Protein Chemistry

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Dr. Mohamed Khomsi

‫ محمد الخمسي‬.‫د‬
Jan / 2023
 Protein Chemistry

Table of contents

 Introduction to Proteins & Amino acids …………………….….. 1

 Classification of Amino acids …………………….….. 6

 Ionization of Amino acids …………………….….. 12

 Physical Properties of Amino acids …………………….….. 16

 Peptide Bond …………………….….. 17

 Structure of Protein …………………….….. 19

 Classification of Proteins …………………….….. 25

 Conjugated Proteins …………………….….. 30

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 Introduction

Bio-Molecules:
- The four main Bio-molecules in the human body are:
(Proteins, Lipids, Carbohydrates, Nucleic acids)

Proteins:
- Are the most Abundant & the most Functionally Diverse molecule in living systems.

Definition of Proteins:
- Are a macromolecule consisting of amino acids connected by peptide bonds.
- They are Organic Nitrogenous compound of High molecular weight.
- Proteins are polymers of amino acids.

Elemental Composition of Protein:

- It Consists of 5 major elements.
- Carbon, Oxygen, Nitrogen, Hydrogen, Sulfur.

Carbon 50-55 %

Oxygen 19-24 %

Nitrogen 13-19 %

Hydrogen 6-7.3 %

Sulfur 0-4 %

1
 Introduction

Functions of Proteins:

(1) Catalytic Function:

- Proteins that have a Catalytic Function are called Enzymes.
E.g. Pepsin, Lipase, DNA Polymerase & Carbonic Anhydrase.
- Enzymes are Biological Catalysts that Speed-up Reactions in Cells.
- Enzymes Reduce Activation Energy of Reactants.

(2) Regulatory and Signalling Function:

- Proteins that have a Regulatory Function are called Hormones & Receptors.
E.g. Insulin & Growth Factors.
- Hormones Regulate Biochemical Processes & Signal Transduction in & between Cells.

(3) Gene Regulatory Function:

- Proteins that have a Gene Regulatory Function are called Nucleoproteins.
- Nucleoproteins are also called Genetic Proteins.
E.g. Transcription Factors & Enhancers.
- Nucleoproteins Regulate Gene Expression (Protein Synthesis).

(4) Protective Function:

- Proteins that have a Protective Function are called Protective.
E.g. Protective are also called Defensive or Immune Proteins.
e.g. Immunoglobulins or Antibodies, Clotting Factors & Snake Venom.

- Some proteins are Toxic e.g Snake venoms.

2
 Introduction

(5) Transportation Function:

- Proteins that have a Transportation Function are called Transporters.
E.g. Hemoglobin, Transferrin, Serum Albumin, Ceruloplasmin.
- Transporters Bind & Carry Ligand in Blood & Lymph.
- Proteins can also Form Channels in the Plasma Membrane.

Protein Transports

Hemoglobin O₂ & CO₂

Transferrin Iron (Fe)

Albumin Fatty Acids (FA)

Ceruloplasmin Cupper (Cu)

(6) Storage Function:

- Proteins that have a Storage Function are called Storage Proteins.
- Storage Proteins are also called Nutrient Proteins.
E.g. Ferritin Stores Iron, Ovalbumin Stores Amino acids Egg, Casein (Milk), Gliadin (Wheat).
- Storage Proteins Store Metal ions & Amino acids in Cells.

(7) Contraction Function:

- Proteins that have a Contraction Function are called Contractile Proteins.
E.g. Actin, Tubulin, Myosin.
- Contractile Protein Produce Ordered Movement & The Force Generators of Muscles.

(8) Structural Function:

- Proteins that have a Structural Function are called Structural Tubes.
E.g. Collagen, Keratin, Elastin.
- Structural Proteins are Insoluble Fibrous Proteins that Give Structure to the Body.

3
 Introduction

Functions of Proteins:

Function Name Examples

Catalytic Pepsin, Lipase,

Enzyme
Function DNA Polymerase, Carbonic Anhydrase

Regulatory
Hormones & Receptors Insulin & Growth Factors
Signaling Function

Gene Regulatory
Nucleoproteins Transcription Factors & Enhancers
Function

Protection
Defensive Proteins Antibodies, Clotting Factors, Snake Venom
Function

Transportation Hemoglobin, Transferrin,

Transporters
Function Serum Albumin, Ceruloplasmin.

Storage
Storage Proteins Ferritin, Ovalbumin, Casein, Gliadin
Function

Contraction
Contractile Protein Actin, Tubulin, Myosin
Function

Structural
Structural Tubes Collagen, Keratin & Elastin
Function

4
 Amino Acids

Name:
- Amino acids.

Symbol:
- AAs.

Overall Formula:
R-CH(NH₂)-COOH

Definition:
- Amino acids are the Micromolecules of proteins.
- They are Organic compounds that contain both Amino group (NH2) & Carboxyl group (COOH).

Structure:
- Amino acids are Organic so they contain a carbon.
- The second carbon after carboxyl carbon is called α carbon.
- The α carbon is attached to:
1- Carboxyl group (COOH)
2- Amino group (NH2)
3- Hydrogen atom (H)
4- Distinctive Side Chain (R)

Type:
- Alpha (α) amino acids & Beta (β) amino acids.
- The Major Building block of Proteins are Alpha (α) amino acids.

- Micromolcule = Monomers = Monomeric unit = Building block.

- The amino group attached to α carbon is called a α amino.
- The carboxyl group attached to α carbon is called a α carboxyl.
- Distinctive = Variable Side Chain (R).
- Amino acids in Living Organisms are both Free Forms & Bound in Peptides & Protein.

5
 Amino Acids

Optical Activity & Stereoisomers:

- All Amino acids have Asymmetric α-Carbon Except Glycine.
- All Amino acids have Optical Isomers Except Glycine.
- All Amino acids have Stereoisomerism Except Glycine.
- Stereoisomerism means amino acids can be L-isomers or D-isomers.
- Most Biological amino acids have the L-configuration.
- L-amino acids have the α-amino group (NH2) on the Left side of the α-Carbon.

- Asymmetric carbon = Chiral Carbon.

- Chiral Carbon is a carbon attached to 4 Different Groups.
- The 4 Different (Distinct) groups Attached to α Carbon are: COOH, NH2, H, R.
- All amino acids have Chiral α-carbon EXCEPT Glycine.
- Glycine have H in Side Chain (R꓿ H).

- Molecules that have chiral carbon have Optical activity & Stereoisomerism.
- Optical activity is ability of molecule to rotate PPL to Left or Right.
- All amino acids are optically active EXCEPT Glycine.
- All amino acids have L & D-forms EXCEPT Glycine.

6
 Amino Acids

Nature:
- Amino acids in Nature are Abundant.
- There is about 300 Naturally Found amino acids.

Mammals:
- Mammals have 2 Types of amino acids.

Proteinogenic amino acids Non-Proteinogenic amino acids

20 amino acids Many amino acids

They Make up Mammalian Proteins They Don’t Make up Mammalian Proteins

They are Coded For by DNA They are Not Coded For by DNA

- Some Proteins Contain New Additional amino acids.

- These amino acids Arise by Post-Translational Modification of amino acid Already Present in Peptide.
- These Modification include Methylation, Acetylation & Phosphorylation.
- E.g. Conversion of Peptidyl Proline to 4-Hydroxyproline.
- E.g. Conversion of Peptidyl Lysine to 5-Hydroxylysine.
- E.g. Conversion of Peptidyl Glutamate to γ-Carboxyglutamate.

Non-Protein Amino Acid:

- Do Not Make Mammalian Proteins, But have Different Functions in the Body.
(1) Ornithine, (2) Citrulline, (3) Homocysteine, (4) Homoserine,
(5) Glutamate-γ-Semialdehyde, (6) β-Alanine, (7) 4-Hydroxyproline, (8) 5-Hydroxylysine.

Non-Proteinogenic amino acids Function

Ornithine Intermediate in Urea Synthesis
Citrulline Intermediate in Urea Synthesis
Homocysteine Intermediate in Cysteine Biosynthesis
Homoserine Product in Cysteine Biosynthesis
Glutamate-γ-Semialdehyde Intermediate in Serine Catabolism
β-Alanine Synthesis of Vitamin B5
4-Hydroxyproline Activation of Collagen
5-Hydroxylysine Activation of Collagen

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 Amino Acids

The 20 Amino Acids

(1) Glycine, (2) Alanine,
(3) Leucine, (4) Isoleucine, (5) Valine,
(6) Phenylalanine, (7) Tryptophan,
(8) Methionine, (9) Proline,
(10) Serine, (11) Threonine, (12) Tyrosine,
(13) Cysteine,
(14) Glutamate, (15) Aspartate,
(16) Glutamine, (17) Asparagine,
(18) Histidine, (19) Lysine, (20) Arginine.

3 Letter 1 Letter 3 letter 1 Letter

Amino acid Amino acid
Abbrev. Abbrev. Abbrev. Abbrev.
Alanine Ala A Lysine Lys K
Arginine Arg R Leucine Leu L
Aspartic acid Asp D Isoleucine Ile I
Asparagine Asn N Phenylalanine Phe F
Cysteine Cys C Proline Pro P
Glutamic acid Glu E Serine Ser S
Glutamine Gln Q Threonine Thr T
Glycine Gly G Tryptophan Trp W
Histidine His H Tyrosine Tyr Y
Methionine Met M Valine Val V

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 Amino Acids

Classification:
- The 20 amino acids are classified according to:

Classification Example

1- Chemical Classification
Non-polar
(Chemistry of the Side chain)
Polar
(Polarity of side chain (R group)
(Ionization of side chain (R group)

Essential
2- Nutritional Classification
Semi-essential
(Needed in Diet or Not)
Nonessential

3- Metabolic classification Pure Ketogenic

Their break down gives: Pure Glucogenic
(Ketone bodies or gives Glucose, or Both) Mixed Glucogenic & Ketogenic

- Polarity = Solubility.
- Ionization = Charge.

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 Amino Acids

Chemical Classification

Amino acids with Non-polar (Hydrophobic) side chains:

Chemistry of Side Chain (R group) Amino Acid

Glycine, Alanine
Leucine, Isoleucine, Valine
(9)
Phenylalanine, Tryptophan
Amino acid with Non-Polar side chains
Methionine
Proline

Glycine
Non-Polar with Aliphatic side chain Alanine

Non-Polar with Branched side chain Leucine

Isoleucine
Valine

Non-Polar with Aromatic side chain

Phenylalanine
(Contains Benzene ring)
Tryptophan

Non-Polar with Sulfur in side chain Methionine

Non-Polar with Secondary α amino group

(It is an Imino acid) Proline

- Nonpolar = Hydrophobic.

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 Amino Acids

Chemical Classification

Amino acids with Polar (Hydrophilic) side chains:

Chemistry of Side Chain (R group) Amino Acid

Serine, Threonine, Tyrosine

(11) Cysteine
Aspartate, Glutamate
Amino acids with Polar side chains Asparagine, Glutamine
Histidine, Lysine Arginine

Serine
Polar with Hydroxyl group (OH) Threonine
Tyrosine

Polar with Sulfhydryl group (SH)

Cysteine

Polar with another Carboxyl group (COOH)

(Acidic Amino acids, Negatively charged)
Aspartic acid = Aspartate
Glutamic acid = Glutamate

Polar with Amide group (CONH) Asparagine

Glutamine

Polar with another Amino group (NH2) Histidine

(Basic amino acids, Positively charged) Arginine
Lysine

- Polar = Hydrophilic.
- Polar amino acids are sub-classified into Charged or Non-charged.
- Non-charged = Unionized = Neutral.
- Charged = Ionized.
- Negatively charged (Acidic: Aspartic, Glutamic).
- Positively charged (Basic: Histidine, Lysine, Arginine).

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 Amino Acids

Chemical Classification

More information on Chemical Classification

- Glycine is the Simplest (Smallest) amino acid.

- Tyrosine, Tryptophan, Phenylalanine are Aromatic.

- Tryptophan, Phenylalanine are Aromatic & Nonpolar, (Contain Phenyl)
- Tyrosine is Aromatic & Polar, (Contain Phenol)

- Methionine & Cysteine contain Sulfur.

- Methionine contains Sulfur Only, Non Polar, CANT form disulfide bridge.
- Cysteine contains Sulfhyhedral (Thiol), Polar, CAN form disulfide bridge.
- 2 Cysteine residues can be connected by a disulfide bridge (-S-S-) to form a Cystine Dimer.
- Disulfide Bridge is a Covalent Bond.
- Cystine Dimer are Formed in the Presence of Mild Oxidizing Agents.
- Cystine Dimer are Broken Easily using Reducing Agents.

- All standard amino acids have a Free Primary α-amino group EXCEPT PROLINE.
- Proline has a Secondary α-amino group called Imino group (NH).
- Proline is a Cyclic structure that forms a five membered ring.

- Tryptophan contains an Indol group

- Histidine contains an Imidazole group
- Arginine contains a Guanido group

- All amino acids Except Glycine have an Asymmetric carbon.

- Isoleucine & Threonine have 2 Asymmetric Carbons.

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 Amino Acids

Nutritional Classification

Amino acids are classified according to their Nutritional Need

Into
(1) Essentail, (2) Semi-Essentail, (3) Non-Essentail.

Classification Explanation Amino acids

Methionine
Phenylalanine
Lysine
Essential Can't be synthesised in body them Threonine
Amino Acids & Valine
(8) Must be taken from diet. Leucine
Isoleucine
Tryptophan
Histidine

They become conditionally essential

They are required in the food of Histidine
Semi-essential
Growing children & Pregnancy Arginine
Amino Acids
(3) They are Not required in the food of Adult Glutamine

Glycine
Alanine
Tyrosine
Can be synthesised in body them
Non-essential Cysteine
&
Amino Acids Proline
Don’t have to be taken from diet.
(9) Aspartate
Asparagine
Serine
Glutamate

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 Amino Acids

Metabolic Classification

Amino acids are classified according to their Metabolic fate in body

Into
(1) Pure ketogenic, (2) Pure Glucogenic, (3) Mixed Ketogenic & glucogenic

Classification Explanation Amino acids

Pure Its breakdown

ketogenic ONLY Leucine & Lysine
Amino acids Gives Ketone bodies

Mixed
Isoleucine
ketogenic Its breakdown
Tryptophan
& Gives BOTH
Tyrosine
Glucogenic Ketone bodies & Glucose
Phenylalanine
Amino acids

Pure Its breakdown The remaining 14

Glucogenic ONLY amino acids
Amino acids Gives Glucose

- His & Arg are required in the food of Growing Children Not Adult.
- Gln & Arg improve patients with Trauma, Post-operative infections, Immunosuppression.

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 Ionization of Amino acids

Ionisable groups of Amino acids:

- All amino acids contain 2 Ionisable groups Except Acidic & Basic Amino acids.
- Acidic & Basic amino acids have 3 Ionisable groups.
- These ionisable groups are the (COOH & NH3+)
- Carboxyl (COOH) is ionized by losing a H+ (Deprotonation) to form Negative (Coo-)
- Amino (NH2) is ionized by gained H+ (Protonation) to form Positive (NH3+)

Ionisable groups of Amino acids:

- In Aqueous Solution, Diprotic amino acids have

negatively carboxyl (Coo-) & positive Amino (NH3+)
which makes them Neutral.

- In Aqueous Solution, Acidic amino acids have

another carboxyl group in their side chain
which makes them Negative.

- In Aqueous Solution, Basic amino acids have

another Amino group in their side chain
which makes them Positive.

- Diprotic a.as only have 2 ionizing groups (e.g. Glycine & Alanine)
- Polyprotic a.as have more than 2 ionizing groups (e.g. Acidic & Basic amino acids)
- 2 Acidic amino acids are Negatively charged.
- 3 Basic amino acids are Positively charged.
- 15 Remaining amino acids are Uncharged (neutral)

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 Ionization of Amino acids
Depending on pH, Amino Acids have 3 forms:

- In Acidic pH amino acids are Positively charged.

- In Aqueous pH amino acids are Uncharged.
- In Basic pH amino acids are Negatively charged.

Solution Acidic Solution Aqueous Solution Alkaline Solution

pH pH < PKa pH = Pka PH > PKa

PH < PI pH = PI PH > PI

Carboxyl groups are

Ionization Deprotonated
Both groups are Both groups are
Of &
Protonated Deprotonated
Amino Acid Amino groups are
Pronated

Protonated Deprotonated Deprotonated

Carboxyl (COOH) is Carboxylate (Coo-) is Carboxylate (Coo-) is
Uncharged Negative Negative
Charge & & &
Protonated Protonated Deprotonated
Amino (NH3+) is Amino (NH3+) is Amino (NH2) is
Positive Positive Uncharged

Net Charge Positive Neutral (Zero) Negative

Migration in Migrates towards DON’T Migrate Migrates towards

Electric Field Cathode in electric field Anode

Special Names Cations Isoelectric Anions

- Water = Aqueous solution = Intermediate pH.

- When AA is dissolved in water it forms Dipolar ion = Zwitterion = Inner salt.
- Inner salt carry both Positive and Negative charges.

- When an AA is dissolved in water is has Amphoteric Properties = Ampholyte.

- Ampholytes act as Acid & Base (Donate & Accept a proton).
- They can Detach & Attach protons to the functional groups.
- The dissociation of carboxyl releases H⁺, which passes to the amino group.

- AA is Buffer that reacts with both bases (OHˉ) & acids (H⁺) to form salts (conjugate base).
Buffer pairs: The COOH/– COOˉ pair can buffer in the pH region around pK1
The NH₃⁺/– NH₂ pair can buffer in the pH region around pK2.

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 Ionization of Amino acids

Isoelectric Point (PI):

- Is the pH at which an amino acid is Electrically Neutral (Zwitterion).
- That is sum of Positive charges = the sum Negative charges (the total charge is Zero).

Calculating Isoelectric Point pI

- PI is calculated by the average of Pka values of ionisable groups.
- pKa values of carboxyl are called pK1 & pKa values of amino group is pk2.
- Acidic amino acids & Basic amino acids have another Ionisable group in their Side chain.
- The Pka value for the ionisable group in the side chain of acidic and basic a.a called pKR.

- Isoelectric point for Diprotic a.a is

PK𝟏 + PK𝟐
pI =
2

- Isoelectric point for Acidic a.a is:

PK𝟏 + PK𝐑
pI =
2

- Isoelectric point for Basic a.a is:

PK𝟐 + PK𝐑
pI =
2

- The Isoelectric Point (PI) (I.E.P).

- pKa of Carboxyl group (COOH) is about 2.
- pKa of Amino group (NH+3) is 8-10.
- PI of Acidic amino acids are Lower & PI of Basic amino acids are Higher.

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 Ionization of Amino acids

Examples Calculating Isoelectric Point:

What is the isoelectric point (pI) of glycine?

Pk1 Pk2
Amino acid
(CooH) (NH+3)
Glycine 2.34 9.6

PK1 + PK2 (2.34 + 9.60)

pI = pI = pI = 5.97
2 2

What is the isoelectric point (pI) of Glutamate?

pK1 pK2 pKR

Amino acid (CooH) (NH+3) (CooH)
Aspartate 2.19 9.67 3.9

PK𝟏 + PK𝐑 (2.19 + 3.9)

pI = pI = pI = 3.0
2 2

What is the isoelectric point (pI) of Histidine?

pK1 pK2 pKR

Amino acid
(CooH) (NH+3) (NH+3)
Histidine 1.8 9.17 6.00

PK𝟐 + PK𝐑 (9.17 + 6.00)

pI = pI = pI = 7.58
2 2

At pH 8, What is the charge of Arginine that has pI 10?

Because pH < pI, Arginine is Positively charged

At pH 10, What is the charge of Lysine that has pI 9.7?

Because pH > pI, Lysine is Negatively charged.

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 Amino Acids

Physical Properties:
- The 4 Physical Properties for amino acids include:
(1) Solubility
(2) Melting Point
(3) Taste
(4) Color

Physical Property Explanation & Example

Solubility of AAs depends upon:

- Polarity, Nature of Solvent (pH), Isoelectric point, Temperature.
Solubility - AAs are soluble in polar solvent e.g. (Water & Ethanol).
- AAs are insoluble in non-polar solvent e.g. (Benzene & Ether).
- AAs are insoluble at an isoelectric point.
- Tyrosine is soluble in hot water.

,h
- Amino acids have Very High Melting points (200-300)ºC
Melting point - They have High Melting point due to Ionic property.

- All amino acids are Tasteless Except:

Taste - Glycine & Alanine: is Sweet
- Arginine: is Bitter

- All amino acids are colorless

Color - They are Crystaline.

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 The Peptide bond

Formation of Peptide bond:

- Amino acids are joined to make Protein.
- Amino acids are joined by a Covalent bond.
- This covalent bond is called a Peptide bond.
- Peptide bond is chemically an Amide linkage.
- This amide linkage is formed between α-Carboxyl group of one AA & α-Amino group another AA.
- This reaction is a Dehydration reaction that eliminates a Water molecule.

Characters of Peptide bond:

- Peptide bonds are generally in a Trans configuration.
- Peptide bonds have Partial Double Bond Nature.
- Peptide bonds are Stable, Rigid & Planar.

- Generally Trans means its NOT always Tran, Can be found in Cis configuration.
Its usually Trans, because of steric interference of the R-groups when in the cis position.
The electrons of O, C, & N in peptide bond are delocalized,
The makes peptide bond have resonance properties,
Because of Resonance peptide bond is: Partial double bond, Stable, Rigid, Planar.
- Stable: peptide bond is chemically more stable than ester bond
- Partial double bond: Shorter than single bond
- Rigid: Prevent free rotation around bond between Carbonyl carbon and Nitrogen.
- Planar means: that αC-C-O-N-H- αC lie on a plane.

Polarity & Ionization of Peptide bond

- The peptide bond is Polar.
- The peptide bond can form Hydrogen bond.
- The peptide bond is Polar but Uncharged.
- It Neither Accept nor Release protons over the pH range of 2–12.

The C=O & NH groups of the peptide bond are Polar, and are involved in Hydrogen bonds.
The Charged groups in polypeptides chain are present only in Terminals & Side chain.

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 Protein (Polypeptide) chains

Naming of Protein Chains

Name of Protein Molecule Number of joined Amino Acids

Dipeptides 2 amino acid residues
Tripeptides 3 amino acid residues
Oligopeptides 2-10 amino acid residues
Polypeptides > 10 amino acid residues
Peptides < 50 (11-49) amino acid residues
Protein Peptides > 50 (Thousands) amino acid residues

Ends of Protein chains

- Protein Chains have 2 Ends: N terminal & C terminal.

N-Terminus C-Terminus

Amino Terminal Carboxyl Terminal

Free Amino end Free Carboxyl end

Left side (Upstream) Right side (Downstream)

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 Examples of Peptides & Proteins

Glutathione
- Is Present in Most Cells.
- Is an Antioxidant.
- Is an Unusual Tri-peptide.
- It is a Tripeptide-Thiol.
- It is a γ-Glutamyl-Cysteinyl-Glycine

Insulin
- Is Hormone produced by Pancreas.
- It contains 51 aa.
- It contains 2 Chains (A Chain & B Chain).
- A Chain contains 21 aa.
- B Chain contains 30 aa
- Insulin contains 3 Disulfide bridges.
- It contains 1 Intrachain disulfide bridge (A chain).
- It contains 2 Interchain disulfide bridge (Between A & B Chains).

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 Structure of Protein

The levels of protein structure include:

Primary Structure, Secondary Structure, Tertiary Structure, Quaternary Structure

1) Primary Structure:
- Linear sequence of amino acids in a Polypeptide chain.

2) Secondary Structure
- Local Folding of short segments of polypeptide chain into Regular Repeating Folded Elements.

3) Tertiary Structure
- Folding of secondary units into Final 3D active mature Subunits & its Domains.

4) Quaternary Structure
- Describes the Number & Arrangement of Polypeptide chains (Subunits, Multimeric) in protein.

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 Structure of Protein

Levels of Structure of Protein

Level of Primary Secondary Tertiary Quaternary

structure structure structure structure structure

Linear Regular Final 3D Arranged

Description Polypeptide Repeating Subunit & Subunits
Chain Folded its Domains
Element

Local Folding of Folding of

Joining of
small segment secondary Joining of
Formed by amino acids in a
polypeptide chain structure subunits
linear sequence
in 3D. into domains

Covalent Non- Covalent Non- Covalent Non-Covalent

Stabilized by
bond bond bond bond

Ionic Ionic
Electrostatic Electrostatic
Bond Peptide Hydrogen Hydrogen Hydrogen
Bond bond Wan der waal Wan der waal
Hydrophobic Hydrophobic
Hydrophilic Hydrophilic

Can form Disulfide bridge Disulfide bridge Disulfide bridge ------

Polypeptide 1 PP chain 1 PP chain 1 PP chain >1 PP chain

chain (Monomer) (Monomer) (Monomer) (Multimer)

Stabilized = Maintained = Preserved

- In Folding of 2ry & 3ry structure the Peptide Bond between –CO & –NH, Do Not Rotate.
- But the Bonds between –Cα & –NH and –Cα & –CO, Rotate Freely.

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 Structure of Protein

More information on Protein Structure

Primary Structure:
- Linear Polypeptide Chain = Linear Polypeptide Sequence = Polypeptide Backbone.
- The primary structure is determined by the Number & Sequence of AA in the protein.
- The primary structure decides the higher levels of organization (Secondary, Tertiary).
- Each polypeptide chain has a unique amino acid sequence decided by the genes.
- Altering sequence of amino acids alters 1ry structure & function causing disease.
- e.g.
- Normal sequence of hemoglobin A (Hb A): contains Glutamic acid in position 6.
- Altering sequence of amino acids causes:
- The hereditary diseases, Sickle cell anemia, & Haemoglobin C Disease
- Abnormal Hemoglobin S (Hb S): contains Valine in position 6
- Abnormal Hemoglobin C (Hb C): contains Lysine in position 6

Secondary Structure:
- The 3 common secondary structures are α-Helix, β-sheet, β-bends.
- The Secondary structure denotes 3D relationship between amino acids (3–4 apart).
- It occurs when Amino acids are linked by Hydrogen bond.
- In secondary structure Hydrogen bonds is between components of peptide bond.
- Components of peptide bond are (C=O & NH).

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 Structure of Protein

More information on Protein Structure

Tertiary structure:
- It is Collection of domains joined by Loops.
- It is formed when alpha and beta linked by Non-covalent.
- It is Biologically Active conformation (a Native Conformation).
- Domain is the basic structural and functional unit of protein.
- Small proteins have One domain.
- Larger proteins (200 aa) have More than One domain.

Quaternary structure:
- Proteins Lose their function when subunits are Dissociated.
- Proteins that consist of 2 polypeptide chains are called Dimeric proteins.
- Proteins that consist of 3 polypeptide chains are called Trimeric proteins.
- Proteins that consist of 4 polypeptide chains are called Tetrameric proteins.
- Proteins that contain Identical polypeptide chains are called Homo proteins.
- Proteins that contain Non-Identical polypeptide chains are called are Hetero proteins
- Hetero proteins can be Similar or Different.
For Example:
- Enzymes are Homo-protein (Identical subunits)
- Haemoglobin are Hetero-Protein (Non-Identical Similar subunits)
- Channel are Hetero-protein (Non-Identical Different subunits)

Haemoglobin:
- Globular protein.
- Hetero-Tetramer, Similar 2α & 2β.

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 Secondary Structures

The 3 Secondary Structures:

(1) α helix, (2) β Sheets, (3) β Turn

α helix:
- it is a Repeating Spiral structure.
- It is formed by twisting the polypeptide chain Clockwise.
- It is a Spiral structure with Side chain extending Outward.
- It is Tightly Packed & stabilized by Intrachain Hydrogen bond.
- H-bond is formed between (C=O) of amino acid & (NH) of residue n+4 (Four Residues along).
- it is a Right handed helix.
Alpha helical segments are found in many globular proteins like Myoglobin.

Number of Amino Acids per turn (n) 3.6 aa

Vertical Length between 2 Amino Acids 1.5 Å

Vertical Length of each Turn (Helix) 5.4 Å

Pitch (p)

Amino acids Commonly found in Alpha helices:

These aminjo acids permit & prefer to adopt helix conformations
are hydrophobic amino acids side chains & methionine, alanine, leucine, glutamate & lysine.

Amino acids Not Commonly found in Alpha helices (Helix breakers):

- Glycine & Proline are infrequent in α helix because they have almost no tendency to form helices.
- Glycine destabilizes α helix is too small & flexible
- Proline breaks & bends α helix because it too rigid and in the cis-conformation

- Neighboring charged amino acids (e.g multiple aspartate residues)

They break α helix by electrical repulsion prevents regular spiral forming.

Amino acids with short side chains that can form H-bond (e.g Ser, Asp, and Asn)
They break α helix because they compete with the main H-bond of peptide bond.
Amino acids with Early branching R-groups (e.g Val and Ile)
They destabilize alpha helix due to steric interactions of the side chains with helix backbone.

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 Examples of Secondary Structures

(1) α helix, (2) β Sheets, (3) β Turn

β Sheets:
- It is also called β-pleated sheet.
- It is the most stable form of secondary structure.
- It is formed by folding of polypeptide chain.
- it is fully extended, Side by side, Pleated lines.
- Pleated means it's NOT straight, because R-group projected Above & Below plane.
- It is formed by the Same chain or Different chain
- The lines can be placed in the Same direction Or Opposite direction
- Same direction = Parallel (e.g Flavodoxin).
- Opposite direction = Antiparallel (Silk).
- Carbonic Anahydrase contains both Paralel & Antiparall.
It is stabilized by intra or interchain H-bond.
- Distance between adjacent amino acids 3.5 A.

β Bend
- It is also called β Turn = Reverse Turn.
- It is formed of 4 amino acids (Tetra peptide).
- It Connects secondary structure elements.
- It usually connects Different Antiparallel β Sheets.
- Glycine & Proline are frequently found in beta turns.
- Glycine gives flexibility & Proline fives bend.
- This allows the protein to attain a more globular compact shape.

α Helix β Sheets
Spiral, Coiled Sheet
One Peptide Chain Two or More Peptide Chain
Mostly Right handed Right or Left handed
Hydrogen bond Intrachain Hydrogen bond Intrachain or Interchain
e.g. Collagen & keratin e.g. Carbonic Anhydrase

** In proteins, the average number of aa in a helix is 11, which gives 3 turns **

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 Denaturation of Proteins

Other Name:
- Unfolding of Protein.

Definition:
- Denaturation is a Process in which Proteins Lose their Shape & Function.

Bond:
- Denaturation Breaks All Non-Covalent Bonds.
- Which alters the Internal Interactions between the Protein's amino acids.
- It also Disrupts Covalent Disulfide bonds between Cysteine.

Structure:
- Denaturation Breaks 4ry, 3ry & 2ry Structures.
- The 1ry structure (amino acid sequence) is Not Disrupted.

Cause:
- Factor Affecting & Causing Denaturation include:
(1) Physical, (2) Chemical, (3) Biological.

Physical Factors Chemical Factors Biological Factors

Temperature Polarity of solvents

High pressure & shear pH of solvents
Enzymes
Irradiation Acids and bases
Chemical Additives

Types of Denaturation:
(1) Reversible Denaturation.
(2) Irreversible Denaturation.

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 Denaturation of Proteins

Effect:
- It Changes Protein's Shape, It Loses its Biological Activity,
- Proteins becomes Dysfunctional & called Denatured.

Denaturation Disrupts Secondary Structure:

Causing Loss of All Regular Repeating Patterns such as α helices & β-pleated sheets
and Adopt a Random Coil Shape.

Denaturation Disrupts Tertiary Structure:

Causing Disruption of Covalent & Non-Covalent bonds between aa Side Chains

Denaturation Disrupts Quaternary Structure:

Causing Dissociation of Subunits or Disruption in their Spatial Arrangement.

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 Hydrolysis of Protein

Other Name:
- Breakdown of Protein.

Definition:
- Hydrolysis is a Process in which Proteins Broken Down into Building Block amino acids.

Bond:
- Hydrolysis Breaks Covalent Peptide Bonds.

Structure:
- Denaturation Breaks 1ry Structures.

Cause:
- Hydrolysis is done by
(1) Enzymes, (2) Strong Chemical.

Denaturation Hydrolysis

Loses Structure & Shape Breaks into Building Blocks Amino acids

High Temperature
Enzyme
Denaturing Agents
Chemicals
Acids or Bases Solution

Loses Biological Activity Produces Peptides & Free amino acids

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 Classification of Protein

- Proteins are Classified on the Basis of Shape & Solubility into 3 Groups:

(1) Simple Proteins, (2) Conjugated Proteins, (3) Derived Proteins

Simple Proteins Conjugated Proteins Derived Proteins

Consist of Consist of Derived from

Protein Part Only Protein Part & Non-Protein Part Simple & Conjugated Proteins

Its Hydrolysis yields Its Hydrolysis yields Produced by

Amino acids Only Amino acids & Other groups Physical or Chemical Treatment

Include Include Include

Fibrous & Globular Lipoproteins, … Peptides, Peptones, Proteases

Derived Proteins:
- They are Derived From Simple & Conjugated Proteins by Physical or Chemical Treatment.
- Physical & Chemical Treatment includes, Hydrolysis, Degradation or Denaturation.
- Examples of Derived Proteins include Coagulated Proteins, Proteases, Peptones, Peptides.

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 Simple Proteins

- There are Three Types of Simple Proteins:

(1) Fibrous Proteins, (2) Globular Proteins, (3) Intermediate Proteins.

Protein Fibrous Protein Globular Protein

Other -----
Scleroproteins (Albuminoids)
Name

Spherical or Globular in Shape.

Long Linear Chains
Shape Formed by Rounded Branched
Forming Stands or Ropes
Condensation of Basic & Acidic a.a

Bonds Held together by Held together by

Intermolecular Hydrogen bonds Cross-linked groups

Solubility Insoluble in Water Soluble in Water, Acids, Alkalis, Salts

Digestion Indigestible Digestible or Indigestible

e.g. e.g.
Structural Proteins Hormones
Example Collagen (Skin) Enzymes
Keratin (Hair) Hemoglobin, Myoglobin
Fibrin (Silk) Immunoglobulin

Intermediate Proteins:
- Their Structure is Intermediate to Linear & Globular Structures.
- They are Soluble in Water.
- e.g. Blood Clotting Proteins Fibrinogen.

- Proteolytic enzymes Can't Hydrolyze Fibrous proteins.

- Hormones e.g. Insulin.
- Enzymes DNA & RNA Polymerase.
- Hemoglobin & Myoglobin are O₂ Carrying Proteins.
- Immunoglobulin = Antibodies.

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 Globular Proteins

Globular Protein Include:

Albumins Gobulins Histone

Soluble Insoluble Soluble

In water in water in water

Coagulated Coagulated
------------
by Heat by Heat

Precipitated by Precipitated by
------------
High Half Saturated
Salt Solution Salt Solution

e.g. e.g. e.g.

Serum Albumin (Blood) Plasma Globulin Chromatin
Ovalbumin (Egg White) Myosin (DNA)

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 Fibrous Proteins

Collagen:
- Collagen is the Most Abundant Protein in Human Body.
- Collagens is a Structural Protein in Extracellular Matrix & Connective Tissue.
- Collagen is Present in Skin, Bone, Teeth, Ligaments, Tendons.
- Collagen Lacks the amino acid Tryptophan.
- Collagen: 1/3 is Glycine, 1/3 is Alanine, Proline, Hydroxyproline, 1% is Hydroxylysine.
- Collagen is a Triple-helix, consists of 3 Left handed chains (al. a2, a3).
- Each chain contains 1000 amino acids.
- Each turn has 3 amino acids.
- The Sequence of 3 amino acids is: Gly-X-Y.
(X = Proline, Y = Hydroxyproline or Hydroxylysine).
- Collagens, on Boiling with Water or Dilute Acids, yield Gelatin.
- Gelatin is Soluble and Digestible.

Keratin:
- Keratins is a Dry structural proteins.
- Keratin is Insoluble & Have High Content of Cysteine.
- There are two types of Keratins: α-keratin and β-keratins.
α-Keratins β-keratins
- Present in Hard & Soft Tissue: - Present in:
Hair, Nails, Skin (Outermost Layer Epidermis) Reptile Skin, beaks, Claws, Feathers,
Horns & Wool. Silk of Silkworms & Spiders.

- Consist of Long Alpha Helixes - Consist of beta pleated sheets

Twisted together-supercoiled-in ropes of They are formed (antiparallel ß-sheets)

three or seven strands.
The super-coiled ropes make a strong but
elastic fiber
Disulfide bridges between alpha-helixes help
to make alpha keratins rigid a hard more.
because the alpha-helixes of the damp fibers
are easily pulled into an extended form.
The extended form is less stable.
It will, in time, return to original alpha helix.
Beta keratins are a class of fibrous proteins
that consist mainly of beta-pleated sheets.
The long, thin fibers secreted by silkworms
and spiders are composed of Fibroin.
Fibroin and other ß-keratins are rich in
amino acids having relatively small R-
groups, particularly glycine, and alanine.

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 Conjugated Proteins

Definition:
- Are Proteins that Consist of a Protein Part United with a Non-Protein Part.

Protein Part:
- The Protein Part Alone is called Apo-Protein.

None-Protein Part:
- The None-Protein Part is Called Prosthetic group (Conjugating group).

Examples of Conjugated Proteins:

(1) Glycoprotein, (2) Proteoglycan, (3) Lipoprotein, (4) Nucleoprotein,
(5) Flavoprotein, (6) Phosphoprotein, (7) Metalloprotein, (8) Chromoprotein

Conjugated Protein Prosthetic group Examples

Elastase,
Glycoproteins Carbohydrate < 4%
Egg Albumin, Serum Albumins, Serum Globulins.

Proteoglycan Carbohydrate > 4% Mucin (Saliva), Ovamucoid (Egg white)

Mucoprotein

Lipoprotein Lipid Serum Lipoproteins (CM, vLDL, LDL, HDL)

Nucleoprotein Nucleic Acids (DNA,RNA) Nucleohistones, Nucleoprotamines

B2
Flavoprotein Flavoprotein enzymes
Riboflavin (FMN, FAD)

Phosphoprotein Phosphoric acid Casein (Milk)

Metal ions Ceruloplasmin (Cu)

Metalloprotein
Fe, Co, Zn, Cu, Mg Carbonic Anhydrase (Zn)

Chromoprotein Colored group Hemoglobin, Cytochrome

- Lipoproteins Transport Lipids like Cholesterol in Blood

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Glutathione

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