Ch. 7 Flashcards
What are the properties of enzymes?
- Most enzymes are proteins
- Work under mild conditions
- Increase reaction rate
- Greater reaction specificity
- Capacity for regulation
What are the working conditions of enzymes?
- Neutral pH
- Low temperature below 100ºC
- Atmospheric pressure
Describe the 2 models of enzyme specificity. Which one accurate?
- Lock and key (inaccurate)
- Substrate (reactant) binds to the enzyme perfectly - Induced fit
- Enzyme is flexible to accommodate the ill-fitting substrate
- Permits a much larger number of weaker interactions between the substrate and enzyme
What are the 3 critical aspects of enzymes?
- Usually bind to substrates with high affinity and specificity
- Active sites (binding pockets) in the enzyme bind to the substrate and promote catalytic reactions - Substrate binding to the active site induces changes in the enzyme
- Enzyme activity is highly regulated in cells
What are the 4 modes of enzyme regulation?
- Bioavailability
- Catalytic efficiency (Activity enzymes regulate covalent modification)
- Covalent modification
- Allosteric regulation (similar to hemoglobin)
How are enzymes chemical catalysts?
- Alter the reaction rate without changing theratio of substrates and products at equilibrium
- Lower the activation energy
- They do NOT change the overall ΔG of the reaction
What is a cofactor?
A small inorganic molecule that aids in the catalytic reaction mechanism within the enzyme active site
What is the function of a cofactor?
Provide additional chemical groups when amino acid functional group are insufficient
What is a coenzyme?
An organic enzyme cofactor
What is NAD+/NADH?
A required component in many redox reactions involving dehydrogenase enzymes
What is a prosthetic group?
A coenzyme that is permanently associated with an enzyme
How does pH/temperature affect enzymes?
Certain enzymes work best at certain pH/temperature –> if you decrease/increase pH/temperature, enzyme activity will decrease
What are the 3 major ways that enzymes increase the rate of a reaction inside cells?
- Stabilize the transition state
- Provide an alternative path for product formation
- Orient the substrates appropriately for the reaction to occur
What is lipoamide? What is its role in catalysis?
- Temporary carrier of acetyl group in reaction catalyzed by pyruvate dehydrogenase
- 2 carbon transfer
How do enzymes catalyze reactions?
- Enzymes bring substrates together
- Geometric and chemical complementarity
- High local concentration
- Optimal orientation
- Bind via non-covalent interactions
What features of the enzyme active site contribute to catalyzing a reaction?
- Provide an optimal orientation of the substrate relative to reactive chemical groups
- Excludes excess solvents
- Binding interactions between substrate and enzyme create a transition state
- Presence of catalytic functional groups
- Sequestered microenvironment of the active site
What facilitates the formation of the transition state?
Bonding interactions of the substrate in the enzyme active site
What inhibits enzymes?
Transition state analogs (stable molecules that mimic the transition state at the active site)l
What are the 3 types of catalysis?
- Acid-base catalysis
- Covalent catalysis
- Metal ion catalysis
What are the 2 types of acid-base catalysis?
- Specific (involves water)
- General (proton transfer involves functional group)
What are the 3 general categories of enzyme-mediated reactions in cells?
- Coenzyme-dependent redox reactions (in lots of metabolic pathways!)
- Metabolite transformation reactions (in anabolic and catabolic reactions)
- Reversible covalent modification reactions (attach/remove molecular tags; recognition)
What are serine proteases?
Enzyme that cleaves the peptide backbone of proteins
What types of catalysis does chymotrypsin use?
- Acid-base catalysis
- Covalent catalysis
What does chymotrypsin do?
Cleaves (hydrolyzes) peptide bonds
Which amino acids are in the catalytic triad of chymotrypsin? What does each one do?
- Asp102: orients His residue
- His57: positions and polarizes -OH of Ser and acts as base (accepts H+)
- Ser195: deprotonates
- TL;DR - Asp positions His which positions Ser which deprotonates
What are steps 1 and 2 of the chymotripsin mechanism?
- Polypeptide binds to active site
- His57 removes proton form Ser195 allowing nucleophilic attack by Ser O- on carbonyl carbon of the peptide
What is step 3 of the chymotrypsin mechanism?
-
His57 donates a proton to amino group of substrate resulting in peptide bond cleavage
- Carbonyl-terminal fragment released as first product
What is step 4 of the chymotrypsin mechanism?
- H2O (reactive) enters active site and His57 acts as base and deprotonates water; resulting -OH acts as nucleophile and attacks carbonyl carbon of covalent acyl-enzyme intermediate
What are steps 5 and 6 of the chymotrypsin mechanism?
- His57 donates proton to Ser195 causing cleavage of acyl-enzyme resulting in the release of amino-terminal fragment
- Product 2 is released and catalytic triad is regenerated
What are two other enzymes with the same catalytic strategy as chymotrypsin (binding pocket)?
What is reversible covalent modification?
- Act as molecular switches that turn on and off cell signaling and gene expression
- Include kinases and phosphotases
- ATP is commonly used as a phosphoryl group source
What is the Michaelis-Menten equation?
- Small Km –> more [ES] –> more readily binds to substrate at low [substrate] (greater affinity for substrate)
- Large Km –> less [E] –> lower affinity for substrate
What is the Lineweaver-Burke equation?
- Used to draw a double reciprocal plot of the enzyme data
- Easier way to determine Vmax and Km
What is Km on a graph?
- Substrate concentration
- Measures how easily the enzyme can be saturated by the substrate
What is Km with respect to enzyme and substrate?
Amount of substrate it takes for an enzyme to reach Vmax/2
What is competitive inhibition?
- Inhibitor looks like substrate
- Inhibitor binds to active site where substrate binds
- Km of enzyme increases
- Vmax of reaction stays the same
What is noncompetitive inhibition?
- Inhibitor doesn’t look like substrate
- Inhibitor binds to different site other than substrate binding site
- Km stays the same
- Vmax decreaes
How do you determine the type of inhibition using Km and Vmax?
- Compare graphs with and without inhibitors
- Competitive inhibition: Vmax is unchanged, Km increases
- Noncompetitive inhibition: Vmax decreases, Km is unchanged
What does Michaelis-Menten graph look like?
What does a Lineweaver-Burke graph look like?
How do you find Vmax and Km on a Michaelis-Menten graph?
How do you find Vmax and Km on a Lineweaver-Burke graph?
