Protein Chemistry

.
)5 9 ‫(الدفعة‬

Part 1
.
Dr. Mohamed Khomsi
Fb: ‫ محمد الخمسي‬.‫د‬
July / 2025
 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 α-amino acids Connected (United by) Peptide Bonds.
- They are Organic Nitrogenous Compound of High Molecular Weight.
- Proteins are Polymers of amino acids.

Elemental Composition of Protein:

- Proteins are Predominantly Constituted by 5 Major Elements.
- Carbon, Oxygen, Nitrogen, Hydrogen, Sulfur.

Carbon 50-55 %

Oxygen 19-24 %

Nitrogen 13-19 %

Hydrogen 6-7.3 %

Sulfur 0-4 %

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 Introduction

Functions of Proteins:

Function Name

Catalytic
Enzyme
Function

Regulatory
Hormones
Function

Gene Regulatory
Genetic Proteins
Function

Protection
Defensive Proteins
Function

Transportation
Transporters
Function

Storage
Storage Proteins
Function

Contraction
Contractile Protein
Function

Structural
Structural Protein
Function

- Some Proteins are Found in Cell Membranes.

- Some Proteins are Toxic E.g. Snake Venoms.

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 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 Carbons.
- The Second Carbon After Carboxyl Carbon is Called α Carbon.
- The α Carbon is Attached to:
1- Amino group (NH2)
2- Carboxyl group (COOH)
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.

Forms:
- Amino acids in Living Organisms are found as Both,
Free Forms & Bound in Peptides & Protein.

- Micromolcule = Monomers = Monomeric Unit = Building Block.

- Distinctive = Variable Side Chain (R).
- Proteins Consist Largely or Entirely of α-amino acids.
- The Major Building Block of Proteins are Called Alpha (α) Amino acids.

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 Amino Acids

Asymmetrical Carbon:
- It is Also Called Chiral Carbon,
- It is a Carbon Attached to 4 Different Groups (Carboxyl, Amino, Hydrogen atom, R group).

Optical Activity:
- Its the Ability of Molecule to Rotate Plane of Polarized Light (PPL),
- Either to the Left or to the Right.

Rotation:
- Levorotatory (L or –) is Used for Substances which Rotate PPL to the Left.
- Dextrorotatory (D or +) is Used for Substances which Rotate PPL to the Right.

Optical Isomers:
- It is Also Called Enantiomers,
- It Occur due to the Presence of an Asymmetric Carbon.
- Optical Isomers Differ From Each Other in their Rotation.
- D- & L-Isomers are Enantiomers Rotate PPL in Equal, but Opposite Directions.
- The Mirror Images of a molecule of amino acid are Non-Superimposable to each other.

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 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.

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 Amino Acids

Nature:
- Amino Acids in Nature are Abundant.
- There are More than 300 Different Amino Acids Described in Nature.

Mammals:
- Mammals (Humans) 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 Hydroxylation, Carboxylation, 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 Proteogenic Amino Acids

- There are 20 Common Amino Acids that Serve as the Building Blocks of Proteins.
- These Amino Acids are the Constituents of Mammalian (Human) Proteins.
(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

A.A Nomenclature is By the First Three Letters of their Name. E.g. Serine (Ser).
- Exception: Isoleucine (Ile), Tryptophan (Trp), Asparagine (Asn) & Glutamine (Gln).

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 Amino Acids

Classification:
- The 20 Amino acids are Classified According to:

Classification Example

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

Leucine
Non-Polar with Branched side chain 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 = Alkyl Hydrophobic group = Can't Enter in Hydrogen Bond Formation.

- All Hydrophobic Amino Acids are Uncharged.
- Glycine is Neither Hydrophobic Nor Hydrophilic.

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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) Aspartic acid = Aspartate

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

Polar with Amide group (CONH) Asparagine

Glutamine

Polar with another Amino group (NH2 or N act as a base) Histidine

(Basic amino acids, Positively charged) Arginine
Lysine

- Polar = Hydrophilic = Can Forms Participate in Hydrogen Bond with H₂o.

- Hydrophilic Amino acids include those with Either Charged or Uncharged side chains
- 6 Polar A.As are Uncharged, Unionized, Neutral, Zero Net Charge
- 5 Polar A.As are Charged, Ionized.
- 2 Negatively Charged A.As (Acidic: Aspartic, Glutamic).
- 3 Positively Charged A.As (Basic: Histidine, Lysine, Arginine).
- Cysteine & Tyrosine Can Lose a Proton at an Alkaline pH.

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 Amino Acids

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 Hydroxy 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's Side Chain & α-amino N Form a Rigid, Five Membered Ring Structure.

- All amino acids Except Glycine have an Asymmetric carbon.

- Isoleucine & Threonine have 2 Asymmetric Carbons.

- Side Chain Features Include:

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

- Heterocyclic a.as include Tryptophan, Proline, Histidine.

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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 by the body Threonine
Amino Acids & Valine
(8) Need to be Supplied through Diet. Leucine
Required for proper growth & maintenance of health. Isoleucine
Tryptophan
Histidine

Can be Synthesized by Adults

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

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
(Need not to be consumed through the diet).
Asparagine
Serine
Glutamate
Glutamine

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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

(2) Its breakdown

Pure ONLY Leucine & Lysine
Ketogenic Gives Ketone bodies
Amino acids

(4)
Mixed Isoleucine
Its breakdown Tryptophan
Ketogenic
Gives BOTH Tyrosine
&
Ketone bodies & Glucose Phenylalanine
Glucogenic
Amino acids

(14)
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 Gaining H+ (Protonation) to form Positive (NH3+).

Ionisable Groups of Amino acids:

- In an Aqueous Solutions (At Physiological PH 7.4),
- Amino acids Can Exist in Different Protonation States,

- Diprotic amino acids are Neutral,

- Because They Have,
- Negative Carboxylate (Coo-) & Positive Ammonia (NH3+).

- Acidic amino acids are Negative,

- Because They Have,
- Another Carboxyl group in their Side Chain.

- Basic amino acids are Positive,

- Because They Have,
- Another Amino group in their Side Chain.

- 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 of Solution, Amino Acids have 3 Forms:

- In Intermediate pH, AAs are Uncharged & Don’t Move in Electric Field.
- In an Acid pH, AAs Carry Positive Charges & Move Towards Cathode.
- In an Alkaline pH, AAs Carry Negative Charges & Move Towards Anode.

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

- When an Amino acid Contains Both Positive Charge & a Negative Charge in the Backbone,
it is Called a Zwitterion and has an Overall Neutral Charge.
- The Zwitterion of an Amino acid Exists at a pH Equal to the Isoelectric Point.
- AA are Amphoteric & Can Act as Both Acids & Bases due to their Zwitterionic Structure.
- AAs Act as Buffer that Reacts with Both Bases (OHˉ) & Acids (H⁺),
- To Form Salts (Conjugate Base or Conjugate Acids).
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,
- the Number of Positive & Negative Charges,
- On a Population of Molecules is Equal (i.e. No Net Charge) (Neutral) (Zwitterion).

Calculating Isoelectric Point pI:

- pI is Determined by the pKa Values of
the Functional Groups (Amine & Carboxyl) in the Molecule.

- 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 pI is a Characteristic Property of Each Individual Amino acid.

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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 (pH), Isoelectric point, Temperature of Solvent.
- Polar & Charged AAs (E.g. Lysine or Glutamic acid),
- are Generally More Soluble in Water,
- Due to Their Ability to form Hydrogen Bonds.
- Non-Polar AAs (E.g. Alanine or Leucine),
- Exhibit Lower Solubility in Water,
Solubility - Non-Polar AAs (E.g. Alanine or Leucine),
- Exhibit High Solubility in Non-Polar Solvents,
(i.e. Benzene, Chloroform, Ether).
- AAs are Insoluble at an Isoelectric Point (pI),
- Due to Net Neutral Charge.
- Solubility Can Increase With Higher Temperatures,
- Tyrosine is soluble in Hot Water.

- They are Solid at Room Temperature.

- Amino acids have Very High Melting Points (200-300) C°.
Melting Point - This Property is Influenced by the Types of Interactions,
- Hydrogen bonds, Ionic Interactions,
- Present Within their Crystalline Structure or Zwitterionic Structure.

- Most amino acids are Tasteless Except:

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

- They Appear are White or Colorless Substances.

Color
- They are Crystalline.

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Amino Acids

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Non-Proteogenic Amino Acids

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Amino Acids

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Amino Acids

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Amino Acids

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Amino Acids

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 Amino Acids

When pH is equal to pK1 (2.3), equal amounts of Forms I & II of Alanine exist in solution.
When pH is equal to pK2 (9.1), equal amounts of Forms II & III are present in solution.

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