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enzymes = biological catalysts Most Enzymes are proteins* proteins ≡ Polypeptides

Substrate attaches reversibly by noncovalent, or weak bonds:Ionic interactions salt bridges between negative and positive group of ionsHydrogen bonds electrostatic attraction between dipolesvan der Waals forces weak interactions due to transitory polarities arising from electron movementsHydrophobic/hydrophilic interactions causes molecules to associate together.

*Recently RNA was found to catalyze some reactions.

Enzymes and their classification

The substance that is acted on by the enzyme is called the substrate

Enzymes react with substrates by means of the active site

It has been estimated that the typical cell contains many thousands of different kinds of enzymes.

The lock-and-key model for enzyme activity.1894-Emil Fisher

• The active site has a rigid shape.• An enzyme only binds substrates that exactly fit

the active site.• Only substrates with the matching shape can fit.• The substrate is the key that fits that lock.

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The induced-fit model for enzyme activity.1958-Daniel Koshland

• Enzyme structure is flexible, not rigid.• Enzyme and substrate adjust the shape of the

active site to bind the substrate.• The range of substrate specificity increases.• Shape changes improve catalysis during reaction.

Increase the rate of reaction by lowering the energy of activation:o Straining bonds in reactants to make it easier to achieve transition stateo Positioning reactants together to facilitate bondingo Changing local environmento Direct participation through very temporary bonding

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Enzymes are catalysts.

Enzymes may recognize and catalyze:• A single substrate.• A group of similar substrates.• A particular type of bond.

Enzyme Specificity and Efficiency

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Enzyme Catalyzed Reaction Mechanism

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Enzymes are divided into six major classes with subgroups and sub-subgroups to define their function more precisely.

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• In most cases, enzyme names end in –ase

• Some are taken from the substrate• Urea: remove -a, replace with -ase = urease• Lactose: remove -ose, replace with -ase = lactase• Amylase: substrate is amylose

• Others are named from the substrate and the reaction catalyzed• Lactate dehydrogenase• Pyruvate decarboxylase

• Some names are historical - no direct relationship to substrate or reaction type• Pepsin • Chymotrypsin • Trypsin• Papain found in papaya• Rennin found in milk• Catalase found in nearly all living organisms

Naming Enzymes

catalase

catalyzes the decomposition of hydrogen peroxide to water and oxygen.

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o Different forms of an enzyme in which a quaternary structure is observed with slight variations in the primary structure.

o Catalyze the same reaction in different tissues or different locations in cells.

In some cases, the same reaction is catalyzed by different enzymes: Isoenzymes (Isozymes)

A B

A B

A B

E

E’

E’’

E ≠ E’ ≠ E’’ however, related multiple versions of the same enzyme

Example: hexokinase and glucokinase

G + Pi G-6-P Brain and other tissues

G + Pi G-6-P Liverglucokinase

hexokinase

Isozymes often have a number of subunits.Example: lactate dehydrogenase (LDH) = 4 subunits of 2 different types.o M and H represent different polypeptide subunits.o H is the main enzyme in the heart.o M is the main enzyme associated with muscle. o consists of five isoenzymes.

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The deficiency or excess of particular enzymes can cause certain diseases or signal problems such as heart attacks and other organ damage.

Isoenzymes concentration in blood serum can be used to identify the organ or tissue involved in damage or disease.

A disease or medical condition can damage an organ and cells die, releasing their content into the blood.

The blood levels of 3 enzymes are commonly assayed in MI (myocardial infraction) situations:creatine phosphokinase CPKaspartate transaminase ASTlactate dehydrogenase LDH

These are elevated following a heart attack and are used to determine the severity of the attack.

Enzymes

• Are most active at an optimum temperature (usually 37°C in humans).

• Show little activity at low temperatures.

• Lose activity at high temperatures as denaturation occurs.

Why is a high fever dangerous?Enzymes lose activity at high temperatures as denaturation occurs.

Normal body T is about 37 °C (98.6 °F)Fever classification Grade °C °Flow grade 38–39 100.4–102.2moderate 39–40 102.2–104.0high-grade 40–42 104.0–107.6hyperpyrexia >42 >107.6

Factors Affecting Enzyme Activity & Inhibition

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Enzymes• Are most active at optimum pH.• The body has an optimum pH of about 7.4.• In certain organs, operate at lower and higher

optimum pH values.• Contain R groups of amino acids with proper

charges at optimum pH.• Lose activity in low or high pH as tertiary

structure is disrupted.

Acidosis is a serious medical condition caused by a drop in pH that , among other things, causes enzymes to denature.

Enzyme Concentration

An increase in enzyme concentration• Increases the rate of reaction (at constant

substrate concentration). • Binds more substrate with enzyme.

An increase in substrate concentration• Increases the rate of reaction (at constant

enzyme concentration).• Eventually saturates an enzyme with substrate

to give maximum activity.

Substrate Concentration

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Reversible Involves noncovalent bindingit can dissociate and allow the enzymeto regain activity.

Irreversible Involves covalent bondingit can not dissociate and thus causing permanent inactivation.

Inhibitors•Are molecules that cause a loss of catalytic activity.•Prevent substrates from fitting into the active sites.•Medicines as well as poisons act as E inhibitors.

E + S ES E + P

+ I

EI no P

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competitive

noncompetitiveInhibitors

In irreversible inhibition, a substance• Bonds with R groups at the active site.• Destroys enzyme activity.

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Structures of selected penicillins in use today as antibiotics

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Selective binding of penicillin to the active site of transpeptidase.

Some bacteria are resistant to penicillin because they produce penicillinase, an enzyme that breaks down penicillin.

Penicillin inhibits transpeptidase, an enzyme that catalyzes the formation of bacterial cell walls.

It does not affect human cell membranes.

Structures of selected sulfa drugs in use today as antibiotics.

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Sulfa drugs inhibit bacterial cell growth because it is structurally similar to PABA, para-aminobenzoic acid. Many bacteria need PABA in order to produce an important coenzyme, folic acid. Folic acid deficiency retards growth and eventually kills the bacteria.

Zymogens (proenzymes) Are inactive forms of enzymes.Are activated when one or more peptides are removed.Such as proinsulin is converted to insulin by removing a small peptide chain.Peptidases are needed to remove the peptide section that turns the inactive form into its active one.Removal of the fragment changes the tertiary structure and turns the zymogen into its enzyme.

Regulation of Enzyme Activity

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An allosteric enzyme is an enzyme in a reaction sequence that binds a regulator substance.

A positive regulator when it enhances the binding of substrate and accelerates the rate of reaction.

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Allosteric regulation

In each biochemical pathway there are one or more enzymes whose catalytic activity can be modulated (increased or decreased) by the binding of a regulator.

A negative regulator when it prevents the binding of the substrate to the active site and slows down the rate of reaction.

Greek allostery translates to “other solid”, “other structure”. Allosteric effect occurs when the binding of a ligand results in a conformational change (other structure) in the enzyme. Such change is associated with increased or decreased enzyme activity.

E1 is an allosteric enzyme: 1. An enzyme in a reaction sequence2. Binds a regulator substance.

A product can act as an inhibitor.An end product binds with the first enzyme (E1) in a sequence when sufficient product is present.

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Feedback inhibition = feedback control

Enzymes:Can function on their ownOr need some help in order to functionThe needed help is provided by a Cofactors or coenzyme.

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small moleculescalled coenzymes Derived from vitaminsPlay a variety of roles that the enzyme alone cannot play.They are recycled and only small amounts are required.

metal ionsAct as Lewis acidsCan coordinate with the enzyme’s R groups, causing them to align in an arrangement that facilitates reaction.

Apoenzyme- An enzyme that requires a cofactor but does not have one bound. It is an inactive enzyme, activation of the enzyme occurs upon binding of an organic or inorganic cofactor.

Holoenzyme- An apoenzyme together with its cofactor. A holoenzyme is complete and catalytically active.

Enzyme Cofactors and Vitamins

Carboxypeptidase A cleaves the C terminal AA of a protein when that AA has a bulky hydrophobic or aromatic side chain.

Zn2+ a cofactor for carboxypeptidase A, stabilizes the carbonyl oxygen during the hydrolysis of a peptide bond.

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After the water molecule loses H+, the remaining

OH- remains bonded to Zn2+.

A CO2 molecule is held in the active site close to

the Zn2+ where it can react with the OH- to form

HCO3-, which is then released from the active

site.

The active forms of carbonic anhydrase requires Zn2+ as a cofactor.carbonic anhydrase

CO2 + H2O HCO3- + H+

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This reactions maintains the proper pH in blood and tissues.

• A coenzyme prepares the active site for catalytic activity.

• An organic molecule bound to the enzyme by weak interactions / Hydrogen bonds

• Most coenzymes carry electrons or small groups

• Many have modified vitamins in their structure

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Coenzymes are small organic molecules.

Coenzymes generally are complex organic molecules that can not be synthesized by some organisms – mammals in particular.

Nicotinamide adenine dinucleotide (NAD+)

Nicotinamide adenine dinucleotide (NAD+) is synthesized from the vitamin niacin.

The Nicotinamide portion is the part of NAD+ responsible for its metabolic functions because it is capable of being reduced and thus can serve as an oxidizing agent to which two electrons and a proton can be added:

A typical reaction in which NAD+ acts as oxidizing agent is the conversion of alcohols to aldehydes or ketones.Here is the conversion of ethanol to acetaldehyde by the alcohol dehydrogenase of liver:

CH3CH2OH + NAD+ → CH3CHO + NADH + H+

LADH (Liver Alcohol Dehydrogenase)

uses the coenzyme nicotinamide adenine dinucleotide (NAD+).

VitaminsIn the early 20th century, scientists detected minute amounts of substances found to be essential in preventing disease and maintaining health.

The substances were called vitamines by Casimir Funk to indicate they were vital for survival and contained nitrogen -that is, they were amines.

The e was later dropped when scientists found that some were not amines.

To date, scientists have identified 13 vitamins.There are 9 water soluble (8 B vitamins and vitamin C) and 4 fat soluble.Among the most common are:

Fat A D E K

Water B C F HFolic acid Biotin

All get DEposited in fatty tissue, acKumulates

Be CareFul with your money H $

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9 Water-Soluble Vitamins = B vitamins and vitamin C

Have polar groups –OH and -COOH and soluble in aqueous solutions.

Cofactors for many enzymes.

Not stored in the body.

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