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transfer of a chemical group
lysis by water
a cleavage reaction NOT using water
change of molecular configuration
joining of two compounds
What enzymes are relevant for treating cystic fibrosis?
digestive enzymes produced in the pancreas, and the presence of elastase in the lung
What enzymes are relevant for the spread of breast cancer?
hydrolytic enzymes are important for ability of cancer cells to invade into the extracellular matrix
proteolytic enzymes that catalyze peptide bond hydrolysis; include pancreatic enzymes like Chymotrypsin, trypsin and elastase, and neutrophil elastase
What kind of amino acid sequences does chymotrypsin bind to?
binds bulky, hydrophobic residues
What kind of amino acid sequences does trypsin bind to?
- binds positively charged residues (eg. arginine, lysine)
- - trypsin is composed of negatively charged amino acid, so it's attracted to positive charged ones when binding
What kind of amino acid sequences does elastase bind to?
binds residues such as glycine, alanine and valine; elastase has a small binding site so only smaller amino acids can fit
What is the active site of an enzyme composed of?
the active site contains amino acid residues that BIND the substrate and separate ones that CATALYZE a reaction; these two residues are NOT the same
- how serine proteases catalyze peptide bond hydrolysis; made up of aspartic acid 102, histidine 57, & serine 195
- the configuration of these 3 amino acids in the enzyme's active site makes serine's -OH (normally a poor nucleophile) unusually reactive
- reactivity of serine's group is comparable to that of an ALKOXIDE (CH2O-) ion
- it attacks peptide bonds of any properly bound substrate
How does the serine protease stabilized the oxanion transition state?
it stabilizes the oxyanion by hydrogen bonds to residues located in a pocket called the oxyanion hole
List the steps of serine protease peptide bond digestion:
- 1. binding of substrate
- 2. attack by serine (alkoxide)
- 3. stabilization of transition state
- 4. release of products (& enzyme regeneration)
What enzyme catalyzes the hydrolysis of peptides on the C-terminal side of phenylalanine, tyrosine and tryptophan?
What amino acids make up the catalytic triad in a serine protease?
Aspartate, histidine and serine
Do enzymes change their structure after catalysis?
No, at the end of the reaction cycle they are the same as when they started
The direction in which a chemical reaction proceeds is determined by:
- 1) the enthalpy (H, change in heat)
- 2) the entropy (S, measure of randomness)
When the Gibbs free energy (G) of a reaction is negative, that reaction is ______:
When the Gibbs free energy (G) of a reaction is positive, that reaction is ______:
When the Gibbs free energy (G) of a reaction is zero, that reaction is ______:
at equilibrium; no further work can be done
How can free energy (G) be made available to do work?
only if the free energy of the Reactants is greater than the free energy of the Products
Is G sensitive to the concentration of reactants and products?
YES free energy is dependent on reaction and product concentrations
At equilibrium, Q=Keq (=0.5 for the conversion of glucose-6-phosphate to fructose-6-phosphate)
When Q>Keq, the reaction goes _________
When Q<Keq, the reaction goes _________
- When Q>Keq, the reaction goes in reverse
- When Q<Keq, the reaction goes forward
What are 4 differences between chemical and biochemical reactions:
- 1) the only time reactions in the body are at equilibrium is at DEATH
- 2) removal of product drives the reaction forward
- 3) reactions proceed under non-standard conditions, hindering the accuracy of prediction G or G knot
- 4) some processes do not take place in solution but are solid phase reactions
free energy of activation, associated with energy barrier to the reaction; the larger G, the slower the reaction
fuel (food) is degraded into smaller molecules with the release of energy; burning fuel to make ATP (or storage)
- reactions or processes that require the input of energy (burning ATP)
- eg. biosyntheses (small molecules are rearranged into macromolecules), mechanical work (muscle contraction), and active transport (membrane potential maintenance)
the _________ of food yields ___
the CATABOLISM of food yields ATP
Enzymes couple ATP (or GTP/CTP) hydrolysis to:
What levels of substrate are suitable for assays of ENZYME concentration?
High, saturating substrate levels are, since the velocity is the highest (as well as being directly proportional to the amount of enzyme and one does not need to be concerned about endogenous substrate of a sample)
What levels of substrate are suitable for assays of SUBSTRATE concentration?
Low substrate levels are best for assays of substrate concentration, since the initial enzyme velocity is directly proportional to the amount of substrate (eg. linearly dependent)
True or False: all exothermic reactions are spontaneous?
False. Delta G can be negative (indicating a spontaneous reaction) even when delta H is positive. This occurs when delta S (the change in entropy) is positive.
True or False: reactions in the body are in equilibrium
How do enzymes affect the energy of reactions?
Enzymes lower the activation energy. They accelerate the rate of reactions, but do not change the potential energy of the substrates or products.
How does the activation energy affect the speed of a reaction?
In general, the larger the activation energy the slower the reaction
velocity (v) of a reaction
the number of product molecules (P) made per unit time(or the disappearance of substrate (S) with time)
How can one determine reaction velocity?
By measuring the amount of product formed per unit time
What kinetic parameters can be extracted from a Michaelis-Menten kinetics graph?
Vmax, the maximum velocity of the catalyzed reaction, and Km, the substrate concentration required to achieve half the maximum velocity
When is Km equal to the substrate concentration in a Michaelis-Menten Kinetics graph?
When the substrate concentration is at half of Vmax
A small Km indicates ______ affinity of enzyme for a substrate, while a large Km reflects a ____ affinity of enzyme for the substrate.
- small Km = HIGH affinity
- large Km = LOW affinity
Lineweaver-Burk Plot (double-reciprocal plot)
- y-intercept = 1/Vmax
- x-intercept = -1/Km
- Slope = Km/Vmax
- used because the graph of v against [S] is asymptotic, making it difficult to determine Vmax
Delta G for ATP hydrolysis (ATP + H2O -> ADP + Pi) is -7.3 kcal/mole. How much energy is required to perform the reverse reaction?
small molecules that help promote catalysis; many vitamins act as cofactors
Which enzyme is deficient in individuals with methylmalonic acidemia?
What is the cofactor for methylmalonyl mutase?
What are the substrates and products of methylmalonyl mutase?
The enzyme converts methylmalonyl CoA to succinyl CoA
True or False: generally, the atoms in an enzyme that bind to a substrate are different than the atoms that participate in the catalysis of a reaction?
What is an oxyanion hole and what is its function?
It is a structural pocket in an enzyme that stabilizes an oxyanion (i.e. stabilizes the transition state)
The initial enzyme velocity is proportional to what?
The amount of substrate
The y-intercept in Lineweaver-Burk plots corresponds to what kinetic parameter?
The x-intercept in Lineweaver-Burk plots corresponds to what kinetic parameter?
The slope in Lineweaver-Burk plots corresponds to what kinetic parameter?
Methylmalonyl acidemia is a profound metabolic disease, characterized by accumulation of a metabolite, methylmalonic acid, in blood and urine. The methylmalonyl mutase enzyme binds two substrates - a coenzyme (coenzyme B12; which is derived from Vitamin B12) and methylmalonylCoA. MethylmalonylCoA is produced during catabolism of certain lipids and amino acids. Sequencing of an infant's enzyme indicates a defect in the substrate binding pocket for Vitamin B12, but not for methylmalonyl CoA. Treatment to alleviate the "failure to thrive" symptoms would therefore most likely include:
C. limiting dietary protein and increased Vitamin B12