Ch. 6 How enzymes work Flashcards
Enzymes
-Enzymes are living systems catalysts
-Most enzymes are proteins, but few are made of RNA
-Most exhibit a high degree of specificity and greater catalytic power than non-biologic catalysts that are specific for that reactant
Ribozymes
-made up of RNA
Catalytic power
-rate enhancement/catalytic efficiency 10^8-10^12
- Enzymes have a higher catalytic power
-Ratio of catalyzed rate: uncatalyzed rate
Specificity of enzymes
- Enzymes are specific to their substrates
-Functional groups on enzymes are arranged so that enzyme can distinguish its substrates from others
Chymotrypsin and its specifity
- Has a reacting binding site and has 3 amino acids bonded to the substrate. Histidine, Serine, and carboxylate.
-Chymotrypsin uses hydrolysis to cleave the polypeptide bond following large aromatic residues
-catalyzed hydrolysis of amide and ester bonds
Role of artificial substrates to study proteases
-Artificial substrates (p-nitrophenyl acetate) mimic the actual substrate of chymotrypsin–> p-nitrophenolate. ( allows the substrate to have color)
Role: to monitor activity of the specific enzyme
- look at study guide
The 6 classes of enzymes and the reactions they catalyze
- Oxidoreductases: Oxidative reduction reactions
- Transferases: Transfer of functional groups
- Hydrolases: Hydrolysis reactions
4.Lyases: Group elimination to form double bonds - Isomerases: Isomerization reactions
- Ligases: bond formation coupled with ATP hydrolysis
How are enzymes named
- Enzymes are usually named after the substrate name and the reaction they catalyze and their names end in -Ase
The meaning of the values of the free energy change of a reaction, the free energy of activation, and the concept of the transition state
Transition state: is the point of the highest energy and is the midway between the reactants and the products
-Free energy activation is the energy-requiring step of the reaction as the energy barrier and is symbolized as ΔG.
Effect of enzyme on activation energy and on free energy change of a reaction
-Enzymes lower the activation energy for a reaction but do not affect its free energy change. The sign of ΔG indicates if the reaction is spontaneous or favorable.
Cofactors
-non A A substrates required for catalytic/enzymatic activity
Coenzyme
-Type of cofactor, it may be derived from vitamins
Cosubstrate
-Type of coenzyme, it enters and exits active site (substrate def.) ( not recycled)
Prosthetic group
- Is permanently attached to the enzyme that remains in the active site between reactions(recycled)
The 3 major chemical catalytic mechanisms
-Acid-base catalysis: A proton is transferred between the enzyme and the substrate
-Covalent catalysis: Involves the use of a nucleophile
-Metal ion catalysis: mediate redox reactions/promote reactivity of active site
The role of an acid and base on the tautomerization of a ketone to an enol
(look at the study guide)
-An acid catalyst (H-A) donates an H+ to the ketones oxygen atom. This lowers the energy of the transition state, therefore, lowering the activation energy for the reaction.
-A base catalyst accepts an H+ lowering the energy of the transition state’
Amino acids involved in acid-base catalysis
- Asp
-Glu
-His
-Lys
-Cys
-Tyr
The reaction coordinate of a reaction involving covalent catalysis
Look at the study guide for the diagram
Amino acids involved in covalent catalysis
- Ser,Tyr
-Cys
-Lys
-His
The role of a metal ion on the alcohol dehydrogenase reaction
-Zn2+ stabilizes the (-) charge on the O atom of the transition state
Types of catalysis used by chymotrypsin
-Uses acid-base catalysis and covalent catalysis and has 3 essential amino acid residues at the active site. It has a serine protease. The reaction occurs in 2 phases that correspond to the formation of a covalent intermediate and its breakdown.
What is the catalytic triad of chymotrypsin
-It promotes peptide bond hydrolysis
-Chymotrypsin uses Acid-Base and covalent catalysis
-It also has a serine protease
-3 essential amino acid residues @ the active site known as the catalytic triad Asp102, His 57, Ser 195.
Roles of each of the catalytic triad amino acid residues
-His 57 acts as a base catalyst and Ser 195 acts as a nucleophile
Understand the steps of the mechanism of peptide hydrolysis by chymotrypsin
- His 57 acts as a base catalyst and accepts H+ from ser 195 hydroxyl group. This results in nucleophilic O-(covalent catalyst) attacking carbonyl C of the substrate. The n-terminal portion of the substrate remains covalently linked to an enzyme
- His 57 acts as an acid catalyst and donates H to N of the scissile peptide bond. This cleaves the bond and Asp promotes the reaction by stabilizing His 57 through hydrogen bonding
- Water then enters the active site and donates a proton to His 57, leaving a hydroxyl group that attacks the carbonyl group of the remaining substrate.
- In the 2nd tetrahedral transition state: His 57 acts as an acid catalyst and donates H+ to ser oxygen and breaks down the transition step(similar to step 2)
- N-terminal portion of the original substrate w/new C-terminus diffuses and the enzyme is regenerated
The role of the oxyanion hole
-is within the active site of chymotrypsin and the transition state stabilized. Forms 3 new H bonds
proximity and orientation effects
increase of reactants and increase of frequency of collisions by bringing reacting groups into close proximity of the active site
-Substrates rotational motions freeze for proper orientation to bind to the enzyme
The induced fit model
-Is the binding of a substrate to enzyme that triggers a conformational change at the active site enhancing catalysis and fully enclosing substrates.
-Glucose + ATP -(hetokinase) glucose-6-phosphate + ADP
How similar are the sequences and structures of the three serine proteases are
-Chymotrypsin,Trypsin, and elastase positions of their catalytic residues in their active sites are identical and have very similar secondary + tertiary structures
How different the active sites of the three serine proteases are and how these determine their specificity
-Chymotrypsin binding site= Ser and binds to large hydrophobic aromatic rings (Phe,Trg,Tyr)
-Trypsin binding site=Asp and binds to basic residues (Arg,Lys)
-Elastase binding site= Val +Thr on walls and binds to small hydrophobic residues(Ala,Gly)
How the activity of proteases can be limited
-By their synthesis as inactive precursors are known as zymogens
-The action of small proteins that pose as substrates but are not hydrolyzed
How zymogens of proteases are activated
-Trypsinogen is activated by the hydrolysis of the peptide bond between Lys 6 and Ile7. Trypsin then cleaves other zymogens including its own leading to auto-activation.
How protease inhibitors limit the activity of proteases
-Protease inhibitors are small proteins that pose as substrates but are not hydrolyzed.
-BPTI is the protease inhibitor of trypsin and poses as the substrate
- Ser 195 of trypsin attacks peptide bind of Lys 15 of BPTI but the bond is not hydrolyzed and halts the formation of the 1st transition state.
