Proteins
Assessment schedule and
grading
Assessme Type Date Percentage of
nt number total marks
1 First Midterm Week 4 5
2 First Practical sheet Week 5 5
3 Second Midterm Week 8 15
4 Practical exam Week 10 15
5 Second practical sheet Week 10 5
6 Presentation Week 11 5
7 Final written exam Week 14 30
8 Oral exam Week 14 10
9 Class work 7 attend.+3 assin.
Proteins
Proteins are the center of action in
biological processes.
Proteins are essential structural
components of cells. They play key roles
in constructing and maintaining living
cells.
All proteins are made up from a set of 20
different amino acids.
Genes encode proteins that are the functional
molecules in cells.
Functions of proteins
Enzymes (biological catalysts) e.g Catalase.
Hormones e.g. Insulin, growth hormone.
Transport proteins e.g, albumin,
hemoglobin
Structural proteins e.g. Collagen.
Protective proteins e.g. Antibodies.
Contractile proteins e.g. Actin and myosin.
Amino acids
Amino acids are the
building blocks for
proteins.
Proteins are polymers of
20 different L-alpha-amino
acids joined together by
peptide bonds.
General structure of amino acids
• All amino acids share a similar structure.
•They contain a central α-carbon atom to which
a carboxylic acid group, an amino group and a
hydrogen atom are covalently bounded.
• The α-carbon atom binds a side chain group
"R“ characteristic for each amino acid.
• In all amino acids, the α-carbon is
asymmetric (four different groups are
arranged around it), except in glycine where
it is symmetric.
• This α-carbon is said to be chiral or
optically active carbon.
Stereoisomers of amino acids
Most amino acids occur in two possible
optical isomers, called D and L.
Only the L-isomer is found in proteins.
Classification of amino acids
Amino acids can be classified according to:
The structure of side chain “R”.
Nutritional requirement.
Metabolic fate.
Polarity of the side chain.
Classification based on structure
I. Aliphatic amino acids.
II. Aromatic amino acids.
III. Imino acid.
IV. Derived amino acids.
I. Aliphatic amino acids
No ring structure in the (R). They are subclassified
into:
A) Aliphatic neutral amino acids:
They are mono-amino; mono-carboxylic acids.
They are divided into:
1- Simple amino acids: Glycine - Alanine.
2- Branched chain amino acids: Valine- Leucine-Isoleucine.
3- Hydroxyl containing amino acids: Serine - Threonine.
4- Sulphur containing amino acids: Cysteine - Methionine.
5- Amino acids with amide group: Asparagine – Glutamine.
B) Aliphatic acidic amino acids:
•They are mono-amino; di-carboxylic acids.
•e.g. Aspartic acid and Glutamic acid.
C) Aliphatic basic amino acids:
•They are di-amino; mono-carboxylic acids.
•e.g. Lysine and Arginine.
A) Aliphatic, neutral amino acids
Simple amino acids
Branched-chain amino acids
Hydroxyl- containing amino acids
Alcoholic amino
acids
Sulphur - containing amino acids
Amino acids with amide group
1ry amino group
B) Aliphatic, acidic amino acids
Mono- amino di-carboxylic acids
C) Aliphatic, basic amino acids
Di- amino mono-carboxylic acids
II-Aromatic amino acids
R = phenyl ring or heterocyclic ring
Basic
aromatic
amino
acid
III- Imino acid
• Proline differs from other 2ry amino group
amino acids in that its side
chain and α-amino N form
a rigid, five-membered ring
structure.
• Proline has a secondary
amino group (rather than a
1ry amino group).
• Because of its unique
geometry, proline is
involved in the formation of
the fibrous structure of
collagen.
Amino acid abbreviations
Formation of cystine residue
A disulfide bond is
formed between the
sulfhydryl or thiol
group (–SH) of each of
two cysteine residues
to produce a cystine
residue.
One mole of cystine is formed
from two moles of cysteine
Classification based on nutritional
requirement
A) Essential amino acids:
•Are those which cannot be synthesized in
the body.
• They must be supplied in the diet.
•They include Val, Leu, Ile, Phe, Trp, Lys,
Met, Thr.
• Both Arg and His are said to be semi-
essential since they are essential only in
infants (they are synthesized in adult liver).
B) Non-essential amino acids:
• Are those which are synthesized in the
body from suitable precursors.
•They are not necessarily to be supplied in
the diet.
•They include the rest of amino acids.
Both essential and non-essential amino
acids are equally needed for normal growth
and good health.
Animal protein = complete protein
Vegetable protein = incomplete protein
Animal and vegetable proteins
Foods of animal origin, such as meat, fish,
eggs, and dairy products, are the richest
dietary sources of all essential amino acid.
Thus, they are proteins of high biological
value (complete protein).
Foods of plant origin are often deficient in
one or more essential amino acids. Thus,
they are protein of low biological value
(incomplete protein).
Classification based on metabolic fate
A) Ketogenic amino acids:
They produce only ketone bodies during
metabolism (Leu & Lys).
B) Ketogenic and glucogenic (Mixed) amino
acids:
They give both glucose and ketone bodies
during metabolism (Phe – Tyr – Trp – Ile –
Thr).
C) Glucogenic amino acids:
They give only glucose during metabolism
(the rest of amino acids).
Ketogenic Mixed Glucogenic
Leucine Phenylalanine Glycine
Alanine
Lysine Tyrosine Valine
Serine
Tryptophan Histidine
Arginine
Threonine Cysteine
Methionine
Isoleucine Proline
Glutamate
glutamine
Aspartate
Aspargine
Classification based on polarity of R group
A) Hydrophobic (water-hating) / Non-polar:
•The side groups “R” carry no charges.
•They do not bind or give off protons or
participate in hydrogen or ionic bonds.
•Thus, they are attracted to lipids or other
hydrophobic groups.
B) Hydrophilic (water-loving) / Polar:
•The side groups are charged.
•They bind or give off protons or participate
in hydrogen or ionic bonds.
•They are attracted to water.
Non polar Polar
(Hydrophobic) (Hydrophilic)
Glycine Serine
Valine Threonine
Alanine Tyrosine
Leucine Cysteine
Isoleucine Lysine
Phenylalanine Arginine
Methionine Histidine
Proline Asparagine
Tryptophan Glutamine
Glutamic acid
Aspartic acid
Functional significance
Hydrophobic amino acids:
They cluster in the interior of protein
molecule and help in its folding.
Hydrophilic amino acids:
They are generally found on the exterior
of proteins (on the surface) to interact with
the surrounding environment.
Functional significance
IV- Derived amino acids
I- Derived amino acids found in protein
After protein synthesis, some amino acids are
modified.
e.g. hydroxy lysine and hydroxy proline are found in
collagen.
II- Derived amino acids not found in protein
(Non- protein amino acids)
They are seen free in cells, e.g. Ornithine, Citrulline,
Homocysteine.
These are produced during the metabolism of amino
acids.
III- Non-α-amino acids
Examples:
-amino butyric acid (GABA): a
neurotransmitter formed from glutamate in
brain.
H2N–CH2–CH2–CH2– COOH
-alanine: a part of coenzyme A.
H2N–CH2–CH2–COOH
Taurine: involved in bile salts formation.
H2N–CH2–CH2–SO3H
Physical Properties of amino acids
1. Solubility:
They are more soluble in polar solvents
compared to non polar ones.
2. Melting Point:
They melt at higher temperatures often
200°C.
3. Taste:
They may be either:
• Sweet (Gly, Ala, Val).
• Bitter (Arg).
• Tasteless (Leu).
Electrochemical properties
(Amphoteric or ionization properties)
• Amino acids can exist as ampholytes (contain
both acidic and basic groups).
In acidic pH, they are cationic (+).
In alkaline pH, they are anionic (-).
- -
R - CH - COO + HA R - CH - COOH + A
(an acid) (anion)
NH3+ NH3+
- - +
R - CH - COO + BOH R - CH - COO + B + H2O
(a base) (cation)
NH3+ NH2
Amino acids react with both acids and bases
Acid-base behavior
Isoelectric point (pI)
• The pH at which the molecule carries no
net charge is known as isoelectric point or
isoelectric pH (pI).
Dipolar form
Characters of amino acid at isoelectric point:
1.The amino acid will carry no net charge.
2.The amino acid will be electrically
neutral with no mobility in an electric
field.
3. The solubility of the amino acid will be
minimum, so it is more liable to
precipitate.
Chemical properties of amino acids
Reactions due to carboxyl group
1. Decarboxylation:
Histidine Histamine + CO2
Tyrosine Tyramine + CO2
Tryptophan Tryptamine + CO2
Glutamic acid Gamma amino butyric acid + CO2
(GABA)
:Amide formation .2
The –COOH group of dicarboxylic amino acids (other
than - carboxyl) combines with ammonia to form the
corresponding amide. For example:
Aspartic acid + NH3 Asparagine
Glutamic acid + NH3 Glutamine
Reactions due to amino group
1. Transamination:
This reaction is used in the synthesis of non-
essential amino acids.
α-amino group (of amino acid) + α- keto acid
New keto acid + New amino acid
2. Oxidative deamination:
•The -amino group is removed from the amino
acid to form the corresponding keto acid and
ammonia.
•In the body, glutamic acid is the most common
amino acid to undergo oxidative deamination.
