Exam 2 Flashcards
Catalyst
- a substance that increases the rate or velocity of a chemical reaction without itself being changed in the overall process
- enzymes are biological catalysts (proteins)
Substrate
- the substance that is acted on by an enzyme
Enzymes are divided into 6 major classes to define their function more precisely
- Oxidoreductase
- Transferases
- Hydrolases
- Lysases
- Isomerases
- Ligases
Oxidoreductases
- catalyze oxidation reduction reactions
- adds/removes electrons and protons from its substrate
ex: alcohol dehydrogenase (oxidation with NAD+)
Transferases
- catalyze transfer of functional groups from one molecule to another
ex: hexokinase (phosphorylation)
Hydrolases
- catalyze hydrolytic cleavage
(cleave bonds by adding a water molecule)
ex: carboxypeptidase A (peptide bond cleavage)
Lysases
- catalyze removal or addition of a group from a double bond, or other cleavages involving electron rearrangement
- remove functional groups via non-hydrolytic reactions.
- Often result in formation of a double bond.
ex: decarboxylation
Isomerases
- catalyze intramolecular rearrangement
2 Types
1) Mutases- transfer functional groups from one position to another
2) Epimerases- invert functional groups about asymmetric carbons
ex: maleate isomerase (cis-trans isomerization)
Ligases
- catalyze reactions in which two molecules are joined
- use the energy from ATP hydrolysis to form bonds between two substrate molecules.
ex: pyruate carboxylase (carboxylation)
Cofactor, or coenzyme
- an organic(nonprotein) small molecule that binds to an enzyme and is essential to carry out the catalytic reaction
- non protein components of enzymes that convert inactive “apoenzymes” to active “holoenzymes”
- not permanently altered by the reaction
- most are derived metabolically from vitamins
Major example of the coenzyme of the Vitamin Niacin and function
- nicotinamide adenine dinucleotide (NAD+)
- oxidation reduction
- capable of acting as an oxidizing agent (reduced)
- conversion of alcohol to aldehydes or ketones, coenzyme of alcohol dehydrogenase
Metalloenzymes
- metal ions that are bound in a prosthetic group like heme
- acts in the same way as a coenzyme,
Example of carboxypeptidase A as a metalloenzyme
- zinc ion in carboxypeptidase A binds the water molecule that attacks the carbonyl of tee scissile bonds and acts as an electrostatic catalyst
How does a reaction proceed?
- spontaneously due to random kinetic energy of reactants 3 types of kinetic energy 1. vibrational 2. rotational 3. translational
What is heats affect on kinetic energy and rate of reaction
- increases them
Transition State
- the unstable (energized) intermediate formed in an enzymic reaction that has properties of both the substrate and the product
- point in a reaction where reactants and products have the highest energy
Activation energy
- the threshold energy required to produce the chemical reaction
Enzymes speed up reactions by _______ the amount of activation required to start a chemical reaction
- lowering
What does it mean that Enzymes are reversible
- typically they bring a chemical reaction to equilibrium instead of completing it
Cellulase enzyme
- hydrolyzes cellulose
- used as a digestive aid and in biofuel production
Collagenase enzyme
- hydrolyzes collagen
- promotes burn and wound healing
Invertase enzyme
- hydrolyses sucrose
- used in manufacture of soft-centered candy
Lipase enzyme
- hydrolyzes lipids
- digestive aid, improves cheese flavor
pectinase enzyme
- hydrolyzes pectin
- clarifies fruit juices
protease enzyme
- hydrolyzes protein
- used in detergents
Apoenzyme
- the nonfunctional protein component of an enzyme lacking its cofactor
Holoenzyme
- the functionally complete apoenzyme plus its cofactor
Two main types of cofactors
- organic:
- coenzymes(CoA, NAD+, biotin) - Inorganic:
- assorted mineral ions (Mg2+, Zn2+)
Prosthetic groups
- tightly bound non protein (organic) components of proteins (heme)
Coenzyme A
- nucleotide cofactor
- derived from pantothenic acid
- carries acyl groups for metabolic processes
- acetyl-CoA most common acyl intermediates
Beri-Beri
- crippling disease
- death due to heart failure bc degeneration of nerve fibers and heart muscle
- dietary deficiency of vitamin B1 (Thiamine), consumption of rice
- Thiamine required by enzymes involved in glucose catabolism and conversion to fats
William Fletcher
- rice bran and germ contained accessory factors that reversed or prevented Beri-Beri disease in chickens and prisoners
Cassimir Funk
- accessory factors contained N-rich substances which he named Vital amines (essential for survival)
Water soluble coenzymes
- NAD+/NADP+
- FMN/FAD
- coenzyme A
- Vitamin C
Lipid soluble enzymes
- Vitamin E
- Vitamin D
- Vitamin A
Vitamin C
- water soluble
- Dehydro” form scavenges free radical electrons within the aqueous compartment of cell.
- helps protect membrane damage by reacting with peroxyls and enhancing the activity of lipid soluble vitamin E
Vitamin E
- regeneration of vitamin E by ascorbic acid
- ascorbate regenerated by reacting with GSH
Vitamin D deficiency
- CAUSES RICKETS
- not a true vitamin or cofactor bc can be synthesized in the body (no enzymic rxns)
- steroid hormone derived from cholesterol in presence of UV light
- Functions to promote Ca2+, PO43- & Mg2+ absorption in intestines.
- Inability to absorb Ca2+, PO43- & Mg2+ results in soft bones that bend during growth and development.
- Children are most susceptible.
Vitamin A deficiency
- get vitamin from animal products and B carotene from plants (carrots)
- Infants and are children most susceptible; high mortalities
- deficiency directly related to polish rice as a staple food in asia
- CAUSES BLINDNESS
Lock and key hypothesis
- Emil Fischer
- enzyme active site(lock) perfectly matches the shape of the substrate (key)
- only allows one substrate to bind to active site and be converted to product
Induced fit model
- Daniel Koshland
- substrates fit into active site like a flexible “hand in glove”
- both the enzyme and substrate are distorted on binding (conformational changes)
- substrate is forced into a conformation approximating the transition state
- enzyme keeps the substrate under strain
How do substrates bind to enzymes?
- non covalent forces
- van der Waals
- electrostatic
- hydrogen bonding
- hydrophobic interations
Enzyme-Substrate reaction 3 steps
1) binds to substrate (only reversible step)
2) conversion of enzyme-substrate complex to enzyme bound to product (intermediate)
- stabilized transition state
3) release of product (rapid)
enzyme-substrate complex vs transition state on rxn coordinate diagram
- ES complex is a stable intermediate that is thermodynamically favored (lower free energy G)
- transition state is an unstable state (highest free energy)
- EP is less favorable that E+P for maximum efficiency
What do delta Gnon and delta Gcat stand for? what do we want to be larger in reaction coordinate diagram? How is this achieved
- delta G non is the transition state
- delta G cat is the Enzyme-substrate complex
- Gcat
Activation energy on rxn coord diagram
- the initial energy state when the reaction begins
- reactants
Transition state on rxn coord diagram
- highest energy point on the diagram between the reactant and product
General acid/base catalysis (GABC)
- important in reactions involving proton transfer
- specialized case of electrostatic catalysis involving the transfer of a positive charge (H+)
What is required for a reaction to be considered catalytic?
- enzyme active site must be restored to its initial state
Lysozyme mechanism of a specific enzyme catalyzed reaction
- lysozyme cleaves a polysaccharide
- lysozyme employs GABC, substrate distortion(strain of D ring) and covalent catalysis to achieve its rate enhancement
Chymotrypsin mechanism of a specific enzyme catalyzed reaction
- catalysis of peptide bonds hydrolysis by a serine proteases
- employs covalent catalysis, GABC and electrostatic stabilization
- involves stabilization of transition states and tetrahedral intermediate states
- oxyanion hole stabilizes the tetrahedral intermediate
Mechanisms of enzyme regulation
- activation
- inhibition
- modification
Substrate level control of enzyme regulation
- direct interaction of substrates and products of each enzyme-catalyzed reaction with the enzyme itself
- the higher substrate concentration, higher rate of rxn
- a large change in S would be required to effect a significant change in enzyme, not used for regulation often
- high levels of product, which can bind to enzyme, inhibit the conversion of substrate to product (product inhibitor)
Why do enzymes need regulation?
- maintenance of ordered state
- conservation of energy
- environmental responsiveness
Feedback control in enzyme regulation
- feedback inhibition
- inhibition or activation of a key step(control points) in the pathway occurs through a allosteric enzyme mechanism
- efficient means to maintain homeostasis of reaction
- an increase in the conc of product leads to a dec in the rate of its production
- control generation of final product by slowing the first step of reaction so machine can regulate concentration of E
Allosteric enzymes
- occurs when the binding of a ligand results in a conformational change in an enzyme
- means other site (other shape) other than active site
- exhibit cooperativity in substrate binding (homoallostery) and regulation of activity by other effector molecules (heteroallostery)
Homoallostery
- cooperative substrate binding
- subunits undergo conformational changes individually
- Shift from T to R form is induced by S
Heterallostery
- inhibitors or activators
- if an enzyme molecule can exist in two conformational states (T and R), then its kinetics can be controlled by any other substance that binds to the protein
- Allosteric inhibitors shift towards T
- allosteric activators shift towards R
T form of monomers (taut)
- low substrate, high inhibitor affinity
R form of monomers(relaxed)
- high substrate and activator affinity
Covalent modification
- the reversible attachment (or modification) of a functional group to/on a protein or enzyme via a covalent bond
ex: - phosphorylation/dephosphorylation
- oxidation/reduction
- proenzymes vs zymogens(irreversible)
Proenzyme
- an inactive enzyme precursor (polypeptide) that must be proteolytically cleaved or hydrolyzed in order to become active
zymogen
- irreversible
- an inactive enzyme precursor (polypeptide) that must be proteolytically cleaved or hydrolyzed in order to become active
- must be cleaved proteolytically in the intestine to yield active enzymes
Ribozymes
- RNA molecules that can act as enzymes
kinetics
- studies the rate at which reactions occur
- also shows the reaction mechanism (how it occurs)
rate laws
- how the rate depends on amounts of reactants
- measure the rate at different starting concentrations
- k= rate constant
ex: if a reactant doubles, initial rate will double
integrated rate laws
- how to calc amount left or time to reach a given amount
half life
- how long it takes to react 50% of the reactants
Arrhenius equation
- how rate constant changes with T
Mechanisms
- link between rate and molecular scale process
Factors that affect rates
- concentration of reactants
- temperature
- catalysts
rate of reaction equation
change in concentration/change in time
- average rate decreases as the reaction proceeds because as the reaction goes forward, there are fewer collisions between reactant molecules
Instantaneous rate in a plot of concentration(y) vs time (x)
- the slope of a line tangent to any curve at any point at the time
- if the ratio is not 1:1
use aA + bB -> cC+ dD
rate= (
Rate law: order
- tell the order of the reaction with respect to each reactant
- overall reaction order can be found by adding exponents on rxns in rate law
first order reaction characteristics
- depends on the first power of the concentration of the reactant
- the larger the k more rapid the rate
- use graph ln A vs t
- straight line with a decreasing slope of -k
first order reaction equation
ln(A)t=-k(t)+ln(A)o t=time -k=slope (A)o=y intercept - in y=mx+b form
Second order reaction characteristics
- 2 reactions come together to form the producy
- plot of 1/A vs time
- has a straight line
- with a slope of positive k
How to determine first or second order when not given a graph
- plug numbers into first order and second order equations
- determine which will have the right characteristics
Half life equation
(A)t=.5 (A)o
- because t1/2 is one half of the original A
- if increase concentration of A
reaction coordinate diagrams
- show the energy of reactants and products (delta E)
- highest point is transition state
- species present at the transition state is called the activated complex
- energy gap between reactants and activated complex is activation energy barrier
Heat in a reaction coordinate diagram
- speeds the reaction, so the amount of molecules that can overcome the activation energy increases
- the curve will flatten and broaden
- reaction rate increases
Arrhenius equation
- relationship between k and Ea
molecularity in reaction mechanisms
- tells how many molecules are involved in the process
Multistep mechanism
- one of the steps are slower than the others
- reaction cannot occur faster than this step, rate determining step
rate enhancement equation
- determines how much an enzyme must stabilize the transition state to achieve observed rate enhancements
- indicates how much faster rxn occurs when catalyzed
to lower activation energy barrier to maintain delta Gcat>delta Gnon do what?
- delta H more negative or delta S more positive
