BIOCHEM - Enzyme Flashcards
organic catalysts where their main function is to speed up metabolic functions in the body.
Enzymes
reaction formula for enzyme
A + B ⇌ P+ Q
formula for forward reaction
A + B to P+Q
formula for backward reaction
P + Q to A+B
symbol is used to denote an equilibrium;
means the forward reaction is equivalent to backward reaction.
⇌
what does A + B ⇌ P+ Q mean
There’s no net of formation of either A+B and P+Q; hence, they are in equilibrium.
symbol used to denote a net forward reaction.
→
formula that shows The predominant is the forward reaction or the formation of P+Q.
A+B → P+Q
portion of the total energy in the system that is available for work
Free energy, ∆G
formula for free energy (Gibbs free)
∆G = ∆H - T∆S
∆G = ∆H - T∆S meaning:
∆G (Gibbs free) is equal to ∆H (Enthalpy) total internal energy MINUS Temperature (T) multiplied by Entropy (∆S)
“heat”, equal to the total change in the
internal energy of the system
Enthalpy, ΔH
extent of disorderliness/randomness of the
system;
becomes maximum(100%) as equilibrium (forward reaction is equal to the reverse reaction) is approached
Entropy, ΔS
∆G = 0 means
Equilibrium, no net change takes place
the forward and backward reactions are equal
“Exergonic”, spontaneous
Product of temperature and entropy is bigger than enthalpy. It gives off energy
∆G ‹ 0 (negative)
“Endergonic”, nonspontaneous
Takes in energy
∆G › 0 (positive)
The downhill movement of the ball is considered ___________ because the starting ball would have a higher energy compared to the end ball.
spontaneous
the energy that must be overcome in order for the reaction to proceed
regardless if it is spontaneous (exergonic) or nonspontaneous (endergonic)
activation energy
the energy of the reactants is higher than the energy of products
exergonic (energy release)
activation energy for reaction proceeds rapidly
low activation energy
activations energy that cause slow reaction
high activation energy
between endergonic and exergonic reactions, which among the two energies of their reactants are far from the activation energy?
Endergonic, because the initial energy of the reactant in exergonic is already high enough that it only needs a small amount of energy
to reach the activation energy as compared to the endergonic reaction.
reactants are at a lower free energy level than the products
endergonic
energy of the products is lower, and the difference in the energy of reactants and products are being release
exergonic reaction
If the reactants are at a lower free energy level than the products
endergonic
If the free energy level of the reactant is higher than the product
exergonic (spontaneous) (energy release)
in exergonic reaction but the energy release is in the form of HEAT.
Exothermic
endergonic reactions that would take up heat
endothermic
FACTORS AFFECTING REACTION RATES:
- TEMPERATURE
- REACTANT CONCENTRATION
- PRESENCE OF CATALYSTS (e.g Enzymes)
If we increase the temperature, the ________ will become faster.
reaction rate
Increase in temperature would result to increase in __________________
The molecules will move faster.
kinetic energy
energy during motion
Kinetic energy
in a chemical reaction, the products will be formed if the molecules of the substrate will collide.
Circulation Theory
One way of increasing the collision in between your substrate molecules will be to increase the _________
movement of the molecules
increase in the concentration of the substrate, would increase the ______ in between the molecules
- Thereby, facilitating in the formation of the product
collision
Ratio of the concentrations of products and reactants
Keq, Equilibrium Constant
It gives as an idea whether the favored reaction occurring is the forward or the backward reaction. (If it is the formation of the products or formation of the reactants is favored).
Keq, Equilibrium Constant
formula of Keq, Equilibrium Constant
Products [P] [Q] over Reactants [A] [B]
(molar concentrations in the bracket)
speeds up the reaction
catalysts
will lower the activation energy (pile of stones in the figure) thereby, facilitating the reaction
enzymes
Proteins that would speed up chemical reactions and are not used up during chemical reactions they catalyzed
ENZYMES
Two steps for enzyme to catalyze:
- They must bind to substrate.
- They would facilitate the catalysis known as the catalytic step.
During the ___________, bonds are being formed or broken.
- Products will then be produced
catalytic steps
steps on enzyme-substrate binding:
a. Substrate Binding (enzymes will bind to the substrate
b. Enzyme-Substrate Complex (catalytic step will occur)
c. Product is formed
d. Product detaching from the enzyme
Portion of enzyme which folds to precisely fit the contours of a substrate via weak electrostatic interactions & facilitates bond reactivity
Active site
Portion of the enzyme where it directly binds to the substrate
Active site
Active sites are _________: it can only bind certain type of substances
- examples are the enzymes that
specifically bind only to hexoses, or
glucose, etc. - e.g., if it binds to glucose, it could not
bind to another monosaccharide
specific
THEORIES ON ENZYME-SUBSTRATE BINDING:
- Lock-and-Key Model
- Induced fit Model
The enzyme’s active site fits the substrate perfectly.
- When the enzyme approaches the substrate, there is already an initial perfect fit between the substrate and the enzyme’s active site.
Lock-and-Key Model
This explains why enzymes are specific when it comes to substrate.
If this enzyme is acting on a protein, any other molecule that isn’t a protein (e.g., Carbohydrate) would not fit the active site and therefore would not be acted upon by the enzyme.
Lock-and-Key Model
limitation of Lock-and-Key Model:
enzymes are very rigid,
1 enzyme: 1 substrate
This is far from the truth because enzymes are proteins and proteins are FLEXIBLE molecules.
Although they are specific when it comes to substrate, they are not really that specific. As long as the substrates are interrelated to one another, enzymes can still act upon it
Lock-and-Key Model
if we follow this model, it would mean that your enzyme should be rigid, should not change its conformation.
- Aside from that, there are enzymes that can bind to several substrates (e.g., hexoses can bind to glucose, galactose, and fructose)
Lock-and-Key Model
This is NOT the best model to explain the enzyme-substrate binding!
Lock-and-Key Model
Enzyme-substrate binding will be explained by:
Induced fit Model
Initially, there is no perfect fit between the active site and the substrate.
Induced fit Model
When the enzyme approaches the substrate, the substrate induces a change in the active site so complementarity will be achieved –
_____________ – eventually achieving a perfect fit
conformational change
Modification of the lock-and-key model.
Induced fit Model
the substrate can change the enzyme by inducing a conformational change in the _________
active site
Also implies that the enzymes can change the substrate by acting on it and turning it to a product
Induced fit Model
example of Induced fit Model
Proteases - Act on a variety of proteins. -Proteins are interrelated to one another structurally
Only made up of protein.
SIMPLE ENZYMES
Small, inorganic, metal ions that are required of some enzymes to activate them.
Metal ions: Cu, Mg, Mn, Fe
- Usually located near the active site
-Helps in binding to the substrate
CO-FACTORS
Act as activators and/or inhibitors of activity
Example: Mg++ stabilizes the carbonyl oxygen in the phosphoenol pyruvate to allow the enzyme enolase to act on it; Mg++ participates in the catalytic activity.
CO-FACTORS
Big, non-protein, organic molecules that are required of some enzymes to activate them.
- Function same with the cofactors.
- Activate or inhibit enzymes.
- Not metallic ions
CO-ENZYME
Participates in binding to the substrate.
Binds to the active site to prepare the active site for substrate binding.
CO-ENZYME
CO-ENZYME Help catalyze reactions by:
- Donate/accept electrons
- transfer group
- Form/break covalent bonds
- Provide functional groups
Common co-enzymes:
- Lipoic acid
- NAD/NADP, FAD
- CoASH
- Vitamins
Lipoic acid :
Decarboxylate alpha-keto acid
NAD/NADP, FAD :
- Redox reaction
- Transfer of electrons
- Dehydrogenation
- Transfer of H+
CoASH:
- Kreb’s Cycle
- Beta oxidation
Vitamins:
- The body needs vitamins such as ascorbic acid, cyanocobalamin and folic acid.
- By themselves, they do not provide energy but instead help unlock energy by acting as co enzymes for some metabolic reactions
The entire enzyme together with all the necessary cofactor plus the protein portion.
● The complete enzyme
HOLOENZYME
● Simple enzyme
● Taken out cofactor or coenzyme, only left with the protein
portion
APOENZYME
There are certain cofactors or co-enzymes that are difficult to separate
from the protein portion of the enzyme because they are covalently
bound to the enzyme.
PROSTHETIC GROUPS
example of PROSTHETIC GROUPS
Heme
The structure shown here that is present not just in hemoglobin but in other
enzymes like catalase.
Heme
Factors Affecting Enzyme Activity
- Temperature
- pH
- Substrate concentration
Enzymes are protein and extremes _________ can denatured enzymes
temperature
as the temperature increases initially, the enzymatic activity increases but up to a certain point only, this point termed as _____________
optimal temperature
The enzymatic activity in the human body is about ________.
More than that the enzymatic activity starts to inactivated or denatured
40
Also have an optimum pH
However, each enzymes have their own specific _________
optimum pH
pepsin optimum pH is around pH _____
(acidic)
pH 1
and enzyme in small intestine optimum pH is around pH _____
pH 8
Initially, if substrate concentration increases, the __________ will also increases
enzymatic activity
substrate concentration and enzymatic activity is __________
directly proportional
once reached the maximum velocity,
the enzymatic activity will no longer increase
because the enzymes are already occupied
saturated
A graph that shows the relationship between the concentration of a substrate and the rate of the corresponding enzyme-controlled reaction.
Michaelis-Menten curve
Initially, as you increase the substrate
concentration it is directly proportional to the reaction rate, up to a certain point.
When the enzyme is saturated, further increasing the substrate concentration leads to _____________.
slower reaction rate
Michaelis-Menten curve [S]
concentration of substrate (mol L-1)
Michaelis-Menten curve [V]
initial reaction rate (mol L-1 s-1)
relationship between initial reaction rate V and substrate reaction rate S
Michaelis-Menten equation
Important Parameters in Michaelis-Menten Equation:
Vmax
Substrate concentration [S]
Vi - reaction rate
Km
○ Maximum velocity of the reaction
○ Never be reach by the chemical reaction
○ ½ Vmax or 50% maximum velocity
Vmax
reaction rate
Vi
Michaelis constant
Km
substrate concentration at 50% of maximum velocity Vm
Michaelis constant Km
How to determine the Km Michaelis constant?
get 50% of Vmax plot it against the x-axis or the substrate concentration
A point/substrate concentration wherein the
reaction is at 50% of the maximum velocity
Michaelis constant Km
the amount of Km if it has low affinity
to the substrate.
Because high substrate concentration results in low saturation
high Km
if the Km is low, the affinity is ______________
at smaller substrate concentration, it immediately reach 50%
50% of the enzyme are already bound
high
- Independent of the reactant concentration
- the reaction rate is constant regardless of how high or low the reactant concentration is.
● Fixed reaction rate of zero reaction rate
Zero reaction rate
Even if we increase the reactant concentration, there is a corresponding increase in the reaction rate
The reaction rate is dependent on the reactant concentration. the more the reactants the more faster the reaction rate
First order reaction
there is a Direct, proportional relationship between reactant concentration and enzyme reaction rate (if we the increased reaction concentration the reaction rate increases)
First order reaction
Plot the reaction of the substrate concentration against the reaction rate. What is obtained is a ____________.
It is a combination of the zero order and the first order
hyperbolic curve
Initially, it follows the first order reaction, mixed, then zero order kinetics becoming independent of the reactant concentration upon reaching the Vmax
Michaelis-Menten Curve
Enzyme with ____________ Km is easily saturated because of its high affinity
Low Km
high affinity enzyme get the substrate resulting into:
easy saturation
the Vmax of low Km high affinity is:
slower compared to high Km low affinity
Michaelis Menten curve converted into linear graph:
1/Vi = (Km/Vmax)1/[S] + 1/Vmax
a double reciprocal (fraction) of each point of Michaelis Menten curve making it into linear function called ___________
Lineweaver-Burke plot
Y= mx + b in algebra means:
y= value of Y in Y-axis
m= slope
x= value of x in x-axis
b = point of intersection (y-intercept)
In Lineweaver Burk plot, Y= mx + b means:
Y = reciprocal of initial velocity (1/Vi)
m = slope (Km/Vmax)
x = 1/[S]
d = 1/Vmax
X intercept = (-1/km) or negative reciprocal of km
is important because it gives an idea of the
different mechanisms of enzyme inhibitors.
Lineweaver Burke plot
Enzyme inhibitors:
Competitive inhibitor
noncompetitive inhibitor
Uncompetitive inhibitor
1/Vmax is not affected. Constant. (down in the point of intersection between the two lines)
X intercept (-1 / Km) is increased (from negative 1/3 to negative 1/4)
Competitive inhibitor
decrease the affinity of the enzyme to the substrate without affecting the overall maximum velocity Vmax of the reaction
increase Km
Competitive inhibitor
Reversible inhibitor because when further increase the amount of substrate, the inhibitor can be bumped off from
the active site.
Competitive inhibitor
The substrate and the inhibitor compete for the same binding site which is the active site.
If it is the substrate that binds to the enzyme, well and good.
if it is the inhibitor that binds the enzyme, this turns the enzyme inactive. “banked off”
this is a ___________ type of inhibition
reversible type of inhibition
in competitive inhibition, inhibitors often resemble the substrate structurally, they
are said to _____________.
molecular analogous
Affinity is not affected
-1 / Km is constant
Vmax is decreased
Noncompetitive inhibitor
It lowers down the overall reaction rate but it will not affect the affinity of the substrate to the enzyme
Noncompetitive inhibitor
Noncompetitive inhibitor are not competing with the same binding site.
the substrate binds to the active site, the inhibitor binds to another site called the ______________________ (site other than the
active site)
allosteric site
both EI and EIS complexes are enzymatically inactive
Allosteric site causes a conformational change to the active site inhibiting the substrate from binding to the active site
causing the reaction rate to decrease
Noncompetitive inhibitor
Occurs when the inhibitor binds only to the ES complex to form the EIS complex
Inhibition is irreversible
Uncompetitive inhibition
Vmax decreased
Km decreased
increase the affinity of this substrate
to the enzyme
Uncompetitive inhibitor
irreversible inhibitors:
Noncompetitive inhibitor
Uncompetitive inhibitor
