Enzymes Flashcards
protein that serves some
catalytic function in the body
enzyme
Allow reactions to occur in the
body that would be impossible
otherwise
enzymes
Has a specific substrate, and
this recognizes its substrate
with extremely high specificity
enzyme
lowers the activation
energy of a reaction
catalyst
area in the enzyme
where the substrate will bind to
active site
will bind to the active site
because it has just the right shape
and composition
substrate
enzyme
changes shape slightly once the
substrate inside the active site
what model
induced fit-binding
complex where enzyme changes
shape as substrate binds
enzyme substrate complex
complex where enzyme leaves the
substrate
enzyme products complex
enzyme will end in this suffix
-ase
breaks down lactose into
galactose and glucose
lactase
Type of enzymes (6)
hydrolase
lyase
ligase
transferase
isomerase
oxidoreductase
catalyzes
hydrolysis (separates a
molecule into two pieces)
what kind of enzyme
hydrolase
cleaves covalent
bonds (other than hydrolysis)
what enyzme
lyase
combines two
molecules
ligase
transfers
functional group
transferase
catalyzes
rearrangement
isomerase
transfers
electrons from one molecule
to another
oxidoreductase
an enzyme and
substrate can be this once the
enzyme operates on its substrate
what kind of bond
covalently linked
needs to bind
to the enzyme before it can operate
on the substrate
cofactor/coenzyme
are globular proteins that
serve as catalyst of biochemical
reactions
enzymes
where the
reactant or substrate binds within
the enzyme called the active site
hydrophobic cleft
also known as active
site
catalytic site
eventually dissociates to form the
product and with subsequent
recovery of the enzyme
Enzyme-substrate complex
This process results to a
lower energy of activation (Eα)
hence facilitating a faster
reaction
dissociation of ES complex
this characteristic of
the reaction remains constant as
illustrated below
enthalpy
study of the
velocity of enzymatic reaction
enzyme kinetics
introduced by
Emil Fischer, wherein the enzyme
and its substrate have
complementary, which means the
substrate fit through the enzyme
active site like a key fits into a lock
lock and key model
introduced by
Daniel Koshland, wherein the loose
binding of the substrate into the
active site of the enzymes induces a
conformational change in the active
site that results in a tighter fitting of
the substrate
induced fit model
proposed a systematic
scheme of classifying and naming
enzymes
International Union of Biochemistry (IUB)
Six general classes of enzymes
oxidoreductase
transferase
ligase
lyase
isomerase
hydrolase
transfers
electron by two processes
oxido-reductases
loss of
electron which usually
manifests as increase
in bonding with oxygen
and/or decrease of
bonding with hydrogen
oxidation
gain of
electron which usually
manifests as increase
in bonding with
hydrogen and/or
decrease of bonding
with oxygen
reduction
the
intermolecular transfer of a
chemical group or moiety
what enzyme
transferase
the breakage of
a chemical bond by addition of
water
what enzmye
hydrolases
the breakage of a
chemical bond by without the
addition of water or not
through oxidation-reduction
what enzmye
lyases
the
intramolecular transfer of a
chemical group or bond
rearrangement within the
same molecule
(isomerization)
isomerase
the formation of a
new chemical by joining two or
more molecules together
ligases
identify the enzyme in pics
+1
nonprotein part in
order to function properly
prosthetic group
vitamins
co-enzmyes or co-factors
co-enzymes
minerals or metals
co-enzymes/co-factors?
co-factors
vitamins that serve as
this are the vitamin B complex and
vitamin C, which are all water soluble
vitamins
co-enzymes
minimum amount of
nutrients that should be taken daily
from dietary source or
supplementation
recommended dietary allowance (RDA)
disorder that is the loss of appetite, peripheral neuropathy, fatigue, loss of muscle coordination (ataxia)
beri-beri
milder form of beri-beri
Wernicke-Korsakoff syndrome
inflammation and scaly appearance of skin
scaly dermatitis
inflammation of cracking of lips corner
angular cheilitis
redness and swelling of the thongue
glossitis
characterized by dermatitis, diarrhea, and memory loss (dementia)
pellagra
convulsions, peripheral neuropathy, irritability, depression
neurologic disruptions
numbness and tingling sensation of extremities
megaloblastic anemia paresthesia
inflammation of gums, joint pains, impaired wound healing, weakness
scurvy
scurvy is deficiency of
ascorbic acid
beri beri and wermicle korsaloff syndrome is deficiency of
thiamine
scaly dermatitis and angular cheilitis is a deficiency of
riboflavin
pellagra is a deficiency of
niacin
neurologic disruptions, anemia, glossitis is the deficiency of
pyridoxine
dermatitis, hair loss, muscle pain is due to the deficiency of
biotin
megaloblastic anemia and neurological defects is due to the deficiency of
folic acid
megaloblastic anemia, paresthesia, neurological defects is due to the deficiency of
cobalamin
metals are electrophilic
groups that aid in the functioning of
enzymes
cofactors
Coordinated by certain amino
acid residues in the enzyme
cofactors
Induce by coordination a
specific lock geometry for the
attachment of substrates and
maintenance of the native
conformation of the enzyme
cofactors
Can also activate certain
bonds in the enzyme and/or
substrate to facilitate
catalysis
cofactors
answer cofactor table
+1
states
that every chemical reaction requires
collision between the reactant
particles and a successful reaction
occurs when the colliding particles
are in proper orientation and collides
with sufficient energy
collision theory of reaction
When the substrate bind at the
enzyme’s active site, it
minimizes the energy of
activation and bring the
substrate particles at a proper
orientation during their
collision
collision theory of reaction
wherein the transition state makes
better contacts with the active site of
an enzyme than the substrate, hence,
sufficient binding energy is not
reached until the substrate enters
the transition state
transition state stabilization
classically theorized that
these occurs as the enzyme
somehow causes the substrate
particles to become distorted toward
the transition state
conformational distortion or stain effect
the
enzyme’s active site is also known as
this, which means that it has much
fewer water molecules as compared
to the exterior of the enzyme
hydrophobic pocket or cleft
effect involving
the lowering of local dielectric
constant surrounding the substrate
particles
desolvation effect
Enhances the electrostatic
interactions of the substrate
particles and the enzyme’s
active site
desolvation effect
Prevents the undue reaction of
water molecules to the
substrate to form unwanted
side products
desolvation effect
Charged functional groups
also stabilizes the reaction
intermediates
desolvation effect
the side chain
functional group of several amino
acids can donate or accept proton,
hence facilitating this
acid-base catalysis
the protonation and
deprotonation results to more
reactive intermediates than the
original substrates, hence, the
reaction occurs at a faster rate
cascade
serves as a base catalyst
for the enzyme acetylcholinesterase
histidine
can form between the
substrate and electrophilic or
nucleophilic group amino acid
residue in the enzyme’s active site
transcient or intermediate covalent bond
can also form this
intermediate covalent bond with the
substrate
prosthetic group
in this, serine
residue forms a transient acyl-serine
covalent bond with the protein
substrate to facilitate the catalysis
chymotrypsin
metal ion is tightly
bound (Fe3+, Cu2+, Zn2+)
metallozenymes
metal ion
is loosely bound (Na+, K+, Mg2+, Ca2+)
metal-activated enzyme
metal is
bound in an organic prosthetic group
(such as in Fe2+ in heme)
organometallic enzyme
Metal can perform any of the
following functions (4)
➢ Bind the substrate in specific
orientation or lock geometry
➢ Mediate electron transfer
➢ Electrostatically stabilize or
shield negative charges
➢ Stabilize the transition state
enzymes are
usually localized within a region or
organelle in the cells
compartmentation
degrade worn
out organelles and
biomolecules, are confined
within the lysosomes
hydrolases
pH of this
organelle optimizes the
activity of hydrolases
acidic pH
the
reversible attachment of a chemical
group to specific amino acid residues
in the enzyme may result to its
activation or deactivation
covalent modification
attachment
of phosphate group is
common way of regulating the
activity of an enzyme
phosphorylation
Accomplished by either, cyclic
adenosine monophosphate
(cAMP), cyclic guanosine
monophosphate (cGMP), or
kinase
covalent modification
is attached on
serine, threonine, or tyrosine
residues
phosphate
adds a large
negative charge to the enzyme
that changes its conformation.
This leads to an increase or a
decrease in the activity of the
enzyme.
phosphate
noncovalent
bonding of small molecules called
effectors to sites in the enzymes
other than the active site
allosteric regulation
Interaction induces
conformational changes that
activate or deactivate the
enzyme
allosteric regulation
enzymes
that are acted upon by such
effectors, made up of several
subunits that contain various
regulatory sites
allosteric enzymes
deactivation of allosteric
enzyme by one of its products
feedback initiation
removal of
some amino acid residues from an
inactive enzyme to convert it to its
active form
proteolytic modification
inactive forms of
enzymes and proteins
zymogens
inactive enzyme
to form trypsin
trypsinogen
inactive
enzyme to form chymotrypsin
chmotrypsinogen
in
proteolytic modification,
specific acid residues are
removed, and the fragments
are joined by this bridges to
make them functional
disulfide bridges
regulation
of the genes that encode for a
particular enzyme
transcriptional control
can directly or indirectly
affect the expression of these
genes
hormones and growth factor
activates a
series of enzymes and
proteins that ultimately affect
gene expression (regulatory
substance is polar)
cascade pathway
if a
regulatory substance is nonpolar,
it crosses the cell
membrane and binds to this
which passes through the
nucleoplasm and binds
directly to a specific segment
in the dna
cytoplasmic receptors
the active site of
the enzyme is not exactly compatible
with its substrate. Upon entry in the
active site, the enzyme changes in
conformation to make a better fit
with the substrate
induced fit model
Proximity effect in catalysis pertains
to what particular phenomenon?
a. The decrease in the energy of
activation as the substrate
molecules enter the active site of
the enzyme
b. Desolvation effect inside the
active site of the enzyme
c. The increase in local
concentration due to the
exclusion of interfering
substances from the active site
d. The transfer of specific chemical
moiety from the enzyme to the
substrate inside the active site
The increase in local
concentration due to the
exclusion of interfering
substances from the active site
Metal ions are important in proper
functioning of many enzymes. How do
they mediate catalysis?
I. Bind to the substrate in a specific
lock geometry which is the proper
orientation for its reaction
II. Serve as mediator of electron
transfer
III. Stabilize nucleophilic substrate
and associated transition state
conformation
I, II, and III
Enzyme facilitates catalysis by
formation of phosphoester bond with the phosphate group of the substrate.
Which amino acid residue can
facilitate such mechanism of
catalysis?
A. Aspartic acid
B. Serine
C. Glutamine
D. Lysine
Serine
Between ES complex formation and
its dissociation to the enzyme and
products, which is the faster process
and why?
a. Formation of ES complex because
it requires more energy
b. Formation of ES complex is faster
because the substrate can readily
bind to the enzyme
c. Formation of ES complex to the
enzyme and products is faster
because the process requires
less energy
d. The dissociation of ES complex to
the enzyme and products is faster
because the products are less
stable than the substrate
c. Formation of ES complex to the
enzyme and products is faster
because the process requires
less energy
Many nutritional deficiency in B
vitamins are associated with what
symptoms?
I. Neurologic
II. Hematologic
III. Cutaneous
I, II, and III
In the formation of molecule A-B
from reactans A and B, the heat
evolved in the reaction is 175 kJ/mol while the energy of activation is 545
kJ.
Among the given substances,
which one was able to facilitate
catalysis for such reaction?
Addition of substance Z which
resulted to the heat evolved in the
reaction at -175 kJ/mol and
energy of activation at 286 kJ.
Enzyme facilitates catalysis by
formation of ester bond with an
alcoholic substrate. Which amino
acid residues can facilitate such
mechanism of catalysis
a. Ser and Tyr
b. Lys and Arg
c. Cys and Met
d. Glu and Asp
Glutamic Acid and Aspartic Acid
The active site of an enzyme has the
following amino acid residues as
critical mediators of catalysis: Ser-
134, His-347, Tyr-121, and Glu-406.
What are the most likely specific
mechanism of catalysis by these
amino acid residues?
a. Conformational distortion and
electrostatic effect
b. Acid-base catalysis and
electrostatic effect
c. Covalent catalysis and
conformational distortion
d. Covalent catalysis and acid-base
catalysis
d. Covalent catalysis and acid-base
catalysis
According to the Collision Theory of
Reaction, what are the requirements
for the formation of the product from
colliding reactant molecules?
a. The reactants molecules should
collide with the reacting
functionalities facing each other
Why are prosthetic groups essential
for many enzymes?
I. They have organic
components that can facilitate
catalysis by covalent bond
formation
II. They have metal ions that can
serve as electron pair
acceptor
III. They have certain amino acids
residues that can serve as
acid-base catalyst
I and II
All of the following are
characteristics of all enzymes
EXCEPT?
a. Made up entirely of amino acid
residues
b. Water-soluble proteins with
spherical shape
c. Facilitate catalysis without being
consumed in the overall process
d. Amino acid side chains that are
critical for facilitating catalysis
e. Catalytic region that stabilizes the
substrate transition state
a. Made up entirely of amino acid
residues
The classic concept of bond strain is
more correctly described in what
way?
a. Chemical bonds of the substrate
is distorted due to the presence of
metal ions in the vicinity of the
active site
b. Transition state makes better
contact with the enzyme than the
substrate due to stabilization
effect of various moieties in the
active site
c. The election cloud of the
substrate is polarized by more
electronegative moieties in the
active site
d. The transfer of electron from one
chemical moiety to another
results to decrease in steric
hindrance
b. Transition state makes better
contact with the enzyme than the
substrate due to stabilization
effect of various moieties in the
active site
Which of the following is a
mechanism of catalysis by coenzymes?
I. They perform intermediate
covalent bond with the
substrate molecules
II. They polarize bonds because
of their electrophilic nature
III. They facilitate electron
transfer
I and II
FoF1 ATPase is the enzyme that
catalyzes ATP synthesis. The enzyme
itself is deactivated by ATP. What
mode of enzyme regulation is being
exemplified?
a. Proteolytic modification
b. Covalent modification
c. Allosteric modification
d. Compartmentation
covalent modification
Glycogen synthase enzyme is
regulated with the addition of
phosphate group on nine serine
residues. What mode of regulation is
being exemplified?
A. Covalent modification
B. Compartmentation
C. Proteolytic modification
D. Allosteric regulation
E. Transcriptional control
A. covalent modification
Enzyme has an all important histidine
residue in its active site such that
substitution with any other amino
acid would result to the loss of
catalytic activity. What are the
possible mechanisms by which this
histidine residue may facilitate
catalysis?
I. Acting as proton acceptor
II. Forming of covalent bond with
the substrate via an ester
bond
III. Serve as stabilizer of
electrophilic substrate
because of its nucleophilic
character
I and II
All of the following are
characteristics of an enzymes
EXCEPT?
a. Has a complementary shape to its
substrate
b. Found somewhere in the interior of
the enzyme
c. Binding site for many different kinds
of molecules
d. Less water content compared to the
cytoplasm
c. Binding site for many different kinds
of molecules
what is the general equaiton for an enzyme-catalyzed reaction
+1 every turn
formation of
the ES complex is slower and
reversible, hence is said to be this
rate determining step
their
model states that the velocity of the
reaction is measured as a function of
substrate concentration until the
maximum velocity (Vmax) of the
reaction is reached as given in the
equation below:
michaelis menten equation
michaelis menten equation
grade yourself accordingly
reaction rate
constant is known as this, and is
actually a composite of the rate constants of ES complex form
michaelis constant
yields a
hyperbolic curve where Vmax is the
horizontal asymptote of the curve
and KM is the substrate concentration
at one-half the Vmax
michaelis menten plot
value of KM
represents this point of the enzyme
for its substrate which is inversely
proportional to the affinity of the
enzyme for the substrate
saturation point
means a high saturation
point of the enzyme which results
from the low affinity of the enzyme
for the substrate
high KM
means a low saturation
point of the enzyme which results
from the high affinity of the enzyme
for the substrate
low KM
substance that slows
down the rate of reaction by binding to a specific region in the enzyme or
the ES complex
inhibitor
three general types of inhibitors
based on their mode of binding
competitive inhibitor
noncompetitive inhibitor
uncompetitive inhibitor
substrate analogue, which
means that its structure is
closely related to that of the
substrate
competitive inhibitor
competes for the same
region in the active site
of the enzyme with the
substrate
competitive inhibitor
Km value and Vmax value in competitive inhibitor
Vmax = same
Km = higher
have an intersection at
the y-intercept
competitive inhibitor
to counteract the effect
of this inhibitor, its
concentration should
be increased
competitive inhibitor
binds to the site in enzyme
other than the active site
noncompetitive inhibitor
vmax and Km in noncompetitive inhibitor
lower vmax
Km = unchanged
have intersection at the
x-intercept
noncompetitive inhibitor
binds to the enzymesubstrate
complex and
usually occurs for a reaction
with two or more substrate or
products
uncompetitive inhibitor
vmax and Km in uncompetitive inhibitor
Vmax = lower
Km = lower
parallel in the
superimposed
Lineweaver-Burk plots
uncompetitive inhibitor
y = mx + b equivalent
check ppt slides
read ppt slides for post lab
+1
