PROTEINS

PART 2
Objectives
1. Differentiate the different bonds present in each structure of
proteins.
2. Describe the different protein structures.
3. Explain the importance of Primary structure.
4. Describe Protein Digestion
5. Provide situation in which protein denaturation is applied.
6. Discuss the impact of protein denaturation.
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

embroyos 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
primary acid sequence of a protein.
Secondary Structure of
Proteins
• This level of structure
describes
Describe the local folding
and Differentiate Primary
patterntoof
Structure the polypeptide
Secondary Structure.
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.
2 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.
2 Orientation of B-Pleated
form
1. Parallel

• 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.
2. ANTI-PARALLEL

• In the anti-parallel
arrangement the hydrogen
bonds are aligned directly
opposite each other, making
for stronger and more stable
bonds.
2. ANTI-PARALLEL
• 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
stucture. 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
pancrease) and petidases (located in the cells
that line the small intestine).
Protein Digestion in 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
After digestion, amino acid absorb in the
circulation and can be metabolize to the ff:
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.
Many of the proteins in our cells is in viscous
solution within our cytoplasm. To continue to
function properly they must remain in solution
and maintain the correct three-dimentional
configuration.
• 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.
What will be the impact of protein
denaturation?