103 Questions
What is the function of ligases?
Paste two pieces together (make a chemical bond), uses ATP
Which enzyme type is responsible for breaking a chemical bond by adding water across it?
Hydrolases
Which coenzyme is a building block of Vitamin B1?
Thiamine Pyrophosphate
What is the common theme associated with Coenzyme A?
Sulfur
Which enzyme type is responsible for rearranging the order of atoms in a molecule (isomerization)?
Isomerases
What is the function of histidine (H57) in the active site of chymotrypsin?
Proton acceptor
Which class of proteases requires Ca++ as a cofactor and is found in Eukaryotes and Eubacteria, but not Archaea?
Calpains
Which enzyme is known for cleaving precursor proteins and is a homodimer with one active site per subunit?
HIV Protease
Which protease has an active site composed of the amino acids His-His-Glu and requires Zn as a cofactor?
Thermolysin
In the liver, Alcohol Dehydrogenase (ADH) uses NAD+ to convert alcohols to which compound?
Acetaldehyde
Which term best describes the relationship between enzymes and effectors?
Allosteric
In enzyme diversity, how many biological reactions/enzyme categories are typically recognized?
Six
Which enzyme is associated with the need for speed in enzyme catalysis?
Chymotrypsin
What type of binding does hemoglobin demonstrate as a case study in enzyme diversity?
Cooperative binding
In enzyme diversity, which term best describes the relationship between substrate binding and cooperativity?
Allosteric
How many families of carbonic anhydrases have been discovered?
8
What metal ion is used by the η family of carbonic anhydrases?
Zinc
What catalytic strategy is employed by the active site of carbonic anhydrases?
Covalent catalysis
What is the medical application of carbonic anhydrases related to artificial lungs?
Carbon dioxide removal
How many splice variations of carbonic anhydrases are produced by humans?
15
What is the role of an apoenzyme?
To form the whole active enzyme
In the context of enzyme diversity, which type of reaction results in swapping functional groups?
Nucleophilic Substitution
What is the preferred state of ATCase when CTP binds to it?
Tense (T) state
What is the function of zymogens?
To require proteolytic activation
What type of kinetics can multiple binding site enzymes follow if they are noncooperative?
Michaelis-Menten kinetics
What is the role of effector binding in enzyme function?
To change the conformation of the enzyme
What is the type of reaction catalyzed by serine proteases like chymotrypsin?
Hydrolysis reaction
What is the catalytic triad of chymotrypsin composed of?
Cysteine, Histidine, Aspartate
What is the main catalytic strategy employed by carbonic anhydrases?
Acid-base catalysis (Approximation)
Why do we need proteases like chymotrypsin?
To synthesize shorter polypeptides
What is the purpose of reversible covalent modifications in proteins?
To activate/inactivate the enzyme
Which type of molecule is Myristic Acid?
A fatty acid
What is the main contribution of carbohydrates to the proteome?
Adding diversity to the proteome
Which color represents nucleotides in the structures referred to in the text?
Green
What is the significance of ADP-ribose in reversible covalent modifications?
It is a common addition to nucleic acids
What is the role of Farnesyl in reversible covalent modifications?
To serve as an intermediate in cholesterol synthesis
What type of modification creates nonproteinogenic amino acids by adding functional groups to activate/inactivate enzymes?
Reversible covalent modifications
What is the color used to represent fatty acids in the structures mentioned in the text?
Red
In the context of enzyme diversity, what is the main difference between apoenzymes and holoenzymes?
Apoenzymes are inactive and lack cofactors, while holoenzymes are active and contain cofactors.
When CTP binds to ATCase, what is the preferred state of the enzyme?
Tense (T) state
What is the catalytic triad of chymotrypsin composed of?
Histidine, Serine, Aspartate
What type of binding does hemoglobin demonstrate as a case study in enzyme diversity?
Homotropic allosteric binding
What metal ion is used by the η family of carbonic anhydrases?
Zinc (Zn)
What is the function of zymogens?
They are inactive and require proteolytic activation.
What is the main contribution of carbohydrates to the proteome?
Stabilization of protein structures
What is the main catalytic strategy employed by carbonic anhydrases?
Nucleophilic addition
What is the function of the oxyanion hole in chymotrypsin's active site?
Stabilizes the tetrahedral intermediate (transition state)
Which class of proteases requires Ca++ as a cofactor and is found in Eukaryotes and Eubacteria, but not Archaea?
Calpains
What is the active site composition of the MMPs proteases?
His-His-Glu
Which metal ion is required by Thermolysin's active site for its function?
Zn
What is the role of Renin in the body?
Helps increase blood pressure and retain water/salt
Which active site residues are split over a heterodimer by Calpains?
(S195) and (G193)
What is the main role of Alcohol Dehydrogenase (ADH) in the liver?
Converts alcohols to acetaldehyde
8.106
$NAD+$ resides in the active site of ADH
What is the specific role of the S1 pocket in chymotrypsin's active site?
Determines placement of cut
What is the main role of HIV Protease in cleaving precursor proteins?
Cleave precursor proteins
What type of kinetics do Michaelis-Menten enzymes follow?
First order kinetics
In the context of reversible reactions, at equilibrium, what is the condition that must be satisfied?
$k_1S = k_{-1}P$
What are the two important equilibrium constants defined for reversible reactions?
Dissociation Constant and Association Constant
What type of reaction does zero order kinetics represent?
Unimolecular reaction
What kinetics does a reversible reaction follow at equilibrium?
$k_1S = k_{-1}P$
What does the condition $k_1S = k_{-1}P$ signify in a reversible reaction?
The reaction is at equilibrium
In Michaelis-Menten kinetics, what is true about catalysis?
It is a first-order reaction
What type of reaction is indicated by the condition $k_1S = k_{-1}P$ in a reversible reaction?
$k_1S = k_{-1}P$ signifies that the reaction is at equilibrium
Which type of kinetics do second-order reactions follow?
Bimolecular kinetics
What is true about catalysis according to Michaelis-Menten kinetics?
It follows first-order kinetics.
In which type of kinetics do Michaelis-Menten enzymes follow?
First order kinetics
What is the interpretation of the condition $k_1S = k_{-1}P$ in a reversible reaction?
The substrate is being both used and created
Which type of reaction does zero order kinetics represent?
Unimolecular reaction
What is the main difference between Michaelis-Menten enzymes and first order kinetics?
Catalysis is not a first order reaction
What type of kinetics can multiple binding site enzymes follow if they are noncooperative?
Michaelis-Menten kinetics
In the context of Michaelis-Menten kinetics, what does the term 'Km' represent?
A dissociation constant for substrate binding
What does the turnover number (kcat) in Michaelis-Menten kinetics indicate?
The number of substrate molecules converted per active site per time
What does the equilibrium constant (KS) in Michaelis-Menten kinetics define?
The association constant for substrate binding
How can the Michaelis-Menten model be simplified when not much product (P) is present and [E·P] is approximately 0?
By ignoring k-3 and k1
What assumption allows the simplification of the Michaelis-Menten model to E + S ⇌ E·S → E + P?
Binding of the substrate is at equilibrium
What is the Michaelis-Menten equation in its most familiar form?
$\frac{\nu_{max}}{\nu_0} = \frac{K_m + S}{S}$
What does it signify if k2 is the rate-limiting step in the Michaelis-Menten kinetics?
$K_m \approx \frac{k_{-1}}{k_1}$
What condition indicates that νmax is reached when the enzyme is fully saturated?
[E·S] = [E]T
What does the abbreviation $\nu_0$ represent in the context of Michaelis-Menten kinetics?
Initial reaction rate
What does the Michaelis constant ($K_m$) represent in Michaelis-Menten kinetics?
The concentration of enzyme-substrate complex at half of its maximum value
What is the main difference between cooperative enzymes and noncooperative enzymes with respect to following Michaelis-Menten kinetics?
Noncooperative enzymes can follow Michaelis-Menten kinetics, while cooperative enzymes cannot.
In the context of enzyme kinetics, what does the condition $k_1S = k_{-1}P$ signify in a reversible reaction?
The reaction is at equilibrium.
Which catalytic strategy is commonly employed by enzymes according to Michaelis-Menten kinetics?
Acid-base catalysis
What is the significance of the oxyanion hole in chymotrypsin's active site?
It stabilizes the transition state of the reaction.
What type of enzyme kinetics do cooperative enzymes exhibit?
Sigmoidal kinetics
In the context of Michaelis-Menten kinetics, what is the significance of the x-intercept in a Lineweaver-Burk plot?
It represents the reciprocal of the Michaelis constant (1/KM)
How does the Hill coefficient (nH) differ in the context of cooperative binding as described by the Hill equation?
It is equal to 1 for non-cooperative binding and greater than 1 for cooperative binding
What effect does a perfectly cooperative binder (n > 1) have on the approximation of θ in the Hill equation?
It leads to an overestimation of θ
What does a Hill plot of Hemoglobin with nH > 1 indicate about its binding characteristics?
Positive cooperativity
How does the slope of a Hill plot relate to the level of cooperativity in ligand binding?
The slope decreases with negative cooperativity and increases with positive cooperativity
What is the relationship described by the Hill equation?
Binding analyses for multiple binding site enzymes
In Michaelis-Menten kinetics, what does a poor enzyme with kcat > k-1 represent?
High catalytic efficiency
What does the condition kcat/km = 1 indicate in the context of Michaelis-Menten kinetics?
Dominance of kcat over km
What does the dissociation constant (KD) represent in terms of enzyme kinetics?
Affinity between enzyme and substrate
What does the condition Km 𝜈0 = 𝜈max/2 indicate in Michaelis-Menten kinetics?
Half-maximal velocity of the reaction
What is the reaction rate for an IRREVERSIBLE reaction?
ν = ΔS - ΔT
Which representation of the reaction data is most suitable for determining the reaction order?
1/[S] vs. time
What is the interpretation of the condition ν = k[S]n?
It indicates first-order kinetics
What is the significance of the slope (k) in the linear response of 1/[S] vs. time?
It represents the rate constant (k)
What does the term 'hyperbolic' refer to in kinetics trends?
A non-linear response in reaction rates
In Michaelis-Menten kinetics, what does ν represent in the equation ν = νmax[S] / (Km + [S])?
Maximum reaction rate
What does the value of Km indicate in Michaelis-Menten kinetics?
The concentration of substrate at half of Vmax
Study Notes
Enzyme Functions and Types
- Ligases are responsible for forming chemical bonds by condensing two molecules with the hydrolysis of ATP.
- Hydrolases break a chemical bond by adding water across it.
Coenzymes and Vitamins
- Thiamine (Vitamin B1) is a coenzyme that is a building block of Coenzyme A (CoA).
- Coenzyme A is associated with fatty acid metabolism and the common theme is energy production.
Enzyme Catalysis
- Isomerases are responsible for rearranging the order of atoms in a molecule (isomerization).
- Histidine (H57) is a key residue in the active site of chymotrypsin, a serine protease.
Proteases
- Calpains are a class of proteases that require Ca++ as a cofactor and are found in Eukaryotes and Eubacteria, but not Archaea.
- Chymotrypsin is a serine protease that cleaves precursor proteins and is a homodimer with one active site per subunit.
- Thermolysin is a metalloprotease that requires Zn as a cofactor.
Enzyme Diversity
- Enzyme diversity recognizes six biological reactions/enzyme categories.
- Carbonic anhydrases are associated with the need for speed in enzyme catalysis.
- Hemoglobin demonstrates cooperative binding, a case study in enzyme diversity.
Carbonic Anhydrases
- There are three families of carbonic anhydrases that have been discovered.
- The η family of carbonic anhydrases uses Zn as a cofactor.
- Carbonic anhydrases employ a catalytic strategy of metal-assisted acid-base catalysis.
- Carbonic anhydrases have a medical application related to artificial lungs.
- Humans produce 14 splice variations of carbonic anhydrases.
Enzyme-Substrate Binding
- Allosteric modulation occurs when an effector binds to an allosteric site, changing the enzyme's activity.
- In noncooperative enzymes, substrate binding does not affect the enzyme's activity.
- In cooperative enzymes, substrate binding affects the enzyme's activity, either positively or negatively.
Protease Functions
- Zymogens are inactive precursors of enzymes that are cleaved to form the active enzyme.
- Chymotrypsin is a serine protease that catalyzes peptide bond hydrolysis.
- The catalytic triad of chymotrypsin is composed of His-His-Glu.
- The oxyanion hole in chymotrypsin's active site stabilizes the negative charge on the tetrahedral intermediate.
Reversible Reactions and Kinetics
- Michaelis-Menten kinetics describe the kinetics of reversible reactions.
- In a reversible reaction, at equilibrium, the condition k1S = k-1P must be satisfied.
- The condition k1S = k-1P signifies that the reaction has reached equilibrium.
- Michaelis-Menten enzymes follow saturation kinetics.
- The turnover number (kcat) in Michaelis-Menten kinetics indicates the enzyme's maximum catalytic rate.
- The equilibrium constant (KS) in Michaelis-Menten kinetics defines the enzyme-substrate binding affinity.
- The Michaelis constant (Km) represents the enzyme's substrate binding affinity.
- Cooperative enzymes exhibit sigmoidal kinetics, while noncooperative enzymes follow Michaelis-Menten kinetics.
Hill Equation and Cooperative Binding
- The Hill equation describes cooperative binding in enzymes.
- The Hill coefficient (nH) represents the level of cooperativity in ligand binding.
- A Hill plot of Hemoglobin with nH > 1 indicates positive cooperativity in ligand binding.
Enzyme Inhibition and Regulation
- In reversible reactions, the dissociation constant (KD) represents the enzyme-inhibitor binding affinity.
- In Michaelis-Menten kinetics, a poor enzyme has kcat > k-1, indicating slow product release.
- The condition Km ν0 = νmax/2 indicates that the enzyme is operating at half-maximal velocity.
- The reaction rate for an irreversible reaction is given by the equation ν = k[S]^n.
This quiz covers the topic of enzyme allosteric regulation, involving a second substrate which can act as an activator or inhibitor. It also discusses the role of ATCase in metabolism and the binding preferences of CTP and ATP for the T/inactive and R/active states.
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