PROTEINS & AMINO

ACIDS
Dr. Ammar Yasir Abdulrahman
Medical Biochemistry
Lecture For First-Year Dentistry Students
 TABLE OF CONTENTS

01 What Are Proteins? 07 The Diverse Functions Of Proteins

02 Classification Of Proteins 08 Protein Denaturation

Amino Acids 09 Protein Synthesis - From DNA To
03
The Building Blocks Of Proteins Functional Protein
04 Classification Of Amino Acids 10 Protein Misfolding And Disease

Formation Of Peptide Bonds -

05 11 Why Proteins Matter In The Mouth?
Linking Amino Acids
Protein Structure - The Four Levels 12 Effects Of Protein Deficiency In Oral
06
Of Organization And Dental Health
What Are Proteins?
● Proteins are large, complex molecules essential for
all biological organisms.
● Proteins are often called the “building blocks of
life” or “workhorses of the cell” because they
perform nearly every task necessary in the body.
● Proteins are both the structural components of cells
and the functional tools that drive metabolic
reactions, regulate gene expression, and mediate
intercellular communication.
● Without proteins, the body wouldn’t be able to
move, think, fight infection, transport oxygen, or
digest food.
Classification Of Proteins
1. Based on Composition: 3. Based on Function:
• Simple Proteins: yield only amino acids upon • Structural: Collagen (connective
hydrolysis. e.g., Albumin, Globulin, Histone. tissues), Keratin (hair, enamel).
• Conjugated Proteins: Contain a non-protein part • Enzymatic: Amylase, Pepsin.
(prosthetic group) such as a metal ion, lipid, • Transport: Haemoglobin, Albumin.
carbohydrate, or nucleic acid. e.g., Glycoproteins, • Hormonal: Insulin, Growth hormone.
Lipoproteins, Haemoglobin. • Protective: Antibodies.
• Contractile: Actin, Myosin.
• Derived Proteins: formed by partial hydrolysis or • Storage: Ferritin (iron), Casein (milk).
chemical modification of simple/conjugated proteins.
e.g., Peptones, Proteoses.
2. Based on Shape:
• Fibrous Proteins: Long, insoluble, structural roles
e.g., Collagen, Keratin
• Globular Proteins: Compact, soluble, functional
roles (enzymes, transport) e.g., Enzymes,
Haemoglobin, Immunoglobulins.
Amino Acids
The Building Blocks Of Proteins
Amino acids are small, organic molecules that form the foundation
of proteins. They are composed of:

● A central carbon atom (called the alpha carbon),

● An amino group (-NH₂), which acts as a base (accepts protons),
● A carboxyl group (-COOH), which acts as an acid (donates
protons),
● A hydrogen atom,
● A variable side chain (R-group), which defines the amino
acid’s identity and chemical properties.
Amino Acids
The Building Blocks Of Proteins
● The side chain, or ‘R-group’, defines each
amino acid’s identity and influences its size,
charge, and reactivity. These differences
allow amino acids to form a diverse range of
proteins, each with a unique structure and
function.
● At the pH of human cells (around 7.4),
amino acids usually exist in a zwitterionic
form, meaning the amino group is
protonated (+) and the carboxyl group is
deprotonated (−), giving the molecule two
charges but an overall neutral state.
Classification Of Amino Acids
The physical and chemical properties of a protein depend largely on the arrangement and
nature of the amino acids in its chain. A key factor is the polarity and charge of the R-group.

01
Nonpolar (Hydrophobic): Amino Acids 03
Acidic (Negatively Charged): Amino
have side chains that do not form Acids contain carboxyl groups in their
hydrogen bonds with water and typically side chains, making them negatively
buried inside the protein structure, away charged at physiological pH.
from the aqueous environment. 👉e.g., Aspartic acid (Aspartate),
👉e.g., Alanine, Valine, Leucine, Glutamic acid (Glutamate).
Isoleucine.

02 Polar (Uncharged): Amino Acids have 04

Basic (Positively Charged): Amino
side chains that are attracted to water Acids have side chains that contain
and can form hydrogen bonds. They are amino groups, making them positively
usually found on the surface of proteins. charged at physiological pH.
👉e.g., Serine, Threonine, Asparagine, 👉e.g., Lysine, Arginine, Histidine.
Glutamine.
 Natural Amino Acid Notation
Amino acid 3 letter 1 letter Amino acid 3 letter 1 letter

Alanine Ala A Leucine Leu L

Arginine Arg R Lysine Lys K

Asparagine Asn N Methionine Met M

Aspartic acid Asp D Phenylalanine Phe F

Polar
Cysteine Cys C Proline Pro P

Glutamic acid Glu E Serine Ser S

Glutamine Gln Q Threonine Thr T Non-polar

Glycine Gly G Tryptophan Trp W

Histidine His H Tyrosine Tyr Y

Isoleucine Ile I Valine Val V

Formation Of Peptide Bonds - Linking Amino Acids
 Amino acids are joined together by covalent bond
called a peptide bond.
 This bond is formed through a dehydration
(condensation) reaction where a molecule of water is
removed as the amino group of one amino acid reacts
with the carboxyl group of another.
 The result is a dipeptide. When more amino acids are
added, a polypeptide chain is formed.
 The linear order of amino acids in this chain is not
random; it is directly encoded by the organism’s
DNA, and every protein has a specific sequence known
as its primary structure. This sequence is genetically
determined and defines the protein’s final function.
Protein Structure - The Four Levels Of Organization
1. Primary Structure:
 The primary structure refers to the linear order of
amino acids, linked one after another by peptide
bonds.
 The primary structure dictates every higher level of
structure and therefore the function of the protein.

 If one amino acid in the sequence is changed, the

protein may fold incorrectly or lose its function
entirely.
 Example: in sickle cell anemia, A single point
mutation replaces glutamic acid with valine in the
β-chain of haemoglobin, causing abnormal sickle-
shaped red blood cells.
Protein Structure - The Four Levels Of Organization
2. Secondary Structure:
As the chain begins to fold, localized structures are
stabilized by hydrogen bonds between the carbonyl oxygen
(C=O) and amide hydrogen (N-H) in the protein backbone.

The two most common secondary structures are:

• α-Helix: A spiral-shaped structure stabilized by
hydrogen bonds at regular intervals.
• β-Pleated Sheet: A flat, zigzagging structure where
polypeptide strands lie side by side.

Secondary structures are crucial for the mechanical

stability and flexibility of proteins.
Protein Structure - The Four Levels Of Organization
3. Tertiary Structure
This is the overall 3D shape of a single polypeptide chain.
It results from interactions between the R-groups of amino
acids, including:
 Hydrogen bonds,
 Ionic bonds,
 Hydrophobic interactions,
 Disulfide bonds (strong covalent bonds between sulfur
atoms of cysteine residues).
The tertiary structure determines the biological activity of a
protein. An enzyme, for e.g., can only bind to its substrate if
the 3D shape of its active site is correct. Tertiary Structure
Protein Structure - The Four Levels Of Organization
4. Quaternary Structure Haemoglobin
Some proteins are composed of multiple
polypeptide chains, called subunits that must
assemble into a larger functional complex.

 These subunits can be identical or different.

 The subunits are held together by the same
types of bonds and interactions as in the
tertiary structure.

👉 Example: Haemoglobin has four subunits

and can only function properly when all four
are assembled correctly.
 • Enzymes: Speed up chemical reactions (Amylase: Breaks down
starch into sugar. Sucrase: Catalyses sucrose hydrolysis).
• Structural proteins: Provide mechanical support (Collagen: In skin
and bones. Keratin: Found in hair, skin, wool and nails).
• Transport proteins: Move molecules around the body
(Haemoglobin: Transports oxygen. Lipoproteins: Transport lipids).
The Diverse • Signal proteins: Transmit and receive biochemical messages
Functions Of (Insulin: Regulates blood sugar. Growth hormone: Regulates
growth).
Proteins • Immune proteins: Defend against pathogens Antibodies
(Immunoglobulins).
• Motor proteins: Enable movement (Actin and Myosin in muscles).
• Storage proteins: (Casein: In milk Stores amino acids and calcium
for infant mammals. Albumin: In eggs serves as a source of amino
acids for the developing embryo).
 Protein Denaturation
 Denaturation: is the process by which proteins lose
their native conformation without breaking peptide
bonds, resulting in the protein losing its biological
activity.
🔥 Causes Of Denaturation

High temperatures: Extreme pH Organic Solvents &

Mechanical agitation:
disrupting hydrogen changes: disrupting chemicals: urea, alcohol, or
shaking or stirring can
bonds and hydrophobic salt bridges and detergents disrupt hydrophobic
unfold proteins and disrupt
interactions, (cooking hydrogen bonding, interactions and hydrogen
weak interactions
an egg causes albumin (gastric acid bonding, (ethanol used in
maintaining structure,
to denature and turn denatures dietary disinfectants denatures
(whisking egg whites).
white). proteins). bacterial proteins).

Heavy Metals (Hg²⁺, Pb²⁺, Ag⁺): bind to thiol (-SH) groups, altering tertiary structure and often
leading to protein precipitation, (mercury poisoning disrupts enzyme structure and function).
Protein Synthesis - From DNA To Functional Protein
Cells produce proteins in two major steps:
1. Transcription: RNA polymerase reads the DNA template
and builds a complementary strand of messenger RNA
(mRNA) inside the nucleus.
2. Translation: The mRNA is transported to the cytoplasm,
where ribosomes read the mRNA and assemble amino acids
in the exact order specified by the genetic code, forming a
polypeptide chain.
 Once the polypeptide is formed, it undergoes:
 Folding into its functional three-dimensional structure.
 Post-translational modifications, such as phosphorylation
or glycosylation, which fine-tune the protein's activity,
stability, or localization.
Protein Misfolding And Disease
 What happens when proteins
misfold? Misfolding and aggregation are linked to serious diseases
• Misfolded proteins fail to achieve
Disease Misfolded Protein Effects
their correct 3D structure
• They tend to aggregate into insoluble Memory loss,
Alzheimer’s Amyloid-β, Tau
clumps neuron death
• Aggregates can disrupt cell function Parkinson’s α-Synuclein Motor dysfunction
and trigger cell death Brain
Huntington’s Huntingtin (polyQ)
 Mechanism of harm: Protein degeneration
aggregates can: Rapid,
• Damage cell membranes Prion Diseases PrP^Sc transmissible
• Interfere with cellular machinery neurodegeneration
• Trigger inflammation and apoptosis Thick mucus in
Cystic Fibrosis CFTR lungs, pancreas
issues
 Why Proteins Matter In The Mouth?
Saliva Protection: Proteins like mucins, amylase,
and lysozyme help protect against tooth decay and
infection by lubricating and cleaning the mouth.

Enzyme Activity: Enzymes help with Enamel Formation: Amelogenin is

digestion and tissue remodeling, also crucial for forming and mineralizing tooth
defending against bacteria. enamel.

Bone Health: Osteocalcin and Collagen in Gums: Collagen supports

osteonectin support the health of healthy gums and periodontal tissues,
the alveolar bone, stabilizing teeth. preventing gum disease.

Wound Healing: Proteins like growth Immunity: Immunoglobulins and

factors and collagen help repair antimicrobial proteins protect against
tissues after oral injuries. pathogens in the mouth.
Effects Of Protein Deficiency In Oral And Dental Health
 Delayed Tooth Eruption and Development:
• Protein-energy malnutrition during early childhood can delay tooth
eruption and impair tooth size and development.
• Mechanism: Reduced collagen synthesis affects odontogenesis.
 Delayed Wound Healing:
• Protein is essential for tissue repair and collagen synthesis, which are
crucial after surgery or extraction.
 Increased Risk of Periodontal Disease:
• Depleted immune function and compromised connective tissue integrity.
• Reduced Salivary Function:
• Decreased saliva flow, increased risk of caries.
 Masticatory Muscle Atrophy:
• Muscle wasting affects chewing efficiency.
 Proteins are essential for structure, enzymes, immunity, signaling, and repair.
 Amino acids are protein building blocks, sequence determines structure & function.
 Protein structure:
• Primary: Sequence
• Secondary: α-Helix, β-Sheet
• Tertiary: 3D folding
• Quaternary: Multiple subunits
 In the mouth, proteins:
• Build enamel (amelogenin)
• Support gums & bone (collagen)
• Aid healing & immunity (growth factors, antibodies)Help lubricate & digest (mucins,
amylase)
 Misfolded proteins can cause disease (e.g., Alzheimer’s, prions).
 Protein deficiency → Delayed tooth eruption, poor healing, dry mouth, higher caries risk.
 Protein synthesis = Transcription + Translation → Folding → Modification