Exam III Flashcards
Which of the following statements is false for an enzyme that follows Michaelis-Menten kinetics? Option A: The relationship between substrate concentration and reaction rate is sigmoidal.
Option B: The initial velocity of the reaction is dependent on substrate concentration.
Option C: The Michaelis-Menten equation assumes that ES maintains a steady state.
Option D: Maximal velocity occurs when the enzyme is entirely in the ES form.
Option A: The relationship between substrate concentration and reaction rate is sigmoidal.
In uncompetitive inhibition, the inhibitor binds only to the ______.
Option A: substrate
Option B: enzyme
Option C: active site
Option D: ES complex
Option D: ES complex
For a reaction A + B → C, if the concentration of B is much larger than A so that [B] remains constant during the reaction while [A] is varied, the kinetics will be Option A: sigmoidal.
Option B: pseudo-first-order.
Option C: unimolecular.
Option D: zero-order.
Option E: hyperbolic.
Option B: pseudo-first-order.
An enzyme is near maximum efficiency when
Option A: its turnover number is near Vmax.
Option B: kcat/KM is near 108 M-1s-1.
Option C: k1 << k-1.
Option D: kcat/KM is equal to kcat.
Option E: KM is large when k2 exceeds k1.
Option B: kcat/KM is near 108 M-1s-1.
But It can be no greater than k1; that is, the decomposition of ES to E + P can occur no more frequently than E and S come together to form ES.
Pseudo-first-order reaction kinetics would be observed for the reaction A + B → C
Option A: if [A] or [B] > [C].
Option B: if [C]>[A] and [C]>[B].
Option C: if [A] or [B] = 0.
Option D: if [C] = 0.
Option E: None of the above.
Option E: None of the above. answer is [B]>>[A]
Different enzymes that catalyze the same reaction, although may be found in different tissues, are known as ______.
isozymes
A two-substrate enzymatic reaction in which one product is produced before the second substrate binds to the enzyme has a ______ mechanism.
ping-pong
A compound that distorts the active site, rendering the enzyme catalytically inactive is called
Option A: a uncompetitive inhibitor
Option B: an allosteric effector
Option C: an inactivator
Option D: a competitive inhibitor
Option E: none of the above
Option A: a uncompetitive inhibitor
Allosteric activators
Option A: bind via covalent attachment.
Option B: stabilize conformations with higher Ks.
Option C: stabilize conformations with higher substrate affinity.
Option D: All of the above.
Option E: None of the above.
Option C: stabilize conformations with higher substrate affinity.
Activator ATP preferentially binds to ATCase’s _____ state
R
Inhibitor CTP preferentially binds to ATCase’s _____ state
T
How do enzymes differ from ordinary chemical catalysts?
- Higher reaction rates
- Milder reaction conditions <100°C and neutral pH
- Greater reaction specificity for substrates and products; rarely have side products.
- Capacity for regulation: capacity for activities varies in response to concentration of other substances such as those that cause inhibitor, covalent modification of enzyme, and amounts of enzymes synthesized
Oxidoreductases
Enzyme that catalyzes oxidation reduction reactions
Tranferases
Enzyme that catalyzes the transfer of functional groups
Hydrolases
Enzyme that catalyzes the hydrolysis of reactions
Lyases
Enzyme that catalyzes group elimination to form double bonds
Isomerases
Enzymes that catalyze isomerization
Ligases
Enzyme that catalyzes bond formation coupled with ATP hydrolysis
what are the 2 forms of complementarity that enzymes have for substrates?
1. geometric: enzyme active site contains indentation that is complementary in shape to substrate
2. electronic: AA residues that form the binding site are arranged to specifically attract the substrate
^both non-covalent
^^this complementarity is the basis for the “Lock and Key” model
the substrate binding site is mostly pre-formed, but does undergo some conformational change upon binding the substrate. What term describes this phenomenon
induced fit
Enzymes are stereospecific because?
They are themselves chiral and form asymmetric sites.
geometric specificity refers to ?
the specificity for substrate based on the identities of the chemical groups on their substrates
T/F: geometric specificity is a more stringent requirement than is stereospecificity
True
partly d/t the fact that steric hindrance may block entry in the first place
T/F: Most enzymes catalyze the reactions of a small range of related compounds although with different efficiencies.
true
the difference is determiend by K value: Ethanol has a lower K value
For example: alcohol dehydrogenase catalyzes the oxidation of ethanol (CH3CH2OH) to acetaldehyde (CH3CHO) faster than it oxidizes methanol (CH3OH) to formaldehyde (H2CO) or isopropanol [(CH3)2CHOH] to acetone [(CH3)2CO], even though methanol and isopropanol differ from ethanol by only the deletion or addition of a CH2 group.
Other Variations in Geometric Specificity:
- A few enzymes are absolutely specific for only one compound.
- Some enzymes, particularly digestive enzymes, are so permissive in their ranges of acceptable substrates that their geometric specificities are more accurately described as preferences.
E.g chymotrypsin, in addition to its ability to mediate peptide bond hydrolysis, also catalyzes ester bond hydrolysis.
__lower/higher__ the K value, the more the substrate binds to the enzyme
lower
How would you describe the geometric specificity of chymotrypsin
Permissive (ie not very geometrically stringent)
it can hydrolyze both peptides and esters, 2 very different groups
Preferred substrates for chymotrypsin are _____, __ terminal amino acids
bulky, C terminal
<em>Recall: the AA to the right of C terminal end can’t be proline.</em>
If a lot of peptides have C terminal ends of bulky AAs, then we can assume that chymotrypsin is involved.
metal ions that are not natural cofactors can do what type of damage?
they can replace Zn2+ and render the active sites of certain enzymes inactive
which amino acid is essential in the functionality/folding of Zinc finger?
His
(Also Cys) - these bind with Zn to form active site
what is the K value for the reaction in which ethanol is turned into acetaldehyde?
K= 10-6
the K values for the other alcohols that have less binding affinity would be larger
NAD+ is an _____________agent in the alcohol dehydrogenase (ADH) reaction
obligatory oxidizing
T/F: in order to complete the catalytic cycle, the coenzyme must return to its original state
True
What stereospecific enzymes are used for
Binding of chiral molecules
Reactions involving prochiral molecules
2 types of processes that enzymes are unable to catalyze alone
Oxidation-reduction reactions
Group-transfer reactions
Cofactors that only transiently associate with a given enzyme molecule
Cosubstrates
4 examples of cosubstrates
NAD
NADH
FAD
FADH2
Enzymatically inactive protein resulting from the removal of a holoenzyme’s cofactor
Apoenzyme
Ratio of the rate of the catalyzed to uncatalyzed reaction
rate enhancement
T/F: catalyst lowers the free energy barrier by the same amount for both the forward and reverse reactions
true
How enzymes achieve their enormous rate accelerations (2)
- Reducing the free energy of the transition state 2.Stabilizing the transition state of the catalyzed reaction
Steps in RNase A mechanism (6)
- His 12 extracts a proton from RNA 2’OH group
- Nucleophilic attack on adjacent phosphorus atom
- His 119 protonates the leaving group
- Water enters active site
- His 12 (now an acid) and His 119 (now a base) facilitate hydrolysis of 2’3’-cyclic intermediate
- enzyme returns to original state
T/F: pH effects on an enzymatic rate may reflect denaturation of the enzyme rather than protonation or deprotonation of specific catalytic residues.
true
transformation of an amine and carboxylic acid into an imine is an example of what kind of catalysis?
covalent
T/F: The nucleophilicity of a substance is closely related to its basicity.
True
possible electrophiles for catalytic mechanisms include: ?
H+
Metal Ions (Mn+)
Carbonyl Carbon
Cationic imines
An important aspect of covalent catalysis is that the more/less stable the covalent bond formed, the more/less easily it can decompose in the final steps of a reaction.
more
less
what are the residue groups that can function as a nucleophile in covalent catalysis?
- Asp
- Cys
- His (unprotonated)
- Lys (unprotonated)
- Ser
mnemonic: ACHeLS
“K” sound for Covalent Catalysis
The active residues in lysozyme’s active site are ?
and which acts first
Asp and Glu
Glu35 acts first by giving off a hydrogen to O1, which stays attached to NAG
lysozyme cleaves the bond between carbon 1 of _____ and carbon 4 of _____
by ____________catalysis
carbon 1 of NAM and carbon 4 of NAG
general acid
how does a lysozyme degrade bacterial cell wall
by hydrolyzing the β(1→4) glycosidic linkages from N-acetylmuramic acid (NAM or MurNAc) to N-acetylglucosamine (NAG or GlcNAc) in cell wall peptidoglycans
what segment of the peptidoglycan is released first from a lysozyme
the segment with the NAG end