proteins and enzymes€¦  · web viewenzymes are the catalysts of biochemical reactions. enzymes...

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Enzymes Enzymes are the catalysts of biochemical reactions. Enzymes catalyze nearly all the myriad reactions that occur in living cells. Uncatalyzed reactions that require hours of boiling in the presence of a strong acid or strong base can occur in a fraction of a second in the presence of the proper enzyme. Reactions involving them occur often at a rate of millions of times per second. The catalytic functions of enzymes are directly dependent on their three- dimensional structures Enzyme terminology There are two general systems that can be used to name enzymes: 1. The older, common, “trivial” system had no rhyme or reason for naming specific enzymes. Often, enzymes were named at the discretion of the individual who discovered them. For example: insulin was named for the “islets of Langerhans”, which are clusters of endocrine cells in the pancreas that secrete insulin. [insulin is derived from the Latin word “insula”, which means “island”] 2. The newer system was developed by the Commission on Enzymes of the International Union of Biochemistry. It names an enzyme by using whatever it is working on to catalyze and adjusting its ending to end in “-ase”. For example, the enzyme that would be used to catalyze the hydrolysis of maltose (a disaccharide) would be called maltase. This equation could be written like this: maltase maltose ---------------- > 2 glucose molecules

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Page 1: PROTEINS AND ENZYMES€¦  · Web viewEnzymes are the catalysts of biochemical reactions. Enzymes catalyze nearly all the myriad reactions that occur in living cells. Uncatalyzed

Enzymes Enzymes are the catalysts of biochemical reactions.

Enzymes catalyze nearly all the myriad reactions that occur in living cells.

Uncatalyzed reactions that require hours of boiling in the presence of a strong acid or strong base can

occur in a fraction of a second in the presence of the proper enzyme. Reactions involving them occur

often at a rate of millions of times per second.

The catalytic functions of enzymes are directly dependent on their three-dimensional structures

Enzyme terminology

There are two general systems that can be used to name enzymes:

1. The older, common, “trivial” system had no rhyme or reason for naming specific enzymes. Often,

enzymes were named at the discretion of the individual who discovered them. For example: insulin was

named for the “islets of Langerhans”, which are clusters of endocrine cells in the pancreas that secrete

insulin. [insulin is derived from the Latin word “insula”, which means “island”]

2. The newer system was developed by the Commission on Enzymes of the International Union of

Biochemistry. It names an enzyme by using whatever it is working on to catalyze and adjusting its ending

to end in “-ase”. For example, the enzyme that would be used to catalyze the hydrolysis of maltose (a

disaccharide) would be called maltase.

This equation could be written like this:

maltase

maltose ---------------- > 2 glucose molecules

In enzyme chemistry, a substrate is “anything acted on by an enzyme”. Notice, I don’t say “reacted with”, because

enzymes don’t react, they simply cause reactions to take place.

So, in the above example, maltose

is a substrate. Maltase is an enzyme

Enzymes, and other catalysts, typically lower the

activation energy of a reaction. The following is a

typical reaction-energy profile.

Page 2: PROTEINS AND ENZYMES€¦  · Web viewEnzymes are the catalysts of biochemical reactions. Enzymes catalyze nearly all the myriad reactions that occur in living cells. Uncatalyzed

Each organism contains thousands of enzymes

Some enzymes are simple proteins consisting of only amino acid units.

Other enzymes are conjugated and consist of a protein part, or apoenzyme, and a nonprotein part, or coenzyme.

A functioning enzyme that consists of both the protein and nonprotein parts is called a holoenzyme.

Apoenzyme + Coenzyme = Holoenzyme

A coenzyme is a small organic molecule that links to an enzyme; its presence is essential to the activity of the enzyme.

Often the coenzyme is derived from a vitamin and one

coenzyme may be associated with different enzymes

For some enzymes, an inorganic component such as a metal

ion (e.g. Ca2+, Mg2+, or Zn2+) is required.

This inorganic component is an activator or cofactor. They act

to “turn on” the enzyme so it can function.

The activator is analogous to a coenzyme; this means they

function similarly.

Another remarkable property of enzymes is their specificity of reaction – that is, a certain enzyme catalyzes the reaction

of a specific type of substance.

Page 3: PROTEINS AND ENZYMES€¦  · Web viewEnzymes are the catalysts of biochemical reactions. Enzymes catalyze nearly all the myriad reactions that occur in living cells. Uncatalyzed

e.g. lactase

The substance acted on by an enzyme is called the substrate.

e.g. Sucrose is the substrate of the enzyme sucrase

Classes of Enzymes1. Oxidoreductases: Enzymes that catalyze the oxidation-reduction between two substrates.

2. Transferases: Enzymes that catalyze the transfer of a functional group between two substrates.

3. Hydrolases: Enzymes that catalyze the hydrolysis of esters, carbohydrates, and proteins (polypeptides).

4. Lyases: Enzymes that catalyze the removal of groups from substrates by mechanisms other than

hydrolysis.

5. Isomerases: Enzymes that catalyze the interconversion of stereoisomers and structural isomers.

6. Ligases: Enzymes that catalyze the linking of two compounds by breaking a phosphate anhydride bond

in ATP.

Rates of Chemical Reactions

A rate is defined as the change in concentration with time, or the speed at which the reactants disappear and products

form.

The reactant must pass through a high-energy transition state. It

is unstable and has characteristics of both reactants & products.

The following is the energy profile for the reaction of water with

carbon dioxide. The dashed lines represent bonds being broken

and bonds being formed.

There are three common ways to increase a reaction rate:

1. Increasing the reactant concentration

2. Increasing the reaction temperature

3. Adding a catalyst

Enzyme KineticsIn 1913, Leonor Michaelis and Maud Menten measured enzyme-catalyzed reaction rates as a function of substrate

concentration. They found most reactions show increasing rate with increasing substrate concentration, but end up

having a maximum velocity.

Page 4: PROTEINS AND ENZYMES€¦  · Web viewEnzymes are the catalysts of biochemical reactions. Enzymes catalyze nearly all the myriad reactions that occur in living cells. Uncatalyzed

Figure 30.4 A Michaelis-Menten plot showing the rate of enzyme-catalyzed reaction

as a function of substrate concentration. The lower left portion of the graph marks

the approximate area where an enzyme responds best to concentration changes.

It is believed that some enzymes work well at low substrate concentrations and others require higher concentrations.

Figure 30.5 Michaelis-Menten plots for two glucose metabolic

enzymes. Hexokinase works best at high concentrations and

glucokinase works best at low concentrations.

An enzyme’s catalytic speed is also matched to an organism’s metabolic needs.

This catalytic speed is commonly referred to as turnover number – the number of molecules an enzyme can react or

“turn-over” in a given time span. For example, the enzyme catalase destroys dangerous hydrogen peroxide and has a

turnover number of 10,000,000/second. This means it breaks down ten million H2O2 molecules per second. Chymotrypsin

is a digestive enzyme that breaks down two peptide bonds every ten seconds to have a turnover number of 0.2/s.

Enzymes offer two major advantages to manufacturing processes and in commercial products:

1. Enzymes cause very large increases in reaction rates even at room temperature.

2. Enzymes are relatively specific and can be used to target selected reactants.

Page 5: PROTEINS AND ENZYMES€¦  · Web viewEnzymes are the catalysts of biochemical reactions. Enzymes catalyze nearly all the myriad reactions that occur in living cells. Uncatalyzed

Industrial uses:

Proteases (proteolytic enzymes) break down proteins. They can be put in laundry detergents to remove blood stains; can

be used to dissolve blood clots.

Lipases digest lipids. Can be put in soaps & detergents to break down fats.

Cellulases, amylases, lactases, and pectinases break down cellulose, amylose, lactose, and pectin, respectively.

Can be in foods (quick cooking oatmeal, pre-peeled citrus fruits, dairy, corn syrup), medicine, fabrics, many others.

Catalysis takes place on a small portion of the enzyme structure called the enzyme active site.

Often this is a crevice or pocket on the enzyme that represents only 1-5% of the total surface area.

Figure 30.6 A

spacefilling model of the

enzyme hexokinase (a)

before and (b) after it

binds to the substrate D-

glucose. Note the two

protein domains for this

enzyme, which are

colored differently.

Lock and key hypothesis: the substrate is a key that fits into an appropriate active site (the lock). This helps explain the specificity

of enzymes. Since enzymes are molecules with some flexibility, the “lock” and “key” are not always rigid. This leads to the

induced-fit model, where the active site adjusts

Figure 30.7 Enzyme-substrate interaction

illustrating both the lock-and-key hypothesis and

the induced-fit model. The correct substrate

(orange square-blue circle) fits the active site

(lock-and-key hypothesis). This substrate also

causes an enzyme conformation change that

positions a catalytic group (*) to cleave the

appropriate bond (induced-fit model).

Page 6: PROTEINS AND ENZYMES€¦  · Web viewEnzymes are the catalysts of biochemical reactions. Enzymes catalyze nearly all the myriad reactions that occur in living cells. Uncatalyzed

Proximity catalysis is when an enzyme acts to brings reactants together.

Productive binding hypothesis is when an enzyme brings the reactants together in proper orientation so that bonds

can break and form.

Strain hypothesis is when the substrate changes shape to fit the active site.

Figure 30.8 Strain Hypothesis: The substrate is being forced toward the product shape by enzyme

binding.

Temperature & pH effectsEssentially, any change that affects protein structure also affects an enzyme’s catalytic function.

If an enzyme is denatured, its activity will be lost.

Thus, strong acids and bases, organic solvents, mechanical action, and high temperature are examples of treatments that

decrease an enzyme-catalyzed rate of reaction.

Page 7: PROTEINS AND ENZYMES€¦  · Web viewEnzymes are the catalysts of biochemical reactions. Enzymes catalyze nearly all the myriad reactions that occur in living cells. Uncatalyzed

Enzyme regulation

Covalent modification – a new group of atoms covalently joins to the enzyme to change the rate of conversion

Enzyme inhibition – decreases activity

Enzyme activation – increases activity

Product inhibition – when a product of a catalyzed reaction builds up, binds to active site, and inhibits its own

production

Feedback inhibition – when the final product of a series of reactions inhibits the enzyme from starting the process over

again. It is like an assembly line. It affects enzymes at the beginning of the molecular assembly line.

Feedforward inhibition – controls enzymes at the end of an assembly line. If there’s an excess of starting materials,

they cause the whole process to move faster.