Chapter 2: Enzymes Flashcards
What is a catalyst?
Do not impact the thermodynamics of a biological reaction
Does an enzyme change the equilibrium position of a reaction?
No, by definition, catalyst do not change the equilibrium position
Do enzymes affect the overall deltaG of a reaction?
No
How do enzymes increase the reaction rate?
By lowering the energy of activation
What are substrates?
The molecules upon which an enzyme acts
What are the major classifications of enzymes? What is the mnemonic?
- LI'L HOT Ligase Isomerase Lyase Hydrolase Oxidoreductase Transferase
In reactions catalyzed by oxidoreductases, the electron donor is known as the _____, and the electron acceptor is known as the ____.
donor: reductant
acceptor: oxidant
Enzymes with dehydrogenase, reductase, or oxidase are usually ______.
oxidoreductases
Enzymes with kinase are usually ____.
transferases
What do kinases catalyze?
The transfer of a phosphate group, generally from ATP, to another molecule
Phosphatase, peptidase, nuclease, and lipase are examples of which enzyme class?
Hydrolases
What do lyases catalyze?
- The cleavage of a single molecule into two products (without water)
- The synthesis of two molecules into a single molecule
What are synthases?
Lyases
What do ligases catalyze? What do they require?
- Addition or synthesis reactions
- Often require ATP
Differentiate endergonic and exergonic reactions.
Endergonic: one that requires energy input (deltaG > 0)
Exergonic: one in which energy is given off (deltaG <0)
Do enzymes affect the kinetics of a reaction?
Yes, by lowering the energy of activation
How do enzymes act? (3)
- By stabilizing the transition state
- Providing a favorable micro-environment
- Bonding with the substrate molecules
What is the active site of an enzyme?
The site of catalysis
What does the lock and key theory hypothesize?
That the enzyme and substrate are exactly complementary
What does the induced fit model hypothesize?
That the enzyme and substrate undergo conformational changes to interact fully
Differentiate cofactors and coenzymes.
- Cofactors: metal cation (minerals)
- Coenzymes: small organic (vitamins)
Differentiate apoenzymes and holoenzymes.
Apoenzymes: enzymes without their cofactors
Holoenzymes: enzymes with their cofactors
What are prosthetic groups?
Tightly bound cofactors or coenzymes
When is an enzyme working at maximum velocity?
When it has become fully saturated, adding more substrate will not increase the rate of reaction
When the reaction rate is equal to half of vmax, km = ?
km = (S)
What is the Michaelis-Menton equation?
v = (vmax (S)) / (Km + (S))
A low Km reflects a ____ affinity for the substrate?
high
What are the two definitions of Km?
- (S) at which half of the enzyme’s active sites are full
- Measure of the affinity of the enzyme for its substrate
Can you alter Km by changing the concentration of substrate or enzyme?
No
What is the intercept of the line with the x-axis in the Lineweaver-Burk plot?
- (1/Km)
What is the intercept of the line with the y-axis in the Lineweaver-Burk plot?
1/v
Why do certain enzymes show sigmoidal (S-shaped) kinetics and not the normal hyperbola in the v vs (S) plot?
Due to cooperativity among substrate binding sites
What are cooperative enzymes?
They have multiple subunits and multiple active sites
What is cooperativity?
Refers to the interactions between subunits in a multisubunit enzyme or protein
Subunits and enzymes may exist in one of two states. What are they?
- Low-affinity tense state (T)
- High-affinity relaxed state (R)
In a cooperative enzyme, what does the binding of the substrate encourage?
- Transition from T state to the R state
- Increases the likelihood of substrate binding by these other subunits
In a cooperative enzyme, what does the loss of the substrate encourage?
- Transition from the R state to the T state
- Promotes dissociation of substrate from the remaining subunits
How can cooperative enzymes be subject to activation and inhibition?
Competitively and through allosteric sites
Give examples of cooperative binding.
- Hemoglobin (acts as a transport protein rather than an enzyme)
- Regulatory enzymes in pathways (ex: PFK-1)
What are the effects of increasing (E)?
Will always increase vmax, no matter the starting concentration
What are the axes in the M&M graph? What kind of curve does that create for monomeric enzymes?
- v vs. (S)
- Hyperbolic curve
What are the axes in the Lineweaver-Burk graph? What kind of curve does that create for monomeric enzymes?
- 1/v vs. 1/(S)
- Straight line
How do the terms enzyme activity, enzyme velocity, and enzyme rate differ?
They are synonyms; do not differ
For every 10oC increase, enzyme activity ____
doubles
What is the optimal temperature for the human body?
37oC = 98.6oF = 310 K
What are the two reasons that explain why enzymes depend on pH to function properly?
- pH affects the ionization of the active site
- Changes in pH can lead to denaturation of the enzyme
How can altering the concentration of salt change enzyme activity in vitro?
Changes in salinity can disrupt bonds within an enzyme, causing disruption of tertiary and quaternary structures, which leads to loss of enzyme function
Define feedback inhibition.
A regulatory mechanism whereby the catalytic activity of an enzyme is inhibited by the presence of high levels of a product later in the same pathway
What is reversible inhibition?
The ability to replace the inhibitor with a compound of greater affinity or to remove it using mild laboratory treatment
What is irreversible inhibition?
Alters the enzyme in such a way that the active site is unavailable for a prolonged duration or permanently; new enzyme molecules must be synthesized for the reaction to occur again
What are the four types of reversible inhibition?
- Competitive inhibition
- Noncompetitive inhibition
- Mixed inhibition
- Uncompetitive inhibition
What is competitive inhibition? Where does the inhibitor bind? How do vmax and Km change?
- Inhibitor is similar to substrate and binds to the active site
- Vmax unchanged
- Km increases
Which inhibition can be overcome by adding more substrate?
Competitive inhibition
What is noncompetitive inhibition? Where does the inhibitor bind? How do vmax and Km change?
- Inhibitor binds with equal affinity to the enzyme and the enzyme-substrate complex
- Vmax decreases
- Km unchanged
What is mixed inhibition? Where does the inhibitor bind? How do vmax and Km change?
- Inhibitor binds with unequal affinity to the enzyme and the enzyme-substrate complex
- Vmax decreases
- Km increased or decreased depending on if the inhibitor has higher affinity for the E or the ES complex
What is uncompetitive inhibition? Where does the inhibitor bind? How do vmax and Km change?
- Inhibitor binds only to the ES complex ONCE the substrate has already bound
- Vmax decreases
- Km decreases
What are allosteric sites?
Non-catalytic regions of the enzyme that bind regulators
If a mixed inhibitor preferentially binds to the enzyme, what happens to the Km value?
Increases Km
Lowers affinity
If a mixed inhibitor preferentially binds to the ES complex, what happens to the Km value?
Decreases Km
Increases affinity
Give a popular real-world example for irreversible inhibition.
Aspirin
What do allosteric enzymes possess?
Multiple binding sites
Differentiate allosteric activators and inhibitors.
Activators: shift that makes the active site more available for binding
Inhibitors: shift that makes the active site less available for binding
Give examples of transient modifications.
Allosteric activation or inhibition
Give examples of covalent modifications.
Phosphorylation/Dephosphorylation and glycosylation
What is a zymogen?
Precursors of an active enzyme
What is the role of zymogens? Give an example.
Critical that certain enzymes (digestive enzymes of the pancreas) remain inactive until arriving at their target site
What are zymogens composed of?
- Contain a catalytic (active) domain and a regulatory domain
- Regulatory domain must be either removed or altered to expose the active site
What is the suffix to most zymogens?
-ogen
