Enzymes Flashcards
Enzymes are catalysts that can and can’t do what
They…
Lower the activation energy
Increase the rate of reaction
Do not alter the equilibrium constant
Are not changed or consumed in the reaction
Are pH and temperature, sensitive with optimal activity at specific pH ranges and temperatures
Do not affect the overall delta G of the reaction
Are specific for a particular reaction or class of reactions
Oxidoreductases
Catalyze oxidation reduction reactions
Transfer of electrons between biological molecules
Often have a cofactor that acts as an electron carrier NAD+ NADP+
Electron donor is known as the reductant
Electron acceptor is known as the oxidant
Dehydrogenase
Reductase
Oxidase
Transferases
Catalyze the movement of a functional group from one molecule to another
Most will be straightforwardly named, but remember that kinases are also a member of this class
Hydrolase
Catalyze the breaking of a compound into two molecules, using the addition of water
Many named for substrate
Phosphatase
Peptidase
Nuclease
Lipase
Lyase
Catalyze the cleavage of a single molecule into two products
Do not require water as a substrate, and do not act as oxidoreductase
The synthesis of two molecules into a single molecule may also be catalyzed by lyase (synthase)
Isomerase
Catalyze reactions between stereoisomers as well as constitutional isomers
Some can be classified as oxidoreductases, transferases, lyases
Catalyze the rearrangement of bond within molecules
Ligases
Catalyze addition or synthesis reactions generally between large similar molecules and often require ATP
Nucleic acid synthesis and repair
What is the impact of enzymes on activation energy?
It lower the activation energy, but not the overall free energy of the reaction
They make it easier for the substrate to reach the transition state
endergonic vs exergonic
Delta G > 0
Delta G < 0
Why are reversible reaction catalyzed by enzymes nonexistent?
They are extremely energetically unfavorable
What stabilizes the special arrangement of the enzyme substrate complex
Hydrogen bonding
Ionic interactions
Transient covalent bonds
Explain the induced fit model
Unlike the lock and key theory, which suggests that the enzymes active site is already appropriately conformed for the substrate, and the substrate has induced a change in the shape of the enzyme, which requires energy, making the bonding of the two endergonic in nature
The release of the enzyme from the active site is exergonic
How are coenzymes and cofactors similar
Small in size
Bind to active site of an enzyme, usually by carrying charge through ionization, protonation, or deprotontation
usually kept at low concentrations
Tightly bound cofactors or co-enzymes that are necessary for enzyme function are known as prosthetic groups
Enzymes without their cofactors are called
Apoenzymes
Enzymes containing their cofactors are called
Holoenzymes
Cofactors are generally
Inorganic molecules or metal ions
Coenzymes are
Small organic groups, the vast majority of which are vitamins or derivatives of vitamins
Water soluble vitamins
B and C
Fat soluble vitamins
A D E K
B1 name
Thiamine
B2 name
Riboflavin
B3 name
Niacin
B5 name
Pantothenic acid
B6
Pyridoxal phosphate
B7
Biotin
B9
Folic acid
B12
Cyanocobalmin
The Michaelis-Menten equation describes what?
How the rate of the reaction depends on the concentration of both the enzyme and the substrate which forms the product
Michaelis-Menten equation
~
—K1~> —Kcat~>
E + S ES E + P
<~K-1-
Under a constant concentration of enzyme, write the equation describing the relationship between velocity and substrate concentration
v = (vmax[S])/(Km+[S])
When the reaction rate is equal to half Vmax
Km = [S]
What is Km
Substrate concentration at which half of the enzymes active site are full
Under certain conditions, it is a measure of the affinity of the enzyme for its substrate
An enzyme with a higher Km has the lower affinity for its substrate, because it requires a higher substrate concentration to be half saturated
Constant value
vmax
Max enzyme velocity
Measured in moles/second
What is the relationship between Vmax and Kcat?
Vmax = [E]Kcat
Kcat
Measures the number of substrate molecules converted to product per enzyme molecule per second
At very low substrate concentrations…
v = (Kcat/Km) x [E][S]
Catalytic efficiency
Kcat/Km
What is the Lineweaver Burk plot?
The double reciprocal graph of the Michaelis-Menten equation
What does the X axis of the Lineweaver Burk plot represent?
1/[S]
What does the Y axis of the Lineweaver Burk plot represent?
1/v
How can one find the Km value in the Lineweaver Burk plot?
Negative reciprocal of X intercept
LB: X intercept is -1/Km
What does an S shaped sigmoidal Michaelis-Menten plot mean?
Cooperativity
Cooperative enzymes have multiple subunits and multiple active sites
Cooperative enzymes are also subject to activation and inhibition both completely and through allosteric sites
Tense versus relaxed states
Low affinity versus high affinity
Binding of the substrate encourages the transition of other subunits from T State to R state which increases the likelihood of substrate binding by these other subunits
Loss of substrate can encourage the transition from the R state to the T state and promote dissociation of substrate from the remaining subunits
Hill’s coefficient>1
Positively cooperative bonding is occurring such that after one ligand is bound the affinity of the enzyme for further ligands increases
Hill’s coefficient<1
Negatively, cooperative binding is occurring such that after one ligand is bound the affinity of the enzyme for further ligands decreases
Hill’s coefficient=1
The enzyme does not exhibit cooperative binding
How does temperature affect enzyme activity?
Enzyme catalyzed reactions tend to double in velocity for every 10°C increase in temperature until the optimum temperature is reached
For the human body this is 37°C
After this the enzyme will denature at high temperatures
Some enzymes that are overheated may regain their function if cooled
How does pH affect enzyme activity?
pH affects the ionization of the active site
Can lead to denaturation
Enzymes that circulate function in human blood optimal pH is 7.4
A pH less than 7.35 is acidemia
How does salinity affect enzyme activity?
Altering the concentration of salt can change enzyme activity in vitro
Increasing levels of salt can disrupt, hydrogen and ionic bonds, causing a partial change in the conformation of the enzyme, and in some cases causing denaturation
How are reversible inhibitors bonded?
Non-covalently
Competitive inhibition
Occupancy of the active site
Can be overcome by adding more substrate
Adding a competitive inhibitor does not alter the value of Vmax
Increase of Km
Noncompetitive inhibition
Bind to an allosteric site instead of the active site
Induces a change in enzyme conformation
Adding more substrate won’t do shit
Decrease vmax
Mixed inhibition
Inhibitor can bind to either the enzyme or the enzyme substrate complex
Has different affinity for each
Do not bind at the active site, but an allosteric site
If the inhibitor preferentially binds to the enzyme it increases the km value
If the inhibitor binds to the enzyme substrate complex it lowers the km value
Vmax is decreased regardless
Uncompetitive inhibition
Lock the substrate in the enzyme
Bind to allosteric site
Lowers Km and Vmax
Allosteric enzymes
Multiple binding sites
Active site is present and at least one other site that can regulate the availability of the active site
Michaelis-Menten plots of cooperative allosteric enzyme kinetics often have a sigmoidal curve
Covalently modified enzymes
The name holds the definition.
Phosphorylation, dephosphorylation, or glycosylation
Zymogens
Zymogens contain a catalytic domain and regulatory domain
The regulatory domain must either be removed or altered to expose the active site
Trypsinogen
the cDNA sequence is…
a DNA copy of the mRNA used to generate a protein
to find the pI of an amino acid with a basic side chain…
we ignore pKa of carboxyl group, avg the side chain and the amino group
role of proline in secondary structure
rigid, causes turns in beta pleated sheets
How does the ideal temp for a rxn change with and without an enzyme catalyst?
ideal temp generally lower w a catalyst than without
