PROTEINS
PREPARED BY MR. ABHIJIT DAS
DEFINITION
A protein is a large and complex molecule made up of
chains of smaller units called amino acids. Proteins are essential for the
structure, function, and regulation of cells and tissues in living organisms.
CLASSIFICATION OF PROTEINS (BASED ON
COMPOSITION)
Proteins can be classified into two main categories based on their composition: simple proteins and conjugated
proteins.
SIMPLE PROTEINS: Simple proteins
are proteins that consist only of amino acids
and do not contain any additional non-protein components. These proteins are
made up of long chains of amino acids that are linked together by peptide bonds. Examples of simple proteins include
albumins, globulins, and histones.
CONJUGATED PROTEINS: Conjugated proteins,
also known as complex proteins, are proteins that contain one or more non-protein components in addition to amino acids.
These non-protein components are called prosthetic
groups. The prosthetic groups play a crucial role in the protein's structure
and function. Examples of conjugated proteins include glycoproteins
(proteins with attached carbohydrates, Ex- FSH/follicle-stimulating hormone), lipoproteins (proteins with attached lipids, Ex- LDL),
and metalloproteins (proteins with attached metal ions, Ex- Haemoglobin).
Conjugated proteins have diverse functions, such as cell signaling, membrane
structure, and oxygen transport.
CLASSIFICATION OF PROTEINS (BASED ON
SOLUBILITY)
Based on solubility, proteins can be classified into
the following categories:
GLOBULAR PROTEINS: These proteins are soluble in water and other aqueous solutions. They
have a compact, three-dimensional structure with hydrophilic amino acid
residues on their surfaces, allowing them to interact with water molecules.
Examples include enzymes, antibodies, and transport proteins.
FIBROUS PROTEINS: These proteins are
often insoluble in water and other aqueous
solutions. They have an elongated, filamentous structure with a high content of
hydrophobic amino acid residues. Fibrous proteins provide structural support
and are commonly found in connective tissues, such as collagen and keratin.
AMPHIPATHIC PROTEINS: These proteins have regions
that are both hydrophilic and hydrophobic,
making them partially soluble in water. They
often have specific functions related to interactions with cell membranes or
lipid environments. Examples include integral membrane proteins and some
signaling proteins.
AMINO ACIDS
DEFINITION
Amino acids are organic compounds that serve as the building blocks of proteins. They are composed of an
amino group (-NH2), a carboxyl group (-COOH), and a side chain (R
group) attached to a central carbon atom. There are 20 different naturally
occurring amino acids that are commonly found in proteins.
The amino group (-NH2) and the carboxyl
group (-COOH) are functional groups that give amino acids their name. The side
chain (R group) varies between different amino acids, and it determines the
specific properties and characteristics of each amino acid.
CLASSIFICATION OF AMINO ACIDS (BASED ON
CHEMICAL NATURE)
NONPOLAR AMINO ACIDS: Nonpolar amino acids have hydrophobic
side chains that do not readily interact with water. They are typically
insoluble in water and prefer to be in hydrophobic environments. Examples of
nonpolar amino acids include:
Alanine (Ala, A)
Valine (Val, V)
Leucine (Leu, L)
Isoleucine (Ile, I)
Glycine (Gly, G)
Methionine (Met, M)
Phenylalanine (Phe, F)
Tryptophan (Trp, W)
Proline (Pro, P)
POLAR AMINO ACIDS: Polar amino acids have hydrophilic
side chains that can interact with water molecules. They are generally more
soluble in water compared to nonpolar amino acids. Examples of polar amino
acids include:
Serine (Ser, S)
Threonine (Thr, T)
Cysteine (Cys, C)
Tyrosine (Tyr, Y)
Asparagine (Asn, N)
Glutamine (Gln, Q)
ACIDIC AMINO ACIDS: Acidic amino acids have side chains
that are negatively charged at physiological pH due to the presence of a
carboxyl group. They can act as acids by donating a hydrogen ion. Examples of
acidic amino acids include:
Aspartic acid (Asp, D)
Glutamic acid (Glu, E)
BASIC AMINO ACIDS: Basic amino acids have side chains
that are positively charged at physiological pH due to the presence of an amino
group. They can act as bases by accepting a hydrogen ion. Examples of basic
amino acids include:
Lysine (Lys, K)
Arginine (Arg, R)
Histidine (His, H)
ALCOHOLIC AMINO ACIDS: Alcoholic amino acids have side
chains that contain hydroxyl groups (-OH). They are often involved in hydrogen
bonding interactions. An example of an alcoholic amino acid is:
Threonine (Thr, T)
SULFUR-CONTAINING AMINO ACIDS: Sulfur-containing
amino acids have side chains that contain sulfur atoms. The sulfur plays
important roles in protein structure and function. Examples of
sulfur-containing amino acids include:
Cysteine (Cys, C)
Methionine (Met, M)
AROMATIC AMINO ACIDS: Aromatic amino acids have side chains
that contain an aromatic ring. They contribute to the hydrophobic core of
proteins and play important roles in protein folding and stability. Examples of
aromatic amino acids include:
Phenylalanine (Phe, F)
Tryptophan (Trp, W)
Tyrosine (Tyr, Y)
CLASSIFICATION OF AMINO ACIDS (BASED ON
NUTRITIONAL REQUIREMENTS)
Amino acids can be classified based on their
nutritional requirements into two main categories: essential
amino acids and non-essential amino acids.
ESSENTIAL AMINO ACIDS: Essential amino acids are those
that cannot be synthesized by the body in
sufficient amounts and must be obtained from the diet.
They are necessary for proper growth, development, and maintenance of bodily
functions. There are nine essential amino acids:
Histidine
Isoleucine
Leucine
Lysine
Methionine
Phenylalanine
Threonine
Tryptophan
Valine
These essential amino acids need to be consumed
through dietary sources, such as protein-rich foods like meat, poultry, fish,
dairy products, legumes, and certain grains.
NON-ESSENTIAL AMINO ACIDS: Non-essential amino acids are
those that the body can synthesize on its own,
and they are not required to be obtained directly from the diet. While they can
be synthesized, their production may still rely on the availability of
essential amino acids or other precursor molecules. There are 11 non-essential amino acids:
Alanine
Arginine
Asparagine
Aspartic acid
Cysteine
Glutamic acid
Glutamine
Glycine
Proline
Serine
Tyrosine
FOUR LEVELS OF ORGANIZATION OF PROTEINS
PRIMARY STRUCTURE: The primary structure refers to the
linear sequence of amino acids in a protein.
SECONDARY STRUCTURE: The secondary structure describes the
local folding patterns within a protein. It is mainly stabilized by hydrogen
bonding between the backbone atoms of amino acids. The two most common
secondary structures are alpha helices and beta sheets. Alpha helices are tightly coiled
structures resembling a spring, while beta sheets consist of extended strands
connected by short stretches of amino acids.
TERTIARY STRUCTURE: The tertiary structure represents the three-dimensional arrangement of the entire protein molecule.
It results from interactions between amino acid side chains, such as hydrogen
bonding, disulfide bridges, hydrophobic interactions, and electrostatic
interactions. The tertiary structure is responsible for
the overall shape of the protein, determining its function and stability.
QUATERNARY STRUCTURE: Quaternary structure refers to the
arrangement of multiple protein subunits (polypeptide chains) to form a
functional protein complex. The subunits in a quaternary structure are held
together by various interactions, such as hydrogen bonds, hydrophobic
interactions, and disulfide bonds.
QUALITATIVE TESTS
BIURET TEST: The Biuret test is a commonly used
test to detect the presence of proteins. It involves adding a reagent
containing copper ions (such as copper sulfate) to the sample. In the presence
of proteins, a violet color develops, indicating a positive result.
NINHYDRIN TEST: The Ninhydrin test is primarily used
to detect the presence of amino acids, which are the building blocks of
proteins. When amino acids react with ninhydrin, a purple or blue color
develops. This color change indicates the presence of proteins.
XANTHOPROTEIC TEST: The Xanthoproteic test is another test
used to detect the presence of proteins. It involves adding concentrated nitric
acid to the sample. If proteins are present, a yellow color develops. Upon
heating, the yellow color may turn orange.
MILLON'S TEST: Millon's test is used to detect
phenolic compounds, such as tyrosine, which is an amino acid found in proteins.
In this test, Millon's reagent (a solution of mercuric nitrate and nitrous
acid) is added to the sample. A red color indicates the presence of phenolic
compounds and hence proteins.
BIURET-MILLIGAN-MORGAN TEST: This test is a
combination of the Biuret test and the Milligan-Morgan test. It is used to
detect proteins in urine. The reagents used in this test include copper
sulfate, potassium sodium tartrate, and sulfuric acid. The presence of proteins
is indicated by the development of a purple or pink color.
BIOLOGICAL ROLE OF PROTEINS
1. Enzymes:
Many proteins act as enzymes, which are biological catalysts that facilitate
and accelerate chemical reactions in the body. Enzymes play a vital role in
metabolic pathways, breaking down substances, building new molecules, and
regulating cellular processes.
2. Structural
Support: Proteins provide structural support and stability to cells and
tissues. They form the framework of cells, tissues, and organs, maintaining
their shape and integrity. For example, proteins like collagen and keratin are
essential for the structure and strength of connective tissues, skin, hair, and
nails.
3. Transport
and Storage: Certain proteins are responsible for transporting molecules, ions,
and gases throughout the body. For instance, hemoglobin, a protein found in red
blood cells, transports oxygen from the lungs to tissues. Similarly, carrier
proteins facilitate the transport of specific molecules across cell membranes.
Proteins can also serve as storage molecules, storing essential substances like
iron (ferritin) or oxygen (myoglobin) until they are needed.
4. Hormones
and Signaling: Proteins act as chemical messengers in the form of hormones.
Hormonal proteins, such as insulin, growth hormone, and adrenaline, regulate
various physiological processes and maintain homeostasis in the body.
Additionally, proteins are involved in cell signaling pathways, transmitting
signals between cells and coordinating cellular responses.
5. Immunity
and Defense: Antibodies, a type of protein produced by the immune system, help
defend the body against foreign substances (antigens) such as bacteria,
viruses, and toxins. Antibodies recognize and neutralize these antigens,
playing a critical role in the immune response.
6. Muscle
Contraction: Proteins, particularly actin and myosin, are responsible for
muscle contraction. These proteins interact to generate the force required for
muscle movement and locomotion.
7. Regulation
and Gene Expression: Proteins regulate gene expression by interacting with DNA
and controlling the transcription and translation processes. Transcription
factors, for example, bind to specific DNA sequences and influence the
expression of genes, determining cell specialization and development.
8. Enzyme
Regulation: Proteins can regulate the activity of enzymes, modulating their
function and controlling metabolic pathways. These regulatory proteins can
activate or inhibit enzyme activity, ensuring that biochemical reactions occur
at the appropriate rates and in response to specific signals.
METABOLISM OF AMINO
ACIDS
DEAMINATION
Removal of an amino group (-NH2)
from an amino acid.
TRANSAMINATION
Ø
Transfer of an amino group
(-NH2) from one molecule to another.
Ø
This process is vital in the synthesis
and breakdown of amino acids.
UREA CYCLE
Ammonia (NH3) is produced during the
breakdown of amino acids.
1.
Carbamoyl Phosphate Formation:
Ammonia combines with bicarbonate and ATP to form carbamoyl phosphate in a
reaction catalyzed by carbamoyl phosphate synthetase I.
2.
Citrulline Formation:
Carbamoyl phosphate combines with ornithine to produce citrulline, with the
help of the enzyme ornithine transcarbamylase.
3.
Argininosuccinate Formation:
Citrulline reacts with aspartate to form argininosuccinate, with the assistance
of the enzyme argininosuccinate synthetase.
4.
Arginine Formation:
Argininosuccinate is cleaved to produce arginine and fumarate by
argininosuccinate lyase.
5.
Urea Formation:
Arginine is hydrolyzed to form urea and regenerate ornithine.
Urea is then excreted from the body primarily
through the kidneys in the urine.
*EASY TO REMEMBER:
Ø Ammonia
+ Bicarbonate + 2 ATP → Carbamoyl Phosphate
Enzyme: Carbamoyl phosphate synthetase I
Ø Carbamoyl
Phosphate + Ornithine → Citrulline
Enzyme: Ornithine transcarbamylase
Ø Citrulline
+ Aspartate → Argininosuccinate
Enzyme: Argininosuccinate synthetase
Ø Argininosuccinate
→ Arginine + Fumarate
Enzyme: Argininosuccinate lyase
Ø Arginine
→ Urea + Ornithine
Enzyme: Arginase
PHENYLKETONURIA
Phenylketonuria (PKU) is a metabolic disorder where
the body can't properly process an amino acid called phenylalanine.
This results in a build-up of phenylalanine in the body, which can lead to intellectual
disabilities, developmental issues, and other health problems if not managed
through a special diet.
ALKAPTONURIA
Alkaptonuria is a rare genetic disorder where the body can't properly break down the amino acids phenylalanine and tyrosine. This leads to a buildup of homogentisic acid, causing urine to turn dark when exposed to air.
JAUNDICE
1. Yellow
Skin and Eyes
2. Excess
Bilirubin in Blood
3. Linked to Liver, Blood, or Bile Duct Issues