Enzymes Flashcards
What is an enzyme
A highly specific protein that functions as a biological catalyst in order to speed up biochemical reactions
One of the fastest enzymes known is
Carbonic anhydrase
What is enzyme specificity due to?
Precise interactions of substrate with enzyme (precision due to 3D structure of enzyme)
What are the six classes of enzymes
- oxidoreductases
- Transferases
- Hydrolases
- Lyases
- Isomerases
- Ligases
Oxidoreductases
Catalyze oxidation-reduction reactions
- transfer electrons between molecules
ex. lactate dehydrogenase
*these reactions require the coenzyme NAD
Transferases
Catalyze the transfer of functional groups between molecules
-ex. alanine transaminase
Hydrolyases
Catalyze hydrolysis by cleaving molecules by the addition of water
ex. trypsin and pyrophosphatase
Lyases
Catalyze the addition of atoms or functional groups to a double bond OR removes them to form a double bond
ex. fumarase
Isomerases
Catalyze the movement of functional groups within a molecule
~generally the simplest enzymatic reactions as only 1 substrate and 1 product
“iso” = same, so within the SAME molecule
ex. alanine racemase
Ligases
Catalyze bond formation or joining two molecules at the expense of ATP
ex. DNA ligase or glutamine synthetase
What is an enzyme without its co-factor?
An apoenzyme
What is the name of a complete catalytically active enzyme?
A holoenzyme
Co-factors can be:
- small organic molecules derived from vitamins called coenzymes or
- metals
What are tightly bound coenzymes called?
Prosthetic (helper) groups
Enzymes may speed up a chemical reaction but properties of the reaction (for example if it occurs at all) depends on _____
Free energy differences
What is free energy (G)
Measure of useful energy
-the ability to do work
What is the free energy change of a reaction? delta G
Informs us as to whether a reaction can take place spontaneously
A reaction can take place spontaneously is delta G is…
Negative (exergonic)
A reaction cannot take place spontaneously if delta G is…
Positive (endergonic)
When is delta G zero?
At equilibrium there is no net change in concentration of products and reactants, so delta G is 0
T/F delta G provides information about the rate of a chemical reaction
False
Can enzymes alter the equilibrium of a chemical reaction
No
X‡ is?
- an unstable arrangement of atoms – chemical bonds are in the process of being broken or formed
- called a Transition State – it has higher ∆G than does S or P
What is the function of an enzyme?
lower the ∆G‡ OR facilitate the formation of the transition state
What is at the heart of enzyme catalysis
Stabilization of the transition state
Enzyme do’s
- lower the ∆G‡ for the reaction
- Stabilise the Transition State
- Make the forward reaction much more favourable
Active site
- Is a 3D cleft or crevice
- Small part part of the total volume of an enzyme
- The substrates bind to the active site on an enzyme by multiple weak attractions
- Binding specificity depends on precisely defined arrangements of atoms in the active site
Lock and Key Theory
Enzyme is a rigid template (lock) and the substrate is a matching key
- Active site of the enzyme is complementary in shape to the substrate
- This theory says that the active site resides are completely immobile
Induced fit theory
This theory takes the flexible nature of protein structure into account
-The active sites some enzymes assume a shape that is complementary to that of the substrate only AFTER the substrate has been bound
*INDUCED FIT b/c the enzyme and substrate slightly change shape to suit each other after they bind
Binding energy…when is maximal binding energy released
- The weak interactions between complementary enzyme and substrate
- Only when the enzyme facilitates formation of the transition state
Transition state analogues
- Potent inhibitors of enzymes
- Very unstable
Kinetics
Study of the rates of chemical reactions
Velocity (V)
The quantity of reactant, A, that disappears in a specified unit of time, t.
Velocity is directly related to concentration of A by a constant, k, called the rate constant
V=k[A]
First-order reactions
Reactions in which V is directly proportional to reactant concentration
- have the unit s^-1
- the initial rate of reaction doubles when the reactant is doubled
Second-order reactions
Involve two reactants and have the units M^-1s^-1
-the initial rate of the reaction quadruples when the reactant is doubled
Michaelis-Menten Model
Initial velocity rises linearly as [S] increases and then begins to level off (plateau)
v0 (initial velocity)= the rate of increase in product with time when [P] is low
–measured for each substrate concentration by measuring the rate of product formation before P accumulates
Km
Michaelis constant… is unique to each enzyme and independent of enzyme concentration
Is equal to substrate concentration at which the reaction velocity is half is maximum value (half of the active sites are filled)
values depend on environmental conditions
Vmax
Directly dependent on enzyme concentration and can only be attained when all the enzyme is bound to substrate
-tells us about the turnover number of an enzyme
Low Km value
Tight substrate binding
Turnover number of an enzyme
Number of substrate molecules that an enzyme can convert into product per unit time when the enzyme is fully saturated with substrate
Kcat
Kcat/Km =
Measure of catalytic efficiency
Lineweaver-Burk plot
Graph of the reciprocal of both sides of the michaelis-menten equation
Sequential reactions
All substrates must bind to enzyme before any product released
*can either be ordered or random
Double displacement reactions
One or more products are released before all substrates bind enzymes
-substrates/products bounce on and off an enzyme (like a ping-pong ball)
Allosteric enzymes
Enzymes that regulate the flux of biochemical compounds in metabolic pathways
- Have a second regulatory site (allosteric site), which is distinct from the active site
- catalyze the committed step of metabolic pathways
- DO NOT CONFORM TO MICHAELIS-MENTEN KINETICS
- activators can lower Km, inhibitors can raise Km
How do feedback inhibitors work?
They bind to a distinct regulatory site on the allosteric enzyme
Phosphofructokinase
Catalyzes the committed step in glycolysis
-ATP acts as an allosteric inhibitor while fructose 1,6-biphosphate acts as an allosteric activator
What are the four mechanisms that enzymes use to form the transition state
- covalent catalysis
- acid-base catalysis
- metal ion catalysis
- stabilization of the transition state
Covalent catalysis
Active site contains a reactive group (usually powerful nucleophile) that becomes temporarily covalently modified during catalysis.
Acid-base catalysis
A molecule other than water plays the role of a proton donor or acceptor (e.g. chymotrypsin uses a histidine residue as a base catalyst to enhance nucleophilic power of serine
Metal ion catalysis
- can bind substrates to increase binding energy
- may generate a nucleophile by increasing acidity of a nearby molecule
- stabilize or shield negative charges by acting as an electrophilic catalyst
Metalloenzymes
Contain tightly bound metal ions (usually Fe 2+, Fe3+, Zn 2+)
Metal activated enzymes
Contain loosely bound metal ions (usually Na+, K+, Mg 2+, or Ca2+)
What is the optimal pH for most enzymes?
Between 5 and 9
3 main types of reversible inhibition
- competitive
- uncompetitive
- noncompetitive
Competitive inhibition
- the inhibitor usually resembles the substrate and binds only to free enzyme (not the ES complex)
- competitive inhibitor reduces the proportion of enzyme molecules bound to the substrate thus decreasing catalysis
- Has no effect on Vmax but increase Km
Uncompetitive inhibition
- inhibitor binds only to the ES complex NOT the free enzyme
- decreases Vmax and decreases Km
Noncompetitive inhibition
- inhibitor can bind simultaneously with the substrate to the enzyme at different binding sites
- can bind to both free enzyme and the enzyme-substrate complex
- decreases Vmax and Km does not change
Irreversible inhibition
-inhibitors form stable covalent bonds with the enzyme
