84 Questions
Which transition metal binds well to O2 but would generate free radicals if free in solution?
Iron (Fe+)
What evolutionary solution is mentioned for capturing the oxygen molecule safely?
Binding oxygen with heme that is protein bound
Which type of structure is myoglobin?
Protein structure
What is the role of the 'proximal' His in myoglobin structure?
It coordinates directly with Fe
Why does CO bind better to free heme than O2?
Similar size and shape to O2
What factor contributes to CO binding about 200x less effectively than O2 in the middle of the protein?
Presence of a distal His residue
How does protein structure affect ligand binding?
By having a complementary binding site for the ligand
What is one reason why lowering the affinity (P50) of myoglobin to oxygen would not help in delivering oxygen to tissues?
It results in too much oxygen bound in the lungs
What is the consequence of the formation of a carbamate in hemoglobin?
Stabilization of the T state
What distinguishes hemoglobin from myoglobin in terms of oxygen binding?
Hemoglobin binds oxygen cooperatively, myoglobin does not
Which factor leads to the release of oxygen in the tissues?
Protonation of His146
What is required for positive cooperativity in hemoglobin's affinity for oxygen?
Quaternary structure with multiple subunits
What role does H+ play in oxygen transport by hemoglobin?
Leads to oxygen release in tissues
What does a sigmoidal binding curve indicate in terms of ligand cooperativity?
Positive cooperativity
What is the quantitative description of cooperativity represented by in a Hill plot?
$Ka = n \times Ka$
How does a drop in pH affect hemoglobin's affinity for oxygen?
Decreases affinity for oxygen
What contributes to the efficiency of oxygen transport in the body?
pH difference between lungs and metabolic tissues
What percentage of carbon dioxide is exported in the form of a carbamate on the amino terminal residues of hemoglobin subunits?
15-20%
What does a small equilibrium dissociation constant (Kd) indicate?
High affinity
Which of the following is NOT a component of a heme group?
Sulfur atom
What characterizes the specificity of proteins in binding to ligands?
Complementary size, shape, charge, or hydrophobic/hydrophilic character
Which type of proteins undergo conformational changes upon ligand binding, allowing for tighter binding?
Globins
How is the equilibrium composition characterized in terms of the equilibrium constant Ka?
[P][L] = Ka[PL]
What does the heme-bound FE cation represent in myoglobin?
+2 (reduced) state
What triggers the conformational change from the T to R state in hemoglobin?
Breaking of ion pairs between the α1-B2 interface
Which state of hemoglobin has a higher affinity for oxygen?
R state (Relaxed state)
What does the binding of O2 cause in the hemoglobin subunits?
Slide of ab pairs past each other and rotation
Who determined the structures of hemoglobin in the presence and absence of Oxygen?
Max Perutz
What is hypothesized to cause the significant conformational change in hemoglobin upon Oxygen binding?
Shift in iron's position in the Heme
What does the binding of O2 in the hemoglobin subunit's pocket trigger?
Localized movement of the proximal His and cascade of movements throughout the subunit
What does Linus Pauling discover that helps lower the standard state free energy change of a reaction?
Transition state stabilization
In enzymatic catalysis, what is the role of the catalytic triad in chymotrypsin?
To stabilize the acyl-enzyme intermediate
What is the function of the acyl-enzyme intermediate in enzymatic reactions?
To lower the activation barrier for the reaction
How does the catalytic triad in chymotrypsin contribute to the catalytic mechanism of the enzyme?
By stabilizing the transition state of the reaction
Which of the following is a key feature of peptide bond formation catalyzed by enzymes like chymotrypsin?
Stabilization of the transition state
What is the primary function of water activation in enzymatic reactions like those catalyzed by chymotrypsin?
To provide nucleophiles for reaction mechanisms
What is the role of Asp-102 in the catalytic triad of chymotrypsin?
Deactivates water for nucleophilic attack by Ser-195
What does Ser-195 do in the catalytic triad of chymotrypsin?
Nucleophilically attacks the carbonyl carbon of the substrate
Why does His-57 interact with Serine in chymotrypsin catalysis?
To transform Serine into a better nucleophile
In chymotrypsin catalysis, what is the function of the catalytic triad in breaking peptide bonds?
Activating the water molecule for nucleophilic attack
Which statement accurately describes the oxyanion hole in chymotrypsin?
It stabilizes the transition state of peptide bond formation
What is the main function of the acyl-enzyme intermediate in chymotrypsin catalysis?
Further stabilize the enzyme-substrate complex
What is the primary function of a Lewis base?
Donating electrons
In acid-base catalysis, what role does water typically play?
Acting as both an acid and a base
Why might general acid-base catalysis be preferred over specific acid-base catalysis?
General catalysis is more efficient
Which amino acid side chain is not usually ionizable and involved in general acid-base catalysis?
Serine
What is the main requirement for general acid-base catalysis when proton transfer from water is slow?
Presence of another proton donor or acceptor
What is the role of histidine in the catalytic triad of chymotrypsin?
Removal of proton from serine for nucleophilic attack
In enzyme catalysis, what is the purpose of the amino acid group in general acid-base catalysis?
Neutralizing charges on intermediates
What is the function of the aspartate residue in chymotrypsin's active site?
Stabilization of the acyl-enzyme intermediate
What occurs during the burst phase in chymotrypsin catalysis?
Release of p-nitrophenol
What is the purpose of water activation in chymotrypsin catalysis?
Formation of the acyl-enzyme intermediate
Which residue in chymotrypsin is responsible for stabilizing the transition state during catalysis?
Aspartate
What effect does His have on water molecules during chymotrypsin catalysis?
Removal of protons to activate water for nucleophilic attack
How do general acids and bases help increase the rate of a reaction in enzyme catalysis?
Avoid the need for extremely high or low pH values
What is one role of covalent catalysis in enzyme catalysis?
Make transient covalent bonds between the enzyme and substrate
What amino acids can act as nucleophiles involved in covalent catalysis?
Serine, thiolate, amine
In chymotrypsin, what accelerates peptide bond hydrolysis?
Metal ion catalysis
What is the role of the catalytic triad in chymotrypsin for peptide bond hydrolysis?
Creates a negative charge to stabilize intermediates
How does acyl-enzyme intermediate formation contribute to enzyme catalysis?
Facilitates the transfer of acyl groups
What does the turnover number, kcat, represent?
The number of substrate molecules converted per unit time by one enzyme molecule
What is the approximate measure of substrate's affinity for enzyme known as?
Km
Why is Km often compared to Kd?
To assess the balance between breakdown and formation of ES complex
Which enzyme has a turnover number of approximately 40 million per second?
Catalase
What is the significance of a lower Km value in enzyme kinetics?
Higher rate of enzymatic reaction
In enzyme kinetics, what does Kcat measure?
[S] at ½ Vmax
Which assumption underlies the comparison between Km and Kd?
[ES] formation is faster than ES breakdown
What does Km represent in terms of substrate concentration and enzymatic reaction?
[S] at which half-maximal velocity is achieved
What are the factors that can affect the rate of an enzymatic reaction?
Enzyme concentration, substrate availability, temperature
What is the primary purpose of studying enzyme kinetics?
To understand the rate of enzymatic reactions
In enzyme assay example with Alcohol Dehydrogenase (ADH), why is NADH production monitored at 340 nm?
NADH has a higher absorbance at 340 nm than NAD-
What does the process of making mutations in enzymes aim to determine?
Essential amino acids for enzyme activity
How are kinetic parameters determined in enzyme kinetics studies?
By repeating experiments under different conditions
What is one of the reasons for differentiating residues involved in catalysis from those involved in substrate binding?
To understand the enzyme's mechanism of action
Why is it important to understand the regulation of enzyme activity?
To control the rate of enzymatic reactions
What does the study of enzyme kinetics provide in terms of biocatalysis?
Precise quantitative descriptions of biocatalysis
What is the effect of increasing substrate concentration on the initial velocity of an enzymatic reaction?
Initial velocity increases
Which enzyme relationship is represented by a hyperbolic curve when plotting initial velocity against substrate concentration?
Michaelis-Menten Enzymes
What is the equation that explains the hyperbolic curve observed when plotting initial velocity versus substrate concentration?
Y is Vo, Vmax is asymptote, X is [S], Km is [S] when Vo is ½ Vmax
What does steady state condition mean in enzyme kinetics?
[ES] formation equals [ES] breakdown
Which assumptions allowed Michaelis and Menten to derive an equation fitting the hyperbolic curve in enzymatic reactions?
k1 and k2 are rate limiting, [P] and [ES] are negligible, and [Efree] = [ET] - [ES]
In Michaelis-Menten kinetics, what does Km represent?
[S] when Vo is half of Vmax
What does Vmax represent in Michaelis-Menten kinetics?
[E] at maximum velocity
Under steady-state conditions in enzyme kinetics, what does d[ES]/dT equal?
0
Test your knowledge on the Hill Equation, hemoglobin's Tense (T) and Relaxed (R) states, O2 binding affinity, and conformational changes triggered by Oxygen binding.
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