Flashcards in Lecture # 7 How Enzymes Work, Introduction to Kinetics Deck (35):
What is an enzyme?
A substance made by an organism that acts as a catalyst. Enzymes lower the activation energy barrier. Most enzymes are proteins, a few RNA molecules are ribozymes, many include cofactors, or coenzymes.
Are some enzymes proteins?
Are some proteins enzymes?
Are all enzymes proteins?
Are all proteins enzymes?
Why don't substances spontaneously combust?
Because of the inherent activation energy barriers for compounds
The barrier to convert substrates to products.
Are enzymes complementary to the substrate thermodynamically favorable? Why or why not?
They are not thermodynamically favorable. By stabilizing the substrate, the enzyme creates an even greater barrier to get the substrate to the transition state. An enzyme that is the same to the transition state puts stress on the substrate and is more thermodynamically favorable.
Isn't it hard to form an enzyme substrate complex if the substrate doesn't fit well?
No, the bonds forming are greater than the chemical bonds already present.
Quantifying Reaction Rates
1)rate constant k = d [p]/dt; rate is not affected by the total dG, but is affected by the energy barrier for the reaction dG+.
The Arrhenius Equation
The relationship between dG+ and the rate constant; k = Ae^-dG+/RT
What do we get from the Arrhenius equation? What does it mean?
K=Ae^-dG+/RT; A is the number of collisions per second; k is inversely and exponentially related to dG+, and directly related to T.
Transfer of electrons
Transfer of functional groups
Single Bond Cleavage (water)
Bond cleavage by elimination
Bond Formation (ATP dep.)
What are the six classes of enzymes?
Hot Lily (Hydrolase, Oxidoreductase, Transferase, Lyase, Isomerase, Ligase.
What are the five mechanisms of catalysis?
SCCAM (Strain, Cage effect, Covalent, Acid-Base, Metal Ion)
Mechanism of catalysis; stabilize ions in a high-energy pattern
Mechanism of catalysis; give and take protons
Mechanism of catalysis; binding two substrates in the correct orientation
Mechanism of catalysis; use of redox co-factors
Mechanism of catalysis; Change of reaction paths
A protective enzyme in saliva that helps to destroy bacteria by breaking polysaccharides in bacterial cell walls. Its mechanism for catalysis is strain.
Enzyme. Mechanism of catalysis is the cage effect
Why is the cage effect an important mechanism in catalysis?
In solution, most molecular collisions aren't in the correct orientation or length of contact. The cage-effect helps take two or more substrates, and puts them in the correct orientations so that reactions can occur.
Gut enzyme that breaks down proteins and peptides. It uses an acid or base (other than H+ or OH-) to add charge stress to the bound substrate. ; mechanism of catalysis (acid-base)
What are the eight amino acids commonly used in Acid-base catalysis?
E, D, K, R, C, H, S, Y
Draw out the Chymotrypsin mechanism
Why do we quantify enzyme kinetics?
Kinetics determines what factors affect the rates of enzyme-catalyzed reactions. Some of those factors include (pH, temperature, ionic strength, mechanism of reactions.)
Transition State Analogs
compounds that mimic the substrate, binds to and stabilizes the enzyme and decreases its activity.
Why do we quantify Enzyme kinetics?
To understand the effects that enzyme concentration,substrate, product, inhibitor, activator concentrations, pH, ionic strength, temperature have on enzymatic functions.