Biochemistry Wk 9 Flashcards
What are enzymes
• Enzymes are biologically active proteins that accelerate the breakdown of food that is eaten.
• Enzymes are biological catalysts. They accelerate reactions, but are not consumed or changed in reactions.
• They are involved in all processes essential for life such as DNA replication and transcription, protein synthesis, metabolism and signal transduction, etc.
The six major classes of enzymes
Oxidoreductases- catalyse oxidation-reduction reactions. (Dehydrogenase)
Transferases- catalyse transfer of C-,N-, or P-, containing groups
Hydrolases- catalyse cleavage of bonds by addition of water (urease)
Lyases- catalyse cleavage of C-C,C-S, and certain C-N bonds (decarboxylase)
Isomerases- catalyse rearrangement of optical or geometric isomers such as mutase
Ligases- catalyse formation of bonds between carbon and O,S,N coupled to hydrolysis of high energy phosphates such as carboxylase
Enzymes and Their Substrates,
Enzymes are 3D structures
Enzymes and Their Substrates, Continued
Consider hexokinase, an enzyme whose job is to transfer a phosphate group from the high energy molecule, adenosine triphosphate,
ATP, to D-glucose.
Enzymes and Their Substrates, Continued
The Active Site
• Active site is lined with amino acid side chains
• The active site is the functional part of an enzyme where catalysis occurs
Enzymes and Their Substrates, Continued
• Glucose, the reactant for hexokinase, fits snugly in the active site. In an enzyme reaction, the reactant is called the substrate.
• Enzymes have specific substrates, a property known as substrate specificity. For example, the active site of hexokinase reacts with
D-glucose, but will not react with L-glucose.
• Enzymes are specific for one enantiomer of the substrate.
Enzymes and Their Substrates, Continued
Co factors- are inorganic substances such as Mg2+
Coenzymes- are small organic molecules derived from vitamins. Riboflavin found in the coenzyme flavin adenine dinucleotide (FAD) is a coenzyme
Enzyme related definitions
Active site- the site in the 3D protein structure at which the substrate binds and is converted to a product
Prosthetic group- a tightly bound cofactor that remains stably bound to the enzyme during the reaction
Apoenzyme- an inactive enzyme, without its cofactor
Holoenzyme- an enzyme with a bound cofactor
Enzymes and Their Substrates, Continued
Enzyme–Substrate Models
• A substrate is drawn into the active site by intermolecular attractions like hydrogen bonding.
• Hydrogen bonding orients the substrate properly within the active site.
• The initial interaction of the enzyme with the substrate is called the enzyme–substrate complex (ES). This complex forms prior to catalysis.
Enzymes and Their Substrates, Continued
1.
There are two enzyme–substrate models:
In the Lock-and-key model, the active site is thought to be a rigid, inflexible shape that is an exact complement to the shape of the substrate. The substrate fits in the active site much like a key fits in a lock.
In the induced-fit model, the active site is flexible, has a shape roughly complementary to the shape of its substrate, and undergoes a conformational change, adjusting to the shape of the substrate when the substrate interacts with the enzyme.
Enzymes as catalysts
Most chemical reactions can be described as the conversion of a substrate to a product. This process often includes a transition state, an intermediate form between substrate and product. This intermediate usually has a higher free energy than the substrate. For this reaction to happen an input of energy required to overcome the barrier. This is the Ea. This accepts the ROR the, the greater the Ea, the slower the reaction
Gibbs Free Energy (G) is used to describe the useful energy in a reaction or the energy capable of doing work.
Catalysts
They increase the ROR by lowering the Ea for the reaction. This means that less energy is required to start the reaction. The rate of reaction is increased
Enzymes affect the activation energy. The activation energy is the difference in free energy between the substrate and the transition state. The transitions state is the intermediary state of the reaction, when the molecule is neither a substrate or product. The transition state has the highest free energy, making it a rare and un-stable intermediate.
An enzyme helps catalyze a reaction by decreasing the free energy of the transition state. As a result, more product will be made because more molecules will have the energy necessary for the reaction to occur and the reaction will occur at a faster rate
Factors That Affect Enzyme Activity
If allowed to sit untouched, the flesh of sliced apples will turn brown by a process known as oxidation, caused by an enzyme.
• If lemon juice is sprinkled on the sliced apple, the vitamin C in the lemon juice will inhibit the formation of this brown color by changing the pH of the environment of the enzyme.
• Enzyme reactions are affected by reaction conditions such as substrate concentration, pH, temperature, and the presence of inhibitors.
Factors That Affect Enzyme Activity, Continued
Substrate Concentration
Maximal velocity: The rate or velocity of a reaction (v) is the number of substrate molecules converted to product per unit time. The rate of an enzyme-catalyzed reaction increases with substrate concentration until a maximal velocity (Vmax) is reached . At a constant concentration of enzyme, an increase in substrate concentration will cause an increase in the enzyme activity up to the point where the enzyme becomes saturated with substrate.
A condition known as steady state is when an enzyme is operating under maximum activit
Factors That Affect Enzyme Activity, Continued
pH
Factors That Affect Enzyme Activity, Continued
• When the enzyme environment is changed by pH, its tertiary structure is disrupted, altering the active site and causing the enzyme’s activity to decrease.
• Enzymes are most active at a pH known as their optimum pH.
• At optimum pH, the enzyme maintains its tertiary structure and its active site.
Factors That Affect Enzyme Activity, Continued
• Changes in pH will also affect the nature of the amino acid side chains in the active site.
• The optimum pH for enzymes is based on the location of the enzymes as shown:
LOOK AT GOODNOTES
Factors That Affect Enzyme Activity, Continued
Temperature
• Enzymes have an optimum temperature at which they are most active.
• The optimum temperature for most human enzymes is normal body temperature, 37 oC.
• Above optimum temperature, enzymes lose activity due to disruption of intermolecular forces stabilizing the tertiary structure.
• At high temperatures, enzymes denature, which modifies the active site.
• At low temperatures, enzyme activity is low due to a lack of energy for the reaction to occur.
Michaelis-Menten kinetics
This diagram illustrates the reaction velocity (v) of a certain enzymatic reaction in relation to its substrate concentration ([S]) in an otherwise stable environment. It yields a solubility curve with an initial steep rise with subsequent plateauing (hyperbolic solubility curve).
The maximum reaction velocity (Vmax) is indicated by the plateau phase which is achieved at maximum substrate concentrations.
KM is defined as the substrate concentration at which the reaction velocity equals 50% of Vmax.
Michaelis-Menten Plot
The Michaelis constant (Km) is related to the affinity of the enzyme for its substrate;
A small Km indicates high affinity because a lower substrate conc is required to half saturate the reaction
A large Km indicates low affinity because a high substrate conc is required to half saturate the reaction
Factors That Affect Enzyme Activity, Continued
Inhibitors
Inhibitors are types of molecules that will cause enzymes to lose activity.
• Enzyme inhibitors prevent the active site from interacting with substrate
to form ES.
• Some inhibitors cause temporary loss of activity, while others cause permanent loss of activity.
Competitive inhibitors
Are similar structure tot he enzyme substrate. They bind the enzyme active site without being converted to product. They block access of the normal substrate to the enzyme. This increases the Km of the enzyme, that is, it takes a greater substrate conc to generate half maximal enzyme activity how V max does not change
Competitive inhibition
With increasing concentrations of inhibitor, the Michaelis-Menten curve flattens and shifts to the right, meaning that the enzyme activity is lower for any given concentration of substrate.
The Vmax’ the maximal rate of the reaction does not change. The enzyme activity can still be maximized, given a high enough substrate concentration.
Non competitive inhibitors
Interact with the enzyme at another site (not the AS) and they affect the ability of the enzyme to catalyse the reaction. They reduce the Vmax of the enzyme. Because the inhibitor is not competing with he substrate for the access to the AS. There is no change to Km
They distort the enzyme and prevent proper binding and catalysis of substrate at the AS
Class of inhibitors
Competitive Non competitive
Km increase No effect
Vmax no effect Decrease
DRUGS for competitive inhibitors
The statin drugs ( lovastatin, simavastatin) used to control blood cholesterol, competitively inhibit 3 hydroxy-3methylglutaryl CoA reducatase in cholesterol biosynthesis
Methrotrexate an antineoplastic drug, competitively inhibits dihydrofolate reductase, depriving the cell of active folate needed for purine and deoxythymdine synthesis, thus interfering with DNA replication during S phase
Noncompetitive inhibitor is allopurinol which inhibits xanthine oxidase
