Enzymes trans - PADAYON! - Biochemistry PDF

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ENZYMESDeiniion Importance/Uses -biological catalysts Majority of enzymes are proteins that speed up the chemical reacions produced by the living cell. -are speciic in the reacion they catalyze, As well as the choice of reactants or substrates.-Used in diverse areas like food manufacturing, paper, l...

Description

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ENZYMES Definition -biological catalysts - Majority of enzymes are proteins that speed up the chemical reactions produced by the living cell.

Importance/Uses -Used in diverse areas like food manufacturing, paper, leather, agriculture, and *different industries. -Useful in *disease diagnosis

-are specific in the reaction they catalyze, As well as the choice of reactants or substrates.

- enzymes are pivotal in all living entities which govern all the biological processes Enzyme Structure -linear chain of amino acids, which give rise to a three-dimensional structure.

The sequence of amino acids specifies the structure, which in turn identifies the catalytic activity of the enzyme. Upon heating, enzyme’s structure denatures = resulting in a loss of enzyme activity, that typically is associated with temperature. (Only a small section of the structure is involved in catalysis and is situated next to the binding sites.)

catalytic site + binding site = enzyme’s active site

I. Objective: Systematically list down the classes, subclasses, sub-sub classes of each individual enzyme Objective I.a. Differentiate the functions of different enzymes

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Mnemonic: Over

The HILL (baligtad lang yung I at L)

According to the International Union of Biochemists (I U B), enzymes are divided into six functional classes and are classified based on the type of reaction in which they are used to catalyze.

Enzyme Classification / Functional Classes Oxidoreductases (oxidation-reduction reactions)

Transferases (transfer of functional groups)

Hydrolases (hydrolysis reactions)

Lyases (addition to double bonds)

Isomerases ( Isomerization reactions)

Description/ Biochemical Property Catalyze redox reaction & can be categorized into oxidase & reductase - catalyzes the transfer of hydrogen or oxygen atom or electrons from one substrate to the other. (Redox reactions). Catalyze the transfer of exchange of certain groups among some substances help in the transportation of the functional group among acceptors and donor molecules Accelerate the hydrolysis of substrates breakdown of the substrate. catalyze the hydrolysis reaction by adding water to cleave the bond and hydrolyze it Promote the removal of a group from the substrate to leave a double bond reaction or catalyze its reverse reaction - catalyzes the non-hydrolytic removal of a group (water, carbon dioxide or ammonia across double bonds) or addition of a group from or to a substrate. Facilitate the conversion of isomerases, geometric isomers/ optical isomers - catalyzes intramolecular changes in the substrate or the structural shifts present in a molecule, thus causing the

Examples Oxidases, Dehydrogenases, Oxygenases, Peroxidases, Catalases

Kinases, Transaminase

Esterase, digestive enzymes, pepsin, lysozyme, acid phosphatase

Decarboxylases, Aldolases

Isomerase, Fumarase, Phosphoglucomutase

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Ligases (formation of bonds with ATP cleavage)

change in the shape of the molecule Catalyze the synthesis of 2 molecular compounds with the release of energy

Citric acid synthetase, ligase

- catalyzes joining of two molecules by forming new bonds.

II. Objective: Discuss the different properties of Enzymes. (REF: book ng teachers ng CAHS) Enzymes, a.k.a. biological catalyst, accelerate biochemical reactions WITHOUT AFFECTING THE NATURE OF THE PRODUCT. Enzymes are proteins with a

MOLECULAR WEIGHT ranging from about 12,000 to more than 1 million

Enzymes react at optimum pH and TEMPERATURE Highest enzymatic reaction Enzymes are inactivated in a liquid medium

PROPERTIES OF AN ENZYME Catalytic Power

Ranging from 25°C - 45°C 37°C 60°C

details Enzymes have HIGH CATALYTIC ACTIVITY: Speeding up reactions as much as 10²¹: Over uncatalyzed levels CONDITIONS Under optimum pH & optimum temperature CATALYTIC POWER= Ratio of the enzyme-catalyzed Rate of Reaction to the uncatalyzed rate:

Specificity

-A molecular Recognition Mechanism -is based on structural complementarities Enzymes are HIGHLY SELECTIVE: Enzyme: specific substrate & specific reaction *SUBSTRATES: substances where enzyme acts

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TYPE of SPECIFICITY (GGSS BoC)

Aka

Explanation

Examples

Bond Specificity

Relative Specificity

-Specific to substrates having the similar bonds and similar structures

Amylase can hydrolyze α-1-4 glycosidic linkage in startch and glycogen

-specificity is LESS

Lipase can hydrolyze ester bond between glycerol and fatty acid in any fats Proteinases hydrolyzes all peptide bonds formed by any amino acids

Group Specificity

Structural Specificity -MODERATE Specificity

-Enzyme specific to type of bond and group surrounding it. -More specific than bond specificity

Endopeptidases like pepsin Exopeptidases Pepsin hydrolyze a peptide bond which the amino group is contributed by an aromatic amino acid (phenyl alalanine, tyrosine, and tryptophan) Trypsin hydrolyze a peptide bond in which amino group is contributed by a basic amino acid (lysine, arginine, and histidine) Chymotrypsin hydrolyze a peptide bind in which the carboxyl group is contributed by an aromatic amino acid Aminopeptidase hydrolyzes the peptide bond from N terminal of protein

Substrate Specificity

Absolute Specificity

An ezyme is to 1 Substrate: 1 Reaction

Carboxypeptidase hydrolyze the peptide bond from C terminal of protein Lactase acts only on lactose Sucrase acts only on sucrose

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Stereoscopic Specificity

Optical Specificity

-specificity is VERY HIGH -Enzymes are specific to its optical configuration -specificity is the HIGHEST SPECIFICITY

Maltase acts only on maltose L-amino acid oxidase acts only on L-amino acids D-amino acid oxidase acts only on D-amino acids α-glucosodic bonds of starch and glycogen are hydrolyzed only by α-glycosidase (αamylase) β-glycosidic bonds of cellulose are hydrolyzed only by βglycosidase (β-amylase)

Geometric Specificity

Co-factor Specificity

-Enzyme can act on different substrates having similar molecular geometry -specificity is VERY LESS -Enzymes are specific to or correct combination of substrate and cofactor Absence of specific co-factor = inactive enzyme

Alcohol dehyfrogenase can oxidize ethanol, methanol, and propanol to yield corresponding aldehydes

Refer to cofactors and coenzyme table

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TYPE of SPECIFICITY Bond Specificity

Group Specificity

Substrate Specificity

Stereoscopic Specificity

ILLUSTRATIONS

PSALM 23 Geometric Specificity

Co-factor Specificity

MODEL LOCK & KEY

SUBSTRATE/ ABSOLUTE SPECIFICITY POSTULATED BY: Emil Fischer

INDUCED FIT

Daniel Koshland

Def Analogy: Lock=enzyme Key=substrate *since enzymes are highly flexible, -interactive process between enzyme and substrate

-substrate adopts to the conformational change on the active site of the enzyme

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Enzyme Naming and Nomenclature

Enzyme commission created a systematic classification way of naming enzymes depending on the reaction they catalyze.

A four digit-number classification number is used to identify the classes, subclasses, sub subclasses and individual entries to specify a particular enzyme.:

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*E.C.2.7.1.1 (EC means Enzyme Commission) Book reference: Garett & Grisham CHARACTERISTIC FEATURES OF ENZYMES Catalytic Power Is Defined as the Ratio of the Enzyme-Catalyzed Rate of a Reaction to the Uncatalyzed Rate

The enzyme jack bean urease catalyzes the hydrolysis of urea:

Specificity Is the Term Used to Define the Selectivity of Enzymes for Their Substrates

In an enzyme-catalyzed reaction, none of the substrate is diverted into nonproductive side reactions, so no wasteful byproducts are produced. It The selective qualities of an enzyme are collectively recognized as its specificity. Molecular recognition (based on structural complementarity) is the basis of specificity. The specific site on the enzyme where substrate binds and catalysis occurs is called the ACTIVE SITE

Regulation of Enzyme Activity Ensures That the Rate of Metabolic Reactions Is Appropriate to Cellular Requirements

Remember *irreversible and reversible reactions

III. Objective: Plot & examine the changes in energy for in enzyme kinetics Importance of ENZYMATIC CATALYST/ ACTIVATION ENERGY for enzymatic activity 1. Biological reactions occur at a very slow pace without enzymatic catalyst. 2. ACTIVATION ENERGY is needed to create sufficient energy for a reaction to occur.

PSALM 23 How exactly does an enzyme work?

Enzyme structure Co-enzymes and Cofactors Activation Energy & Free Energy

A. ENZYME STRUCTURE ACTIVE SITE SUBSTRATE

pocket of the enzyme where the catalytic reaction takes place molecule that binds to the active site, as acted upon by the enzyme recognizes each other through structural complementarity & is bound by weak forces

ENZYME-SUBSTRATE COMLPLEX

Hydrogen bonds

weak forces: Ionic bonds Van der Waals interactions

B. CO-ENZYMES AND COFACTORS Enzyme may also require non-protein components that prepare the active site for catalytic activity. *although most enzymes function on their own

CO-ENZYMES



-ORGANIC MOLECULES -serve as intermediate carriers of functional groups in conversion of substrates to products Some are tightly bound & are difficult to separate referred to as The prosthetic group forms a complex with protein that is catalytically active called A catalytically inactive protein without a prosthetic group is called



COFACTORS

PROSTHETIC GROUPS of the enzyme HOLOENZYME

APOENZYME

-METAL IONS/ INORGANIC MOLECULES

PSALM 23 C. ACTIVATION ENERGY & FREE ENERGY *All reactions involve energy.

ΔG ° or ΔG Ea

d Free Energy

- represents the free energy change associated with the formation of the substance from the elements in their most stable forms as they exist under standard conditions.

Free Energy

- Energy associated with a chemical reaction that can be used to do work

Change in Standard Free Energy or Change in Free Energy *Δ means delta Activation Energy

-determines if the reaction will occur or the direction it proceeds -is the difference in the free energy of reactants and products -There is an energy barrier that separates the energy levels of the reactants and products. Energy must be added to the reactants to overcome the energy barrier, which is recovered when products are formed. - The energy barrier is known as Ea, the activation energy. The activation energy is distinct from the ΔG, or free energy difference between the reactants and products.

Transition State

-reactive condition - is a very short-lived configuration of atoms at a local energy maximum in a reaction-energy diagram -is central to understanding catalysis, because enzymes function by lowering activation energy. -transitory of molecular structure in which the molecule is no longer a substrate but not yet a product.

The reaction: 1. starts with the reactants’ certain level of energy 2. and reaches the transition state or activation energy (ΔG°) where additional energy is absorbed 3. and lastly energy is released to form a product. SPONTANEOUS REACTION: Free Energy of Product is lower than (...