2.2 ENZYMES Flashcards
activation energy (Ea)
he energy barrier that blocks the tendency for a chemical reaction to occur.
active site
The region on the surface of an enzyme or ribozyme where the substrate binds, and where catalysis occurs.
allosteric activation
when the binding of one ligand enhances the attraction between substrate molecules and other binding sites
allosteric inhibition
a form of noncompetitive inhibition: a molecule that binds to the enzyme at an allosteric site. This site is not at the same location as the active site. Upon binding with the inhibitor, the enzyme changes its 3D shape.
chemical change
a process that leads to the chemical transformation of one set of chemical substances to another
catalyze
to increase, the rate of (a chemical reaction) by catalysis
chemical change
the process that causes products to have different properties than reactants because their atoms and molecules are arranged differently.
chemical kinetics
chemical kinetics – an area of chemistry dealing with speeds/rates of reactions
1) rates of reactions affected by four factors
2) concentrations of reactants
3) temperature at which reaction occurs
presence of a catalyst
4) surface area of solid or liquid reactants and/or catalysts
conenzyme
a subset of cofactors that are organic (carbon-based) molecules.
cofactor
non-protein helper molecules
catalyze
means to increase the reaction rate by using an enzyme that’ll reduce the activation energy
confirmations change
a change in the shape of a macromolecule, often induced by environmental factors such as:
- temp
- pH
- enzyme concentration
- substrate concentration
catalysis
The process by which a substance speeds up a chemical reaction without being consumed or altered in the process
covalent modification
enzyme-catalyzed alterations of synthesized proteins and include the addition or removal of chemical groups
enzyme
biological catalyst: proteins and RNA (ribozymes)
enzyme activation
the process of the increasing rate of the enzyme reaction
enzyme inhibition
a molecule that disrupts the normal reaction pathway between an enzyme and a substrate
Enzyme inhibitors can be either competitive or non-competitive depending on their mechanism of action
prevent the formation of an enzyme-substrate complex and hence prevent the formation of product
Inhibition of enzymes may be either reversible or irreversible depending on the specific effect of the inhibitor is used
enzyme-catalyzed reaction
a reaction that occurs converting the substrate into products and forming an enzyme products complex once an enzyme will grab on (bind) to one or more reactant molecules
enzyme-substrate complex
the structure formed when the substrate is held within the active site of the enzyme; initiates chemical reaction
feedback inhibition
The end product of a metabolic pathway acts on the key enzyme regulating entry to that pathway, keeping more of the end product from being produced.
induced fit
a continuous change in the conformation and shape of an enzyme in response to substrate binding. This makes the enzyme catalytic which results in the lowering of the activation energy barrier causing an increase in the overall rate of the reaction.
irreversible modification
involves the addition or removal of some type of group, most commonly the phosphoryl group, onto or from the enzyme. The addition of phosphoryl groups involves the use of ATP (energy source) and requires a protein called protein kinase. On the other hand, proteins that can remove phosphoryl groups from enzymes are called protein phosphatases. Unlike proteolytic cleavage, the addition or removal of phosphoryl groups is reversible.
kinase
an enzyme that adds phosphate groups (PO43−) to other molecules
maximum velocity
rate attained when the enzyme sites are saturated with substrate, i.e. when the substrate concentration is much higher than the KM.
metabolic pathway
series of chemical reactions in a cell that build and breakdown molecules for cellular processes
Michaelis constant (KM)
the substrate concentration at which the reaction rate is half of its maximal value (or in other words, it defines the substrate concentration at which half of the active sites are occupied). It indicates the affinity of an enzyme for a given substrate: the lower the KM value, the higher the affinity of the enzyme for the substrate.
non-covalent modifications
a type of reversible protein modification that allows enzymes to be turned on or off when special molecules bind noncovalently to the enzyme
noncompetitive inhibitor
an inhibitor that binds to an allosteric site resulting in decreased efficacy of the enzyme
orientation
the exact way that reactant molecules must make direct contact with each other in order to form a bond
phosphatase
an enzyme that removes a phosphate group from a protein
physical strain
this occurs when a molecule has an additional amount of internal energy which an unstrained molecule does not
protein-protein interaction
are physical contacts of high specificity established between two or more protein molecules as a result of biochemical events steered by interactions that include electrostatic forces, hydrogen bonding, and the hydrophobic effect
reversible modification
is the making and breaking of a covalent bond between a non-protein group and an enzyme molecule. The most common reversible modification is the addition and removal of phosphate groups through the processes of phosphorylation and dephosphorylation
saturable
capable of being saturated.
substrate
a molecule upon which an enzyme acts, in order to catalyze chemical reactions
thermodynamics
a branch of science dealing with the transfer of energy from one place to another and from one form to another
transition state
an enzyme-catalyzed reaction, the reactive condition of the substrate after there has been sufficient input of energy (activation energy) to initiate the reaction.
uncatalyzed reaction
reaction proceeds via a one-step mechanism (one transition state-observed)
Explain why spontaneous reactions often proceed very slowly.
these type of reaction often proceed very slowly because they require extra energy in order to reach the necessary activation energy for the reactants to overcome the transition state, and become lower energy
products
Describe what an enzyme is, why it is needed, and how they help chemical reactions proceed in living cells.
what: these proteins act as catalysts in reactions
why: they stabilize the structure of the transitions state by binding substrates to their active sites. This in turn lowers the free energy of the transition state, which in turn decreases the rate of the chemical reaction. Enzymes do not however change the Gibbs free energy of the chemical reaction.
how:
Explain the role of the active site.
The active site of an enzyme is the region that binds the substrates(and cofactor if any) The interaction of the enzyme and substrate at the active site promotes the formation of the transition state. the enzyme changes shape on substrate binding.
Describe the process of enzyme action, including how they increase the rate of chemical
reactions.
Enzymes are proteins that act as catalysts within living cells. Catalysts increase the rate of chemical reactions occurs without being consumed or permanently altered themselves.
The basic mechanism by which enzymes catalyze chemical reactions begins with the binding of the substrate to the active site on the enzyme. The active site is the specific region of the enzyme which combines with the substrate. Mechanism of enzyme action is well explained in terms of lock and key model of enzyme action.
The active site was thought to have a fixed structure (the lock), which exactly matched the structure of a specific substrate (the key). Thus the enzyme and substrate interact to form an enzyme-substrate complex. The substrate is converted to products that no longer fit the active site and are therefore released, liberating the enzyme.
Explain each component of a free energy diagram for an uncatalyzed vs. enzyme-catalyze
reaction.
The addition of a catalyst to a reaction lowers the activation energy, increasing the rate of the reaction. The activation energy of the uncatalyzed reaction is shown by Ea, while the catalyzed reaction is shown by Ea’. The heat of reaction (ΔH) is unchanged by the presence of the catalyst.
Explain each element of an enzyme kinetics curve.
The rate of reaction when the enzyme is saturated with substrate is the maximum rate of reaction, Vmax.
The relationship between rate of reaction and concentration of substrate depends on the affinity of the enzyme for its substrate. This is usually expressed as the Km (Michaelis constant) of the enzyme, an inverse measure of affinity.
For practical purposes, Km is the concentration of substrate which permits the enzyme to achieve half Vmax. An enzyme with a high Km has a low affinity for its substrate, and requires a greater concentration of substrate to achieve Vmax.”
Describe how reaction rates change with differences in substrate concentration
The rate of a chemical reaction increases as the substrate concentration increases. Enzymes can greatly speed up the rate of a reaction. However, enzymes become saturated when the substrate concentration is high.
Explain why enzymes are sensitive to environmental conditions.
they’re sensitive to environment conditions such as:
1) Temperature: Raising temperature generally speeds up a reaction, and lowering temperature slows down a reaction. However, extremely high temperatures can cause an enzyme to lose its shape (denature) and stop working.
2) pH: Each enzyme has an optimum pH range. Changing the pH outside of this range will slow enzyme activity. Extreme pH values can cause enzymes to denature.
3) Enzyme concentration: Increasing enzyme concentration will speed up the reaction, as long as there is substrate available to bind to. Once all of the substrates is bound, the reaction will no longer speed up, since there will be nothing for additional enzymes to bind to.
4) Substrate concentration: Increasing substrate concentration also increases the rate of reaction to a certain point. Once all of the enzymes have bound, any substrate increase will have no effect on the rate of reaction, as the available enzymes will be saturated and working at their maximum rate.
Contrast the different mechanisms used by cells to regulate enzyme activity
Enzymes can be regulated by other molecules that either increase or reduce their activity. Molecules that increase the activity of an enzyme are called activators, while molecules that decrease the activity of an enzyme are called inhibitors.
feedback inhibition, reversible covalent modification of enzymes, proteolytic activation of the enzyme, feedback regulation, and regulation of isozymes.
Distinguish between different types of reversible inhibitors.
Irreversible: permanently change enzymes conformations by covalent modification (binding)
ex: allosteric inhibition
reversible: cause temporary changes in the enzyme confirmation via non-covalent modification (binding) when they undergo the process of induced fit
ex: competitive, uncompetitive, and noncompetitive
Describe how enzymes work together in metabolic pathways that can be regulated by feedback
inhibition.
Metabolic pathways are a series of reactions that multiple enzymes catalyze. Feedback inhibition, where the pathway’s end product inhibits an upstream step, is an important regulatory mechanism in cells.
