Glossary of Biology - Enzymes

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What are enzymes?
They are protein catalysts that accelerate reactions
How do they manage this?
They reduce the initial energy (activation energy) necessary for them to proceed
Does the enzyme change anything else?
What about the equilibrium point of the reaction?
Nope, it just changes the rate at which it is attained
What happens to the enzymes during reactions?
They are neither consumed nor changed
Are enzyme reactions reversible?
Most are reversible. The product synthesized by an enzyme can also be decomposed by the same enzyme
Does the free energy change of the two reactions change?
No, it changes by a magnitude of 0
Do enzymes bind to anything, or are they selective?
They are very selective
How many reactions do they catalyze?
Some may catalyze only one type of reaction, or one specific class of closely related reactions
What does Urease do?
Urease selectively catalyzes the breakdown of urea
What does chymotrypsin do?
It selectively catalyzes the hydrolysis of specific types of peptide bonds, enabling it to catalyze the hydrolysis of more than one type of peptide
What is the molecule upon which an enzyme acts called?
It is called a substrate
When the substrate binds to the area on each enzyme that is specific for it, what does it form?
A substrate complex
What is this area called?
The active site
What is the shape of it?
It is a three-dimensional shape into which the substrate fits and is held at a particular orientation
What are the two models describing the formation of an enzyme-substrate complex?
The lock and key theory, and the induced fit hypothesis
What is the lock and key theory?
It holds that the spatial structure of an enzyme’s active site (the lock) is exactly complementary to the spatial structure of its substrate (the key)
What is the induced fit hypothesis?
It describes the active site of an enzyme as having some flexibility of shape
What happens when the appropriate substrate comes into contact with the active site?
The conformation of the active site changes such that it surrounds the substrate, creating a close fit
What happens if the substrate is the wrong shape?
It will not induce a conformational change in the enzyme’s active site, thereby preventing the formation of an enzyme substrate complex
What do studies suggest is the more plausible of the two?
Studies suggest that the induced fit hypothesis is more plausible
What are cofactors?
They are nonprotein molecules that many enzymes require the incorporation of before becoming catalytically active
How do they aid?
They aid in the binding of the substrate to the enzyme by stabilizing the enzyme in an active conformation
What is an enzyme called that is devoid of its necessary cofactor?
It is called an apoenzyme
What does this infer?
It means it is catalytically inactive
What is an enzyme called that contains its cofactor?
It is called a holoenzyme
How are cofactors bound to their enzymes?
They are bound by weak noncovalent interactions or by strong covalent bonds
What are tightly bound cofactors called?
Prosthetic groups
What are two important types of cofactors?
Metal cations
What are some examples of metal cations?
Zn2+, Fe2+ and small organic groups
What is an example of an organic cofactor?
What are the organic groups called?
What is special about coenzymes?
They cannot be synthesized by the body and are obtained from the diet as vitamin derivatives
What can the lack of a particular vitamin lead to?
It can impair the action of its corresponding enzyme and lead to disease
What is the rate of an enzyme-catalyzed reaction related to?
Concentrations of the enzyme and the substrate, and environmental variables such as temperature and pH
What happens when the concentration of the substrate is low compared to that of the enzyme?
Many of the active sites are unoccupied and the reaction rate is low
What happens when the substrate concentration is increased?
It leads to proportional increases in the rate of reaction, because unoccupied active sites on the enzyme readily bind to the additional substrate
What happens once most of the active sites are occupied?
The reaction rate will level off
Even if I add tons more?
Yep, even if you add tons more
What happens at high concentrations of substrate?
The reaction rate approaches its maximal velocity
What is this also known as?
What does this imply?
It means that even by adding a ton of substrate, you can’t relieve noncompetitive inhibition
What is the Michaelis-Menten model and when was it proposed?
It was proposed in 1913, and it says that an enzyme-substrate complex, ES, is formed at rate k1 from enzyme E and substrate S. The ES complex can either dissociate into E and S at rate k2, or form product P at rate k3.
What is the relationship between the three rates?
It is defined by the Michaelis constant, Km
What is the constant?
(k2 + k3) / (k1), or the ratio of the breakdown of the ES complex to its formation
What does this mean in lay terms concerning reaction rate?
When the reaction rate is equal to _ Vmax, Km = [S] and can be understood as the point at which half of the enzyme’s active sites are filled
What about when [S] is less than Km?
Changes in substrate concentration greatly affect the reaction rate
What is the opposite of this, when [S] is higher than Km?
When that occurs, V approaches Vmax
What are the effects of temperature?
Well, the rates of enzyme-catalyzed reactions tend to double for every 10C increase in temperature
This occurs until what point?
This occurs until the optimal temperature is reacted
What is the optimal temperature for most enzymes in the human body?
For most, the optimal temperature is 37C
What happens at higher temperatures?
The enzymes become denatured
What does this mean?
It means their 3-dimensional structure is destroyed and the enzyme becomes nonfunctional
Can enzymes ever renature?
Some can. Some that are partially denatured can sometimes regain their activity upon being cooled
What are the effects of pH?
For each enzyme there is also an optimal pH above and below which enzymatic activity declines
What is the maximal activity of many human enzymes?
It occurs around pH 7.2
What is significant about the pH 7.2?
It is the pH of most body fluids
What are exceptions to this?
Pepsin, which works best in highly acidic conditions of the stomach like pH of 2, and pancreatic enzymes, which work optimally in the alkaline conditions of the small intestine at pH of 8.5
What is an allosteric enzyme?
It has two or more active sites that may be composed of more than one subunit
What does an allosteric enzyme do?
It oscillates between two configurations, an active state capable of catalyzing a reaction, and an inactive state that cannot
What does the interaction between an allosteric enzyme and regulator accomplish?
It can stabilize either configuration, depending on the type of regulator involved
What are the two types of regulators?
There are allosteric inhibitors and allosteric activators
What does an inhibitor do?
It prevents an enzyme from binding to its substrate by stabilizing the inactive conformation
What does an activator do?
It stabilizes the active configuration, promoting the formation of enzyme-substrate complexes
What is another allosteric effect that involves increased affinity of an enzyme for its substrate?
Sometimes binding of a regulator at the allosteric site or the binding of a substrate at one of the enzymes active sites, may stimulate the other active sites on the enzyme to bind more efficiently by increasing their affinity for the substrate
What is an example of this?
Malonate differs from succinate only in having an additional methylene group, and is consequently recognized as succinate by the enzyme succinate dehydrogenase
What are the three inhibitors for enzymatic activity?
Feedback inhibition, reversible inhibition, and irreversible inhibition
What is feedback inhibition?
It occurs when the end product of a sequence of enzymatic reactions becomes an allosteric inhibitor of one of the preceding enzymes in the sequence
What is this used for?
It allows organisms to avoid overproduction of metabolites
What is reversible inhibition?
Reactions with weak enzyme-inhibitor complexes that dissociate easily are referred to as reversible inhibition reactions
What are the two types?
Competitive inhibitors and noncompetitive inhibitors
How do competitive inhibitors work?
They compete with the substrate directly by binding to the active site of the enzyme
How are the structures of competitive inhibitors and substrates related?
Because they bind at the same site, they usually have similar structures
How can the presence of competitive inhibitor molecules be overcome?
By adding sufficiently high substrate concentrations
How do noncompetitive inhibitors work?
They work by binding to other sites on the enzyme and cause a conformational change such that the enzyme can no longer bind substrate at its active site
What is irreversible inhibition?
In this type, permanent damage is done to the active site, either by tight, covalent bonding of the inhibitor to the enzyme, or by denaturization of the 3-D structure of the active site
What does this prevent?
It prevents the formation of the enzyme-substrate complex
What is a zymogen?
It is an enzyme that is secreted in an inactive form
How can a zymogen become active?
It can be cleaved under certain physiological conditions to the active form of the enzyme
What are important examples of zymogens?
Pepsinogen, trypsinogen, and chymotrypsinogen
What are they cleaved into?
They are cleaved in the digestive tract to yield the active enzymes pepsin, trypsin, and chymotrypsin

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