Chapter 6: Enzymes Flashcards
What are 2 good reasons to use proteins/enzymes as catalysts? How do they catalyze?
Greater reaction specificity (enzymes make the desired pathway most favorable) and capacity for regulation.
Enzymes catalyze by providing an environment (active site) within which a given reaction can proceed more rapidly – they bind
substrates. This lowers the activation energy without affecting the overall Free Energy. The active site is lined with residues that bind the
substrate and catalyze its chemical transformation. These active site residues also contribute to substrate specificity.
An enzyme increases the rate of a reaction (reaches equilibrium faster) but does not alter reaction equilibria.
How can energy barriers be a good thing?
They prevent the spontaneous decay of all biomolecules.
What are most enzymes?
Most enzymes are Globular Proteins (but some RNA also catalyze reactions – Ribozymes).
When are the terms ‘binding site’ vs. ‘active site’ used?
Binding site is referring to a ligand/receptor relationship. Active site is referring to an enzyme/substrate relationship.
What is the Michaelis Complex formula (2 forms)? What is it describing?
Enzyme-Substrate Complex – Allows for development of Kinetic Equations.
v = vmax [S] / Km + [S]
or
v = Kcat [E]tot [S] / Km + [S]
(where Km is the Michaelis Constant: The substrate concentration at which the reaction rate is ½ Vmax).
List 3 ways enzymes lower transition state energy barriers.
They rearrange covalent bonds during catalysis (Lego example). Amino side chains may form a transient covalent bond with a substrate
and activate it for reaction or a group may be transiently transferred from the substrate to the enzyme.
They organize reactive groups into close proximity.
Via the energy associated with formation of non-covalent interactions between the substrate and the enzyme. Energy such as Hydrogen
bonds, Ionic bonds, Van Der Waals, and Hydrophobic Interactions.
What state of the substrate do the enzymes evolve to fit via induced fit process? How does this affect specificity?
The transition state. Because of this, the enzyme will not interact to the same degree with another molecule.
What is Km? Kcat?
Substrate concentration at ½ Vmax where V is initial velocity measuring binding speed. Kcat is the ‘Turnover Number’ meaning the
number of substrate molecules that one enzyme can convert per second.
Km = Kd only when K2 (dissociation of the enzyme from the substrate to form the product) is rate limiting (very slow). This is very rare.
What does the term ‘Steady State’ imply?
Rate is continuous.
What are the 2 different Types of Enzyme Mechanisms?
In ‘Sequential mechanism’, random or ordered can happen – one is made before the other and a ternary complex (ES1S2) will form. Lines
in Lineweaver-Burk plot cross over. In ‘Ping-Pong’, no ternary complex is formed and the first substrate modifies the enzyme. Lines in
Lineweaver-Burk plot do NOT cross over.
What is an inhibitor? Describe the 3 different types of inhibition.
Compounds that decrease enzyme’s activity.
Competitive: The inhibitor competes with the substrate for the active site. Lines in Lineweaver-Burk plot intersect at y-axis.
Uncompetitive: The inhibitor binds at a different site AFTER substrate binds. Lines in Lineweaver-Burk plot are parallel.
Noncompetitive/Mixed: A little bit of both above. Lines in Lineweaver-Burk plot intersect left of y-axis.
What is Chymotrypsin? What 3 Amino Acids are in the Catalytic Triad?
A protease that cleaves peptides on the C-Terminal Side of Phenylalanine, Tyrosine, and Tryptophan residues.
Catalytic Triad = Asp, His and Ser.
What are the 2 key Amino Acid residues in the Enolase mechanism?
Lysine and Glutamate.
