ENZYMES Flashcards
1
Q
all reactions in our body are mediated by
A
ENZYMES
2
Q
are protein that catalyzes and increases reactions without being changed in the overall process
A
ENZYMES
3
Q
among the many biological reactions that are energetically possible, enzyme selectively channel ____
A
REACTANTS which are referred to as SUBSTRATES
4
Q
direct all metabolic events
A
ENZYMES
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
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
7
Q
GLUCOSE molecular formula
A
C6H12O6
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
9
Q
first used the term enzyme, which literally means “in yeast”
1878, GERMAN PHYSIOLOGIST
A
WILHELM KUHNE
10
Q
the word enzyme literally means
A
“IN YEAST”
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
12
Q
when did Eduard Buchner received a nobel prize in biochemical research & his discovery of cell free fermentation
A
1907
13
Q
Essential for breakdown of nutrients that are used to supply energy and chemical building blocks.
A
ENZYMES
14
Q
TRUE OR FALSE
most enzymes are proteins
A
TRUE
15
Q
one of the most important role of an enzyme
A
CATALYSIS
16
Q
most enzymes are proteins except
A
RIBOZYMES
17
Q
are nucleic acids but act as enzymes
A
RIBOZYMES
18
Q
structurally, most of the enzymes are
A
GLOBULAR
19
Q
considered as the most efficient catalyst known
A
ENZYMES
20
Q
enzymes can speed the rate of reaction by a factor up to
A
10, 20
more than a thousand folds
21
Q
non enzymatic catalyst typically enhance the rate of the reaction by factors of
A
10, 10
22
Q
the substance wherein the enzymes act upon
A
SUBSTRATE
23
Q
has a specific geometric shape wherein specific substrate would fit in
A
ACTIVE SITE
24
Q
The basic function of an enzyme
A
INCREASE THE RATE OF A REACTION
25
Most enzymes act **specifically** with **how many reactant** (called a **substrate**) to **produce products**
ONLY ONE
26
enzymes are **regulated** from a state of what activities
low to high and vice versa
27
the **minimum energy** needed to start a chemical reaction
ACTIVATION ENERGY
28
# WITH OR WITHOUT ENZYME
**higher** activation energy is needed
WITHOUT ENZYME
29
# WITH OR WITHOUT ENZYME
**lower** activation energy is need
WITH ENZYME
30
Enzyme that is capable of **hydrolyzing** or **breaking down lactose** to form **glucose** & **galactose**
LACTASE
31
Most genetic disorders are due to a **deficiency** in
ENZYME FUNCTION
32
a **hereditary** disease that is caused by the **lack** of a **liver** enzyme **phenylalanine hydroxylase**.
PHENYLKETONURIA
pku
33
**Phenylektonuria** is caused by the lack of what enzyme
PHENYLALANINE HYDROXYLASE
34
if **nawala** si phenylalanine hydroxylase, what set of enzyme would take effect
TRANSAMINASE
35
**transaminase** will lead to the accumulation of a substance known as
PHENYLPYRUVIC ACID
36
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***.
PHENYLALANINE
37
ratio of the case of pku
1:150,000
38
* **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**)
PHENYLKETONURIA
39
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
PHENYLKETONURIA
40
in **testing pku**, reaction is needed to be checked within **how many hours** after taking the milk
24 hours
41
to **ensure** the test for pku, **how many days** should the baby be **retested** to catch earlier false negatives
7 - 10 days
42
long term effect of pku
irreversible brain damage & mental retardation
43
**treatment** of pku
**elimination** of **phenylalanine** from the diet
44
RA about **newborn screening**
RA 9288
45
Enzymes may **require** a **non-peptide (non-protein) component** as a
COFACTOR
46
The **peptide component** is called
APOENZYME
47
**cofactor** is called
COENZYME
48
**combined functional unit** of **apoenzyme + coenzyme** is called
HOLOENZYME
49
**Cofactors** that are **tightly bound** to the **polypeptide** are called
PROSTHETIC GROUPS
50
an enzyme has what structure
complex 3D structure
51
* Important part of an enzyme.
* The **shape** and the **chemical environment** inside this **permits a chemical reaction to proceed more easily**.
ACTIVE SITE
52
are the **reactants** that are **activated by the enzyme**.
SUBSTRATE
53
* 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.
APOENZYME
54
**inactive** protein
APOENZYME
55
* **nonprotein** portion
* **activates** enzyme
* cofactor
* **binds** specifically to **apoenzyme** to **complete** the **shape** of the **active site**
COENZYME
56
* **active** protein
* capable of performing its job by **catalysis**
* product of apoenzyme + coenzyme
HOLOENZYME
57
* 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.
PROENZYME OR ZYMOGEN
58
**proenzyme** is also known as
ZYMOGEN
59
either one or more **inorganic ions** or **metal ion activator**
COFACTOR
60
**complex organic** or **metalloorganic** molecule
COENZYME
61
the site **other than** the active site
ALLOSTERIC SITE
62
* acts as **transient carriers** of specific functional groups
* Derived from **vitamins**, **organic nutrients**
COSUBSTRATE
63
* 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.
PROSTHETIC GROUPS
64
FMN
Flavin mononucleotide
65
FAD
Flavin adenine dinucleotide
66
enzymes that contain **tightly bound metal ions**
METALLOENZYMES
67
common **suffix** for enzymes
-ase
67
**hydrolyze** proteins
PROTEASES
67
**remove hydrogen** atoms
DEHYDROGENASE
68
catalyze **rearrangement** in **configuration**
ISOMERASE
68
may be added to identify **multiple forms** of an enzyme
ALPHANUMERIC DESIGNATORS
68
# NOMENCLATURE
MODIFIERS used to indicate
* substrate
* source
* regulation
* MOA (mechanism of action)
68
68
names that do not end with -ase
TRIVIAL NAMES
69
69
MAJOR CLASSES OF ENZYMES
| 6
Oxidoreductases
Transferases
Hydrolases
Lyases
Isomerases
Ligases
| OTHILL
69
7th class of enzyme
TRANSLOCASES
69
* Catalyze a variety of **oxidation-reduction** reactions
* Common names include **dehydrogenase**, **oxidase**, **reductase** and **catalase**
OXIDOREDUCTASE
70
* 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)
TRANSFERASE
71
essential for the **synthesis** of **DNA** and **RNA** (polynucleotides)
POLYMERASE
72
* Catalyze **hydrolysis reactions** where a molecule is **split** into two or more smaller molecules by the **addition of water**
HYDROLASES
73
**split** protein molecules
PROTEASES
74
essential for **HIV replication**
HIV PROTEASE
75
plays a major role in **apoptosis**
CASPASE
76
splits **nucleic acids** (DNA & RNA)
NUCLEASES
77
Nucleases can be divided into
**EXO**nuclease
**ENDO**nuclease
78
progressively splits off **single nucleotides** from **one end** of DNA or RNA.
EXONUCLEASE
79
splits DNA or RNA at **internal sites**
ENDONUCLEASE
80
* catalyzes **dephosphorylation** (**removal** of **phosphate groups**).
* Example: **calcineurin** (aka **protein phosphatase 3**)
* Tacrolimus, Sirolimus, Everolimus and Cyclosporin A are the calcineurin inhibitors
PHOSPHATASE
81
* 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**.
LYASES
82
* Catalyze atomic **rearrangements** within a molecule.
* Examples include **rotamase**, **protein disulfide isomerase (PDI)**, **epimerase** and **racemase**
ISOMERASES
83
* Catalyze the reaction which **joins** two molecules
* Examples include **peptide synthase**, **aminoacyl-tRNA synthetase**, **DNA ligase** and **RNA ligase**
LIGASES
84
means that **there is no net change** in the concentrations of the reactants and products
REACTION EQUILIBRIA
85
**Rate enhancements** that enzymes bring about are in the range of ____ **orders of magnitude (MO)**
5 - 17
86
* 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**
REARRANGEMENT OF COVALENT BONDS
87
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.
WEAK, NONCOVALENT
88
* 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**
BINDING ENERGY
89
* 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).
LOCK AND KEY THEORY
90
**Lock & key theory** is first postulated by
EMIL FISCHER
91
* 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**.”
LOCK & KEY HYPOTHESIS
92
An enzyme must be **complementary** to the
REACTION TRANSITION STATE
93
**optimal interactions** (weak interactions) between the enzyme and substrate occur only in the
TRANSITION STATE
94
* 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).
INDUCED FIT THEORY
95
**Induced fit theory** is postulated by
DANIEL KOSHLAND
96
In **induced fit theory**:
enzymes are
REUSABLE
97
In **induced fit theory**:
active site changes
SHAPE
98
This explains the enzymes that can **react with a range of substrates of similar types**.
INDUCED FIT THEORY
99
# 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**
CATALYSIS BY PROXIMITY
100
# 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**
ACID-BASE CATALYSIS
101
# 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).
PROXIMITY
102
# 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.
ORIENTATION
103
# 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**
COVALENT CATALYSIS
104
# 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
METAL ION CATALYSIS
105
# 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.
DESOLVATION
106
# MECHANISMS TO FACILITATE CATALYSIS
**Involvement** of **charged enzyme functional groups** in stabilizing otherwise unstable intermediates in the chemical mechanism can also correctly be called
ELECTROSTATIC CATALYSIS
107
# 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**
CATALYSIS BY STRAIN
108
# MECHANISMS TO FACILITATE CATALYSIS
the **most important rate enhancing mechanism** available to enzymes
CATALYSIS BY STRAIN
109
# 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**.
TRANSITION STATE STABILIZATION
110
# 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**.
INDUCED FIT
111
112
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.
ENZYME KINETICS
113
Describes how **reaction velocity** varies with **substrate concentration**
MICHAELIS MENTEN EQUATION
114
k1, k-1, and k2
RATE CONSTANTS
115
Michaelis constant
(k-1 + k2) / k1
116
# ASSUMPTIONS
**[S] >[E]**, so [ES] at any time is **small**
RELATIVE CONCENTRATIONS OF E & S
117
# 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**
STEADY STATE ASSUMPTION
118
# 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**
INITIAL VELOCITY
119
# 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**
small Km
120
# CHARACTERISTICS OF Km
Reflects **low affinity of E for S** because a **high concentration of S** is needed to **half-saturate** the enzyme
Large Km
121
The **rate of reaction** is ____ to the **enzyme concentration** at **all substrate concentrations**
DIRECTLY PROPORTIONAL
122
# ORDER OF REACTION
**[S] < Km**, the **velocity** of reaction is **roughly proportional** to the **enzyme concentration**
FIRST ORDER
123
# ORDER OF REACTION
**[S] > Km**, the **velocity** is **constant** and **equal** to **Vmax**; the **rate of reaction** is then **independent** of **substrate concentration**
ZERO ORDER
124
* 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**
LINEWEAVER-BURK PLOT
125
**lineweaver-burk plot** is also called
DOUBLE-RECIPROCAL PLOT
126
substance that can **diminish** the **velocity** of an enzyme catalyzed reaction
INHIBITOR
127
* 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**
COMPETITIVE INHIBITION
128
**competitive inhibitors** are also termed as
SUBSTRATE ANALOGS
129
* 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
COMPETITIVE INHIBITION
130
131
# CONSEQUENCES OF COMPETITIVE INHIBITION
At **high levels of substrate** all of the inhibitor is **displaced by substrate**.
Vmax is unchanged
132
# CONSEQUENCES OF COMPETITIVE INHIBITION
**Higher substrate concentrations** are **required** to **reach** the **maximal velocity**.
Km is increased
133
# NONCOMPETITIVE INHIBITION
At **high levels of substrate** the **inhibitor** is **still bound**.
Vmax is decreased
134
# NONCOMPETITIVE INHIBITION
Noncompetitive inhibitors **do not interfere** the **binding** of substrate to enzyme
Km is not changed
135
# FACTORS AFFECTING ENZYME REACTIONS
The **rate of enzyme catalyzed reaction** ____ with **substrate concentration** until a **maximal velocity (Vmax) is reached**
INCREASES
136
# FACTORS AFFECTING ENZYME REACTIONS
The rate of enzyme-catalysed reactions **increases** as the temperature rises to the ____
OPTIMUM TEMPERATURE
137
# FACTORS AFFECTING ENZYME REACTIONS
**Above** a certain temperature, activity begins to **decline** because the enzyme begins to ____
DENATURE
138
Enzymes are usually **damaged** above about **what temperature**
45C
139
example of enzyme that work best at a pH of about **2.0**
GASTRIC PROTEASE
140
molecules that **regulate allosteric enzymes** that bind **noncovalently** at a site **other than the active site**
EFFECTORS
141
# EFFECTORS
**inhibit** enzyme activity
NEGATIVE EFFECTORS
142
# EFFECTORS
**increases** enzyme activity
POSITIVE EFFECTORS
143
* 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**)
HOMOTROPIC EFFECTORS
144
The effector may be **different** from the substrate
HETEROTROPIC EFFECTORS
145
A form that may be **more** or **less active **than the **unphosphorylated** enzyme
PHOSPHORYLATED FORM
146
(**degrades** glycogen)
Glycogen phosphorylase
147
(**synthesize** glycogen)
Glycogen synthase
148
**Alter** the **total population of active sites** rather than influencing the efficiency of existing enzyme molecules
INDUCTION & REPRESSION OF ENZYME SYNTHESIS
149
Enzymes that are needed at **only one stage of development** or **under selected physiologic conditions** are subject to
REGULATION OF SYNTHESIS
150
Enzymes that are in **constant use** are **NOT** regulated by
ALTERING THE RATE OF ENZYME SYNTHESIS
151
a **common form** of enzyme regulation in which the product **inhibits the enzyme**
FEEDBACK INHIBITION
152
enzymes are **most active** at what temperature
OPTIMUM TEMPERATURE
| usually 37C in humans
153
153
enzymes show **little activity** at what temperature
LOW TEMPERATURES
154
enzymes **lose activity** at what temperature as **denaturation occurs**
HIGH TEMPERATURES
155
what is **disrupted** in the structure of enzymes at **high** or **low** **pH**
TERTIARY STRUCTURE
156
* **HMG Coenzyme A reductase** inhibitors
* **lower** serum lipid concentration
STATINS
157
* inhibitors of **viral reverse transcriptase**
* **block replication of HIV**
EMTRICITABINE and TENOFOVIR DISOPROXIL FUMARATE
158
158
**antihypertensive** agents
ACE inhibitors
159
inhibitors of **alanyl alanine carboxypeptidase-transpeptidase**, thus **blocking cell wall synthesis**
Lactam Antibiotics (Penicillin and Amoxicillin)
160
may indicate **tissue damage** accompanied by **increased release of intracellular enzymes**, thus **useful as a diagnostic tool**
ELEVATED ENZYME ACTIVITY
161
**aminotransferase** is also called
GLUTAMATE
162
* 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
ISOENZYMES
163
**isoenzymes** are also called
ISOZYMES
164
present in **more than 5%** in **myocardial** muscles
CK2 (MB)
165
**Creatine kinase** is also called
CREATININE PHOSPHOKINASE (CPK)
166
each **isoenzyme** is a ____ composed of 2 polypeptides
DIMER
167
* Appears approximately **4 to 8 hours** following onset of **chest pain**, and reaches a **peak in activity** at approximately **24 hours**
CK, CREATININE KINASE
168
* 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**
LACTATE DEHYDROGENASE
169
ENZYME INDUCER
**P**henobarbital
**R**ifampicin
**C**arbamazepine
Phenytoin
Griseofulvin
Smoking
Chronic addiction
## Footnote
REMEMBER: **PRC**
170
ENZYME INHIBITOR
Cimetidine
Ketoconazole
Fluconazole
Miconazole
