Chapter 6: How Enzymes work Flashcards
What are enzymes?
o Speed up biochemical reactions
o They are catalysis; they increase rate of interactions. They are recycled and are rescued. After the reaction they come out intact and work again.
In enzymes: Ribozymes, catalytic power, degree of specificity (examples), and rate enhancement
- Ribozymes: they used to say that all the enzymes are proteins but recently some are made of RNA(ribozymes)
- Catalytic power:
- Degree of Specificity: catalyze hydrolysis peptite bond following large aromatic residue (ex. phenylalanine, tryprophan, tyrosine). Catalyze hydrolysis of amide and ester bonds.
- Rate of enhancement: the ratio of the catalyzed rate divided by the uncatalyzed rate. Pp3. Tells you how many times the rate of the rxn has been increased.** The range is typically 10^8 to 10^12 are typical for enzymes.**
Chymotrypsin (as an example of a protease)-catalyzed reaction, and its specificity
- Catalyzed rxn: Known as hydrolysis (cleavage by water); the breaking of water. They are cleaving a peptide bond.
- Specificity: Can recognize the side chain [pp5]
- Known as protease; because the substrate is another protein.
Role of artificial substrates to study proteases
- To distinguish the fragments and chymotrypsin from each other they use artificial substrates. The artifical will mimic the actual substrate. Chymotrypsin can recognize esters and break the bond. And then the activity of chymotrypsin can be monitored.
The 6 classes of enzymes and reactions they catalyze
These enzymes have subclasses and then more subclasses. They are identified by a four-digit number.
How enzymes are named
- They are named after the substrate name and the rxn they catalyzed. [Ex pp8]
- The ends always end with -ase. *There are exceptions to both of these rules
- Another example is [pp9]
- Specific for alanine: alanine aminotransferase
- There are some names that are very specific while other can be broad.
The meaning of the values of the free energy change of a reaction, the free energy of activation and the concept of transition state
- Values of free energy: conversion of reactants to products
- Free energy of activation: The amount of energy needed to add for the rxn to occur.
- Concept of transition state: It cannot be detected but it can be proposed. The highest point of energy.
- Delta G of the rxn is zero. It means equilibrium: the rates are equal (forward and reverse)
- The sign of delta G indicates if the rxn is spontaneous or favorable
Effect of enzyme on activation energy and on free enrgy change of a reaction
** The height of the activation energy determines the rate of the reaction. Enzymes lower the rate (highest peak) speeding up the rxn. **
Enzymes on free energy: Enzymes lower the activation energy but they do not affect the free energy.*
The meaning of cofactors, coenzymes, co-substrates and prosthetic groups
- Cofactor- a non AA substrates required for catalystic/ enzymatic activity
- coenzyme- type of cofactor; may be dervied from vitamins
- cosubstrate- type of coenzyme; enters and exits active site
- prosthetic group- tightly bond co enzyme that remains in active site before reaction
The 3 major chemical catalytic mechanisms
- Acid-base catalysis; a proton is transferred between enzyme and the substrate
- covalent catalysis; involves the use of a nucleophile
- metal ion catalysis
The role of an acid and base on the tautomerization of a ketone to an enol
The un-catalyzed reaction is slow because the carbanion-like transition state has a high activation energy
An acid catalyst (H-A) donates H+ to the ketones oxygen atom.
This lowers the energy of the transition state, therefore, lowering the action energy for the reaction,
A base catalyst (:B) accepts a H+ lowering the energy of the transition state
| The acid stabilizes the negative charge of oxygen on ketone.
The E decreases and so does the activation energy
Amino acids involved in acid-base catalysis
- Asp
- Glu
- His
- Lys
- Cys
- Tyr
The reaction coordinate of a reaction involving covalent catalysis
- Covalent catalysis involves a two- part reaction process
- covalent bond forms between catalyst and substrate during TS
Amino acids involved in covalent catalysis
-AA that act as nucleophiles in covalent catalysis
The role of a metal ion on the alcohol dehydrogenase reaction
- metal ions mediate redox rxns and promote reactivity of the acitve site
Understand the steps of the mechanism of peptide hydrolysis by chymotrypsin
- His 57 acts as a base catalys and accepts H+ form Ser 195 hydroxyl group. Resulting nucliophile O- (covalent catalyst) attacks carbonyl C of substrate
- His 57 acts as an acid catalyst and donates H to N of scissle pepetide bond–> bond cleaveage and decomposition of tetrahedral Ts; c-terminal portion cleaved; Asp stabilizes His 57 via H-bonding.
- N-termnial poriton of substrate remains covalently linked ot enzyme= covalent intermediate.
The induced fit model
- the binding of substrate to enzyme triggers a **conformational change ** at the active site enhancing catalysis
- glucose + ATP = glucose-6-phosphate + ADP
How similar the sequences and structures of the three serine proteases are
- sequence variation occurs on the surface of the enzyme; but the positions of the catalytic residues in the 3 active sites are virtually identical
- Chymotrypsin, trypsin and elastase have also very similar secondary and tertiary structures.
- Although similar the serine protesase have different substrate specificities. Their binding sites have differnt sizes and specific residues.
How zymogens of proteases are activated
- Zymogens= inactive precurosr of protease
- They synthesize in the pancreas
- Activated by protelysis
