PROTEINS

What is Protein?
• The proteins are the more complex molecules
in the living cells.
• A human body has around 100.000 differents
types of proteins.
• A protein is a biological macromolecule
composed by one or several peptides.
• A peptide is a polymer (= chain) of amino acids
(AA) linked between them by a peptide bond.
• Protein = AA > 100; Peptide = 10 ≤ AA ≤ 100;
Oligopeptide = AA ≤ 10 (including
• Tripeptide (AA = 3); Dipeptide (AA = 2))
 What is Protein?
 Proteins are organic nitrogenous compounds formed of C,
H, O & “N”
 Proteins are the polymers of 20 naturally occurring amino
acids

 Amino acids are organic acids in which one H is replaced

by NH3 usually at α carbon (next to COOH group)
 All amino acids have in common
 central α carbon to which COOH & H & NH2 are
attached
 α carbon is also attached to a side chain called R group
which is different for each amino acid
 N and C terminals

 There are 3 categories of Amino acids

1. Primary protein amino acids
2. Non primary protein amino acids
3. Non protein amino acids
 Functions of Protein
 Dynamic
1. Transport of molecules across cell membrane or between
cells
 Haemoglobin carries oxygen
 Protein carriers carry glucose across cell membrane
 Transfer in carry iron
 Albumin carries Ca, fatty acids and bile pigments
2. Catalytic role : Enzymes that are protein in nature
3. Metabolic regulations : some hormones are protein like
Insulin
4. Contraction of the muscle : actin and myosin are proteins
5. Storage : ferritin is storage form of iron

 Structural
1. They are components of cell membrane, cytoplasm and cell
organelles
2. Mechanical support
 Collagen and elastin - ligaments tendon and blood vessels
 Keratin - skin, hair and nails
 Ossien - bone
 Amino acid
• The amino acid is the basic unity of the
protein.

The amino acid is composed by a

carbone (C) on which is linked:

• An amino group (NH2)

• An acid group (COOH)
• A variable chemical group (R)
• A hydrogen (H)
Standard acid aminos
Standard acid aminos
Standard acid aminos
Amino acid abbrevation table
 1. Structure
A. Aliphatic (have no ring structure)
1. Neutral : (NH2=COOH) ex. Glycine
2. Basic : (NH2>COOH) ex. arginine
3. Acidic : (COOH>NH2) ex. Aspartic acid
4. With NH2 in their side chain ex.
Asparagine

B. Aromatic (with benzene or phenol rings)

Ex. Phenylalanine & tyrosine

C. Heterocyclic (has also other types of

rings)
Ex. Histidine & tryptophan
 Conformation of Proteins
 Proteins have a 3 dimensional shape (primary,
secondary and tertiary structure) that is required for its
function .. Some proteins formed of 2 or more
polypeptide chains have also a quaternary structure
 Primary : refers to no. and sequence of a.a in
polypeptide chain (straight)
 Secondary : as a result of coiling and folding of the
polypeptide chain, it takes two forms either (α-helical)
or (β-pleated sheets)
 Tertiary : it is the three dimensional structure of each
polypeptide chain, it takes the form of either (fibrous)
or (globular) domains
 Quaternary : in proteins of 2 or more polypeptide
chains .. An example of this is hemoglobin made of 2 α
and 2 β chains
THE PROTEIN STRUCTURE

The primary structure:

•T h e p r i m a r y s t r u c t u r e
corresponds to the amino acids
sequence according the mRNA
gene.

•We see the primary structure

only during a short time, i.e,
during the elongation process of
the protein synthesis.
The secondary structure:
•The variable chemical groups (R) of
the AA have differents properties:
Hydrophobic, hydrophilic, charges (+)
or (-) , -SH groups…

Intramolecular chemical
interactions: Hydrogen bonds,
Disulfide bridges, Ionic bonds,
hydrophobic and hydrophilic
interactions…

Alpha-helice and
Beta-sheet structures
The tertiary structure:
• The tertiary structure is the final form of the protein.

• The function of the protein is strongly

related to its final form (structure).

•The final structure can be destroyed in case of a

heating process or extrem pH =
Denaturation process

Biological function is lost!

The quaternary
structure:
In case of proteins composed
by tertiary assembled
subunits
(Hemoglobin, Immunoglobin)
 Protein classification
According their compositions:
1. Holoprotein = Protein composed only by
amino acids.
2. Conjugated protein = protein composed by
amino acids and by something else
(carbohydrates: Glycoprotein, lipids: lipoprotein).

According
their
functions:
 2. Optical Activity
 All amino acids are Optically active and show D & L
Isomers as they contain an asymmetric α carbon
except “glycine” which is non optically active
 D-amino acids : with their NH2 to the right of α
carbon
 L-amino acids : with their NH2 to the left of α carbon

 All of the amino acids in our body are of the L-amino

acids (3aks el sugars)
 3. Polarity of “R”
1. Non polar (hydrophobic) ( have no reacting groups)
(least soluble in water) (do not bind or give protons)
Ex. Alanine , leusine
 Their side chains tend to coalesce interiorly in an
aqueous solution (hydrophobicity) like a drop of
oil in water

2. Polar (hydrophilic) (have reacting groups)

A. Polar Uncharged (have Neutral polar functional
group that can hydrogen bond with water)
(containing OH, SH OR NH )
B. Polar Charged (have an active reactive group)
(offering or demanding protons) so they may
be ACIDIC or BASIC
 4. Nutritional Value
1. Essential amino acids
• Cant be synthesized in the body so must be
taken in the diet Ex. Valine , leucine , isoleucine ,…..

2. Non essential amino acids

• Can be synthesized in the body Ex. Glycine ,
alanine , aspartic ,…..
 Arginine and Histidine are called semi-essential
because they are synthesized in the body in a
rate enough for adults but not for growing
individuals
 5. Metabolic Fate
1. Ketogenic amino acids
• Give rise to ketone bodies and fats in the catabolic
way Ex. Leucine
2. Glucogenic amino acid
• Give rise to carbohydrates … Ex. glycine, serine ,….
3. Mixed amino acids
• Part will enter the metabolic pathway .. The
other into glucose pathway
• Ex. Lysine , tryptophan ,….
 Properties of Amino Acids
1. Optical activity
2. Amphoteric property
• In solution, amino acids act as both acid and
alkali d.t the presence of acidic group (COOH-) and
basic group (-NH2)
3. Isoelectric point (zwitter ion state)
• It’s the pH at which the protein carries equal +ve
and –ve charges
• At this point
 Proteins and enzymes loose their function
 Their viscosity in solution becomes maximal
 Their solubility becomes minimal (easily
precipitated)
 Formation of Proteins
 Amino acids peptide and polypeptides protein
 Amino acids form peptides in a “dehydration”
reaction (peptide bonds)
 Polypeptides contain 10-100 amino acid .. Peptides
with more than 100 amino acids are called proteins
 2 types of bonds are responsible for the structure
1. Covalent (strong bonds)(favor stability resist
denaturation)
A. Peptide bonds : COOH combines NH3 with removal
of water
B. Disulphide bonds : between 2 Cysteine a.a in the
same or diff polypeptide chains
2. Non covalent (weak bonds)(favor protein folding)
A. Hydrogen bonds
B. Hydrophobic bonds (help stabilize protein structure)
C. Ionic bonds )repulsive or attractive)
 The peptide bond
• The amino acid (AA) molecules are linked each
other one by peptide bonds.

• A peptide bond is a covalent bond between the

carboxylic group (CO) of one amino acid and the
amino group (NH2) of another amino acid
molecule.

• The formation of a peptide bond releases a water

molecule (H2O) = reaction of condensation.

• The assembly of several AA molecules gives a

peptide (AA ≤ 20).

• The assembly of several peptides gives a protein

(AA ≥ 20).
 Denaturation of Proteins
 Loss of native structure by many causes leading to
changes in secondary, tertiary and quaternary
structure due to rupture of non covalent bonds
(never peptide bond) with loss of biological activity
 All levels of structure are disrupted except primary
(strong peptide bond)
 Causes
 Physical causes : heating above 70, powerful
shaking, repeated freezing and melting, UV and high
pressure
 Chemical causes : urea, alcohol, strong bases &
acids, salts of heavy metals as Mg
 Effects
 Decreased solubility and rate of diffusion
 Increased viscosity due to unfolding
 Loss of activity
 Change in antigenic property
 Protein synthesis
(= Transcription + Translation)
• The protein synthesis has 2 steps:
the transcription of the DNA into a mRNA, and
the translation of the mRNA into a protein.
• The proteins are assembled from amino acids
according the informations provided by the RNA
messenger.
• The translation is the application of the genetic
informations provided by the mRNA. The amino
acids are free inside the cytoplasm before to be
assembled to form the proteins during the
translation step.
•Translation = Ribosome + amino acids + tRNA
+ mRNA
 Essential and non-essential amino acids
• An essential amino acid is an indispensable amino
acid that cannot be synthesized by the human
body: THEY ARE PROVIDED BY THE
NUTRIENTS (FOODS)
• A conditionally non-essential amino acid is an
amino acid which becomes essential in some
cases (premature baby).
• A non-essential amino acid can be synthesized by
the human body.
Thank You.