Proteins 5.

Composition
 are made up of amino acids
 the general formula is as follows
 chief constituents of all cells of the body
General formula of amino acid
 more complex than either the carbohydrates or
fats
 derived from the Greek word “proteios” which
means of first importance
 all proteins contain the elements carbon, hydrogen,
oxygen, and nitrogen
 most proteins also contain sulfur, some contain
phosphorus, and a few, such as hemoglobin,  the amino group has a lone pair of electrons which
contain some other elements impart basic characteristics
 have a very high molecular weights  the COOH possesses an acidic hydrogen as a result
 a polymer of amino acid of the pi electron delocalization
 also an energy source (4 kcal/gram)  the carbon has a weakly acidic hydrogen as a result
 necessary for the formation of the various of the electron attracting inductive effect of the
 enzymes and hormones found in the body nitrogen of the NH2 group
 the carbon is called alpha carbon as well as
1. Source asymmetric carbon
-through Nitrogen cycle  depending on the amino acid, the R group can be
varied:
 acidic side chains
 basic side chains
 non-polar side chains
 polar but neutral side chains
 also, the R groups of the amino acid can give rise to
specific interactions especially if these are imagined
as extending out of the of the protein chain, that is,
the groups will determine both the structure and
the function of each protein molecule
 the body can synthesize some but not all of the
amino acids that it needs
 those that cannot synthesize but are needed by the
2. Functions
body are called essential amino acids
 building of new cells
 the essential amino acids are: (PVT MATHILL)
 maintenance of existing cells
 Phenylalanine
 replacement of old cells
 Valine
3. Specific functions
 Tryptophan
 structure – hair, skin, bones, nails, connective
 Methionine
tissues (keratin & collagen)
 Arginine (can be synthesized but too
 catalysis – enzymes
slow to be of practical value)
 transport – hemoglobin
 Threonine
 movement – myosin and actin in muscles
 Histidine (only required during
 hormones – insulin (maintenance of blood
childhood)
sugar)
 Isoleucine
 protection – antibodies
 Leucine
 storage –ferritin stores iron, iron is a heme
 Lysine
component
 regulation
4. Major types
a. fibrous protein – collagen, for structural purposes
b. globular proteins - haemoglobin

6. Structure
 consist of many amino acids joined together by
a peptide bond (linkage)
 on hydrolysis, yields proteoses, peptones,
polypeptides, tripeptides, dipeptides, and finally
amino acids
7. The three dimensional structure of proteins
 primary structure
 refers to the number and sequence of
amino acids
 held together by peptide bond
 the sequence of the amino acids
determines the protein’s three-
dimensional structure and suggests its
functional role and relationship to other
proteins
 polypeptides that have similar amino acid
sequences and functions are said to be
homologous
 sequence comparisons among homologous
polypeptides have been used to trace the
genetic relationships of different species
Primary structure of insulin
Secondary Structure
 refers to the arrangement of the amino acids
such as coiled (-helix )and pleated shape ( -
pleated sheet)
 consists of several repeating patterns
 held together by peptide bonds, H-bonds &
disulfide bonds
-helix
 the chain of the -helix are twisted in such a
manner that its shape resembles a right handed
coiled spring
 the shape is maintained by numerous
intramolecular hydrogen bonds that exist
between the backbone of the N–H of the
amino acid and the C=O of the carboxylic acid
group
 because of the several structural constraints
certain amino acids do not foster helix
formation such as amino acid sequences with
large numbers of charged amino acids and
bulky R groups are incompatible with helix
structures
pleated
 the chain of the pleated sheet is maintained
by intermolecular hydrogen bonds. The
hydrogen bonding is between
backbone C=O and HN groups
 consists of parallel and antiparallel
 in parallel pleated sheet, the polypeptide
chains are arranged in the same direction while
antiparallel chains run in opposite directions
 antiparallel are more stable than the parallel
because fully collinear hydrogen bonds form.
Secondary structure
Hair The alpha helix is not so unknown to us, u see it
every day and wash it frequently
Silk Clothing The beta pleated sheet can be found in
our clothing.
Tertiary structure
 refers to the specific folding and bending of the
coils into specific layers or fibers
 gives their specific biologic activity
 many polypeptides fold in such a fashion that
amino acid residues that are distant from each
other in the primary structure come into close
proximity
Two types
a.) Fibrous proteins
b.) Globular proteins
Tertiary Structure
Quaternary structure
These are fibrous protein playing structural roles.
Keratin is also a fibrous protein. NAILS
 the structures are stabilized by:
 covalent bond – are created by chemical
reactions that alter a polypeptide’s structure
during or after its synthesis. This is referred to
as posttranslational modifications. Most
prominent is the disulfide bonds found in many
extracellular proteins which partly protect
protein structure from adverse changes in pH or
salt concentration.
 disulfide bond - found in many extracellular
proteins which partly protect protein structure
from adverse changes in pH or salt
concentration. Intracellular proteins do not
contain disulfide bridges because of high
cytoplasmic concentrations of reducing agents.
 hydrogen bonding between polar groups on
side chains
 salt bridge between two amino acids with
ionized side chains, that is, between an acidic
amino acid and a basic amino acid held together
by simple ion-ion attraction – significant only in
regions of the protein where water is excluded
because of the energy required to remove
water molecules from ionic groups near the
surface.
 hydrophobic interactions – as the polypeptide
folds, the hydrophobic R groups are brought
into close proximity because they are excluded
from water. Then the highly ordered water
molecules are released from the interior,
increasing the disorder of the water molecules.
 The favorable disorder change is a major
driving force in protein folding
 Determines how the different subunits of the
protein fit into an organized whole
 Held together by hydrogen bonds, salt bridges,
and hydrophobic interactions
 Example is the hemoglobin
 SIMPLE PROTEIN

9. Properties
 the amino acids in the protein molecule are
linear
 the continuing pattern of peptide bonds is the
backbone of the protein molecule, the R groups
are called the side chains
 colloidal in nature
 Amphoteric in nature (zwitterions)
 Possesses isoelectric point
 easily precipitated by:
-alcohol – concentrated inorganic acids
-salts (salting out) – radiation
-salts of heavy metals - Heat
-alkaloidal reagents

Zwitterions
 RCOOH does not exist as is but in the form of
RCOO and H+
 RNH2 also does not exist as is but as RNH3+
 And amino acid has both the COOH and the NH2
8. Classification
on the same molecule, and in solution, the
> simple proteins – on hydrolysis yield amino acids
COOH donates the H+ (proton) to the NH2
> conjugated proteins – on hydrolysis would yield
H
amino acids and some other types of compounds
usually a non-protein compound 
> derived proteins – do not occur naturally but are R  C  COO
partial hydrolysis products of protein molecules 
NH3+
  Compounds that have a positive charge on one
side and a negative charge on the other are
called zwitterions
 Amino acids are not only zwitterions in water
solution but in solid form as well
 Because of this characteristic, amino acids are
considered to be internal salts and therefore
ionic compounds
 Ionic compounds have high melting points and
fairly soluble in water and so are amino acids
Isoelectric point (pI)
 The pH where molecules have equal (+) and ()
charges. At pH lower than the pI, protein
molecules have a net of (+) charge; at pH higher
than the pI, the protein molecules have a net of
() charge. This explains the buffer action of
protein molecules
 Also, the water solubility of large molecules
such as proteins often depends on the repulsive
forces between like charges on their surface
 When protein molecules are at the pH where
net charges can either be (+) or (), the protein
molecules repel each other but at the pI, this
repulsion forces are smallest
 At pI, protein molecules tend to clump together
to form aggregates, reducing their solubility,
therefore, proteins are least soluble in water at
this point and can be precipitated from their
solutions
Denaturation
 Protein conformation are stabilized by the 2o
and 3o structures and through aggregation of
subunits in 4o structure
 Any physical or chemical agent that destroys
these structures changes the conformation of
the protein and the process is called
denaturation
 Denaturation changes the 2o , 3o and 4o
structures. It does not affect the 1o structure
 If denaturation occurs to a small extent, then it
can be reversed
1. Heat cleaves the H-bonding so boiling of protein
solution destroys the -helix. In other proteins,
especially globular proteins, heat causes the
unfolding of the polypeptide chains and because of
subsequent intermolecular protein–protein
interaction, precipitation or coagulation takes place.
This is what happens to boiled egg.
2. Urea breaks the H–bonding and causes the
unfolding of globular proteins
3. Detergents change protein conformation by
opening up the hydrophobic regions
4. Acids, bases, affect the salt bridges as well as the H–
bonding because they change the pH resulting in
the protonation of some protein side groups
5. Salt concentration – the solubility of proteins varies
considerably.
Fibrous proteins, for example, are insoluble in
water but the addition of small amount of salt, a
process called salting in, often improves solubility
significantly. The binding of salt ions to the protein’s
ionizable groups decreases interaction between
oppositely charged groups on the protein molecules.
Water molecules then can form solvation spheres
around these groups.
When large amounts of salt are added to a
protein in solution, a precipitate forms. The large
number of salt ions can effectively compete with the
protein for water molecules, that is, the solvation
spheres surrounding the protein’s ionized groups are
removed. As a result proteins will precipitate out. This
process is called salting out is usually reversible.
6. Reducing agents can break the disulfide bonds
reducing them to SH groups. The protein in keratin has
a high percentage of disulfide bonds and is responsible
for the shape of the hair. In either the permanent wave
or straightening, the hair is first treated with reducing
agent that cleaves some of the disulfide bonds. This
allows the molecules to loose their rigid orientations
and become flexible. Then the hair is set in the desired
shape and then an oxidizing agent is applied. The
oxidizing agent reverses the reaction, forming the new
disulfide bonds
7. Heavy metals attack the disulfide bonds by forming
salt bridges resulting to insoluble precipitate.
8. Mechanical stress – stirring and grinding actions
disrupt the delicate balance of forces that maintain
protein structure. The foam formed when egg white is
beaten vigorously contains denatured protein

10. Tests
 Xanthoproteic test – means yellow, works only
on proteins that consists of amino acids
containing a benzene ring, such as tyrosine or
phenylalanine
 Biuret test – formation of a violet color of a
solution, works for substances that contain two
or more peptide linkages; considered to be the
general tests for proteins
 Millon’s test – formation of a white precipitate
that on heating turns brick-red; specific for
amino acid tyrosine
 Hopkin’s-Cole test – purple color at the point of
contact between two liquids; specific for the
amino acid tryptophan
 Ninhydrin test – production of blue-purple
color, indicates the presence of free amino
acids or peptide groups