Chapter Eight Flashcards
Despite the diversity, all enzymes operate by …
facilitating the formation of the transition state.
Nucleophile:
How does a nucleophile participate in a chemical reaction?
Electrophile:
nucleophile is a chemical that is attracted to regions of positive charge in another molecule; participates in a chemical reaction by donating electrons to an electrophile
electrophile is a chemical that is electron deficient; electrophiles are attracted to nucleophiles (electron-rich molecules/regions)
What are the four common strategies that enzymes employ to catalyze specific regions?
- covalent catalysis
- general acid-base catalysis
- metal ion catalysis
- catalysis by approximation and orientation
Describe the four common catalytic strategies:
- the active site contains a reactive group (powerful nucleophile) that becomes temporarily covalently modified in the course of catalysis
- molecule (other than water) plays a role of a proton donor/acceptor
- done in various ways:
A. metal ion can serve as an electrophilic catalyst– stabilizing a negative charge on a reaction intermediate
B. metal ion may generate a nucleophile– increasing acidity of a nearby molecule (ex. water)
C. metal ion may bind to the substrate– increasing the number of interactions with the enzyme; increasing binding energy - when a reaction includes two distinct substrates; they are placed and oriented properly on a single binding surface of an enzyme (enhance reaction rate)
Binding energy:
the free energy released in the formation of the weak interactions between enzyme and substrate that facilitate the formation of the transition state
When is binding energy at the max?
Why? What does this promote?
when the enzyme binds to the transition state
this results in favoring the transition state and promotes catalysis
What are the modulators of enzymatic activity (3)?
- temperature
- pH
- inhibitory molecules
Temperature […] the rate of enzyme-catalyzed reactions.
enhances
Why does temperature enhance the rate of most reactions?
there is an increased in the Brownian motion which makes enzyme-substrate interactions more likely
In organisms that maintain constant body temperature are […]. The effect of outside temperature on enzyme activity is […].
In organisms that assume the temperature of the ambient environment […]. The effect of cooler temperature is […] and warmer temperature is […].
endotherms; minimized
ectotherm; inactive biochemical activity; active biochemical activity
What are the three types of reversible inhibition?
- competitive
- uncompetitive
- noncompetitive
Explain each type of reversible inhibition and describe its overall effect:
- Competitive inhibition: inhibitor resembles the substrate and binds to the active site EI; diminishes the rate of catalysis
- Uncompetitive inhibition: substrate-dependent inhibition where the inhibitor binds only to the ES complex; diminishes the rate of catalysis
- Noncompetitive inhibition: inhibitor and substrate can bind simultaneously to an enzyme molecule at different binding sites; decreasing the number of active enzymes
Which reversible inhibition can be resolved? How?
competitive inhibition– it can be overcome by sufficiently high concentrations of substrate
What are the effects of Km and Vmax during competitive inhibition? What do these changes mean?
Km– value is increased; this means more substrate is needed to obtain the same reaction rate
Vmax– remain the same– with more substrate to overcome inhibitors, the value of Vmax will be reached (enzymes will be still fully active with large amount of substrate)
What are the effects of Km and Vmax during uncompetitive inhibition? What do these changes mean?
Km– value is lowered; no product form is made to reach the rate of the reaction (lower concentration of S is required to form 1/2 maximal concentration of ES)
Vmax– value is lowered; inhibitor only binds to the ES complex which doesn’t proceed to form any product (always present so lowers Vmax)
What are the effects of Km and Vmax during noncompetitive inhibition? What do these changes mean?
Km– unchanged; a substrate can still bind to the enzyme
Vmax– lowered; inhibitor lowers the concentration of functional enzyme (dilute solution results)
Double-reciprocal plots: How can you distinguish competitive inhibition?
y-axis– same Vmax whether or not inhibitor is present
x-axis– increase in Km app compared to Km
greater slope with presence of inhibitor
Double-reciprocal plots: How can you distinguish uncompetitive inhibition?
y-axis– Vmax is reduced (1/Vmax is increased)
x-axis– Km is reduced (1/Km is increased)
slopes are equivalent; parallel lines result
Double-reciprocal plots: How can you distinguish noncompetitive inhibition?
y-axis– Vmax is decreased (1/Vmax is increased)
x-axis– Km is unchanged
greater slop with inhibitor present
Irreversible inhibitors […] bind either […] or […] to an enzyme. These result in […] modification.
tightly; covalently; noncovalently; functional group
What are the four categories of irrevesible inhibitors?
- group-specific reagents
- affinity labels (substrate analogs)
- suicide inhibitors
- transition-state analogs
Group specific reagents: modify […] of […].
specific R groups; amino acids
Affinity labels: molecules that […] modify […] and are […] similar to an enzyme’s susbtrate. They are more specific for the active site than […].
covalently; active site residues; structurally; group specific
Suicide inhibitors– […] modified substrates. The mechanism of catalysis generates a chemically […] that […] the ezyme through […] modification.
chemically; reactive intermediate; inactivates; convalent
Transition-state: A compound resembling the […] of a […] reaction.
transition state; catalyzed
Why is protein TO important (2)? What class of enzymes participate in the breakdown of proteins?
- preoteins must be degraded so amino acid constituents may be recycled
- ingestion of protein must be broken down into small peptides and amino acids for absorption
proteolytic enzymes
General mechanism of proteolytic enzymes:
enzymes cleave proteins by a hydrolysis reaciton (water to a peptide bond)
Chymotrypsin cleaves […] bonds selectively on the […] termianl side of the large […] amino acids.
These consist of … (5).
peptide; carboxylic; hydrophobic
- tryptophan
- tyrosine
- phenylalanie
- methionine
- isoleucine
How does chymotrypsin use covalent modification as its catalystic strategy (2)?
- there’s use of a powerful nucleophile to attack the unreaction carbonyl group of the substrate
- nucleophile becomes covalently attached to the substrate temporarily
What is the nucleophile chymotrypsin uses to attack the carbonyl group?
reactive serine residue
How was histidine found to be an important reside in catalysis?
affinity labeling
What residues are part of the catalytic triad?
serine 195, histidine 57, aspartate 102
