enzymes Flashcards
What are some examples of processes that would take a very long time in the absence of enzymes?
○ Extracting energy from glucose
○ Burning hydrocarbon fuels
○ Nitrogen fixation
○ Digesting food
What are the two ways a reaction can be accelerated?
- Adding heat: Increases the number of reactants with sufficient energy to overcome the activation energy barrier.
- Adding a catalyst: Decreases the activation energy barrier but does not react.
What are enzymes?
○ Mostly proteins.
○ Have primary, secondary, tertiary, and quaternary structures.
○ Typically globular proteins.
○ Their structure is determined by the same forces that govern protein structure (e.g., hydrogen bonds, Van der Waals interactions).
What are the key characteristics of enzymes as catalysts?
○ They accelerate reaction rates.
○ They are regenerated at the end of the reaction.
○ Can increase reaction rates by 106 to 1020 fold.
○ Highly specific for their substrates.
○ Do not produce side reactions.
What are some common features of enzyme nomenclature?
○ Enzyme names typically end in “-ase”.
○ The name often describes the process, substrate, product, or chemical reaction.
Ex: Citrate synthase, alcohol dehydrogenase, pyruvate decarboxylase.
How are enzymes regulated?
Enzymes are regulated through
* allosteric regulation
* competitive inhibiton
* reversible covalent modification
* gene expression and subcellular localization
* feedback inhibition
* Ionic signals
* substrate availability
Their structures are flexible & changing their shape can alter their function
What determines the speed of a thermodynamically favorable biochemical reaction?
the size of the activation energy barrier.
Do enzymes affect the free-energy change (ΔG) of a reaction?
No, they only affect the activation energy.
How do enzymes reduce the free energy of the transition state?
○ Removing substrates from aqueous solution (desolvation).
○ Proximity and orientation effects.
○ Taking part in the reaction mechanism.
○ Stabilizing the transition state.
What is the active site of an enzyme?
- The region of the enzyme where catalysis occurs.
- Usually a small portion of the protein.
- Contains key amino acids involved in binding and catalysis.
- Determines affinity, specificity, and rate of the reaction.
- Complementary to the substrate or transition state.
- Shape, hydrophobic interactions, hydrogen bonds, and ion pairs contribute to substrate binding.
Describe the lock and key model of enzyme-substrate binding.
This model suggests a rigid interaction where the enzyme’s active site is a perfect fit for the substrate, like a lock and key.
Describe the induced fit model of enzyme-substrate binding.
This model proposes that the active site changes shape as the substrate binds, leading to a more precise fit
What are the advantages of desolvation in enzyme catalysis?
- Removal of the water shell accelerates reactions.
- Enhances polar interactions (hydrogen bonds, ion pairs).
- Prevents side reactions
How do proximity and orientation effects contribute to catalysis?
○ Chemical reactions require substrates to come together in the correct orientation.
○ Active sites bind substrates close to each other (proximity) and in the correct geometry (orientation).
○ This can enhance reaction rates by up to a thousandfold.
How can enzymes participate in reactions?
○ Some enzymes use functional groups in the active site to participate in reactions.
○ These groups may act as:
■ Acid/base catalysts
■ Covalent catalysts
■ Metal ion catalysts
○This can be achieved through amino acids or cofactors (or both).
What are cofactors?
- Molecules or compounds that enhance the reactive potential of polypeptides.
- They provide new reactive functional groups. Can be:
■ Metal ions (e.g., Fe, Zn, Cu, Na, Mg, K)
■ Coenzymes (organic molecules)
● Cosubstrates (e.g., NAD+)
● Prosthetic groups (e.g., FAD)
What is the difference between an apoenzyme and a holoenzyme?
- Holoenzyme: The functional enzyme with its prosthetic group attached.
- Apoenzyme: The protein portion of an enzyme without its prosthetic group.
How does transition state stabilization contribute to catalysis?
○ Binding the transition state lowers the activation energy (ΔG‡).
○ Enzyme active sites bind the transition state better than the substrate.
○ Transition state analogs are potent inhibitors because they bind with higher affinity than the substrate.
What is V0 in enzyme kinetics?
Initial velocity, or the rate of product formation at the beginning of a reaction.
What is Vmax in enzyme kinetics?
The maximum rate of product formation when the enzyme is saturated with substrate
What is Km in enzyme kinetics?
The Michaelis constant.
○ Analogous to Kd in ligand binding.
○ Reflects the affinity of the enzyme for its substrate.
○ A smaller Km indicates higher affinity.
○ V0 = 50% Vmax when [substrate] = Km.
What are some mechanisms for regulating enzyme activity that affect the intrinsic activity of the enzyme?
○ Competitive inhibition
○ Allostery
○ Reversible covalent modification
○ Ionic signals (e.g., Ca2+ ions)
What are some mechanisms for regulating enzyme activity that do not affect the intrinsic activity of the enzyme?
- Regulation of gene expression
- Changes in subcellular localization
How do competitive inhibitors work?
○ Bind reversibly to the active site.
○ Resemble the substrate or transition state but do not react.
○ Physically block the active site, preventing substrate binding.
○ Reduce the number of available active sites, leading to lower reaction rates.
○ Cause an apparent increase in Km.
○ Increasing substrate concentration can overcome competitive inhibition.
○ Vmax remains unchanged.
Why are transition state analogs better competitive inhibitors than substrate analogs?
They bind to the enzyme with higher affinity, effectively blocking substrate binding
What are allosteric enzymes?
○ Often oligomeric (multi-subunit) enzymes.
○ Exhibit cooperativity, similar to hemoglobin.
○ Show a sigmoidal relationship between substrate concentration and reaction velocity.
○ Have different states (T and R) with varying active site geometries.
○ Allosteric effectors can bind to sites other than the active site and affect the equilibrium between the T (low activity) and R (high activity) states.
Positive effectors stabilize the R state and increase enzyme activity
Negative effectors stabilize the T state, decreasing enzyme activity
What is homoallostery?
The binding of a substrate molecule to one subunit of an allosteric enzyme, which affects the binding of substrate to other subunits.
What is heteroallostery?
The binding of a molecule other than the substrate (an allosteric effector) to a site other than the active site, which modulates the enzyme’s catalytic activity.
What are the two states of allosteric enzymes?
○ T state: Tense state, low activity
○ R state: Relaxed state, high activity
How do allosteric activators and inhibitors affect enzyme activity?
- Allosteric activators favor the R state (high activity).
- Allosteric inhibitors favor the T state (low activity).
What is reversible covalent modification?
○ Covalent modification of an amino acid residue that alters the 3° structure of a polypeptide, affecting enzyme activity.
○ Phosphorylation is the most common type, often occurring on Ser, Thr, or Tyr residues
How does phosphorylation regulate enzyme activity?
○ Phosphorylation adds a phosphate group to an amino acid residue.
○ Increases the size, polarity, and negative charge of the residue.
○ Can either increase or decrease the activity of the target enzyme.
What enzymes catalyze phosphorylation and dephosphorylation?
○ Protein kinases: Catalyze the phosphorylation of proteins using ATP.
○ Protein phosphatases: Catalyze the dephosphorylation of proteins by hydrolysis.
Both kinases and phosphatases are often regulated themselves
phosphorylation= adding a phosphate group
dephosphorylation = removal of a phospahet group
