By
Prof. Souad M. Aboazma
AMINO ACID CHEMISTRY
 Definition.
 Characters.
 Classification:
 Amino acids can be classified according to :
 Number of amino and carboxyl groups in the amino
acid
 Nutritional : either essential or non essential amino
acids
 Metabolic: either glucogenic or ketogenic amino acids
 Charge and polarity of side chain
i) According to the number of
amino and carboxyl
groups in the amino acid
 Neutral amino acids
 Acidic amino acids
 Basic amino acids
Neutral amino acids
1-Aliphatic amino acids:
Glycine , Alanine, Valine , Leucine , Isoleucine.
2) Aromatic amino acids:
Phenyl alanine, Tyrosine, Tryptophan.
3) Hydroxy amino acids:
Serine, Threonine, Tyrosine.
4) Sulphur- containing amino acids:
Methionine, Cystiene , Cyst in
5) Heterocyclic amino acids as histidine,tryptophan
6) Imino acids as proline &hydroxyproline,
Acidic amino acids
Aspartic acid and Glutamic acid .
Basic amino acids
Arginine and Lysine
Heterocyclic amino acids
Histidine ,Tryptophan, Proline and Hydroxyproline
ii Nutritional Classification:
1) essential amino acids:
Phenylalanine , Treptophan,Histidin .
Methionine , Threonine .
Leucine , Valine , Isoleucine.
Arginine, Lysine .
2) non essential amino acids
Glycine , alanine , serine , tyrosine , praline ,
hydroxyl praline , cystiene , cystin , aspartic acid
& glutamic acid
iii Metabolic Classification:
1- Glucogenic amino acids
2- Ketogenic amino acid as leucine
3- Both glucogenic and ketogenic amino acids as
Tyrosine, phenylalanine, tryptophan, lysine &
isoleucine
iv According to charge and
polarity of side chain
1- Hydrophobic, non polar uncharged amino acids
as alanine,valine,leucine isoleucine &methionine
2- Hydrophilic polar:
a- Uncharged polar amino acid as serine,threonine
b- Charged polar amino acids
Positively charged
Negatively charged
Properties of amino acids
 I. Physical properties:
 Soluble in water, strong acid and base.
 All are optically active due to presence of asymmetric
carbon atom except glycine.
 They have all the biological importance of proteins.
 They are amphoteric due to presence of 2 groups [COOH (acidic) –NH2 (basic)], so they react with both
acids and alkalies.
* Iso-electric point [IEP]
It is the pH at which the amino acid or proteins carry
both +ve and –ve charge to form Zwitter ions. These
ions are electrically neutral (do not move in electric
field) and are easily precipitated. Each amino acid has
its specific I.E.P.
Zwittern ion:
It is the dipolar ion of amphoteric compounds (amino
acid and proteins) produced when the pH of the
medium is at the I.E.P. It carries both +ve and –ve
charges and thus it is electrically neutral (does not
move in electric field).
II. Chemical properties
A- Reactions due to NH2 group:
1- Reaction with acids to form salt
2-Reaction with nitrous acid to liberate nitrogen . in all
amino acids except proline and hydroxyproline.
3- Reaction with acetyl chloride ( acetylation reaction)
Amino acid reacts with acetyl chloride to give acetyl amino
acid.
4- Reaction with CO2 to form carbamino compounds
5- Reaction with methyl iodide ( methylation reactions)
6- Deamination of amino acids
 Oxidative deamination: Produces α – keto aid and
NH3.
 Reductive deamination: Produces fatty acid and NH3.
 Hydrolytic deamination: Produces hydroxyl fatty acid
and NH3
B- Reactions due to COOH group:

Reaction with strong alkalies to form salt

Reaction with alcohols to form esters

Decarboxylation reaction:
To form primary amines
e.g Histidine  Histamine.
Tryptophan  Tryptamine.
Serine

Ethanolamine.
C- Reaction due to both NH2
and COOH group
Amino acids condense with each other by COOH group
at one amino acid with NH2 of other amino acid to
form peptide bond. If 3 amino acids condense together
they form tripeptide .
D-Reactions due to radical R:
 According to the side chain amino acids give colour
reaction as :
- sulfur test for sulfur containing a.a.
- Xanthoproteic test for aromatic a.a.
- Rosenheim test for tryptophan (indol ring).
- Millon’s test for phenol group as tyrosine.
- Ninhydrin reaction :all amino acids give blue
colour except proline which give yellow colour.
PROTEIN CHEMISTRY
Definition
Proteins are organic complex nitrogenous
compounds of high molecular weight, formed of C, H,
O, N [N= 16%]. They are formed of a number of amino
acids linked together by peptide linkage [-CO-NH-].
The carboxylic group of the first amino acid units with
the amino group of the second amino acid and so on.
Biological importance of
proteins
 They provide the body with nitrogen, sulfur, and some vitamins.
 Formation of enzymes and protein hormones.
 Formation of supporting structures in the body as bone, cartilage, skin,
nails, hair and muscles.
 They enter in the formation of buffer system of the blood.
 They enter in the formation of haemoglobin
 They include plasma proteins, which carry hormones, minerals and
lipids (in the form of lipoprotein complex).
 They enter in formation of antibodies (immunoglobulins).
General properties of proteins




Proteins are substances of high molecular weight.
Proteins form colloidal solution and having its
same properties as:
Tyndall effect & Brownian movement
Proteins are non dialyzable due to their large molecules.
Proteins are amphoteric which liable to react with acid and
alkali. Each protein has its own isoelectric point. Protein acts
as a buffer solution which resists the change of its pH by
addition of acid or alkali.
•Denaturation
Denaturation of protein
it is a change in native state (physical, chemical, and
biological properties) of proteins without destruction of
their peptide linkages ,but destruction of secondary bonds
leading to unfolding protein molecule.
 Denaturating agents:

Physical: High temperature, high pressure, X-ray,
ultraviolet rays- mechanical agitation.
Chemical: Strong acids, strong alkalies, organic
solvents, heavy metals.
Results of denaturation:
 Physical:
Decrease solubility, Iincrease viscosity and can not be
crystallized.
 Chemical:
 Unfolding of the protein molecule.
 Destruction of some subsidiary hydrogen bonds.
 Exposure of some groups as (SH) of cystiene.
 Biological:
 Loss of activity, if it is hormone or enzyme.
 Loss of antigen antibody reaction
(allergicmanifestation). Easily digested
 .

Folloculation of proteins
 It
is a precipitation of denaturated
protein at its I.E.P.
 This folloculation is dissolved again by
changing pH from the I.E.P by
addition of acid or alkali (reversible).
Coagulation of prteins
 Boiling of the folloculated protein changing
it to coagulum.
 This coagulum can not dissolved again even
by changing the pH (irreversible).
Precipitation of proteins
Proteins are precipitated from solution by many ways:
 At I.E.P.
 By high concentrations of neutral salts as ammonium
sulfate, Mg sulfate, Na chloride.
 By heavy metals e.g. silver nitrate, lead acetate.
 By strong acids e.g. trichloro acetic acid (TCA),
phosphotungestic acid, picric acid.
 By organic solvents which are miscible with H2O e.g.
ethyl alcohol, methyl alcohol, acetone….
Fractionation of proteins
 Precipitation by neutral salts
 Electrophoresis:
 It is the migration of proteins in an electric field.
Proteins in alkaline medium migrate to anode.
 Proteins in acidic medium migrate to cathode.
 When a sample of plasma proteins is subjected to electrophoresis,
albumin will be the fastest in migration followed by α – globulin, β
– globulin, γ – globulin.
 This method is used to diagnose any abnormalities in plasma
proteins.

 Ultracentrifugation: Centrifugation of proteins at very
high speed according to molecular weight.
 Chromatography & dialysis.
Classification of proteins
Prpteins can be classified on the basis of their
solubility, shape,biological functions,or chemical
composition
1-Classification of proteins according to their
solubility:
 Proteins soluble in H2O,or other biological solvents
(Albumin –globulin- Histones – Protamin - prolamin –
glutelins)
 Proteins not soluble in most protein solvents
[albuminoids] as nail and hair.
2-According to their shape:
 A- Globular proteins : axial ratio is more than 10,more
stable as keratin & myosin in muscles.
 B-Fibrous proteins : axial ratio is less than 10 , less
stable as albumin & globulin.
3-according to their biologic
functions :
 Enzymes: e.g. dehydrogenases, kinases
 Storage proteins: ferritin , myoglobin
 Regulatory proteins: DNA-binding protein, peptide
hormones
 Structural proteins: collagen
 Protective proteins: clotting factors , immunoglobulins
 Transport proteins: hemoglobin , plasma lipoproteins
 Motile proteins: actin, tubulin
4-according to their chemical
composition
A-Simple proteins: On hydrolysis, they produce
only amino acids as albumin ,globulins, glutellin
Prolamines,protamines,histones,
albuminoids(scleroproteins).
albuminoids (scleroproteins)
 They are fibrous proteins.
 Insoluble in H2O, dilute acids and alkali, and all
neutral solvents.
 Not digested by proteolytic enzymes.
 Found in animal tissues and having supportive and
protective function as keratin ,elastin ,collagen &
gelatin.
B-Conjugated proteins (compound protein)
 These are formed of protein part and non protein part.
According to non protein part, they are divided into:
1- Glycoproteins and Mucoproteins:
Protein conjugated with carbohydrate e.g.
certain hormones [FSH, LH, TSH] & Immunoglobulins
IMMUNOGLOBALINS (IGs)
 Globulins are mainly formed in reticuloendothelial system in macrophages and
lymphocytes.
 Immune system is divided into :
 B-cells (Bone marrow): concerned with circulating
humeral antibodies.
 T-cells (Thymus glands): concerned with cell mediated
immune response as graft rejection, hyypersensitivity
reactions and defense against malignant cells and viral
infection.
Lipoproteins:
 Protein conjugated with lipids either [phospholipids-
triglyceride- cholesterol] e.g. Chylomicrons – VLDL –
LDL – HDL.
 It is the transport form of lipids in blood.
Phosphoproteins:
 Protein conjugated with phosphoric acid thruogh
hydroxylic group of serine, threonine &tyrosine
 Casienogen is an example for phosphoproteins (the
main protein of milk ).
Metalloproteins
 Proteins conjugated with metals e.g.
 Ceruloplasmin = protein + Cu.
 Insulin = protein + zinc.
Chromoproteins:
 Hemoglobin containing Fe-porphyrin (red color).
 Chlorophyll containing Mg-porphyrin (green color).
 Flavoproteins: These are enzymes containing FMN,
FAD (yellow color).
Nucleoproteins:
Proteins conjugated with nucleic acids e.g. Histone
associated with DNA in chromosomes.
C-Derived proteins
These are the denaturated or hydrolytic products of
either simple or conjugated proteins.
1- Primary protein derivatives:
 These results from alteration of proteins from its native
state without hydrolysis:
 Metaproteins: Due to the effect of acid or alkali e.g.:
 Acid or alkali metaprotein.
 Gelatin [denaturated collagen].
 Coagulated proteins: Due to the effect of heat e.g.
 Coagulated albumin and globulin.
2-Secondary protein derivatives:
 These are the hydrolytic priducts of proteins

Proteoses:
 Result from partial hydrolysis of proteins.

Peptones:
 Result from further hydrolysis of proteases.
 Soluble in H2O.
•Peptides:
 Resulting from further hydrolysis of peptones.
• Amino acids
Structure of proteins:
 Proteins are formed of a large number of
amino acid linked togther by peptide bonds
(polypeptide chain).
 There are four orders of protein structures
Primary structure of Proteins:
 Referred to the number, type and
sequence of amino acids in the
polypeptide chain.
 Any change in one of amino acids in
polypeptide chain produces a
physiological defect.
 The main bond in this structure (peptide
bond) –CO-HN-
Secondary Structure of Proteins
 The polypeptide chain will be folded to give a specific
conformational form which may be :
The α-Helix
The α-helix is a common secondary structure encountered in
proteins of the globular class. The formation of the α-helix
is spontaneous and is stabilized by H-bonding between
amide nitrogens and carbonyl carbons of peptide bonds
spaced four residues apart. This orientation of H-bonding
produces a helical coiling of the
peptide backbone such that the R-groups lie on the exterior
of the helix and perpendicular to its axis.
β-pleated Sheets
β-sheets are composed of 2 or more different regions of
stretches of at least 5-10 amino acids. The folding of
the polypeptide backbone aside one another to form βsheets is stabilized by H-bonding between amide
nitrogens and carbonyl carbons. β-sheets are said to be
pleated. This is due to positioning of the α-carbons of
the peptide bond which alternates above and below
the plane of the sheet.
It formed by hydrogen bonds or disulfide bonds
between two extended polypeptide chains or
between two regions of single chain. β-pleated
sheets exist in two forms: parallel (the adjacent chains
are aligned in the same direction with respect to Nterminal and carboxy terminal residues) and
antiparallel (the two chains are arranged in opposite
direction ) .
- Loop sheets:
 Half of the residues in a typical globular protein are
present in α helices or β pleated sheets, the remainder
reside in loop or coil conformation which form the
antigen- binding sites of antibodies.
 These loops should not be confused with random
coils which are biologically unimportant
conformations of denatured proteins
- supersecondary structures (motifs):
 α helices or β pleated sheets form recognizable
supersecondary motifs,such as:
 β– α – β: ( two strands of β sheets connected by α
helix
 β – hair pin-: two antiparallel β sheets connected by
short regions of loop.
helix-turn-helix (HTH) is a major structural motif
capable of binding DNA. It is composed of two α
helices joined by a short strand of amino acids
Tertiary Structure of Proteins
Tertiary structure refers to the complete threedimensional structure of the polypeptide units of a
given protein. Secondary structures of proteins are
coiled to constitute distinct structure called
domain. Domains arefundamental functional
three dimentional structural units of
polypeptides. Therefore, tertiary structure also
describes the relationship of different domains to
one another within a protein molecle
The core of a domain is built from
combinations of secondary structural
elements (motifes).
The interactions of different domains is
governed by several forces: These include
hydrogen bonding, hydrophobic
interactions, electrostatic interactions and
van der Waals forces.
Forces Controlling Tertiary Protein
Structure
1-Hydrogen Bonding:
Polypeptides contain numerous proton donors and
acceptors both in their backbone and in the R-groups
The environment in which proteins are found also
contains H-bond donors and acceptors of the water
molecule. H-bonding, therefore, occurs not only
within and between polypeptide chains but with the
surrounding aqueous mediumof the amino acids.
2- Hydrophobic Forces:
Proteins are composed of amino acids that
contain either hydrophilic or hydrophobic
R-groups. It is the nature of the interaction
of the different R-groups with the aqueous
environment that plays the major role in
shaping protein structure.
The hydrophobicity of certain amino acid Rgroups tends to drive them away from the
exterior of proteins and into the interior.
This driving force restricts the available
conformations into which a protein may
fold.
3- Electrostatic Forces:
 Formed between oppositely charged groups in the side
chains of amino acid. e.g.
 ε- amino group of lysine and carboxyl group of
aspartate.
 Lysine – NH3+ …………….-OOC-aspartate
4- van der Waals Forces:
There are both attractive and repulsive van der Waals
forces that control protein folding. Attractive van der
Waals forces involve the interactions among induced
dipoles that arise from fluctuations in the charge
densities that occur between adjacent uncharged nonbonded atoms. Repulsive van der Waals forces involve
the interactions that occur when uncharged nonbonded atoms come very close together but do not
induce dipoles. The repulsion is the result of the
electron-electron repulsion that occurs as two clouds
of electrons begin to overlap.
5- Disulphide bonds:
Formed between 2 cystiene
residue, it connect 2
polypeptide chain or 2
sections in one chain. It is
covalent bond.
Quaternary Structure of Proteins
Many proteins contain 2 or more different
polypeptide chains that are held in
association by the same non-covalent forces
that stabilize the tertiary structures of
proteins. Proteins with multiple polypetide
chains are oligomeric proteins. The
structure formed by monomer-monomer
interaction in an oligomeric protein is
known as quaternary structure.
Oligomeric proteins can be composed of multiple
identical polypeptide chains or multiple distinct
polypeptide chains. Proteins with identical
subunits are termed homo-oligomers. Proteins
containing several distinct polypeptide chains are
termed hetero-oligomers. Hemoglobin, the
oxygen carrying protein of the blood, contains two
α and two β subunits arranged with a quaternary
structure in the form, α2β2. Hemoglobin is,
therefore, a hetero-oligomeric protein.
Protein folding
 Protein folding is the process by which a string
of amino acids (the chemical building blocks
of protein) interacts with itself to form a
stable three-dimensional structure during
production of the protein within the cell. The
folding of proteins thus facilitates the
production of discrete functional entities,
including enzymes and structural proteins,
which allow the various processes associated
with life to occur
Importance of folding protein molecules
Protein folding is essential for the production of
structures that can perform particular functions
in the cell . Also it prevents inappropriate
interactions between proteins, in that folding
hides elements of the amino acid sequence which
if exposed would react non-specifically with other
proteins.
Protein misfolding
 Under favorable conditions, most proteins have no
problem quickly folding to their native structures.
However, there are some proteins which appear
unable to fold without the presence of other helper
proteins, called chaperones. In the absence of
chaperones, these proteins will fail to achieve their
native state and instead may associate with other
unfolded polypeptide chains to form large aggregate
structures.
Inappropriate folding is one way in which a
protein imbalance may arise – the misfolded
protein may be nonfunctional or suboptimally
functional, or it may be degraded by cellular
machinery
Protein misfolding diseases
 In many cases, misfolded proteins are
recognised to be undesirable by a group of
proteins called heat shock proteins, and
consequently directed to protein degradation
machinery in the cell. This involves
conjugation to the protein ubiquitin, which
acts as a tag that directs the proteins to
proteasomes, where they are degraded into
their constituent amino acids.
 Hence many protein misfolding diseases are
characterised by absence of a key protein, as it has
been recognised as dysfunctional and eliminated
by the cell’s own machinery. Diseases caused as a
consequence of misfolding, include cystic fibrosis
& other disease .
 In addition, some cancers may be associated with
misfolding. Many protein misfolding diseases are
characterised not by disappearance of a protein
but by its deposition in insoluble aggregates
within the cell.
Diseases caused by protein
aggregation include Alzheimer’s
disease (deposits of amyloid beta
and tau), Type II diabetes (depositis
of amylin), Parkinson’s disease
(deposits of alpha synuclein),