Biochemistry Chapter 3: Enzymes Flashcards
definition of Km
Concentration of substrate needed to reach reaction rate of 1/2 of Vmax
analog
compound with a structure similar to another molecule, allowing it to mimic, activate, inhibit, or interfere with the function of the original molecule in a biological system, depending on its specific properties and the context of its interaction.
Suicide Inhibition
occurs when an enzyme binds the inhibitor (structurally a substrate analogue) and forms an irreversible complex with it, usually through a covalent bond.
Difference between phosphorlyase and phosphatase
Phosphorlyase adds phosphate (It adds a phosphate group without ATP by breaking a bond using inorganic phosphate)
Phosphtase removes phosphate It removes a phosphate group using water (hydrolysis).
kcat
turnover number. is the maximum number of substrate molecules an enzyme can convert to product per active site per unit time when the enzyme is fully saturated with substrate. It is expressed as:
Hill coefficient greater than 1
cooperativity
Hill coefficient = 1
Non-cooperative (independent binding) Each ligand binds independently, with no effect on affinity.
hill coefficient < 1
Negative cooperativity. Binding of one ligand decreases the affinity for subsequent ligands.
Difference between specificity and affinity
Specificity refers to an enzyme’s ability to distinguish and act on a particular substrate among many options, while affinity describes how tightly an enzyme binds to its substrate, often measured by the Kₘ value.
Km vs Kd
Kₘ (Michaelis constant) measures the substrate concentration at which an enzyme operates at half of its maximum velocity (Vmax). A lower Kₘ means higher affinity because the enzyme reaches half-max activity at a lower substrate concentration.
K_d (Dissociation constant) measures the binding affinity between two molecules, such as a ligand and a receptor (or an antibody and an antigen). It represents the equilibrium between bound and unbound states. A lower K_d means higher affinity, as it indicates that the two molecules stay bound more tightly and dissociate less.
Which type of inhibitor does NOT alter the KM/Vmax ratio of an enzyme?
Uncompetitive (slope doesn’t change between inhibited and not inhibited)
catalytic efficiency
kcat/km
When experiments are performed on enzymes that display traditional Michaelis–Menten kinetics, what shape does the graph of V0 versus substrate concentration [S] have?
Hyperbolic
What is the order with respect to each reactant and the overall reaction order? And the rate law?
What are the units for k for 0 order, 1st order and 2nd order (rate constant)
What is the Arrhenius Equation?
How to use the Arrhenius Equation
protein unfolding is typically what rate order
A general unimolecular reaction follows:
Folded protein -> Unfolded protein
Rate=k[FoldedProtein]
Therefore, it’s first order
Steady state assumption
E + S in decreasing, E + P is increasing
Michaelis constant (Km) is defined as:
Remember E + S <> ES –> E + P
How do you find Vmax from this graph?
y-intercept (1/Vo) (when y = 0)
Which enzyme is used both in gluconeogenesis and glycogenolysis?
glucose 6-phosphatase catalyzes the final step of both gluconeogenesis and glycogenolysis.
Relationship between Kcat and Vmax
High Kd vs low Kd
High Kd = doesn’t bind well
Low Kd = binds well
Specific activity
is a measure of enzyme purity. It is defined as the amount of enzyme activity (in units) per milligram of total protein in a sample. The higher the specific activity, the purer the enzyme preparation.
difference between k and K for protein folding
Assuming that only the native and unfolded states can be observed under experimentally available conditions, what is the most likely shape of the curve for the dependence of the fraction of folded protein upon denaturant concentration?
sigmoidal curves. protein folding is cooperative
once part of the protein unfolds, the rest unfolds quickly.
How can protein folding be both unimolecular and sigmoidal?
✅ First-order kinetics applies to single molecules → Unfolding rate depends only on folded protein concentration.
✅ Cooperative unfolding applies to the whole population → Leads to a sigmoidal curve when plotting fraction folded vs. denaturant.
Answer is C. AAs are typically L form
Enzymes catalyze chemical reactions by stabilizing:
Transition State
How Proteases Act as Hydrolases:
Hydrolases are enzymes that break chemical bonds using water (H₂O).
Proteases are a type of hydrolase that specifically break peptide bonds in proteins via hydrolysis.
Lyase activity
“Lyases break molecules by removing functional groups, often forming double bonds or ring structures in the process.”
Cytochrome P450
Enzyme that adds oxygen atoms to substrates (e.g., drugs, toxins, hormones) to make them more water-soluble for excretion.
making something more polar helps metabolize it
Michaelis–Menten equation
enzymes that play a key role in apoptosis (programmed cell death). Once activated, they cleave proteins at specific sites to systematically dismantle the cell.
Caspases
Why protein kinase?
What kind of enzyme performs each of these reactions?
