a particular type of chemical bond, irrespective of the rest of the molecular structure. This is the most general of the common specificities. Give examples.
Linkage specificity
- Phosphatases - hydrolyze phosphate–ester bonds in all types of phosphate esters.
- Proteases, such as trypsin, chymotrypsin, and elastase, are enzymes that selectively hydrolyze peptide bonds.
94
the enzyme will act on a particular stereoisomer. Chirality is inherent in an enzyme's active site because amino acids are chiral compounds. Give example.
Stereochemical specificity
- An L-amino acid oxidase will catalyze the oxidation of the L-form of an amino acid but not the D-form of the same amino acid. Because we use only D-sugars and L-amino acids, the enzymes involved in digestion and metabolism recognize only those particular stereoisomers.
95
a measure of the rate at which an enzyme converts substrate to products in a biochemical reaction.
Environmental effects: Factors that affect enzyme activity include:
Enzyme activity
(1) Temperature
(2) pH
(3) substrate concentration, and
(4) enzyme concentration
96
a measure of the kinetic energy (energy of motion) of molecules.
At higher temperatures, molecules are moving __ and __ more frequently. This concept applies to collisions between substrate molecules and enzymes. As the temperature of an enzymatically catalyzed reaction increases, so does the __.
Temperature
- faster
- colliding
- rate (velocity) of the reaction
97
Beyond the optimum T, the increased energy begins to cause disruptions in the tertiary structure of the enzyme
denaturation
98
For human enzymes, the optimum temperature is around 37°C, normal body temperature. A person who has a fever where body core temperature exceeds 40°C can be in a life-threatening situation because such a temperature is sufficient to initiate enzyme __.
denaturation
99
The “destroying” effect of temperature on bacterial enzymes is used in a hospital setting to __ medical instruments and laundry. In high-temperature, high-pressure vessels called __, super-heated steam is used to produce a temperature sufficient to denature bacterial enzymes.
- sterilize
- autoclaves
100
Although instruments can be sterilized by dry heat (160°C) applied for at least 2 hours (h) in a dry air oven, autoclaving is a quicker, more reliable procedure. The autoclave works on the principle of the __. __ is pumped out of the chamber, and __ under pressure is pumped into the chamber until a pressure of __ atmospheres (atm) is achieved. The pressure causes the temperature of the steam, which would be 100°C at atmospheric pressure, to rise to __. Within 20 minutes (min), all the bacteria and viruses are killed.
- pressure cooker
- Air
- steam
- 2
- 121°C
101
the pH at which an enzyme exhibits maximum activity.
The charge on acidic and basic amino acids located at the active site depends on pH. Small changes in pH (less than one unit) can result in __ and subsequent __ of catalytic activity.
__ help maintain the optimum pH for an enzyme.
Optimum pH
- enzyme denaturation
- loss
- Biochemical buffers
102
* Optimum pH usually falls within the physiological pH range of __.
* Exceptions: __, which is active in the stomach, functions best at a pH of 2.0. On the other hand, __, which operates in the small intestine, functions best at a pH of 8.0. The amino acid sequences present in them are those needed such that the R groups present can maintain __ at low (2.0) and high (8.0) pH values, respectively.
- 7.0–7.5
- Pepsin
- trypsin
- protein tertiary structure
103
* At pH outside the optimum, __ or __ of groups on the substrate could also take place. The interaction between the altered substrate and the enzyme active site may be __ than normal—or even __.
* An interesting bacterial adaptation to an acidic
environment occurs within the __.
- protonation
- deprotonation
- less efficient
- impossible
- human stomach
104
These acidic conditions significantly reduce the enzymatic activity of any __ present in pickled foods
harmful microorganisms
105
* Many years prior to the discovery of the causal
agent, stomach and duodenal ulcers were thought to be due to __, __ and __, among others.
* __, a clinical pathologist who had examined many stomach biopsy specimens noticed a parallel between the severity of the __ and the number of __ present.
* In 1981, he met __, a trainee doctor. Marshall was looking for a research topic and learned that Warren had a list of patients whose gastric biopsies showed “curved” bacteria.
- excess stomach acid
- emotional stress
- spicy food
- J. Robin Warren
- inflammation
- bacteria
- Barry James Marshall
106
* Marshall was unsuccessful in developing an
animal model, so he decided to experiment upon __. In 1984, following a baseline endoscopy which showed a normal gastric mucosa, he drank a __. Three days later he developed nausea and achlorhydria (absence of hydrochloric acid in the gastric secretions). Vomiting occurred and on day 8 a repeat endoscopy and biopsy showed marked gastritis and a positive __. At day 14, a third endoscopy was performed and he then began treatment with __ and __. He recovered promptly and thus had fulfilled Koch’s postulates for the role of H. pylori in __.
- himself
- culture of the organism
- H. pylori culture
- antibiotics; bismuth
- gastritis
107
Professor Marshall and Dr Warren were awarded the __ for their 1982 discovery of “the bacterium Helicobacter pylori and its role in gastritis and peptic ulcer disease.”
2005 Nobel Prize in Medicine
108
How do the enzymes present in the H. pylori bacterium function in the acidic environment of the stomach?
Present on the surface of the bacterium is the enzyme urease, an enzyme that converts urea to the basic substance ammonia. The ammonia then neutralizes acid present in its immediate vicinity; a protective barrier is thus created. The urease itself is protected from denaturation by its complex quaternary structure.
109
-called “suicide bags” because they are membrane-bound vesicles containing about fifty different kinds of __ that degrade large biological molecules into small molecules. If the hydrolytic enzymes of the lysosome were accidentally released into the cytoplasm of the cell, the result would be the __ and __. Because of this danger, the cell invests a great deal of energy in maintaining the integrity of the lysosomal __. An additional protective mechanism relies on the fact that lysosomal enzymes function optimally at an acid pH (pH 4.8). Should some of these enzymes leak out of the lysosome or should a lysosome accidentally rupture, the cytoplasmic pH of 7.0-7.3 renders them inactive.
Lysosomes
- hydrolases
- destruction of cellular macromolecules
- death of the cell
- membranes
110
The enzyme-catalyzed reaction must occur in two stages:
1. The formation of an enzyme-substrate complex. This binding of the substrate to the active site of the enzyme is a rapid step.
2. Conversion of substrate into product and release of the product and enzyme. This step is slower and limits the rate of the overall reaction.
111
An enzyme’s __ is the number of substrate molecules transformed per minute by one molecule of enzyme under optimum conditions of temperature, pH, and saturation.
turnover number
112
Because enzymes are not consumed in the reactions they __, the cell usually keeps the number of enzymes __ compared with the number of substrate molecules. This is efficient; the cell avoids paying the __ of synthesizing and maintaining a large workforce of enzyme molecules. Thus, in general, the concentration of substrate in a reaction is much __ than that of the enzyme.
- catalyze
- low
- energy costs
- higher
113
If the amount of substrate present is kept constant and the enzyme concentration is __, the reaction rate __ because more substrate molecules can be accommodated in a given amount of time.
- increased
- increases
114
immediate species that provide an alternative pathway, with lower activation energy, through which a reaction can occur
enzyme-substrate complex
115
- the active site has a fixed geometric shape
- only a substrate with a matching shape can fit into it
lock-and-key model
116
- the 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
induced-git model
117
factors that affect the rate of enzyme activity
- temperature
- pH
- concentration of substrate
- concentration of enzyme
118
Reaction rate increases with ___ until the point at which the protein is denatured and activity drops sharply.
temperature
119
Maximum enzymatic activity is possible only within a narrow __ range; outside this __ range, the protein is denatured, and activity drops sharply
- pH
- pH
120
reaction rate increases with __ until full saturation occurs; then rate levels off.
substrate concentration
121
reaction rate increases with increasing __, assuming __ is much lower than that of the substrate
enzyme concentration; enzyme concentrations
122
a microorganism that thrives in extreme environments, environments in which humans and most other forms of life could not survive.
- environments include the hydrothermal areas of Yellowstone National Park and hydrothermal vents on the ocean floor where temperatures and pressures can be extremely high.
extremophiles
123
1. __ (optimal growth at pH levels of 3.0 or below)
2. __ (optimal growth at pH levels of 9.0 or above)
3. __ (high salinity, a salinity that exceeds 0.2 M NaCl needed for growth),
4. __ (a temperature between 80°C and 121°C needed to thrive)
5. __ (a high hydrostatic pressure
needed for growth)
6. __ (extremely dry conditions needed for growth)
7. __ (a temperature of 15°C or lower needed for growth).
1) Acidophiles
2) alkaliphiles
3) halophiles
4) hyperthermophiles
5) piezophiles
6) xerophiles
7) cryophiles
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The enzymes present in extremophiles are called __. An __ is a microbial enzyme active at conditions that would inactivate human enzymes as well as enzymes present in other types of higher organisms.
- extremozymes
- extremozyme
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Because industrial processes usually require higher temperatures and pressures than physiological processes, __ have characteristics that have been found to be useful.
* The enzymes present in some detergent formulations, which must function in __, are the result of research associated with high-temperature microbial enzymes. Similarly, __ laundry detergents contain enzymes originally characterized in cold environment microbial organisms.
- extremozymes
- hot water
- cold water-wash
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The development of commercially useful enzymes using extremophile sources involves the following general approach:
1. Samples containing the extremophile are gathered from the extreme environment where it is found.
2. DNA material is extracted from the extremophile and processed.
3. Macroscopic amounts of the DNA are produced using the polymerase chain reaction (PCR).
4. The macroscopic amount of DNA is analyzed to identify the genes present that are involved in extremozyme production.
5. Genetic engineering techniques are used to insert the extremozyme gene into bacteria, which then produce the extremozyme.
6. The process is then commercialized.
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Regulation of enzyme activity within a cell is a necessity for many reasons; mainly due to __ (If the cell runs out of __, it will die).
Illustrations:
1. A cell that continually produces large amounts of an __ for which __ is always very low is wasting energy. The production of the __ needs to be “turned off.”
2. A product of an __ that is present in plentiful (more than needed) amounts in a cell is a waste of energy if the enzyme continues to catalyze the reaction that produces the product. The enzyme needs to be “turned off.”
- energy conservation
- chemical energy
- enzyme; substrate concentration
- enzyme
- enzyme-catalyzed reaction
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mechanisms by which enzymes within a cell can be “turned on” (3)
(1) feedback control associated with allosteric enzymes
(2) proteolytic enzymes and proenzymes/zymogens
(3) covalent modification
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Characteristics of allosteric enzymes
1. All allosteric enzymes have __; that is, they are composed of two or more protein subunits.
2. All allosteric enzymes have two kinds of binding sites: those for __ and those for __.
3. __and __ binding sites are distinct from each other in both __ and __. In most cases, the one is on one protein chain and the other is on another.
4. __ at the regulatory site causes changes in the overall three-dimensional structure of the enzyme, including structural changes at the active site
- quaternary structure
- substrate
- regulators
- Active; regulatory
- location; shape
- Binding of a molecule
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- In allosteric enzymes, One product can function as a __ by fitting into the effector binding site.
- Binding of the effector in the effector binding site causes a __ of the enzyme that closes the active site and inactivates the enzyme.
- negative feedback effector
- conformational shift
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__ is not the only mechanism by which an allosteric enzyme can be regulated; it is just one of the more common ways. Regulators of a particular allosteric enzyme may be products of entirely different pathways of reaction within the cell, or they may even be compounds produced outside the cell (hormones).
Feedback control
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___– an inactive form of enzyme; converted by __ (hydrolysis of the protein) to the active form when it has reached the site of its activity. Give examples.
- Proenzyme or zymogen
- proteolysis
- digestive and blood-clotting enzymes
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proenzymes of the digestive tract and their activator and enzyme
1. proelastase - trypsin - elastase
2. trypsinogen - trypsin - trypsin
3. chymotrypsinogen A - trypsin + chymotrypsin - chymotrypsin
4. pepsinogen - acid pH + pepsin - pepsin
5. procarboxypeptidase - trypsin - carboxypeptidase A, carboxypeptidase B
134
__ is a process in which enzyme activity is altered by covalently modifying the structure of the enzyme through __ of a chemical group to or __ of a chemical group from a particular amino acid within the enzyme’s structure.
Covalent modification
- attachment
- removal
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* The most common type of protein modification is __ or __ of an enzyme.
* Typically, the phosphoryl group is added to (or removed from) the R group of a __, __, or __ in the protein chain of the enzyme. Notice that these three amino acids have a free —OH in their R group, which serves as the site for the addition of the phosphoryl group.
* For some enzymes, the active (“turned-on” form) is the __ of the enzyme (e.g. triacylglycerol lipase); however, for other enzymes, it is the __ that is active (e.g. glycogen synthase).
- phosphorylation (by protein kinases)
- dephosphorylation (by phosphatases)
- serine, tyrosine, or threonine
- phosphorylated version
- dephosphorylated version
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chemicals that can bind to enzymes and either eliminate or drastically reduce their catalytic ability.
Enzyme inhibitors
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Give examples of enzyme inhibitors and their functions
* arsenic - binds to the thiol groups of cysteine amino acids in the proteins, interfering with the formation of disulfide bonds needed to stabilize the tertiary structure of enzymes
* Penicillin - inhibits several enzymes that are involved in the synthesis of bacterial cell walls
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Three (3) modes of inhibition:
(1) irreversible inhibition
(2) reversible competitive inhibition
(3) reversible noncompetitive inhibition
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Irreversible enzyme inhibitors
* In general, such inhibitors do NOT have structures similar to that of the enzyme’s normal substrate.
* Usually bind very tightly, sometimes even covalently, to the enzyme. This generally involves binding of the __ to one of the __ of an amino acid in the active site. Inhibitor binding may __ the active site binding groups so that
the __ cannot form.
* Alternatively, an inhibitor may interfere with the __ of the active site, thereby effectively eliminating catalysis.
* Irreversible inhibitors, which include __ and __, generally inhibit many different enzymes.
- inhibitor
- R groups
- block
- enzyme-substrate complex
- catalytic groups
- snake venoms; nerve gases
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* The neurotransmitter __ is released following a nerve impulse
* It diffuses across the __ (the space between the nerve and muscle cells) and binds to the __ in the postsynaptic membrane of the muscle cell
* __ and __ then flow into and out of the cell, respectively. This generates the nerve impulse and causes the __.
- acetylcholine
- nerve synapse
- acetylcholine receptor protein (R)
- Na+; K+ ions
- muscle to contract
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The transmission of nerve impulses at the __ involves many steps, one of which is the activity of a critical enzyme, called __, which catalyzes the hydrolysis of the chemical messenger, __, that initiated the nerve impulse.
- neuromuscular junction
- acetylcholinesterase
- acetylcholine
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- Inhibitors of acetylcholinesterase are used both as poisons and as drugs. Among the most important inhibitors of acetylcholinesterase are a class of compounds known as __. One of these is the nerve agent __ that forms a covalently bonded intermediate with the active site of acetylcholinesterase. Thus, it acts as an __
- The covalent intermediate is stable, and acetylcholinesterase is therefore inactive, no longer able to break down __. Nerve transmission continues, resulting in __. Death may occur as a result of __. Antidotes for poisoning by organophosphates, which include many insecticides and nerve gases, have been developed. The antidotes work by __ the effects of the inhibitor. One of these antidotes is known as PAM, an acronym for __. This molecule displaces the organophosphate group from the active site of the enzyme, alleviating the effects of the poison.
- organophosphates
- Sarin (isopropylmethylfluorophosphate)
- irreversible, noncompetitive inhibitor
- acetylcholine
- muscle spasms
- laryngeal spasm
- reversing
- pyridine aldoxime methiodide
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Two types: (a) Reversible competitive inhibitors:
* often referred to as __; that is, they are molecules that resemble the structure and charge distribution of the natural substrate for a particular enzyme. Because of this resemblance, the inhibitor can occupy the enzyme active site. However, no reaction can occur, and enzyme activity is inhibited.
* This inhibition is __ because the inhibitor and the substrate compete for binding to the enzyme's active site.
* The degree of inhibition depends on their __. If the inhibitor is in excess or binds more strongly to the active site, it will occupy the active site more frequently, and enzyme activity will be greatly decreased.
- structural analogs
- competitive
- relative concentrations
144
__ is a vitamin required for the transfer of methyl groups in the biosynthesis of methionine and the nitrogenous bases required to make DNA and RNA. Humans cannot synthesize __ and must obtain it from the diet. __, on the other hand, must make it because they cannot take it in from the environment.
__ (PABA) is the substrate for an early step in it synthesis.
If the correct substrate (PABA) is bound by the enzyme, the reaction occurs, and the bacterium lives. However, if the __ is present in excess over PABA, it binds more frequently to the active site of the enzyme. No __ will be produced, and the bacterial cell will __.
In addition to it being supplied in our diets, we obtain it from our __.
- Folic acid
- folic acid
- Bacteria
- para-Aminobenzoic acid (PABA)
- sulfa drug
- folic acid
- die
- intestinal bacteria
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The __, the first antimicrobics to be discovered, are competitive inhibitors of a bacterial enzyme needed for the synthesis of the vitamin folic acid.
- the prototype of which was discovered in the 1930s by __, are structural analogs of PABA and thus __ of the enzyme
that uses PABA as its normal substrate.
- sulfa drugs (sulfonamide)
- Gerhard Domagk
- competitive inhibitors
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- The formation of an enzyme–competitive inhibitor complex is a __ because it is maintained by __. With time (a fraction of a second), the complex breaks up.
- The empty active site is then available for a __. Substrate and inhibitor again compete for the empty active site.
- Thus the active site of an enzyme binds either inhibitor or normal substrate on a random basis. If inhibitor concentration is __ than substrate concentration, the __ the occupancy process. The reverse is also true. Competitive inhibition can be reduced by simply increasing the __.
- reversible process
- weak interactions (hydrogen bonds, etc.).
- new occupant
- greater
- inhibitor dominates
- concentration of the substrate
147
A __ is a molecule that decreases enzyme activity by binding to a site on an enzyme other than the active site. The substrate can still occupy the active site, but the presence of the inhibitor causes a change in the __ of the enzyme sufficient to prevent the catalytic groups at the active site from properly effecting their catalyzing action.
noncompetitive enzyme inhibitor
- structure
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Examples of non-competitive inhibitors include the __. The binding sites for these ions are __ (—SH; also called __) groups located away from the active site. __ are formed, an effect that disrupts secondary and tertiary structure.
Unlike the situation in competitive inhibition, __ the concentration of substrate does not completely overcome the inhibitory effect in this case.
- heavy metal ions Pb2+ (lead ion), Ag+ (silver ion), and Hg2+ (mercury ion)
- sulfhydryl
- thiol
- Metal sulfide linkages
- increasing
149
The specificity of __ depends upon the presence of a __, a cluster of hydrophobic amino acids brought together by the three-dimensional folding of the protein chain. The flat aromatic side chains of certain amino acids (tyrosine, tryptophan, phenylalanine) slide into this pocket, providing the binding specificity required for catalysis at the catalytic site
These enzymes are called __ because they have the amino acid serine in the catalytic region of the active site that is essential for the __ of the peptide bond.
- chymotrypsin
- hydrophobic pocket
- serine proteases
- hydrolysis
