Chapter 3 Enzymes

X on a graph

point of saturation

How do enzymes catalyze reactions?

An enzyme can catalyze a reaction by making a substrate molecule split into two or more molecules. Or can catalyze the reaction of joining together two molecules, to make a dipeptide.

The effect of enzyme concentration

To look at the effect of enzyme concentration it is best to look at right at the beginning of the reaction. This is because, once the reaction is underway, the amount of substrate in each reaction begins to vary, because substrate is converted to product at different rates in each of the five reactions.The more enzyme present, the more active sites will be available for the substrate to slot into. As long as there is plenty of substrate available, the initial rate of reaction increase linearly with enzyme concentration.

Biological catalysts

a molecule which speeds up a chemical reaction but remains unchanged at the end of the reaction

Active site

a region, usually a cleft or depression, to which another molecule or molecules can bind.

Reversible inhibitors

can be washed out of the solution by dialysis, there are two categories.

Irreversible inhibitors

combine with the functional groups of the amino acids in the active site, irreversibly.

End-product inhibition

using the end product of a chain of reactions as a non-competitive reversible inhibitor. As the enzyme converts substrate to product, it is slowed down because the end product binds another part of the enzyme and prevents more substrate binding. However, the end product can lose its attachment to the enzyme and go on the be used elsewhere, allowing the enzyme to reform into its active site.

Advantages of immobilized enzymes

- you can re-use enzymes which lowers cost -more tolerant to changes in temperature and ph

Factors that affect enzyme action

-The effect of enzyme concentration -The effect of substrate concentration -Temperature and enzyme activity -ph and enzyme activity

Course of a reaction

-When the enzyme and substrate are first mixed there are a large number of substrate molecules. At any moment, virtually every enzyme molecule has a substrate molecule in its active site. -The rate at which the reaction occurs depends only on how many enzymes can convert the substrate into a product, release it and then bind another substrate molecule. -However, as more and more substrate is converted into product, there are fewer and fewer substrate molecules to bind with enzymes. Enzyme molecules may be 'waiting' for substrate molecules to hit their active sites. As fewer substrate molecules are left, the reaction gets slower and slower, until it eventually stops.

Vmax

An enzyme's maximum possible rate, V stands for velocity. At Vmax all the enzyme molecules are bound to substrate molecules- the enzyme is saturated with substrate.

The peak of the effect of temperature on enzyme activity

As temperature continues to increase, the speed of movement of the substrate and enzyme molecules also continue to increase. However, above a certain temperature, the structure of the enzyme molecule vibrates so energetically that some of the bonds holding the enzyme molecule in its precise shape begin to break. The enzyme molecule begins to lose its shape and activity and is said to be denatured, this is often irreversible. At first, the substrate molecules fit less well into the active site, slowing down the reaction until eventually they don't fit at all and the reaction cannot occur.

How many types of substrate molecules does an enzyme act on?

Each type of enzyme will usually act on only one type of substrate molecule. This is because the shape of the active site will only allow one shape of molecule to fit. The enzyme is said to be specific for this substrate.

What type of proteins are enzymes?

Enzymes are globular proteins and are therefore foiled into a precise three-dimensional shape, with hydrophilic R groups on the outside of the molecule ensuring that they are soluble.

Enzymes and activation energy

Enzymes decrease the amount of activation energy needed to have a chemical reaction. When a substrate binds to the active site of an enzyme, the shape of its molecule is slightly changed. This makes it easier to change the substrate into a product thus reducing the activation energy.

Enzyme-product complex

Interactions between R groups of the enzyme and the atoms of the substrate can break or encourage formation of, bonds in the substrate molecule, forming one two or more products. The rate at which substrate molecules can bind to the enzyme's active site, be formed into products and leave can be very rapid.

pH and enzyme activity

Most enzymes work fastest at a pH of somewhere around 7. Some however, such as the protease pepsin, have a different optimum pH. The lower the pH, the higher the hydrogen ion concentration. Hydrogen ions can interact with the R groups of amino acids, which affect the ionic bonding and thus the 3D arrangement of the enzyme molecule. When the shape is different the chances of the substrate molecule fitting are reduced, a pH very different from the optimum pH can completely denature the enzyme.

What is an enzyme inhibitor?

a molecule which binds to the enzyme and reduces or 'inhibits' the enzyme's function. If an inhibitor molecule binds only briefly to the site, there is competition between it and the substrate for the site. If there is much more of the substrate present than the inhibitor, substrate molecules can easily bind to the active site in the usual way, and so the enzyme's function is unaffected. Inhibitors usually reduce the rate of enzymic reactions. Inhibition can be lethal but in most situations is essential to keep reactions controlled.

Measuring rate of reaction

amount of product formed/unit of time

Immobilized enzymes

an enzyme attached to an inert, insoluble material to render it immobilized.

Catalase

an enzyme found in the tissues of most living organisms and catalyzes the breakdown of hydrogen peroxide into water and oxygen.

Induced fit hypothesis

an enzyme has a particular shape into which the substrate fits, but the enzyme, and sometimes the substrate, can change shape slightly as the substrate molecule enters the enzyme in order to ensure a perfect fit. This makes the catalysis even more efficient.

The effect of substrate concentration

as substrate concentration increases, the initial rate of reaction also increases. Again, this is only what we would expect: the more substrate molecules there are around, the more often an enzymes active site can bind with one. However, if we go on increasing substrate concentration keeping the enzyme concentration constant, there comes a point where every enzyme active site is working continuously. If more substrate is added, the enzyme simply cannot work faster; substrate molecules are effectively 'queuing up' for an active site to become vacant. The enzyme is working at its maximum possible rate.

Temperature and enzyme activity

at low temperatures the reaction only takes place very slowly, this is because the molecules are moving relatively slowly. Substrate molecules will not often collide with the active site, and so binding between substrate and enzyme is a rare event. As temperature rises, the enzyme and substrate molecules move faster. Collisions happen more frequently so that substrate molecules enter the active site more often. Moreover, when they do collide, they do so with more energy. This makes it easier for bonds to be formed or broken so that the reaction can occur.

Competitive inhibitors

compete with the substrate molecules for the active site. The inhibitors action is proportional to its concentration and resembles the substrates structure closely. Can be reversed by increasing the concentration of the substrate.

Extracellular

enzymes that are secreted by cells and catalyze reactions outside cells, for example digestive enzymes

Intracellular

enzymes that operate within cells,

Affinity

how quickly a substrate and an enzyme react together. measured by the Michaelis-Menten constant. The higher the __________ of the enzyme for the substrate, the lower the substrate concentration needed for this to happen.

Non-competitive inhibitors

not influenced by the concentration of the substrate, it inhibits by binding to the enzyme but not at the active site. The resulting distortion ripples across the molecule to the active site, making the enzyme unsuitable for the substrate. A type of allosteric inhibition. May or may not be reversible depending on whether the inhibitor binds permanently or not.

Enzyme

protein molecules that are described as biological catalysts, increase the rate at which chemical reactions occur.

Enzyme-substrate complex

the combined structure created when the substrate is held in place by temporary bonds which form between the substrate and some of the R groups of the enzyme's amino acids.

Activation energy

the extra energy needed to convert a substrate into a product, this can be done by heating the substrate. Mammals such as humans use this method to speed up metabolic reactions.

Lock and Key Hypothesis

the idea that the enzyme has a particular shape into which the substrate fits exactly. The substrate is the key whose shape fits into the lock of the enzyme. Was later modified in light of evidence that enzyme molecules are more flexible than is suggested by a rigid lock and key.

Substrate

the molecule or molecules which bind to the active site of the enzyme. The shape of the active site allows it to fit perfectly

Initial rate of reaction

the rate of an enzyme-controlled reaction is always the fastest at the beginning

Michaelis-Menten constant (Km)

the substrate concentration at which an enzyme works at half its maximum rate (1/2 Vmax) At this point half the active sites of the enzyme are occupied by substrate. Thus, this constant measures the affinity of the enzyme for its substrate. A high Km means a lot of substrate must be present to saturate the enzyme, meaning the enzyme has low affinity for the substrate.

Optimum temperature

the temperature at which an enzyme catalyzes a reaction at a maximum rate. Most mammals have an optimum temperature of around 40 degrees Celsius. We keep ours at 37 degrees Celsius to ensure enzyme-catalyzed reactions occur at close to their maximum rate. It would be dangerous to maintain a body temperature of 40 degrees Celsius, as even a slight raise above this would begin to denature enzymes.

Turnover rate

the typical rate at which an enzyme molecule can convert a substrate molecule into a product. the typical rate is estimated to be around one thouand substrate molecules into product per second.