Lecture # 6: Proteins & Enzymes(Chapter 2)

Objectives:1- Discuss protein structure and functions.

2- Discuss protein denaturation.

3- Explain how enzymes function. Protein of influenza virus Antibody

Proteins are polymers of aminoacids

The word protein is derived from the Greek word proteios, meaning “of first importance”

Proteins

Proteins ate the most versatile molecules in the body

Fatty acidAminoacid

Aminoacids They are hydrocarbon chains (R) with an amino group and a carboxylic acid group linked by a central carbon with an hydrogen attached to it

R

Carboxylic acid group

Amino group

What makes the difference between different aminoacids is the side chain (R) attached to the central carbon

20 amino acids are used to make all the proteins and they are identical except for the radical (R) group

Peptide bond

Dipeptide

H2O+

DEHYDRATION SYNTHESIS

Dehydration synthesis creates a peptide bond that joins amino acids

Dipeptide Synthesis

•Dehydration synthesis creates a peptide bond that joins amino acids

H

H

(b)

Amino acid 1

Peptide bond

A dipeptide

Amino acid 2

O+

+

OH

H

R1

N C C

H

H

O

OH

H

R2

N C C

H

H

OH

R1

N C C

O

OH

H

R2H

N C C H2O

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Dipeptide Synthesis

Dipeptide

It is any molecule composed of two or more amino acids joined by peptide bondsPeptide:

Peptides named for the number of amino acids:Dipeptides have 2 Tripeptides have 3Oligopeptides have fewer than 10 to 15 Polypeptides have more than 15Proteins have more than 50

A proteins is a large folded chain of more than 50 aminoacids (usually from 50 to 10,000 aminoacids)

Protein of influenza

virusAntibody

The antibody helps disable the virus by binding with it. The antibody is able to carry out this binding because it has a shape that is complementary to that of the virus molecule

Proteins have three to four levels of structural complexity:1- Primary structure2- Secondary structure

3- Tertiary structure4- Quaternary structure

It is the unique three dimensional shape of protein crucial to functionConformation:

Proteins have four levels of structural complexity:

Protein Shape

Primary structure

Secondary structure

Tertiary structure

Quaternary structure

It is the complex bending and folding that gives a protein its final tridimensional shape of globular or fibrous shapes.

It is the protein’s sequence of aminoacids, which is encoded in the genes.

It is the arrangement of the aminoacid chain due to hydrogen bonds between atoms at different parts of the chain.

It is the association between two or more peptide chains to form a protein complex.

Primary structureIt is the protein’s sequence of aminoacids, which is encoded in the genes.

The way that aminoacid chains are arranged in the space due to hydrogen bonds between the aminoacids next or near to each other

dO -dH+

dH+

dH+dO -

dO - dH+

dO -

Secondary structure

Tertiary structureIt is the complex bending and folding that gives a protein its final tridimensional shape of globular or fibrous shapes

Fibrous proteins: They form extended sheets or strands. They are tough, durable, and generally insoluble in water. They usually play structural roles

Globular proteins: They are compact, generally rounded, and readily disperse in water forming a colloid

Quaternary structureIt is the association between two or more peptide chains to form a protein complex

Antibodies

Four Levels of Protein Structure

It is the extreme conformational change that destroys function

Conformation: It is the unique three dimensional shape of protein crucial to functionProteins have the ability to reversibly change their conformation:Enzyme functionMuscle contractionOpening and closing of cell membrane pores

Denaturation:

Extreme heat or pH can denature the proteins

Conjugated Proteins:They are proteins that contain a non-amino acid moiety called a prosthetic group

Hemoglobin contains four complex iron containing rings called a heme moieties

Heme moieties

1- Structure– keratin – tough structural protein

• gives strength to hair, nails, and skin surface– collagen – durable protein contained in deeper layers of skin, bones,

cartilage, and teeth

2- Communication– some hormones and other cell-to-cell signals– receptors to which signal molecules bind

• ligand – any hormone or molecule that reversibly binds to a protein

3- Membrane Transport– channels in cell membranes that governs what passes through– carrier proteins – transports solute particles to other side of membrane– turn nerve and muscle activity on and off

Protein Functions

4- Catalysis– enzymes

5- Recognition and Protection– immune recognition– antibodies – clotting proteins

6- Movement– motor proteins - molecules with the ability to change shape

repeatedly

7- Cell adhesion– proteins bind cells together– immune cells to bind to cancer cells– keeps tissues from falling apart

Enzymes and Metabolism

Net energy released by

reaction

ENERGY

PRODUCTS

Glucose + Fructose

SucroseREACTANTS

Energy hill

PRODUCTS

HYDROLYSIS

ENERGYExergonic reaction

REACTANTS

Activation energy

SucroseREACTANTS

Activation energy

PRODUCTS

Glucose + Fructose

ENERGY

ENERGY

Total released energy

Most chemical reactions do not occur or occur very slowly spontaneously

Net energy released by

reaction

SucroseREACTANTS

Activation Energy: The amount of energy required to start a chemical reaction

Many reactions needs a great amount of energy for activation

To provide this amount of energy, the temperature will increase to values that would damage the cells

However, the human organism digest starch with the help of enzymes.

For example: To digest starch in the laboratory, you must boil it in an acid solution. We could not tolerate these conditions in our body

They have a high activation energy

PRODUCTS

A + B

1000 C

370 C

A BREACTANTS

Enzymes:

Lower activation energy

They are proteins that bind to the reactants and lower their activation energy

SUBSTRATE

Enzyme

High activation energy SUBSTRATE

SUBSTRATE

Enzymes and Activation Energy

Time

Free

ene

rgy

cont

ent

Time

Energy levelof products

Energy levelof reactants

Activationenergy

Netenergyreleasedbyreaction

Activationenergy

Netenergyreleasedbyreaction

(a) Reaction occurring without a catalyst (b) Reaction occurring with a catalyst

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Enzymatic Reaction Steps

Sucrase (enzyme)

1 Enzyme and substrate

Sucrose (substrate)

Enzyme–substrate complex

2

Enzyme and reaction products

3Glucose Fructose

O

O

Active site

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1The substrate approaches the active site on enzyme molecule

Active site: It is the portion of an enzyme that binds with and transforms a substrate

2The substrate binds to the active site forming the enzyme-substrate complex

This binding is highly specific. The substrate fit a particular enzyme like a lock and key. This selectivity is called enzyme-substrate specificity

The enzyme remains unchanged and is ready to repeat the process

The enzyme breaks the covalent bonds between monomers in substrate by adding H+ and OH- from water (hydrolysis)

3

The reaction products are released: glucose and fructose

One enzyme molecule can consume millions of substrate molecules per minuteThe fastest-working enzymes can carry out 100,000 chemical transformations per second, without themselves being changed

The temperature optimum for all human enzymes is the body temperature (37 degrees C)

Factors that change enzyme shape:The pH and temperature alters or destroys the ability of the enzyme to bind to substrate. The enzymes vary in optimum pH:- salivary amylase works best at pH 7.0- pepsin works best at pH 2.0

Cofactors and CoenzymesCofactor:They are inorganic substances that are required by some enzymes

About 2/3rds of human enzymes require a nonprotein cofactorSome cofactors are iron, copper, zinc, magnesium and calcium ions

They bind to enzyme and induces a change in its shape, which activates the active site, which is essential to function

They accept electrons from an enzyme in one metabolic pathway and transfer them to an enzyme in another

Coenzymes:They are organic cofactors that facilitate the work of the enzymes. Many coenzymes are derived from water-soluble vitamins (niacin, riboflavin)

Niacin

Riboflavin

Enzyme 1 Enzyme 2

Enzyme 1 Enzyme 2

Metabolic Pathway: It is a chain of reactions, with each step usually catalyzed by a different enzyme

Coenzymes accept electrons from an enzyme in one metabolic pathway and transfer them to an enzyme in another

Coenzyme

Metabolic Pathway: It is a chain of reactions, with each step usually catalyzed by a different enzyme.

A B C DEnzyme 1 Enzyme 2 Enzyme 3

A is initial reactant, B+C are intermediates and D is the end product.

Initial reactant

Product

Intermediates

Enzyme 1 Enzyme 2 Enzyme 3

Intermediates