2.

1 Protein: Definition, Classification, Composition, Function, metabolism

Definition:
Protein is a complex organic nitrogenous compound composed of amino acids linked
together by peptide bonds. The number of amino acids present varies from about a hundred to
several thousands in different proteins. - Some proteins are composed of only one polypeptide
chain while others are composed of two or more polypeptide chains (multi subunit proteins) held
together by non-covalent bonds. Each protein has a unique amino acid sequence and a well-
defined three-dimensional structure known as the conformation.

Sources: Meat, fish, milk, egg, pulses yogurt, beans, nuts, lentils, soy products, quinoa, sea
foods, green peas cheese and vegetables.

The general properties of proteins

1. High molecular weight substances.

2. It constitutes more than 50% of the dry weight of the cell.

3. It presents in different shapes; fibrous and globular.

4. The globular is soluble in water and diluted salt solution with different degrees

5. The chemical and physical properties depend on the amino acids forming the protein.

6. The biological properties and 3D conformation depend also on the constituting amino acids.

7. All proteins are amphoteric compounds.

8. They precipitate by heat, in alcohols and in their isoelectric point

Classification:
Proteins can be classified according to three different criteria:
 Proteins can be classified on the basis of the chemical composition.
 Proteins can be classified on the basis of shape.
 Proteins can be classified on the basis of their biological function
Protein is classified into three groups (types) on the basis of the chemical composition -
 Simple Protein
 Conjugated Protein
 Derived Protein

Simple Protein: The protein which gives only amino acid on hydrolysis is called simple protein.
These are pure protein and have no non-protein group in the molecules. Ex. Albumins, globulins,
chymotrypsins, ribonuclease-A etc.

Conjugated Protein: These protein contain amino acid units with one or more additional non-
protein (prosthetic) group or groups. Eg; lipoproteins, glycoproteins, Nucleoproteins,
phosphoproteins, hemoproteins, flavoproteins, metalloproteins, phytochromes, cytochromes,
opsins, and chromoproteins.

Class Prosthetic Example and Source

Nucleoproteins Nucleic acid DNA & RNA (Nucleus of cells)
Glycoproteins Carbohydrate Egg, wheat etc
Phosphoproteins Phosphoric acid Milk (caesin) Egg yolk etc
Lipoproteins Lipid Phospholipid, Cholesterol
Metalloproteins Metals Copper (ceruloplasmin), Iron (siderophilin)

Derived Protein: These proteins are not found in nature as such. They are products of hydrolysis
of the native protein molecules. The gradual stages are as follows:
Protein —— Proteoses —— Peptones —— Peptides —— Amino acids

Proteins can be classified on the basis of their shape into two main classes:
 Globular proteins
 Fibrous proteins

Globular proteins:
 They are generally soluble in water.
 The polypeptide chains are tightly folded into a globular shape.
 Example: enzymes, hemoglobin, myoglobin

Fibrous proteins:
 They are insoluble in water
 Their polypeptide chains are arranged in long strands (elongated in the form of fibers).
 Example: Collagen, elastin, keratin.

Proteins can be classified on the basis of their biological function into:

 Catalytic function (enzymes)
 Transport function (hemoglobin, albumin, transferrin)
 Nutrient and storage proteins (e.g., casein & ferritin)
 Contractile or mobile proteins (e.g., actin, myosin)
  Structural function (Keratin, elastin, collagen)
 Defense proteins (e.g., antibodies / immunoglobulins, fibrinogen and thrombin)
 Regulatory function, some hormones are proteins (Growth hormone, somatotropin)
 Some toxins are proteins.

Composition of Protein:
 Protein molecules are organic molecules made of the elements carbon, hydrogen,
nitrogen, oxygen, and sulfur. Protein molecules are made of amino acids, which are
assembled into long chains called polypeptide chains in the primary structure.
 The secondary structure is determined by the dihedral angles of the peptide bonds.
 The tertiary structure is determined by the folding of protein chains in space.
 Association of folded polypeptide molecules to complex functional proteins results in
quaternary structure.

Primary structure: The order of amino acids is in the chain.

Secondary Structure: The folding of the polypeptide chain into a specific coiled structure held
together by disulfide and hydrogen bonds.

Tertiary structure: The arrangement of twisted chain into layers, crystals and fibers.

Quaternary structure: Some protein molecules are made of subunits and the arrangement of
subunits are called quaternary structure.
Classification of Proteins

Based on the molecular shape, proteins can be classified into two types.

1. Fibrous Proteins:

When the polypeptide chains run parallel and are held together by hydrogen and disulfide bonds,
then the fiber-like structure is formed. Such proteins are generally insoluble in water. These are
water-insoluble proteins.

Example – keratin (present in hair, wool, and silk) and myosin (present in muscles), etc.

2. Globular Proteins:

This structure results when the chains of polypeptides coil around to give a spherical shape.
These are usually soluble in water.

Example – Insulin and albumins are common examples of globular proteins.

Properties of protein:
 Proteins are colloidal in nature.
 They are generally soluble in water, weak salt solution, dilute acids and alkalis.
 Proteins undergo coagulation by heat and strong acid.
 Each protein has got a particular isoelectric pH at which it can be precipitated.
 Proteins are denatured by many kind of physical or chemical treatment such as shaking,
change of temperature, change of reaction, addition of neutral salt etc.

Functional importance of Protein:

1. It acts as a growth material for the organism.
2. It repairs the wear and tear of the body.
3. To increase flesh, body weight etc. Cells mostly contain protein.
4. It forms buffer system of the body and helps in O2 carriage e.g. hemoglobin.
5. It acts as a part of fuel of organism.
6. It helps to carryout muscle contraction, e.g. Myosin.
7. It provides energy to the body e.g. 4.1 kcal/gm.
8. Maintains colloidal osmotic pressure etc.
9. It helps in the formation of enzymes, hormones, antibody (immunity) e.g. catalase,
pepsin, amylase, lipase, insulin, glucagon, thyroxine, immunoglobins etc.
What is protein and why is it necessary?

Proteins are the building blocks of living beings. Protein is present in every human cell. An
amino acid chain forms the basic building block of proteins. For our body to repair damaged
cells and create new ones, we need protein in our daily diet. Children, teenagers, and pregnant
women all need protein for healthy growth and development.

What is protein deficiency?

When protein consumption is insufficient to meet our body’s needs, we have a protein
deficiency. Worldwide, an estimated 1 billion people experience inadequate protein intake. Up to
30% of South Asia and Central Africa children have insufficient protein intake, making these
regions among the worst affected.

What are the four types of proteins?

Primary, secondary, tertiary, and quaternary structures are the four levels of complexity that can
be used to characterize the entire structure of a protein.

Metabolism of Protein:

 Protein metabolism entails the creation of proteins and amino acids, known as anabolism,
as well as the breakdown of proteins into amino acids, known as catabolism.
 Amino acids in the cellular pool come from dietary protein and from the destruction of
cellular proteins.
 The amino acids in this pool need to be replenished because amino acids are outsourced
to make new proteins, energy, and other biological molecules.
 Mechanical digestion of protein begins in the mouth and continues in the stomach and
small intestine.
 Chemical digestion of protein begins in the stomach and ends in the small intestine.
 The body recycles amino acids to make more proteins.

Main events of protein metabolism:

 Breakdown of amino acids (known as deamination – removal of the amine group from
the molecule)
 Removal of ammonia from the body by synthesis of urea
 Synthesis of non-essential amino acids
 Synthesis of clotting factors for blood coagulation.
 Protein metabolism occurs in the liver
 Proteins are broken down into amino acids by enzymes which are transported to the liver
 When protein is broken down into amino acids (deaminated) it produces nitrogen which
produces ammonia (NH3)
 NH3 is produced when amino acids are ‘deaminated’ (removed of an amine group from
an amino acid due to surplus) for energy.
 NH3 is a waste product which is toxic.
  The liver converts excess ammonia into urea (NH2CONH2) (less toxic / harmless) via
urea cycle
 Transported to kidneys and excreted (some excreted via sweat).

Process of protein metabolism:

Digestion of protein:
Aim of digestion of proteins, is to break the peptide bonds holding the proteins and amino acids
together.
The enzymes that break down proteins are called proteases (e.g. pepsin, trypsin and
chymotrypsin)
 Pepsin – stomach
 Trypsin – small intestine or pancreas
 Chymotrypsin – small intestine or pancreas.

From the Mouth to the Stomach:

a. The first step in protein food digestion involves chewing.

b. The teeth begin the mechanical breakdown of the large food pieces into smaller pieces
that can be swallowed.
c. The salivary glands provide some saliva to aid swallowing and the passage of the
partially mashed food through the esophagus.
d. The mashed food pieces enter the stomach through the esophageal sphincter.
e. The stomach releases gastric juices containing hydrochloric acid and the enzyme, pepsin,
which initiate the breakdown of the protein.
f. The acidity of the stomach facilitates the unfolding of the proteins that still retain part of
their three-dimensional structure after cooking and helps break down the protein
aggregates formed during cooking.
 g. Pepsin, which is secreted by the cells that line the stomach, dismantles the protein chains
into smaller and smaller fragments.
h. Chemical breakdown of large protein molecule requires more time and long mixing. The
powerful mechanical stomach contractions churn the partially digested protein into a
more uniform mixture called chyme.
i. Protein digestion in the stomach takes a longer time than carbohydrate digestion, but a
shorter time than fat digestion.
j. Eating a high-protein meal increases the amount of time required to sufficiently break
down the meal in the stomach. Protein food remains in the stomach longer, making us
feel full longer.

From the Stomach to the Small Intestine:

The stomach empties the chyme containing the broken down protein food into the small
intestine, where the majority of protein digestion occurs.

The pancreas secretes digestive juice that contains more enzymes that further break down the
protein fragments.

The two major pancreatic enzymes that digest proteins are chymotrypsin and trypsin.
The cells that line the small intestine release additional enzymes that finally break apart the
smaller protein fragments into the individual amino acids.

The muscle contractions of the small intestine mix and propel the digested proteins to the
absorption sites.

The goal of the digestive process is to break the protein into dipeptides and amino acids for
absorption.

Protein Absorption:

In adults, essentially all protein is absorbed as tripeptides, dipeptides or amino acids and this
process occurs in the duodenum or proximal jejunum of the small intestine.

The peptides and/or amino acids pass through the interstitial brush border by facilitative
diffusion or active transport.

Very little protein makes it to the large intestine if you are not eating excessive amounts. If you
have smelly flatulence, this may be a sign you are eating too much protein because the excess is
making it to the colon where you gut microbes are digesting it and producing smelly gas.

Once passed through the membrane, the amino acids or peptides are released into the intestinal
blood stream and are transported to the liver by the hepatic (liver) portal vein. This is known as
the enterohepatic (from intestine to liver) circulation.

In the liver, 50-65% amino acids are used to synthesize protein, nitrogen containing compounds
and form purine/pyrimidine bases.

In some cases, they may be converted to energy.

The liver regulates the amino acid levels in the blood. The amino acids that do not stay in the
liver pass through and are transported to the rest of the body to be taken up and utilized by other
cells. Most branch chain amino acids pass through the liver.

Amino acid Catabolism:

In the liver, catabolism of amino acid takes place releasing ammonia.

Ammonia is toxic, so the liver transforms it into urea (less toxic than ammonia), which is then
transported to the kidney and excreted in the urine.

Urea (NH2-CO-NH2) is a molecule that contains two Nitrogen (2N) and is highly soluble in
water. This makes it a good choice for transporting excess nitrogen out of the body.

Nitrogen is also excreted in the feces, skin, hair, and nails. In skin, hair, and nails the nitrogen is
bound to protein as this is the building block of each.
Because amino acids are building blocks that the body reserves in order to synthesize other
proteins, more than 90 percent of the protein ingested does not get broken down further than the
amino acid monomers.

The very first step in their catabolism is removal of –NH2 group and formation of corresponding
keto-acid. The ammonia which is liberated, quickly converted to urea and it is incorporated in
some other a-acid. Catabolism of a-acid involves the following process:

1. Transamination 2. Deamination

3. Urea formation 4. Decarboxylation

Transamination:
It is the process of conversion of amino acid into keto acid. In this process amino group of one
amino acid (donor) is transferred to an α-keto acid (recipient) resulting in the formation of a new
amino acid and a new keto acid.

The donor amino acid is converted into a new keto acid and the recipient keto acid is converted
into a new amino acid.

Transamination is a reversible process and is catalyzed by the enzyme transaminase or amino

transferase. Co-enzyme for the reaction is vitamin B6 (Pyridoxine).

Transamination takes place principally in liver, kidney, heart and brain.

Deamination:
Deamination is a process in which amino group (-NH2) is removed from the amino acid, which
then changes to an α-keto acid. In this process amino group is removed as ammonia.
Ammonia released during deamination is either converted into ammonium salt or into urea.
Deamination usually takes place in liver and kidney cells to catabolize excess of amino acids.

Urea formation (Urea Cycle):

When production of ammonia exceeds beyond a certain level it become toxic. Excess of
ammonia produced during the deamination of amino acids is converted to less toxic substance,
urea, before been excreted in the urine.

Formation of urea is a cyclic process and the cycle is known as urea cycle. This cycle was first
outlined by Hans Krebs and Kurt Henseleit in 1932; hence it is also known as Kreb’s Hanseleit
cycle.

The chief site for urine formation is liver and after its formation urea passes into the blood
stream and from blood to kidneys and finally excreted into the urine.
Urea synthesis takes place in five steps. Each step is catalyzed by a specific enzyme. Out of these
five enzymatic reactions, two take place in the mitochondria and three take place in the
cytoplasm.

Urea formation cycle is also known as ornithine cycle as it involves conversion of amino acid
ornithine to citrulline though glutamic acid which is derived from aspartic acid by transamination
and/or form α-ketoglutaric acid and ammonia.

Steps of the urea cycle

A. The mitochondrial stage:

1. Carbamoyl phosphate is formed from Ammonia (NH3) and Bicarbonate (H2CO3), by

the enzyme Carbamoyl phosphate synthetase (CPS).

NH3 + CO2 + 2ATP → carbamoyl phosphate + 2ADP + Pi

2. Carbamoyl phosphate is converted to Citrulline with catalysis by Ornithine

transcarbamylase,

Carbamoyl phosphate + ornithine → citrulline + Pi

B. The cytosolic stage:

3. Citrulline condenses with Aspartate to form Argininosuccinate. This reaction is

catalyzed by Argininosuccinate synthatase.

Citrulline + ATP + aspartate → argininosuccinate + AMP + PPi

4. Argininosuccinate is cleaved to form Arginine and Fumarate by the enzyme

Argininosuccinase (Arginosuccinate lyase).

Argininosuccinate → arginine + fumarate

5. Arginine is cleaved to form Urea and Ornithine by the enzyme Arginase.

Arginine → urea + ornithine

6. The ornithine is then transported back to the mitochondria by the enzyme Ornithine
translocase to begin the urea cycle again.
7 intermediates of the Krebs Cycle:
1. Oxaloacetate 2. Pyruvate
3. X-ketoglutarate 4. Fumarate
5. Succinyl coenzyme A 6. Acetyl coenzyme a
7. Acetoacetate

What happens when the urea cycle goes wrong?

 If there is a problem with the urea cycle, then the level of ammonia in the blood will rise,
causing hyperammonemia.
 Ammonia is able to cross the barrier between the bloodstream and the brain.
 Once it enters the brain, it can stop the TCA cycle by depleting one of the metabolites, α-
ketoglutarate.
 This means that these brain cells cannot make energy, ultimately leading to their death.
 This eventually will lead to neurological problems, which can be as severe as irreversible
brain damage.

What is the Urea Cycle?

In humans and mammals, almost 80% of the nitrogen excreted is in the form of urea, which is
produced through a series of reactions occurring in the cytosol and mitochondrial matrix of liver
cells. These reactions are collectively called the urea cycle or the Krebs-Henseleit cycle.
Ammonia is a toxic product of nitrogen metabolism which should be removed from our body.
The urea cycle or ornithine cycle converts excess ammonia into urea in the mitochondria of liver
cells. The urea forms, then enters the blood stream, is filtered by the kidneys and is ultimately
excreted in the urine.

The overall reaction for urea formation from ammonia is as follows:

2 NH3 + CO2 + 3ATP ------> Urea (NH2.CO.NH2) + Water (H2O) + 3 ADP

Amino acids are divided into two categories: essential and non-essential amino acids.

Essential amino acids are not made by the human body and must instead be acquired from
our diet.

The 9 essential amino acids are: histidine, isoleucine, leucine, lysine, methionine,
phenylalanine, threonine, tryptophan, and valine.

Non-essential amino acids, by contrast, are synthesized by the human body.

Nonessential amino acids include: alanine, arginine, asparagine, aspartic acid, cysteine,
glutamic acid, glutamine, glycine, proline, serine, and tyrosine.