Proteins

1. PROTEINS
Introduction
 Twenty percent of the human body is made up of proteins. Proteins are the large,
complex molecules that are critical for normal functioning of cells.
 They are essential for the structure, function, and regulation of the body’s tissues
and organs.
 Proteins are made up of smaller units called amino acids, which are building blocks
of proteins. They are attached to one another by peptide bonds forming a long chain
of proteins.
 A protein is a naturally occurring, extremely complex substance that consists of
amino acid residues joined by peptide bonds.
 Proteins are present in all living organisms and include many essential biological
compounds such as enzymes, hormones, and antibodies.
Where does protein synthesis take place?
Protein synthesis occurs in the ribosomes of cells. In eukaryotic cells, ribosomes are
found as free-floating particles within cells and are also embedded in the rough
endoplasmic reticulum, a cell organelle.
Where is protein stored?
Proteins are not stored for later use in animals. When an animal consumes excess
proteins, they are converted into fats (glucose or triglycerides) and used to supply
energy or build energy reserves. If an animal is not consuming sufficient protein, the
body begins to break down protein-rich tissues, such as muscles, leading to muscle
wasting and eventually death if the deficiency is severe.
What do proteins do?

2. Proteins are essential for life and are essential for a wide range of cellular activities.
Protein enzymes catalyze the vast majority of chemical reactions that occur in the
cell. Proteins provide many of the structural elements of a cell, and they help to bind
cells together into tissues. Proteins, in the form of antibodies, protect animals from
disease, and many hormones are proteins. Proteins control the activity of genes and
regulate gene expression.
General properties of proteins
1. Found in all living organisms.
2. Involved in processes such as digestion of food, cell structure, catalysis, movement,
energy manipulation etc.
3. Complex molecules.
4. Polymers of amino acids.
5. Taste: Tasteless. Hydrolytic products are bitter
6. Odor: Odorless
7. Molecular weight: High molecular weight (macromolecules)
8. Viscosity: long molecules (fibrous) more viscous than globular proteins.eg.
Fibrinogen more viscous than albumin.
9. Hydration: Amino and carboxyl group are easily hydrated.
10.Solubility: Forms colloidal solutions instead of true solutions in water
11.Nature of amino acid determines the pH of proteins.
12.Protein shape is determined by the sequence of amino acids.
Classification of proteins
Classification based on structure:
 Fibrous proteins
 Globular proteins
 Intermediate proteins
Globular proteins:
Globular proteins are generally compact, soluble, and spherical in shape.
Fibrous proteins:
Fibrous proteins are typically elongated and insoluble.
Classification based on composition:
 Simple proteins
 Conjugated proteins
 Derived proteins
1. Simple proteins:

3. A protein that contain amino acids only.
Examples: albumin, globulins and histones
2. Conjugated proteins:
A protein that have some non-protein moiety in its structure along with protein part.
3. Derived proteins:
Proteins derived from simple and conjugated proteins by physical or chemical
treatment. Examples: peptones, peptides and denatured proteins.
Classification based on functions:
 Structural proteins, enzymes, hormones
 Pigments, transport proteins, contractile proteins
 Storage proteins, toxins.
Functions of proteins
Proteins perform many different functions:
Class of proteins Function in the body Examples

4. Structural Provide structural
components
 Collagen in tendons
and cartilage
 Keratin in hair, skin,
wool, and nails
Contractile Movement of muscles  Myosin and actin
contract muscle fibers
Transport Carry essential
substances throughout
the body
 Hemoglobin transports
oxygen
 Lipoproteins transport
lipids.
Storage Store nutrients  Casein stores protein in
milk.
 Ferritin stores iron in
the spleen and liver.
Hormone Regulate body
metabolism and
nervous system
 Insulin regulates blood
glucose level
 Growth hormone
regulates body growth
Enzyme Catalyze biochemical
reactions in the cell
 Sucrose catalyzes the
hydrolysis of sucrose
 Trypsin catalyzes the
hydrolysis of proteins
Protection Recognize and destroy
foreign substances
 Immunoglobulin
stimulate immune
response
Other functions of proteins
 Proteins help mediate cell responses, such as the protein rhodopsin, found in the
eye and involved in the vision process.
 Proteins make up a large protein of muscle fiber and help in the movement of
various parts of our bodies.
 Skin and bone contain collagen, a fibrous protein.
 Protein is vital in the maintenance of body tissue, including development and repair.
 Protein is the major source of energy.
 Protein is involved in the creation of some hormones, help control body functions
that involve the interaction of several organs and help regulate cell growth.
 Protein produces enzymes that increase the rate of chemical reactions in the body.

5. Amino acids
Amino acids are the basic structural constituents of naturally occuring proteins. They
all consists of amino group (NH+3), a carboxylate group (COO-), a hydrogen atom
and a substituent group R, called side chain, bounded to a central carbon atom.
There are 20 standard amino acids.
Amino acid structure:
An amino acid contains both a carboxylic group and an amino group. Amino acids
that have an amino group bonded directly to the alpha-carbon are referred to as
alpha amino acids.

6. Every alpha amino acid has a carbon atom, called an alpha carbon, Cα; bonded to
a carboxylic acid, –COOH group; an amino, –NH2 group; a hydrogen atom; and
an R group that is unique for every amino acid.
Classification of amino acids:
There are 20 amino acids. Amino acids have been classified under various ways:
--- Structure
 With side chain containing Aliphatic side chains
 With side chain containing Hydroxyl groups
 With side chain containing Sulfur atoms
 With side chain containing Acidic groups or their amides
 With side chain containing Basic groups
 Containing Aromatic rings
 Imino acid
--- Polarity
 Non polar
 Polar
--- Nutritional
 Essential and non-essential
Classification based on essentiality:

7. Essential amino acids are the amino acids which you need through your diet because
your body cannot make them. Whereas non-essential amino acids are the amino
acids which are not an essential part of your diet because they can be synthesized by
your body.
Peptide bonds
Amino acids are linked together by ‘amide groups’ called peptide bonds.
During protein synthesis, the carboxyl group of amino acid at the end of the growing
polypeptide chain reacts with the amino group of an incoming amino acid, releasing
a molecule of water. The resulting bond between the amino acids is a peptide bond.
Structure of proteins
The sequence of a protein is determined by the DNA of the gene that encodes the
protein (or that encodes a portion of the protein, for multi-subunit proteins).
A change in the gene's DNA sequence may lead to a change in the amino acid
sequence of the protein. Even changing just one amino acid in a protein’s sequence
can affect the protein’s overall structure and function.
To understand how a protein gets its final shape or conformation, we need to
understand the four levels of protein structure: primary, secondary, tertiary, and
quaternary
1. Primary Structure
• The simplest level of protein structure, primary structure is simply the sequence of
amino acids in a polypeptide chain.
• The hormone insulin has two polypeptide chains A, and B. The sequence of the A
chain, and the sequence of the B chain can be considered as an example for
primary structure

8. 2. Secondary structure
Secondary structure refers to local folded structures that form within a polypeptide
due to interactions between atoms.
The most common types of secondary structures are α helix and the β pleated
sheet. Both structures are held in shape by hydrogen bonds, which form between
the carbonyl O of one amino acid and the amino H of another.

9. 3. Tertiary structure
The overall three-dimensional structure of a polypeptide is called its tertiary
structure. The tertiary structure is primarily due to interactions between the R
groups of the amino acids that make up the protein.
Important to tertiary structure are hydrophobic interactions, in which amino acids
with nonpolar, hydrophobic R groups cluster together on the inside of the protein,
leaving hydrophilic amino acids on the outside to interact with surrounding water
molecules.
Also, Disulfide bonds, covalent linkages between the sulfur-containing side chains
of cysteine’s, are much stronger than the other types of bonds that contribute to
tertiary structure
There are several types of bonds and forces that hold a protein in its tertiary
structure.
 Hydrophobic interactions greatly contribute to the folding and shaping of a
protein. The "R" group of the amino acid is either hydrophobic or hydrophilic. The
amino acids with hydrophilic "R" groups will seek contact with their aqueous
environment, while amino acids with hydrophobic "R" groups will seek to avoid
water and position themselves towards the center of the protein.
 Hydrogen bonding in the polypeptide chain and between amino acid "R" groups
helps to stabilize protein structure by holding the protein in the shape established
by the hydrophobic interactions.
 Due to protein folding, ionic bonding can occur between the positively and
negatively charged "R" groups that come in close contact with one another.
 Folding can also result in covalent bonding between the "R" groups of cysteine
amino acids. This type of bonding is called a disulfide bridge. Interactions
called van der Waals forces also assist in the stabilization of protein structure.
These interactions pertain to the attractive and repulsive forces that occur
between molecules that become polarized. These forces contribute to the
bonding that occurs between molecules.

10. 4. Quaternary structure
When multiple polypeptide chain subunits come together, then the protein attains its
quaternary structure.
 Hemoglobin is an example of a protein with quaternary structure. Hemoglobin,
found in the blood, is an iron-containing protein that binds oxygen
molecules. It contains four subunits: two alpha subunits and two beta
subunits.

11. How to Determine Protein Structure Type:
The three-dimensional shape of a protein is determined by its primary structure. The
order of amino acids establishes a protein's structure and specific function. The
distinct instructions for the order of amino acids are designated by the genes in a
cell. When a cell perceives a need for protein synthesis, the DNA unravels and is
transcribed into an RNA copy of the genetic code. This process is called DNA
transcription. The RNA copy is then translated to produce a protein. The genetic
information in the DNA determines the specific sequence of amino acids and the
specific protein that is produced. Proteins are examples of one type of biological
polymer. Along with proteins, carbohydrates, lipids, and nucleic acids constitute the
four major classes of organic compounds in living cells.
Denaturation of proteins
Loss of native structure by many causes leading to changes in secondary,
tertiary and quaternary structure due to rupture of non-covalent bonds (never
peptide bonds) with loss of biological activity.
 All levels of structure are disrupted except primary (strong peptide bond).
Causes:
Physical causes – heating above 70, powerful shaking, repeated freezing and
melting, UV and high pressure.
Chemical causes – urea, alcohol, strong acids and bases, salts of heavy metals as
MG.
Effects:
 Decreased solubility and rate of diffusion
 Increased viscosity due to unfolding
 Loss of activity
 Change in antigenic property.
What foods are high in protein?
Protein can be found in both plant and animal-based foods. Figure 2 shows the
protein content found in a typical serving of common animal and plant-based foods.
For more information on how to estimate healthy portion sizes, see measuring
portion sizes with your hands.

12. Figure 2. High protein foods.

13. Is there a difference between animal and plant
based proteins?
As we can see in Figure 2, both animal and plant-based foods can be rich sources of
protein. But do they have the same quality?
The quality of a protein can be defined in many ways; however, all definitions relate
to the distribution and proportion of essential and non-essential amino acids they
contain. In general, animal-based proteins are of higher quality as they contain
higher proportions of essential amino acids compared to plant-based proteins.
There is a common misconception that plant-based proteins completely lack certain
essential amino acids. In fact, most plant-based proteins will contain all 20 amino
acids but tend to have a limited amount of certain essential amino acids, known as
their limiting amino acid(s). This means, if a small number of plant foods are
consumed as the only protein sources, they are unlikely to supply enough essential
amino acids to meet our requirements. For people who consume little to no animal-
based foods, such as vegans or vegetarians, it is important that they consume
protein from sources with complementary limiting amino acids. For example,
consuming rice (limited in lysine and thiamine but high in methionine) and beans
(limited in methionine, but high in lysine and thiamine) will provide complementary
amino acids that can help meet essential amino acid requirements.
Animal and plant-based proteins also differ in their bioavailability and digestibility.
The digestible indispensable amino acid score (DIAAS) is the recommended method
for determining dietary protein digestibility and is expressed in values below or
sometimes even above 100.3 A DIAAS of over 100 indicates that the protein has
very high digestibility and quality and is a good complement protein to those that
have lower qualities. Animal-based proteins tend to have higher DIAAS scores
compared to plant-based proteins (Table 2). As most people consume protein from a
variety of sources the quality and digestibility of protein is not usually a concern.

14. How much protein do we eat every day?
In general, Europeans eat enough protein and deficiency is rare among most developed
countries (figure 3). As the diet of Europeans already exceeds the required level, EFSA
has not recommended an increase in current protein intakes.
Figure 3. Protein intake across European countries.
Conclusion
Protein is essential for life; it supplies the essential amino acids needed for the growth
and maintenance of our cells and tissues. Our requirement for protein depends on our
stage of life and most Europeans consume enough to meet their requirements. As most
people consume a varied diet, the quality and digestibility of the proteins they eat should
not be a concern as long as the total amount of protein meets their daily needs. As we
eat foods and not nutrients, we should choose protein-rich foods that not only provide
essential amino acids but also support a healthy and sustainable diet.
References
1. EFSA (2012). European Food Safety Authority, Scientific Opinion on Dietary
Reference Values for protein. EFSA Journal 2012; 10(2):2557
2. UK food composition database.

15. 3. Consultation, F.E., 2011. Dietary protein quality evaluation in human nutrition.
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