PROTEINS P2 REVIEWER
primary acid sequence of a protein.
CELLULAR FUNCTION OF PROTEINS
Enzymes are biological catalyst –ex: Pepsin, Trypsin
Defense Proteins include antibodies (Immunoglobulins)
which are specific protein molecules produced by
specialized cells of the immune system in response to
foreign antigens.
Transport Protein carry material from place to another
in the body. Ex: transferrin, Hemoglobin and Myoglobin.
Regulatory Protein controls many aspects of cell
function, including metabolism and reproduction. Ex:
Insulin and Glucagon
Structural proteins provide mechanical support to large
animals and provide them with their outer coverings.
Ex: Keratin
Movement Proteins are necessary for all forms of
movement. Ex. Actin and Myosin, Flagella of sperm cell.
Nutrient Protein serves as source of Amino acids for
embryos or infants. Ex: Albumin and Casein
PROTEIN STRUCTURE
Primary Structure of Proteins
-It is the amino acid sequence of the protein chain.
-This structure will determine its biological active form.
-It results from the covalent bonding between the
amino acids in the chain.
-The amino acid sequence of a protein is encoded in
DNA. Proteins are synthesized by a series of steps called
transcription (the use of a DNA strand to make a
complimentary messenger RNA strand - mRNA) and
translation (the mRNA sequence is used as a template
to guide the synthesis of the chain of amino acids
which make up the protein).
-Genes can change by the process of mutation during
the course of evolution.
-A mutation in gene can result in a change in the
Secondary Structure of Proteins
-This level of structure describes the local folding
pattern of the polypeptide backbone and is stabilized
by hydrogen bonds between N-H and C=O groups. The
most common are the orderly repeating forms known
as the a helix and the b sheet.
-The secondary structure is the result of hydrogen
bonding between the amide Hydrogen and carbonyl
oxygens of the peptide bonds.
Types of Secondary Structure
1. α-Helix 2. β-Pleated Sheet
1. α-Helix
The most common type of Secondary structure may it
be in coiled of helical conformation.
Special Feature:
-Every amide hydrogen and carbonyl oxygen associated
with the peptide backbone is involved in a hydrogen
bond when the chain coils into an α-Helix.
- Every carbonyl oxygen is hydrogen bonded to an
amide hydrogen four amino acids away in the chain.
Structural Property of a-helix
- It has great mechanical strength and is applied very
efficiently in both the fibrous protein of skin and those
of muscle.
Proteins having an α-Helix structure
Fibrous Proteins – are structural proteins arranged
in fibers or sheets that have only one type of
secondary structure.
α-Keratins – are fibrous proteins that form the
covering (hair, nails, and fur) of most land animals.
2. β-Pleated Sheet
The second common secondary structure in
proteins resembles the pleated folds of drapery.
All the carbonyl oxygen and amide hydrogens in a
B-pleated sheet are involved in hydrogen bonds,
and the polypeptide chain is nearly completely
extended.
Orientation of B-Pleated form
1. PARALLEL
-Beta sheets are parallel
if the polypeptide strands run in the same
direction, N-terminus to C-terminus. The N-
terminus of one beta strand will be opposite the N-
terminus of the other beta strand.
-The parallel arrangement is less stable because the
geometry of the individual amino acid molecules
forces the hydrogen bonds to occur at an angle,
making them longer and thus weaker.
2. ANTI-PARALLEL
-Beta sheets are anti-parallel
if the polypeptide strands run in opposite
directions. The N- terminus of one beta strand will
be opposite the C-terminus of the other beta
strand.
-In the anti-parallel arrangement, the hydrogen
bonds are aligned directly opposite each other,
making for stronger and more stable bonds.
-An anti-parallel beta-pleated sheet forms when a
polypeptide chain sharply reverses direction. This
can occur in the presence of two consecutive
proline residues, which create an angled kink in the
polypeptide chain and bend it back upon itself.
Silk Fibroin
- A protein whose structure is an antiparallel B-
pleated sheet.
- The polypeptide chains of a B-pleated sheet are
almost completely extended, and silk does not
stretch easily.
- Glycine accounts for nearly half of the amino acids
of silk fibroin. Alanine and serine account for most
of the others,
Tertiary Structure of Proteins
Tertiary structure is the complete three-
dimensional (3-D) structure of a polypeptide. It is
formed spontaneously and stabilized both by side
chain interactions and, in extracellular proteins, by
disulfide bonds. This folding brings distant
sequences in a linear polypeptide together into a
stable structure
The structure is maintained by the following
molecular interactions:
- Van der Waals Forces between the R groups of
non-polar amino acids that are hydrophobic.
- Hydrogen bonds between the polar R group of the
polar amino acids
- Ionic bonds (salt bridges) between the R groups of
oppositely charged amino acids
- Covalent bonds between the thiol-containing
amino acids.
Globular proteins generally have a more compact
and rounded shape and have functional roles (they
do something)
Quaternary Structure
• some proteins are made up of multiple
polypeptide chains, also known as subunits. When
these subunits come together, they give the
protein its quaternary structure.
• The forces that hold the quaternary structure of a
protein are the same as those that hold the tertiary
structure.
• Prosthetic group – when a non-protein group is
added to the functional protein. Ex: Glycoprotein
PROTEIN DIGESTION
• Is the degradation of protein by cellular enzymes
in a process called hydrolysis.
• The macromolecules are the proteins or
polypeptides themselves, and the subunits are the
amino acids.
• It takes place in two different phases: - In the
stomach
- In the small intestine.
Both of these phases of digestion are based on
several types of enzymes that are called
Proteinases and Proteases.
• Proteases –endo & exo peptidases:
- Enzymes that degrade proteins by hydrolysis of
peptide bonds
• Proteinases- endo peptidases; proteases that
show specificity for intact proteins

Protein Digestion in Mouth & Salivary Glands
-Chewing and crushing rich foods and mix them
with saliva to be swallowed.
Protein Digestion in Stomach
- It is the start of protein digestion.
• Gastrin – Stimulates Parietal cells to secrete HCl;
Chief cells of the gastric glands to secrete
pepsinogen
• HCl / Hydrochloric Acid – Denatures protein
structure. Activates pepsinogen (Zymogen) to
pepsin.
• Pepsin- Hydrolyzes proteins to smaller
polypeptides and some free amino acids.
Protein Digestion in Intestine
• The remainder of protein digestion occur in the
small intestine as the result of the action of
enzymes such as trypsin (secreted by the pancreas)
and peptidases (located in the cells that line the
small intestine).
• Secretin – Stimulates the pancreas to secrete
bicarbonate into the small intestine to neutralize
the gastric HCl
• Cholecystokinin- Stimulates secretion of several
pancreatic enzyme with activity optima pH 7 to 8.
• Trypsin
- Activates Chymotrpsinogen →chymotrypsin
- Further hydrolyze the peptides that were
produced by pepsin in the stomach specifically the
peptide bonds next to Lys and Arg.
• Chymotrypsin - Cleaves peptide bonds next to
Phe, Tyr, Trp, Met, Asp and His
Denaturation of Protein
• Occur when the organized structures of a
globular protein, the a-helix, the B-pleated sheet
and tertiary folds become completely disorganized.
However, it does not alter the primary structure.
Factors that cause Denaturation
• Temperature
As the temperature increase, molecular movement
also increase and the bonds within the cells vibrate
more violently which results to disruption of
protein structure.
Coagulation- occur as the protein molecules unfold
and become entangled. At this point, they are no
longer in solution; they have aggregated to become
a solid.
• pH
A high concentration of hydrogen ions (low pH) will
result in more groups being protonated. Carboxyl
groups (aspartic acid, glutamic acid, the carboxy
terminus) and phenolic groups are uncharged when
protonated. The nitrogen groups (amines on lysine,
guanidino of arginine, and imidazole in histidine,
etc.) are charged when protonated
• Organic Solvents
-Polar organic solvents, such as rubbing alcohol (2-
propanol), denatured proteins by disrupting
hydrogen bonds within the protein, in addition to
forming hydrogen bonds with the solvent, water
Nonpolar regions of these solvents interfere with
hydrophobic interactions in the interior of the
protein molecules, thereby disrupting the
conformation.
• Heavy metals
- Mercury (Hg2+) or Lead (Pb2+) may form
negatively charged side chain groups.
- Heavy metals may also bind to sulfhydryl groups
of a protein that can accompanied by loss of
function.
• Detergents
Detergent have hydrophobic region and
hydrophilic. When detergents interact with
proteins, they disrupt hydrophobic interactions,
causing the protein chain to unfold.
• Mechanical Stress
- Stirring, whipping, or shaking can disrupt the
weak interactions that maintain protein
conformation. This is the reason that whipping egg
whites produces a stiff meringue.