Chapter 6: How Enzymes Work Flashcards
What is the definition of ribozymes?
Ribozymes are enzymes that are made of RNA. (Most enzymes are made of proteins but ribozymes are made of RNA).
What is the definition of an enzyme?
Biocatalysts (living system catalysts) speed up biochemical reactions.
1. Increase the rate of reaction. Recycled and reused. Participate in the reaction but are reused when the reaction is finished.
2. Exhibit a high degree of specificity and greater catalytic power than non-biologic catalysts
3. Act under mild conditions
Define the degree of specificity of enzymes.
Most enzymes are highly specific for their reactants (called substrates) and products. The functional groups in the active site of an enzyme are arranged so that the enzyme can distinguish its substrates from among many others that are similar in size and shape and can then mediate a single chemical reaction involving those substrates.
What is the catalytic power of enzymes?
Enzymes have higher catalytic power than non-biologic. Enzymes differ from nonbiological catalysts in that the activities of many enzymes are regulated so that the organism can respond to changing conditions or follow genetically determined developmental programs.
What is enzyme rate enhancement?
The ratio of the catalyzed rate/uncatalyzed rate.
Shows us how many times the reaction has been increased by a catalyst
What is Chymotrypsin as an example of a protease?
Chymotrypsin is a digestive enzyme found in the pancreas. Chymotrypsin is a part of the Hydrolases class of enzymes.
It is composed of 2 domains and a substrate (reactants) binding pocket/side where 241 essential amino acids reside.
Hydrolysis of polypeptide substrates takes place in a cleft between the two domains, near the side chains of three residues (His 57, Asp 102, and Ser 195). This area of the enzyme is known as the active site. The active sites of nearly all known enzymes are located in similar crevices on the enzyme surface.
Chymotrypsin catalyzed reaction and its specificity
Chymotrypsin catalyzes the hydrolysis of the peptide bond following almost any large nonpolar aromatic residue such as Phe, Trp, or Tyr. It can also catalyze the hydrolysis of other amide bonds and ester bonds.
Protease
Proteases are enzymes that act on and break down proteins. Can similarly be called a proteinase or a peptidase
What is hydrolysis?
Cleavage by water
Role of artificial substrates to study chymotrypsin and other proteases
They mimic the actual substrate. The peptide bond is an ester and the have a bulky side chain that is recognized by Chymotrypsin. This helps us analyze protease in different environments.
The 6 classes of enzymes and reactions they catalyze
How enzymes are named
All biochemical reactions involve either the addition of some substance to another, or its removal, or the rearrangement of that substance.
The name of an enzyme frequently provides a clue to its function. In some cases, an enzyme is named by incorporating the suffix-ase into the name of its substrate. For example, fumarase is an enzyme that acts on fumarate. Chymotrypsin can similarly be called a proteinase, a protease, or a peptidase. Most enzyme names contain more descriptive words (also ending in-ase) to indicate the nature of the reaction catalyzed by that enzyme. For example, pyruvate decarboxylase catalyzes the removal of a CO2 group from pyruvate:
What is the meaning of the value of the free energy change of a reaction?
The amount of energy released in the conversion of reaction to a product under standard conditions.
ΔG < 0 favorable or spontaneous reaction
ΔG > 0 unfavorable or non-spontaneous reaction
What is the meaning of the value of free energy of activation?
Energy-requiring step of the reaction is called the free energy of activation
What does the concept of transition state mean in chemical reaction processes?
The point of highest energy is known as the transition state (TS)
Do enzymes have an effect on activation energy’s free energy change?
No. Enzymes LOWER the activation energy, but they do NOT affect the free energy
What is the meaning of cofactors?
In some cases, the amino acid side chains of an enzyme cannot provide the required catalytic groups, so a tightly bound cofactor participates in catalysis. For example, many oxidation-reduction reactions require a metal ion cofactor, since a metal ion can exist in multiple oxidation states, unlike an amino acid side chain.
What are coenzymes?
A coenzyme is defined as an organic molecule that binds to the active sites of certain enzymes to assist in the catalysis of a reaction.
Two types of coenzymes are co-substrates or prosthetic groups. co-substrates are consumed.
What are the 3 major chemical catalytic mechanisms?
- Acid-Base Catalysis: Many enzyme mechanisms include acid-base catalysis, in which a proton is transferred between the enzyme and the substrate. This mechanism of catalysis can be further divided into acid catalysis and base catalysis.
- In Covalent Catalysis, the second major chemical reaction mechanism used by enzymes, a covalent bond forms between the catalyst and the substrate during the formation of the transition state.
- Metal Ion Catalysis occurs when metal ions participate in enzymatic reactions by mediating oxidation-reduction reactions, or by promoting the reactivity of other groups in the enzyme’s active site through electrostatic effects.
What is the role of an acid and base on the tautomerization of a ketone to an enol?
If a catalyst (symbolized HOA) donates a proton to the ketone’s oxygen atom, it reduces the unfavorable carbanion character of the transition state, thereby lowering its energy and hence lowering the activation energy barrier for the reaction. This is an example of acid catalysis since the catalyst acts as an acid by donating a proton. Note that the catalyst is returned to its original form at the end of the reaction.
Which amino acids are involved in acid-base catalysis?
These groups can act as acid or base catalysts, depending on their state of protonation in the enzyme’s active site. The side chains are shown in their protonated forms, with the acidic proton highlighted.
What is the reaction coordinate of a reaction involving covalent catalysis?
Covalent catalysis involves a two- part reaction process
Which amino acids are involved in covalent catalysis?
In their deprotonated forms (right), these groups act as nucleophiles. They attack electron-deficient centers to form covalent intermediates.
Is this keto-enol tautomerization reaction shown accelerated by an acid or base catalyst?
The same keto-enol tautomerization reaction shown above can be accelerated by a catalyst that can accept a proton, that is, by a base catalyst. Here, the catalyst is shown as :B, where the dots represent unpaired electrons. Base catalysis lowers the energy of the transition state and thereby accelerates the reaction.
Is this keto-enol tautomerization reaction shown accelerated by an acid or base catalyst?
An acid catalyst (H-A) donates a H+ to the ketone’s oxygen atom. This lowers the energy of the transition state, therefore, lowering the activation energy for the reaction
Define Covalent Catalysis
In covalent catalysis, the second major chemical reaction mechanism used by enzymes, a covalent bond forms between the catalyst and the substrate during formation of the transition state. Consider as a model reaction the decarboxylation of acetoacetate. In this reaction, the movement of electron pairs among atoms is indicated by red curved arrows
What is the catalytic triad of chymotrypsin?
Asp 102, His 57, and Ser 195 are arrayed in a hydrogen-bonded network. Atoms are color-coded (C gray, N blue, O red), and the hydrogen bonds are shaded yellow.
What are the steps of the catalytic mechanism of chymotrypsin and other serine proteases?
Asp, His, and Ser in peptide bond hydrolysis.
1.Removal of the Ser hydroxyl
proton by His 57 (a base catalyst)
allows the resulting nucleophilic
oxygen (a covalent catalyst) to
attack the carbonyl carbon of the
substrate.
- The tetrahedral intermediate (first TS)
decomposes when His 57, now acting as an acid catalyst, donates a proton to the nitrogen of the
scissile peptide bond. This step cleaves the bond. Asp 102 promotes the reaction by stabilizing His 57 through
hydrogen bonding. This creates the “real” intermediate which is the acyl-enzyme covalent intermediate. - Water then enters the active site.
It donates a proton to His 57 (again a base catalyst), leaving a hydroxyl group that attacks the carbonyl group of the remaining substrate. This step resembles Step 1 above. - In the second tetrahedral intermediate, His 57, now an acid catalyst, donates a proton to the Ser oxygen, leading to the collapse of the intermediate. This step resembles Step 2 above.
- The N-terminal portion of the original substrate, now with a new C-terminus, diffuses away, regenerating the enzyme.
Describe step 1 of the catalytic mechanism of chymotrypsin and other serine proteases
- The peptide substrate enters the active site of chymotrypsin so that its scissile bond (red) is close to the oxygen of Ser 195 (the N-terminal portion of the substrate is represented by RN, and the C-terminal portion by RC).
- Removal of the Ser hydroxyl
proton by His 57 (a base catalyst)
allows the resulting nucleophilic
oxygen (a covalent catalyst) to
attack the carbonyl carbon of the
substrate.
Describe step 2 of the catalytic mechanism of chymotrypsin and other serine proteases
The tetrahedral intermediate (first TS)
decomposes when His 57, now acting as an acid catalyst, donates a proton to the nitrogen of the
scissile peptide bond. This step cleaves the bond. Asp 102 promotes the reaction by stabilizing His 57 through
hydrogen bonding. This creates the “real” intermediate which is the acyl-enzyme covalent intermediate.
Describe step 3 of the catalytic mechanism of chymotrypsin and other serine proteases
Water then enters the active site.
It donates a proton to His 57 (again a base catalyst), leaving a hydroxyl group that attacks the carbonyl group of the remaining substrate. This step resembles Step 1 above.
Describe step 4 of the catalytic mechanism of chymotrypsin and other serine proteases
In the second tetrahedral intermediate, His 57, now an acid catalyst, donates a proton to the Ser oxygen, leading to the collapse of the intermediate. This step resembles Step 2 above.
Describe step 5 of the catalytic mechanism of chymotrypsin and other serine proteases
The N-terminal portion of the original substrate, now with a new C-terminus, diffuses away, regenerating the enzyme.
What is the role of the oxyanion hole in a catalytic mechanism?
The transition state is stabilized in the “oxyanion hole”
What does efficient catalysis depend on?
Proximity and orientation effects
How does the active site microenvironment of an enzyme promote catalysis?
Induced fit model
The binding of substrate to enzyme triggers a conformational change at the active site enhancing catalysis.
What are the conformational changes in hexokinase? Hexokinase, which catalyzes the phosphorylation of glucose by ATP (Reaction 1 of glycolysis).
What are the varying specificities of the enzymes chymotrypsin, trypsin, and elastase?
These enzymes have similar mechanisms but exhibit different substrate specificity or chemical characters called specificity pockets
- Chymotrypsin preferentially cleaves peptide bonds following large hydrophobic residues.
- Trypsin prefers the basic residues Arg and Lys, and Val
- Elastase cleaves the peptide bonds following small hydrophobic residues such as Ala, Gly, and Val (these residues predominate in elastin, an animal protein responsible for the elasticity of some tissues).
How are zymogens of proteases activated?
The inactive precursor of chymotrypsin is called chymotrypsinogen, and it is synthesized by the pancreas along with the zymogens of trypsin (trypsinogen), elastase (proelastase), and other hydrolytic enzymes. All these zymogens are activated by proteolysis after they are secreted into the small intestine.
An intestinal protease called enteropeptidase activates trypsinogen by catalyzing the hydrolysis of its Lys 6-Ile 7 bond. Enteropeptidase catalyzes a highly specific reaction; it appears to recognize a string of Asp residues near the N-terminus of its substrate:
How do protease inhibitors limit the activity of proteases?
The activity of proteases is limited by the action of protease inhibitors and by synthesizing the proteases as inactive precursors (called zymogens) that are later activated when and where they are needed.
