Chapter 5: Enzymes Flashcards
What are enzymes?
Organic substances that act as biocatalysts that increase the rate of chemical reactions.
What is the nature of enzymes?
Most enzymes are protein in nature. Some are RNA in nature and are called ribozymes.
How are enzymes produced or consumed in chemical reactions?
They are neither produced nor consumed in chemical reactions.
Do enzymes change chemically at the end of a reaction?
No
How do enzymes affect the equilibrium of a reaction?
It doesn’t affect the equilibrium constant (-G stays the same).
How specific are enzymes in their actions?
They are highly specific in their action. They act on specific substrate or few related substrates.
How are enzymes made?
They are produced by living cells, cellular catalysts, but can work in vivo and vitro.
What is the amount of enzymes needed for a chemical reactions?
They are needed in very small amounts for a chemical reaction.
Nomenclature old method:
- Pepsin
- Trypsin
- Chymotrypsin
- Rennin
Nomenclature new method
- Hydrolase: substrate + ase: sucrase, glucosidase, urease, arginase.
- Other actions: substrate + action of enzyme: lactate dehydrogenase, pyruvate carboxylase, adenylate cyclase.
Enzyme specificity
Enzymes are highly specific in their actions, interacting with 1 absolute specificity or few related substrates of relative specificity.
What are enzymes highly specific?
Enzymes specificity is due to the nature and arrangement of the chemical groups at the catalytic site.
What is the importance of enzyme specificity?
- Digestive enzymes are of low specificity allowing a few numbers of enzymes to digest all food.
- Metabolic enzymes are of high specificity to be well regulated.
Chemical nature of enzymes is divided into?
- Simple protein enzymes: formed of only amino acids.
- Conjugated protein enzymes.
Conjugated protein enzymes are divided into?
- Protein part (apoenzyme).
- Non protein part (cofactor).
What enzymes are protein in nature?
All enzymes are proteins in nature except for ribozymes, which are RNA in nature.
What enzymes are protein in nature?
All enzymes are proteins in nature except for ribozymes that are RNA in nature.
What are holoenzymes?
Apoenzymes and cofactors together.
What happens to apoenzymes alone?
Inactive
Cofactors
- Coenzyme: prosthetic group or co-substrate.
- Metal ion: mettaloenzymes or metal activated enzymes.
Coenzymes (organic)
Prosthetic group: tightly bound to apoenzyme by covalent or non-covalent forces.
Co-substrate: loosely bound to apoenzymes.
Metal (inorganic)
Metalloenzyme: cation is tightly bound to the apoenzyme.
Metal activated enzymes: cation loosely bound to apoenzyme.
Enzymes are large protein molecules that contain a small specific regions each such as:
- Active sites (catalyst sites) or substrate binding sites: complementary to the substrate.
- Allosteric site: binds with organic modifiers.
Active sites
- Amino acids arranged in a specific manner that makes the enzyme specific to one substrate or few related substrates.
- The active site is rich in many groups such as:
- COOH
- SH
- OH
- NH2 - The active site is rich in certain amino acids:
- Serine and Cysteine
- Glutamate and aspartate
- Histidine
What are the theories that can explain the mechanism of the enzyme’s actions?
- Induced fit theory.
- Lowering the energy of activation.
Induced fit theory
When the substrate approaches the enzyme, the active site becomes similar to the substrates so the substrate fits into the enzyme forming an Enzyme-Substrate complex that gives enzyme+product.
Lowering the energy of activation
- For any substrate to give product, it should be placed at a high energy called the energy of activation. Enzymes decrease the energy of activation.
- Enzymes don’t affect the equilibrium constant, G stays the same.
- G = Energy of products - substrate.
What are the factors that affect the rate of enzyme catalyzes reactions?
- Concentration of substrates [S].
- Concentration of Enzymes [E].
- Concentration of cofactors [C].
- Concentration of products [P].
- Temperature
- PH
How many factors change at a time?
Only 1 factor is changed at a time, while the remaining factors should remain constant.
When should the velocity be measured?
At the beginning of the reaction (initial velocity or Vi).
Concentration of a substrate [S]
- Velocity of a reaction.
- Km (Michaelis constant).
- Michaelis-Menten equation.
- Significance of Km.
- Lineweaver- Burk plot (double reciprocal plot).
Velocity of a reaction
Number of substrate molecules converted per unit time.
1. Increase in [S] = Increase in velocity of a reaction, directly proportional.
2. When Vmax (maximal velocity) is reached, further increase in [S] won’t increase the velocity of a reaction.
Km (Michaelis constant)
Substrate concentration the produces half the Vmax.
1. At Vmax, all enzymes are saturated with substrates so further increase in [S] will not increase the reaction velocity.
2. Before Km: the reaction is responsive to the increase of [S] which will lead to a linear curve.
3. After Km: the reaction is less responsive to increased [S] which will lead to a non-linear curve.
Michaelis-Menten equation
Describes the behavior of many enzymes when [S] is changed.
Vi= Vmax [S]/ Km + [S]
Significance of Km
- Index for the affinity of the enzymes to substrates ( the lower the Km, the higher the affinity).
- Isoenzymes have different Km’s.
- If there is an enzyme that binds to several substrates, each substrate will have a different Km.
- If there is an inhibitor that decreases the binding of the substrate to the enzyme, it will decrease the affinity which will increase the Km.
Lineweaver-Burk plot (double reciprocal plot)
- Michaelis-Menten equation gives a non linear (hyperbolic) curve at Vmax, and increase in [S] will not increase the velocity.
- The curve is converted into a linear one by taking the reciprocal of both the [S] and V and plot in 1/[S] and 1/V (double reciprocal plot).
- This will give a linear relationship so at any [S], we can obtain a velocity for the lower reaction.
Concentration of enzymes [E]
- An increase in [E] will lead to an increase in the velocity until a certain point (Vmax).
- Beyond Vmax, further increase in [E] will not increase the velocity.
- [S] is the limiting factor.
Concentration of Cofactors [C]
- Increase in [C] will increase velocity of the reaction until a certain point (Vmax).
- Beyond Vmax, further increase in [C] will not increase the Vi.
- The [E] is the limiting factor.
Concentration of products [P]
- Increase in the concentration of products will lead to the decrease of the velocity of a reaction.
- Decrease in the concentration of products will lead to increase of the velocity of a reaction.
Temperature
- Optimum temperature of most enzymes is 37 degrees Celsius.
- Below this temperature, a decrease in velocity will occur due to decrease in collision between the enzyme and substrate . For example, 0 C will lead to the stopping of a reaction.
- At 70C the reaction stops due to denaturation.
What is the optimum temperature for plant enzymes?
50C
PH
- Each enzyme has its optimum PH at which the reaction reaches maximum velocity.
- Below or above this optimum Ph, the reaction will decrease.
- The optimum Ph for most enzymes is between 5-9.
- Optimum Ph for pepsin is 2.
- At Ph 2 units above or below the optimum Ph will lead to stopping of reaction.
Optimum Ph for pepsin
2
Why can the Ph affect the catalytic activity of the enzyme?
- Slight changes in Ph: alteration of the charges on the substrate no active site of enzyme.
- Extreme changes in Ph: Denaturation which will lead to irreversible inhibition of the enzyme action.
Inhibitors
Any substance that can decrease the activity of an enzyme catalyzed reaction.
What are types of enzyme inhibitors?
- Competitive inhibitors.
- Allosteric inhibitors.
- Other inhibitors.
Competitive inhibitors
- The inhibitors is similar (structural analogue) to the substrate.
- The inhibitor competes with the substrate for binding with the active site of the enzyme which decreases the rate of chemical reaction.
- The inhibition depends on the concentration of the inhibitor and the substrate. An increase in the concentration of the substrate will remove the inhibition (reversible inhibition).
What is the effect of competitive inhibitors on Km and Vmax?
- Km is increased.
- No effect on Vmax.
What are example of competitive inhibitors?
- Sulfonamide or sulfanilamide.
- Allopurinol.
- Dicumarol and warfarin.
- Statins.