Proteins

By:
Roselita O. Natividad
Nat. Science – Ateneo de Zamboanga University

• chief constituents of all cells of the body

• 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, contain some other elements
• have a very high molecular weights
• a polymer of amino acid
• also an energy source (4 kcal/gram)
• necessary for the formation of the various
enzymes and hormones found in the body
 What are Polymers?
• A polymer is a large molecule or a macromolecule which
essentially is a combination of many subunits. The term
polymer in Greek means ‘many parts’. Polymers can be
found all around us. From the strand of our DNA which is a
naturally occurring biopolymer to polypropylene which is
used throughout the world as plastic.

• Polymers may be naturally found in plants and animals

(natural polymers) or may be man-made (synthetic
polymers). Different polymers have a number of unique
physical and chemical properties due to which they find
usage in everyday life.
1) Source
– through nitrogen cycle

Air nitrogen
denitrifying bacteria nitrogen-fixing bacteria

Soluble cpds in soil Soil nitrates

decay synthesis synthesis

Animal waste product Plant protein

metabolism digestion and synthesis

Animal protein
2. Functions
• building of new cells
• maintenance of existing cells
• replacement of old cells

3. Specific functions
• structure – skin, bones, hair, nails (collagen and keratin)
• catalysis – enzymes
• transport – hemoglobin
• movement – myosin and actin in muscles
• hormones – insulin (maintenance of blood sugar)
• protection – antibodies
• storage
• regulation
4. Major types
1) fibrous protein – for structural purposes
2) globular proteins

5. Composition
• are made up of amino acids
• the general formula is as follows

COOH

H  C  NH2

R
• the amino group has a lone pair of electrons which impart basic
characteristics
• the COOH possesses an acidic hydrogen as a result of the pi
electron delocalization
• the carbon has a weakly acidic hydrogen as a result of the electron
attracting inductive effect of the nitrogen of the NH2 group
• the carbon is called alpha carbon as well as asymmetric carbon
• 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
– structure – chief constituents of skin, bones, hair, and
fingernails. Two important structural proteins are collagen and
keratin
– catalysis – called enzymes which catalyze reactions
– movement – muscle expansion and contraction are involved in
every movement. Muscles are made up of protein molecules
called myosin and actin
– transport – hormones
– protection – storage
– regulation
• the body can synthesize some but not all of the amino acids that it
needs
• those that cannot synthesize but are needed by the body are called
essential amino acids
• the essential amino acids are:
– arginine (can be synthesized but too slow to be of practical
value)
– histidine (only required during childhood)
– isoleucine
– leucine
– lysine
– methionine
– phenylalanine
– threonine
– tryptophan
– valine
6. Structure
• consist of many amino acids joined together what is called a
peptide linkage
• on hydrolysis will yield 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
secondary structure
• consists of several repeating patterns
• refers to the arrangement of the amino acids such as coiled and
pleated shape
• held together by peptide bonds, H-bonds disulfide bonds
• can be in the form of an -helix and  -pleated sheet
• 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 amino acid four residues away while the R
groups extend outward from the helix
• 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
• 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
Alpha - helix Beta-pleated Sheet
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
• 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
Quaternary structure
• 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
• Reasons for common occurrence of multisub-unit proteins
• 1. Synthesis of separate subunits may be more efficient than
substantially increasing the length of a single polypeptide chain
• 2. In supermolecular complexes such as collagen fibers, replacement of
smaller, worn-out or damaged components can be managed effectively
• 3. The complex interactions of multiple subunits help regulate a
protein’s biological function

Structure of proteins at different levels

8. Classification
• simple proteins – on hydrolysis yield amino acids
• conjugated proteins – on hydrolysis would yield amino acids and
some other types of compounds usually a non-protein compound
• derived proteins – do not occur naturally but are partial hydrolysis
products of protein molecules
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
• the six atoms of the peptide backbone are rigid and lie in the same
plane, and two adjacent peptide bonds can rotate relative to one
another about the C – N and C – C bonds
• colloidal in nature
• easily precipitated by:
– alcohol – concentrated inorganic acids
– salts (salting out) – radiation
– salts of heavy metals – amphoteric in nature
– Heat – posses isoelectric point
– alkaloidal reagents – zwitterions
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 on the same
molecule, and in solution, the COOH donates the H+ (proton)
to the NH2
H

R  C  COO

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
• To be passed
1. Amino acids are said to be amphoteric, why is that?
2. Biuret test is considered to be a general test for proteins,
why is that? Will amino acid gives positive test with Biuret?
3. Denaturation is the loss of protein function from structural
change or chemical reaction. At what level of protein
structure or through what chemical reaction does each of
the following denaturation agents act?
- Heat
- Strong acid
- Mechanical stress
4. Explain the action of egg white as an antidote in mercury
poisoning.
Questions:
1) Define the following terms:
a) -carbon c) isoelectric point?
b) peptide bond

2) Differentiate the terms in each pair below:

a) globular and fibrous proteins
b) simple and conjugated proteins

3) Distinguish between proteins, peptides and

polypeptides.

4) List six functions of proteins in the body.

5) What are the elements found in all proteins?

6) Indicate which of the following amino acids are polar, nonpolar,
acidic, or basic:
a) glycine f) tyrosine
b) glutamic acid g) histidine
c) praline h) lysine
d) cysteine i) asparagines
e) valine j) leucine

7) What are the three major functions of proteins?

8) What are the two major types of proteins?

9) What are essential amino acids? List them down.

10) What is the bond that holds amino acids together to form a protein
molecule?
11) What structure is responsible for the number and sequence of amino acids to
form the protein molecule?

12) Write the general formula for amino acid?

13) What property describes the acidic and basic characteristic of proteins?

14) What happens to the solubility of proteins at its isoelectric point?

15) What is the role of a reducing agent in the straightening of a curly hair?

16) Explain the action of egg white as an antidote in mercury poisoning?

17) Indicate the level(s) of protein structure to which each of the following
contributes:
a) amino acid sequence c) -pleated sheet
b) hydrogen bond d) disulfide bond