Enzymes Flashcards
What are enzymes?
Enzymes are biological catalysts
–> Speed up chemical reactions without being consumed or changed
What is the difference between apoenzyme and holoenzyme?
Apoenzyme - without the prosthetic group
Holoenzyme - with the prosthetic group
Two general ways to increase the
speed of a chemical reaction:
- Heat (denature, speeds up everything (nonspecific) problem is that cell needs specificity)
- Add a catalyst
Enzymes are typical globular proteins:
Biological catalyst
Same structure as other proteins
1o, 2o, 3o (not regulated often) and sometimes 4o (regulated by allostery)
Structure determined and/or stabilized by the same non-covalent interactions (hydrophobic interactions, H-bonds, ion pairs, van der waals, disulphide bonds)
Enzymes are Highly ….
Specific and Non-random
General properties of enzymes vs.
non-biological catalysts
-Higher reaction rates
- Milder reaction conditions (37 degree C, ph of 7, high pressure)
- Greater reaction specificity (act on certain number of molecules)
- Capacity for regulation
BECAUSE conformational change in protein structure is possible
Also important in cooperativity
Why is ATP a “high energy” molecule?
- decreased electrostatic repulsion
- resonance stabilization
- increase entropy via breaking phosphoanhydride bond
- Free energy released for breaking a
phosphoanhydride bond is -30 kJ/mol (more than -25 kJ/mol)
In biological systems, a reaction will proceed only if the free energy of the ____ is less than the free energy of the _____.
products; reactants
delta G = negative means
-Reaction is exergonic and
“thermodynamically favorable” (energy released)
-R>P
-doesnt mention speed!
Define Enthalpy and Spontaneous
Enthaply: type/number of bonds
Spontaneous: rate/speed –> does the reaction want to go, when it does move what speed?
Increase entropy means …
decrease enthalpy, decrease in high energy bonds
The Speed of a Favourable Biochemical
Reaction is Determined by the Size of the _________________
Activation Energy Barrier
Facts about ∆G‡
- ∆G‡ = GTS - GR
- Increase ∆G‡ = slower rxn
- Decrease ∆G‡ = faster rxn
How does enzymes affect reaction rates (kinetics)?
Increasing temp will increase speed of rxn, therefore more collisions
Enzyme do not influence __, they influence ___. Enzymes effect ___, they do not effect ___.
- ∆G
- ∆G‡
- Kinetics
- Thermodynamics
Catalysts lower the activation energy
barrier by:
- Removing substrates from aqueous solution (desolvation) - H2O
- Proximity and orientation effects -> physically bring correct orientation
- Taking part in the reaction mechanism -> change transition state
- Stabilizing the transition state -> decrease transition state
Design of the active site in enzymes contributes to:
- Affinity (how tightly the molecules bind)
* Specificity (what molecules bind)
Induced Fit Model?
Substrate binding changes the shape
of an active site - induced fit
New interactions between the substrate and active site influence the enzyme conformation (shape).
Desolvation?
Removing substrates from
aqueous solution
The sequestering of substrates in a
non-aqueous environment has
several advantages:
- Prevents interference by water molecules
- Formation of H-bonds is more effective in a non-aqueous environment
- It eliminates the energy barrier imposed by ordered solvent molecules (water)
Proximity and Orientation
Effects in Catalysis
May account for a thousand-fold increase in reaction rates
Enzymes assist in the formation of the
transition state by taking part in the
reaction mechanism
- Positioning certain aa side chains in the active site where they can react with the substrates
- -acid-base catalysis (residue taking part in rxn)
- covalent catalysis/nucleophilic catalysis
- –transient covalent bond between substrate and enzyme
- Provide other chemical substances at the active site-cofactors
- -metal ion catalysis
Amino Acid Side Chains in Acid-Base
Catalysis
These groups can
act as acid (with hydrogen) or base (without hydrogen) catalysts, depending on their state of protonation.
4.Stabilizing the transition state
- The Active Site Binds the Transition State Better Than it Binds the Substrate
- Free energy of the transition state is lowered
The more tightly an enzyme
binds the transition state relative to
the substrate the _____ the catalytic
activity of the enzyme
greater
Transition state analogs are POTENT inhibitors of many enzymes b/c
- bind to enzyme with higher affinity compared to substrate (compete with substrate)
- rational basis for drug design (take new info, and design molecules)
- versus serendipitous drug discovery
Relationship between Kd and affinity:
- decrease kd = increase affinity
- increase kd = decrease affinity
Competitive Inhibition of
Enzyme Activity
- Inhibitors are similar to the substrate in shape and size but differ chemically in such a way that they cannot react
- CO is a competitive Inhibitor of O2 binding to HB
- Substrate and inhibitor compete for the same site on the enzyme
- overcome by increase number of substrates, decrease inhibitor = non covalent bonds break -> substrate gets in
Allosteric enzymes show a _______ relationship between reaction velocity and substrate concentration
sigmoidal
Heteroallostery?
An allosteric enzymes catalytic activity is
modulated by the noncovalent binding of specific molecules at a site other than the active site
Effector vs inhibitor
Negative effector, allosteric inhibitor
Positive effector, allosteric activator
Allosteric enzymes have two states:
T (tense, low activity) –> Allosteric Activator
R (relaxed, high activity) –> Allosteric Inhibitor
The addition of a phosphate
group results in:
-A large increase in size.
-A large increase in polarity/hydrophilicity.
-The addition of two negative charges.
-The capability of making multiple new H
bonds.
Phosphorylation CHANGES enzyme activity by modifying the protein’s precise 3-D shape.
