leen fraihat, rawan ahmad · leen fraihat, rawan ahmad ## scientific team – يملعلا...

Mais Abu Zainah, Sama Abulhaj,

Leen Fraihat, Rawan Ahmad

##

SCIENTIFIC TEAM 1 –الفريق العلمي

مبسم الله الرحمن الرحي

Enzymes

Electronegativity

N2-O2-F2 ——> the most EN

have Partial negative charge -8

important in Hydrogen bonding

Non covalent interactions are making bonds without sharing electrons.

Hydrophobic reactions are important in folding proteins

Introduction into Biochemistry - Enzymes

Lecture 1

Date : 4/7/2021

كلام الدكتور والخمري الأسود :

:السلايدالأزرق

الأخضر: شرح أو توضيح خارجي


bio chemistry is deals with understanding the function-structure

relationship.

and deals with organization of interactions between different molecules in

different tissues , cells and organs

biochemistry important in disease diagnose :* we Can use glucose as

biomarker in diabetic persons

and important in drug making:

-certain drugs to specific diseases

محددمعرفة شكل البروتين )الانزيم( يسهل عملية صنع الأدوية لجعلها تتلائم مع موقع الارتباط ال

-targeted treatment :in cancer we use targeted chemotherapy with lower side

effects


Enzymes introduction:

)عمل البروتين يقوم على التشاركية )لا يعمل لوحده

Proteins can bind to different molecules -Large: proteins -Small:ions (mg+2/ Zn+2…)

Ligands are small molecules EGFR :epidermal Growth Factor Receptor -The ligand of it is EBF Cytokines are ligands for our immune system -Specificity determines function


The main function of enzymes is to accelerate reaction + need less time

Reactant (substrate)—enzyme—-> product

حقيقة هذا غير موجود لانه بمجرد تكون المنتج ينفصل عن الانزيمEP


قد يحتوي الانزيم على اكثر من(active site) لكن ذلك لا يعني انه غير(specific) فقد يكون هنالك

هو انزيم يحفز عدة تفاعلات pyruvate dehydrogenase complexعلاقة بين تلك المواقع :

لكن جميعها ذات صلة )مترابطة(


Regulatory site

-Regulate the active site

-Regulate the speed of reactions

Active site

Binding site. تحمل المادة المتفاعلة Catalytic site مكان حدوث التفاعل


Trypsin has an (ASP)in active site which has -Bly charged so it helps in

degradation of (Lys and Arg) which are +vly charged

In B , they are aromatic amino acids

In C ,the amino acids are small and non polar so the active site is small and

non polar(hydrophobic interactions)

Chairality determines specificity


Active site exist far away from each other but they get close to each other

by protein folding

The extra amino acids determine and regulate the activity of active site


لا يوجد الموقع النشط على سطح الانزيم وانما بداخله وذلك لمنع دخول الماء

Active sites have polar or non polar residues to fit the substrate


Weak attraction: non covalent bonds and include :

1. Hydrophobic interactions

2. Electrostatic interactions

3. Van der weals interactions

4. Hydrogen bonding

بالتوفيق ..


How do substrates fit into the active site of enzymes?

- We have two theories or two models about how substrates fit into the

Active Site of Enzymes

1- Lock-and-key model (old)

(The structure of the substrate is compatible with the active site of the

enzyme)

• Here, the substrate fits directly into the active site.

• Not really !!

• Proteins are dynamic in nature. • Some enzymes can bind different substrates. • Some enzymes catalyze multi-substrate reactions.

- So why is this model considered wrong ?

It is not 100% accurate because :-

- Proteins can change their structures

Just like lego

with relatively different structures


- And enzymes can bind with with relatively different structures

- Note : some enzymes can bind different substrates but with

specificity. For example (Carbonic Anhydrase) reaction in which it

binds to carbon dioxide (CO2) and water in which these substrates are

different but the enzyme in this case is specific to these two

substrates another example is Tripson which can bind to different

peptides but these peptides what they have in common is that they

have Lysine and Arginine.

2- Induced fit model

• Enzymes are flexible and active sites can be modified by binding of substrate.

In the case of Carbonic Anhydrase Enzyme, (CO2) binds on

the Active Site of Carbonic Anhydrase so it changes the

structure of the Active Site a little bit so that water can fit

into the Active Site which means that induced fit happened

to allow a second substrate to bind to the active site.

Which is a more accurate model


- (And what happens initially the substrate binds to the enzyme and the structure of

the Active Site changes)

- we can see here when the substrate which is in red when it binds to the enzyme the

enzyme structure changes and that's because this substrate will do interaction with the

amino acids in the active site which means there is going to be hydrogen bonding,

electrostatic, hydrophobic interactions which means there is going to be attraction and

repulsion .

- An amino acid located in the enzyme gets closer to the substrate because of repulsion

so the structure of the active site will change according to the substrate.

How do enzymes accelerate reactions?

Types of energy :

• There are two forms of energy • potential - capacity to do work (stored)

Enzyme

Substrate

- we have to know that this is the amount of energy stored in bonds of molecules. - It is the energy which is stored within an object and in chemistry it is the energy that is stored in bonds\ in covalent bonds.


• kinetic - energy of motion

• Potential energy is more important in the study of biological or chemical systems. • Molecules have their own potential energy stored in the bonds connecting atoms in molecules. • It is known as free energy or G (for Josiah Gibbs). • It is the energy that is available for reactions.

Free energy (G)

• The difference between the free energy values between reactants and products (free-energy change ∆G) :

∆G = Gproducts – Greactants

Potential energy is what's really important when talking about enzymatic reactions not Kinetic energy.

Like CO2 and H2O for example there is an energy

stored between (H) with (O) and (C) with (O) and

so on, and this energy is called the free energy.

- Free energy is the energy that is stored within molecules and each

molecule has it's own free energy so the free energy in water molecule is

different than the energy that is stored in CO2 molecule.

The free energy


∆ G accounts for the equilibrium of the reaction and

enzymes accelerate how

quickly this equilibrium is

reached.

note that the energy stored in the transition state is

higher than the energy stored in the substrate

and that's because the transition state is an

intermediat between the substrate and the product

certain amount of energy

stored in the substrate

certain amount of energy

stored in the product

the activation energy

when using enzyme

the activation energy

when not using

enzyme

the (Y) axis here shows the amount of energy inside the molecule

for the reaction to happen we have to convert the substrate into a product and

this product has a different energy (G) than the energy of the substrate and in

order to do this conversion we need to add some energy (Activation Energy) in

order to reach the transition state and the substrate will turn into a product

The transition state isn't stable so in order to preserve it we need a huge amount

of energy. And this energy is necessary to convert the substrate into a product

and this energy as we said is called the (Activation Energy)


What does it mean?

∆G = Gproducts – Greactants

- If ∆G is negative, Gproducts is less than Greactants, energy is

not needed to drive the reaction, but released, making the

forward reaction (from left to right) spontaneous (the reaction is

called exergonic).

((it means that the amount of energy in the reactants is sufficient to

turn the reactants into products, in this type we have an accessive

amount of energy that leaves as heat))

- If ∆G is positive, Gproducts is more than Greactants , an input of

energy is needed, making the reaction not spontaneous (the

reaction is called endergonic).

- The reverse reaction is exergonic and , thus, spontaneous.

- If ∆G is zero, both forward and reverse reactions occur at equal rates; the reaction is at equilibrium.

In chemical

reactions in general

as well as

enzymatic reaction

In chemical

reactions

in general

In all of these reactions ∆G is constant and never changes whether we

added an enzyme or not because both (G) substrate and (G) of product

are constant


What do Enzymes do?

Any enzymatic reaction goes through a transition state (ES) that

has a higher free energy than does either S or P.

The difference in free energy of the transition state and the

substrate is called the activation energy.

Enzymes lower the activation energy, or, in other words, enzymes

facilitate the formation of the transition state at a lower energy.

• At the highest energy level, the substrate configuration is most

unstable and is most tightly bound to the enzyme.

• The bonds or the electronic configuration are maximally

strained.

* all reactions whether they were spontaneous or non-spontaneous

they need the activation energy.

* If spontaneous (exergonic) reaction happened in the human body

the extra energy could be stored in our bodies as energy molecules

like ATP molecules and heat some times specially in winter.

If we have a reaction from A ---> B and it's and exergonic reaction the

reverse reaction from B ---> A will be an endergonic


Alternative pathways

• Substrates often undergo several

transformations when associated with the

enzyme and each form has its own free

energy value.

• The activation energy corresponds to the

complex with the highest energy.

• The energy of activation does not enter

into the final ΔG calculation for a reaction.

in reality in enzymatic reaction we have more than one transition state

from this diagram we can see multiple

forms of molecules or multiple transitions

states each one of them has it's own

energy (G)


the activation state of any enzymatic reaction is the one that has the highest energy.

the activation energy is the difference of energy between the transition state and the

substrate.

activation energy for catalyzed reaction = energy of the transition state with the highest

(G) -- the energy of the substrate.

How do enzymes catalyze reactions?

1- Proximity of substrates together. 2- Orientation of the active site to fit the substrate in the best fit

possible. 3- Changing the energy within bonds allowing the breakup and

formation of bonds. 4- Catalysis is the end result.

For example if we have two substrates

(A,B) in order for them to be combined

together an enzyme must be used, this

enzyme will turn A,B into (C) substrate

while leaving them to combine together,

without using an enzyme will take

millions of years

what is meant here is that it is not

important for A to collide with B but what

is important is for the collision to be at

the right angle or the right group so

what enzymes do that they bind to

substrate and then they put them in the

right angels and the right orientation to

catalyze reactions.


Examples of possible mechanisms to do so : • Catalysis by bond strain • Catalysis involves acid/base reactions • Covalent catalysis

In some cases, enzymes use a combination of these

mechanisms.


Catalysis involves acid/base reactions

• The R groups of amino acids act as donors (acids) or acceptors (bases) of protons. • Examples: histidine, aspartate

usually in the active site of enzymes that depend on acid-base

reaction we have amino acids like these ones

A question for smarties: In the stomach, gastric acid decreases the pH to 1 to 2 to denature proteins through disruption of hydrogen bonding. The protease in the stomach, pepsin, is a member of the aspartate protease superfamily, enzymes that use two aspartate residues in the active site for acid–base catalysis of the peptide bond. Why can they not use histidine like chymotrypsin?


المطلوب حفظه من الجدول :

1) Amino Acids that are involved in catalysis in acid base catalysis and stabilization.

التي يتم ذكرها في السلايدات أو التي يأتي ذكرها من الدكتور مهمة ليس من الضروري حفظ أسماء الإنزيمات لأننا سنأخذها لاحقًا ، في حين أن الإنزيمات

فيجب حفظها

leen fraihat, rawan ahmad · leen fraihat, rawan ahmad ## scientific team – يملعلا...

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