Enzymes Flashcards
enzymes are…
catalysts of biological reactions; accelerate reactions by millions fold
common features for enzymes and inorganic catalysts:
- Catalyze only thermodynamically possible reactions 2. Are not used or changed during the reaction.
- Don’t change the position of equilibrium and direction of the reaction
- Usually act by forming a transient complex with the reactant, thus stabilizing the transition state
specific features of enzymes:
- Accelerate reactions in much higher degree than inorganic catalysts
- Specificity of action
- Sensitivity to temperature
- Sensitivity to pH
enzymes have an optimum ____ at which they function most efficiently
temperature
enzymes, like all proteins, ____ at high temperature and lose activity
denature
enzymes will denature above ____
45-50 degrees C
most enzymes have temperature optimum of ____
37 degree C
every enzyme has a pH optimum because ionizable amino acids, such as ___, ____, and ____ participate in the catalytic reactions
histamine; glutamate; cysteine
the pH sensitivity of enzymes results from the effect of _______
pH on the ionic charge of amino acid side chains of enzymes
each enzyme has max activity at a particular pH (optimum pH); for most enzymes the optimum pH is ___
7
contain firmly bound metal ions at the enzyme active sites (examples: iron, zinc, copper, cobalt)
metalloenzymes
example of metalloenzyme
carbonic anhydrase contains zinc
coenzymes act as _____; ____, _____ or groups of atoms can be transferred
group-transfer reagents; hydrogen, electrons
classification of coenzymes
metabolite coenzymes (synthesized from common metabolites) and vitamin-derived coenzymes (derivatives of vitamins)
_____ cannot be synthesized by mammals, but must be obtained as nutrients
vitamins
TPP is….
thiamine pyrophosphate; a derivative of thiamine (vitamin B1)
TPP participates in reactions of:
- oxidative decarboxylation, 2. transketo-lase enzyme reactions
PLP is…
pyridoxal phosphate; derived from vitamin B6 family of vitamins
PLP is a coenzyme for enzymes catalyzing _______
reactions involving amino acid metabolism (isomerizations, decarboxylations, transamination)
6 classes of enzymes
oxidoreductases, transferases, hydrolases, lyases (synthases), isomerases, ligases (synthetases)
oxidoreductase enzymes
dehydrogenases, peroxidases, oxidases
transferase enzymes
hexokinase, transaminases
hydrolase enzymes
alkaline phosphatase, trypsin, esterases, peptidases, glycosidases
Lyase (synthase) enzymes
fumarase, dehydratases, pyruvate decarboxylase
isomerase enzymes
Triose phosphate isomerase, phosphogluco-mutase, alanine racemase
ligase (synthetase) enzymes
pyruvate carboxylate, DNA ligase
oxidoreductases
catalyze oxidation-reduction reactions
transferases
catalyze group transfer reactions
hydrolases
Catalyze hydrolysis reactions where water is the acceptor of the transferred group
lyases
Catalyze lysis of a substrate, generating a double bond in a nonhydrolytic, nonoxidative elimination
isomerases
catalyze isomerization reactions
ligases (synthetases)
catalyze ligation, or joining of two substrates; require chemical energy (ex: ATP)
specific region in the enzyme to which substrate molecule is bound
active site
characteristics of active sites
- specificity
- small three dimensional region of the protein
- binds substrates through multiple weak interactions (noncovalent bonds)
- there are contact and catalytic regions in the active site
active site of lysozyme
consists of six amino acid residues which are far apart in sequence
the active site contains _____ and binds substrates through multiple ______
functional groups (-OH, -NH, -COO, etc.); weak interactions (noncovalent bonds)
Fischer theory (lock and key model)
the enzyme active site (lock) is able to accept only a specific type of substrate (key)
specificity of enzymes
absolute, relative, stereospecificity
absolute specificity
one enzyme acts only on one substrate (example: urease decomposes only urea; arginase splits only arginine)
relative specificity
one enzyme acts on different substrates which have the same bond type (example: pepsin splits different proteins)
stereospecificity
some enzymes can catalyze the transformation only substrates which are in certain geometrical configuration, cis- or trans-
One international unit (IU) of enzyme catalyzes conversion of 1 µmol of substrate to product per minute
definition of enzyme activity
the specific activity of an enzyme is a measure of the number of ____ protein
IU/mg
rate of catalysis
At a fixed enzyme concentration [E], the initial velocity Vo is almost linearly proportional to substrate concentration [S] when [S] is small but is nearly independent of [S] when [S] is large
rate rises linearly as ____ and then levels off at ____
[S] increases; high [S] (saturated)
first researchers who explained the shape of the rate curve (1913)
Leonor Michaelis and Maud Menten
During reaction enzyme molecules, E, and substrate molecules, S, combine in a reversible step to form an ______
intermediate enzyme-substrate complex (ES complex)
indicates the speed or efficiency of a reaction
rate constant (k)
In fixed, saturated [S], _____
the higher the concentration of enzyme, the greater the initial reaction rate (this relationship will hold as long as there is enough substrate present)
in a tissue or cell, different chemical agents (______) can inhibit the enzyme activity
metabolites, substrate analogs, toxins, drugs, metal complexes, etc.)
inhibitor (I) binds to an enzyme and prevents the formation of _____ or break it down
ES complex
after combining with enzyme (EI complex is formed) can rapidly dissociate
reversible inhibitors
EI complex is held together by _____ and enzyme is inactive only when bound to inhibitor
weak, noncovalent interactions
3 basic types of reversible inhibition
competitive, uncompetitive, noncompetitive
competitive inhibition
- Inhibitor has a structure similar to the substrate thus can bind to the same active site
- The enzyme cannot differentiate between the two compounds
- When inhibitor binds, prevents the substrate from binding
- Inhibitor can be released by increasing substrate concentration
example of competitive inhibition
benzamidine competes with arginine for binding to trypsin
noncompetitive inhibition
- Binds to an enzyme site different from the active site
- Inhibitor and substrate can bind enzyme at the same time
- Cannot be overcome by increasing the substrate concentration
uncompetitive inhibition
Uncompetitive inhibitors bind to ES not to free E
This type of inhibition usually only occurs in multisubstrate reactions
irreversible enzyme inhibition
very slow dissociation of EI complex
Tightly bound through covalent or noncovalent interactions
irreversible inhibitors
group-specific reagents
substrate analogs
suicide inhibitors
group-specific reagents
react with specific R groups of amino acids
substrate analogs
–structurally similar to the substrate for the enzyme
-covalently modify active site residues
suicide inhibitors
- Inhibitor binds as a substrate and is initially processed by the normal catalytic mechanism then generates a chemically reactive intermediate that inactivates the enzyme through covalent modification
- Suicide because enzyme participates in its own irreversible inhibition
methods of regulation of enzyme activity
allosteric control, reversible covalent modification, isozymes (isoenzymes), proteolytic activation
allosteric enzymes have a second ______distinct from the active site
regulatory site (allosteric site)
allosteric enzymes contain more than one _____
polypeptide chain (they have quaternary structure)
bind noncovalently to allosteric site and regulate enzyme activity via conformational changes
allosteric modulators
2 types of modulators
negative (inhibitor) and positive (activator)
negative modulators
–binds to the allosteric site and inhibits the action of the enzyme
–usually it is the end product of a biosynthetic pathway - end-product (feedback) inhibition
positive modulators
–binds to the allosteric site and stimulates activity
–usually it is the substrate of the reaction
____ attachment of a molecule to an amino acid side chain of a protein can modify activity of enzyme
covalent
common covalent modification of protein activity
phosphorylation of ATP
multiple forms of an enzyme which differ in amino acid sequence but catalyze the same reaction
isoenzymes
isoenzymes can differ in:
kinetics, regulatory properties, the form of coenzyme they prefer, and distribution in cell and tissues
isoezymes are coded by _____
different genes
some ____ are regulated by enzymes that exist in different molecular forms (isoenzymes)
metabolic processes
tetramer (four subunits) composed of two types of polypeptide chains, M and H
lactate dehydrogenase
5 isozymes of LDH
H4 – heart HM3 H2M2 H3M M4 – liver, muscle
high affinity, best in aerobic environment
H4
lowest affinity, best in anaerobic environment
M4
important for diagnosis of different diseases
isoenzymes
many enzymes are synthesized as ____ (zymogens) that are activated by ______
inactive precursors; proteolytic cleavage
_____ only occurs once in the lifetime of an enzyme molecule
proteolytic activation
examples of specific proteolysis
•Digestive enzymes
–Synthesized as zymogens in stomach and pancreas
•Blood clotting enzymes
–Cascade of proteolytic activations
•Protein hormones
–Proinsulin to insulin by removal of a peptide
different enzymes that catalyze sequential reactions in the same pathway are bound together
multienzyme complexes
different activities may be found on a single, multifunctional polypeptide chain
multifunctional enzymes
“channeling” of reactants between active sites; Occurs when the product of one reaction is transferred directly to the next active site without entering the bulk solvent
metabolite channeling
metabolite channeling can greatly _____of a reaction
increase rate
channeling is possible in _____ and _____
multienzyme complexes; multifunctional enzymes
enzymes can be complex or ____, which contain a ____ and a _____ called a ____
holoenzymes; protein part; nonprotein part; cofactor
when enzymes only contain protein, they are called ____
simple
complex or holoenzymes consist of a protein part called the ____ and a nonprotein part called the ____
apoenzyme; cofactor
cofactors can be either ____ or ____
prosthetic groups; coenzymes
prosthetic groups are usually small _____ molecules or atoms that are usually tightly bound to the ____
inorganic; apoenzyme
coenzymes are large ____ molecules that are loosely bound to the _____
organic; apoenzyme
common covalent modification of protein activity
phosphorylation
donor molecule in phosphorylation
ATP
example of modified protein after phosphorylation
glycogen phosphorylase
protein function after phosphorylation
glucose homeostasis, energy transduction
you can make phosphorylation more or less active by _____
adding or removing a phosphate group
