Enzymes Flashcards
In the absence of enzymes, digesting a meal could take
50 years
How can a reaction be accelerated
Adding heat or adding a catalyst which increases reaction rates, not consumed in the reaction
Are enzymes proteins
With few exceptions, enzymes are proteins. Primary structure, secondary structure, tertiary structure, and quaternary structures. Typically, globular proteins. Structure is governed/determined by the same forces.
Are enzymes catalysts
Accelerate reaction rates. Regenerated at the end of the reaction. 10^6 to 10^20-fold increase in reaction rates Highly specific, A + B → C + D, No side reactions
How do we name Enzymes
Typically end in -ase, Name often describes the process: Substrate name (or the product name) or Chemical Reaction.
How are enzymes regulated
Distinguishes enzymes from non-biological catalysts. As proteins, enzyme structures are (to an extent) flexible. Changing the shape of an enzyme changes its function.
How will reactions proceed
In all systems, biological or otherwise, a reaction will proceed only if the free energy of the products is less than the free energy of the reactants.
What is an exergonic reaction
When delta G is negative: Reaction is exergonic and “thermodynamically favourable” (spontaneous). Thermodynamically favorable reactions DO NOT NECESSARILY proceed at measurable rates
What state as the highest free energy
Transition state
What determines the rate of reaction
Activation energy determines the rate of reaction
Do enzymes affect the free-energy change, reactants, transition state or products?
Enzymes do not affect the free-energy change (delta G) of the reaction! Enzymes are with reactants and the products, and the transition state complex.
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 are active sites
Region of enzyme where catalysis occurs. Usually only a small portion of the protein. Key amino acids are in the active site: Binding and Catalysis Determines affinity, specificity, and rate. Complementary to substrate/transition state: Shape, hydrophobic interaction, hydrogen bonds and ion pairs.
What is the Active Site of Lysozyme
The active site is a 3-D cleft/crevice within the 3-D shape of the protein
What is the complementarity in substrate binding
Interactions between substrate and enzymes? Groups that are hydrophobic, hydrogen bond donors, hydrogen acceptors and ion pairs, these are paired with their complement in the binding site. Design of the active site contributes to: Affinity andSpecificity
What is Desolvation
Exclusion of water provides three advantages: Removal of water shell accelerates reactions, Enhances polar interactions (hydrogen bonds, ion pairs), Prevents side reactions. “Induced Fit.”
What is “Induced Fit”
Some enzymes change shape when substrate binds. Closes off active sites (excludes more water) and brings catalytic groups together.
What is Induced Fit
Some enzymes show a pronounced conformation change upon binding of substrate
What is the Induced Fit Model
Active site changes as substrate(s) bind
How does proximity and orientation play a role in binding sites
Chemical reactions only occur if substrates come together in the right orientation to react. Active sites bind substrates close to each other (proximity) and in the correct geometry (orientation). May account for a thousand-fold increase in reaction rates. All enzymes do this.
What are Participation Reactions
Some enzymes participate in the reactions by positioning functional groups near the substrates in the active site.
What are examples of participation reactions
Acid/base catalysts, Covalent catalysis and Metal ion catalysis
Which amino acid side chains can act as acid-base catalysis
Asparate (Asp), Glutamate (Glu), Histidine (His), Lysine (Lys), Cysteine (Cys) and Tryptophan (Tyr)
What amino acid side chains can act in nucleophilic catalysis
Serine (Ser), Tryptophan (Tyr), Cysteine (Cys), Lysine (Lys) and Histidine (His)
What are holoenzymes
When the polypeptide is combined with the prosthetic group to form the functional tertiary structure it can be referred to as the holoenzymes.
What are apoenzymes
Without the prosthetic group, the polypeptide can be referred to as the apoenzyme.
What are holoproteins and apoproteins
Holoprotein and apoprotein can be used respectively to refer to non-enzymatic proteins with or without prosthetic groups (ex: apomyoglobin is the myoglobin polypeptide chain without heme associated).
What is Transition State Stabilization
Binding the transition state will aid in lowering delta G. Parts of the protein interact with the unstable transition state. Enzyme active sites bind the transition better than they bind the substrate.
How does tightness of an enzyme bind relate to catalytic activity
The more tightly an enzyme binds the transition state relative to the substrate the greater the catalytic activity of the enzyme.
What are transition state analogs
Transition state analogs are POTENT inhibitors of many enzymes. Bind to enzyme with higher affinity compared to substrate.
What is V0 in enzyme kinetics
Initial velocity (rate of production formation)
What is Vmax in enzyme kinectics
Maximum rate or product form
What are the mechanisms can affect the intrinsic activity of the enzyme
Competitive inhibition, allostery, reversible covalent modification and ionic signals (such as Ca2+ ions)
What are the mechanisms do not affect the intrinsic activity of the enzyme
Regulation of gene expression and changes in subcellular localization
What are competitive inhibitors
Substances that bind reversibly in the active site. Resemble the substrate or transition state but do not react. Physically blocks active site
What does it mean when a competitive inhibitors blocks the active site
Fewer active sites available. Lower reaction rates (inhibited, curve shifts right) and and Apparent increase in Km.
How does the Vmax change when the substrate concentration overcomes inhibition
No change in Vmax
What are inhibitors
Inhibitors are similar to the substrate in shape and size but differ chemically in such a way that they cannot react
How do competitive inhibitors affect the apparent affinity for enzyme and substrate
Competitive inhibitors decrease the apparent affinity (increase Km) for enzyme and substrate
What are allosteric enzymes
Many enzymes are oligomeric (multi subunit). Like hemoglobin, enzyme activity may be cooperative. Sigmoidal relationship between substrate and reaction velocity. Reflects different states (geometries) and active site. Change between low activity (T) and high activity (R) states. Compounds besides the substrate may affect the equilibrium between T and R states. Allosteric effectors (positive/negative; activators/inhibitors). Quite common in regulation.
What is a positive homoallostery
Active site is available and it leads to product formation
What is a negative heteroallostery
One of the active sites is taken up by an inhibitor so it leads to no product formation or reduced product formation
Do allosteric enzymes have different states
They have two states, a T state (low activity) and R state (high activity)
What state does the allosteric activators favour
Favours the R state
What is Reversible Covalent Modification
Covalent modification of an amino acid residue changes the tertiary structure. Phosphorylation is the most common type of reversible covalent modification. (Ser/Thr/Tyr – OH becomes phosphorylated. Increases size, polarity, and charge significantly.) May increase or decrease activity of the target enzyme
What is the reversible phosphorylation of enzymes
Protein kinases catalyze the phosphorylation of proteins. Protein phosphates catalyze the dephosphorylation of proteins by hydrolysis. These are enzymes, often regulated themselves.
