2.16 Role of Proteins

Proteins are very important molecules in our cells. They are involved in virtually all cell functions. Each protein within the body has a specific function.

Some proteins are involved in support or composition of body parts (structural roles), while others are involved in various physiological activities like bodily movement or in defence against germs (functional roles).

Table 2.4: List of Structural Proteins

Table 2.5: List of Functional Proteins

STEAM Activity 2.2 (from textbook)

Title: The presence or absence of protein in a given sample can be confirmed by biochemical tests.

Intermediate Level

Amino Acids in Detail

• Central α-carbon
• Hydrogen atom
• Amino group (-NH₂)
• Carboxyl group (-COOH)
• R group (variable)

Types of Amino Acids:

Peptide Bond Formation

• -OH from carboxylic acid group of one amino acid
• -H from amino group of another amino acid
• These combine to form water
• A peptide bond is formed between C and N

• N-terminal end (amino group)
• C-terminal end (carboxyl group)

Polypeptide: - Many amino acids linked by peptide bonds

Levels of Protein Structure

Classification of Proteins

Roles of Proteins

Significance of Amino Acid Sequence

• Point mutation in β-globin gene
• Glutamic acid replaced by valine at position 6 in β-chain
• Causes sickle-shaped red blood cells
• Leads to pain and organ damage

• Two α-chains (141 amino acids each)
• Two β-chains (146 amino acids each)

Sickle Haemoglobin (Hbˢ): - One difference: Glutamic acid → Valine at position 6 in β-chain

Important Points

• 1. Proteins play most of the critical roles in cells and are required for the structure, functioning, maintenance, and regulation of body systems.
• 2. Proteins are the main structural components of the cell.
• 3. All proteins contain C, H, O, N, while some contain P, S.
• 4. Few proteins have Fe, I, Mg incorporated into the molecule.
• 5. Chemically, proteins can be defined as polymers of amino acids or polypeptide chains.
• 6. A protein may consist of a single polypeptide or more than one polypeptide.
• 7. Amino acids are the building blocks of proteins.
• 8. There are many amino acids known to occur, but only 20 are commonly found in proteins.
• 9. Each amino acid contains a carbon atom called the α (alpha) carbon.
• 10. To this α-carbon, the following are attached:
• - A hydrogen atom
• - An amino group (-NH₂)
• - A carboxyl group (-COOH)
• - A variable group known as the -R group
• 11. The R group has a different structure in each of the 20 biologically important amino acids and determines their individual chemical properties.
• 12. Two simplest amino acids: Glycine and Alanine.
• 13. Essential amino acids: Cannot be produced by our bodies; must be acquired through diet. There are nine essential amino acids.
• 14. Non-essential amino acids: Can be synthesized in the human body. There are eleven non-essential amino acids.
• 15. Peptide bond: When two or more amino acids bind with each other to form a condensed molecule, a bond called a peptide bond is formed.
• 16. On hydrolysis of proteins, peptide bonds are broken to release multiple amino acids.
• 17. Peptide bonds are vital for the maintenance of primary structure of proteins.
• 18. Dipeptides and polypeptides are formed by the condensation of amino acids on the ribosome under the instructions of mRNA. This process is known as translation.
• 19. During peptide bond formation:
• - The -OH from the carboxylic acid group of one amino acid
• - And the -H from the amino group of the other amino acid
• - Are liberated and form a water molecule.
• - A bond is established between the C of the carboxylic acid group and the N of the amino group.
• 20. A dipeptide has two ends: N-terminal end and C-terminal end.
• 21. Primary structure: A linear polypeptide with a specific sequence and number of amino acids.
• 22. Secondary structure: α-helix or β-pleated sheet formed by H-bonding.
• 23. Tertiary structure: Globular shape formed by folding of α-helix and β-pleated sheets.
• 24. Quaternary structure: More than one globule attached together by hydrophobic interaction.
• 25. Significance of amino acid sequence: Even a point mutation can disturb the sequence of amino acids, causing severe defects like sickle cell anemia.
• 26. Sickle cell anemia: Caused by a point mutation in the β-globin gene; glutamic acid is replaced by valine at position number six in the β-chain.
• 27. Classification of proteins:
• - Fibrous proteins: Fibre or filament-like; secondary structure; insoluble; elastic; cannot be crystallized.
• - Globular proteins: Spherical or globule-like; tertiary or quaternary structure; soluble; inelastic; can be crystallized.
• 28. Roles of proteins:
• - Structural: Collagen, elastin, keratin, histone.
• - Functional: Enzymes, hormones, antibodies, haemoglobin, fibrinogen, ovalbumin, casein.

Remember

• - Proteins = polymers of amino acids
• - Amino acids = building blocks of proteins
• - 20 amino acids commonly found in proteins
• - Essential amino acids = 9; must be in diet
• - Non-essential amino acids = 11; made by body
• - Peptide bond = bond between two amino acids
• - Dipeptide = two amino acids
• - Polypeptide = many amino acids
• - Primary structure = sequence of amino acids
• - Secondary structure = α-helix or β-pleated sheet
• - Tertiary structure = globular shape
• - Quaternary structure = more than one globule
• - Fibrous proteins = fibre-like; insoluble; structural
• - Globular proteins = spherical; soluble; functional
• - Sickle cell anemia = point mutation; glutamic acid → valine at position 6 in β-chain

Common Mistakes

• 1. Confusing proteins and amino acids – Proteins are polymers of amino acids; amino acids are the monomers.
• 2. Thinking all amino acids are essential – Only 9 are essential; 11 are non-essential.
• 3. Confusing essential and non-essential amino acids – Essential = must be in diet; Non-essential = can be made by the body.
• 4. Thinking peptide bonds are the same as glycosidic bonds – Peptide bonds are between amino acids; glycosidic bonds are between sugars.
• 5. Forgetting the difference between primary, secondary, tertiary, and quaternary structure – Primary = sequence; Secondary = α-helix/β-sheet; Tertiary = globular; Quaternary = multiple globules.
• 6. Confusing fibrous and globular proteins – Fibrous = fibre-like, insoluble, structural; Globular = spherical, soluble, functional.
• 7. Thinking all proteins are enzymes – Enzymes are just one type of protein. There are also structural proteins, hormones, antibodies, etc.
• 8. Forgetting the role of R groups – R groups determine the chemical properties of amino acids and the folding of proteins.
• 9. Thinking sickle cell anemia is caused by a large mutation – It is caused by a point mutation (single nucleotide change).
• 10. Confusing the number of amino acids in haemoglobin chains – α-chains have 141 amino acids; β-chains have 146 amino acids.
• 11. Forgetting the position of the mutation in sickle cell anemia – Glutamic acid is replaced by valine at position 6 in the β-chain.
• 12. Thinking all proteins are soluble – Fibrous proteins are insoluble; globular proteins are soluble.
• 13. Confusing the bonds involved in protein structure – Primary = peptide bonds; Secondary = hydrogen bonds; Tertiary = ionic, disulfide, hydrophobic; Quaternary = hydrophobic.

Quick Revision

• Proteins play most of the critical roles in the cells and are required for the structure, functioning, maintenance, and regulation of the body systems.
• Proteins are the main structural components of the cell.
• All proteins contain C, H, O, and N, while some contains P, S.
• Few proteins have Fe, I, and Mg incorporated into the molecule.
• Chemically proteins can be defined as polymers of amino acids or polypeptide chains.
• A protein may consist of a single polypeptide or more than one polypeptide.
• 2.12.2 Amino acids: Amino acids are the building blocks of proteins.
• There are many amino acids known to occur, but only 20 are commonly found in proteins.
• The amino acids are built on a common plan.
• Each contains a carbon atom. It is called α (alpha) carbon. To this a hydrogen atom, an amino group (-NH₂), a carboxyl group (-COOH) and a variable group known as -R group are attached.
• The R group has a different structure in each of the 20 biologically important amino acids and determines their individual chemical properties.
• Two simplest amino acids i.e., glycine and alanine.
• 2.12.3 Essential and non-essential Amino acids:
• Essential amino acids: The essential amino acids are those amino acids which cannot be produced by our bodies and they should essentially be acquired through our diet.
• They can be obtained from foods like milk, egg, fish, chicken, meat, vegetables, lentils etc.
• They can serve to build and repair muscle and bones act as precursor molecules for the synthesis of hormones and neurotransmitters.
• One can face the deficiency of essential amino acids and consequently suffer many health problems if not regularly taken in diet.
• There are nine essential amino acids which include, lysine, leucine, isoleucine, histidine, methionine, phenylalanine, threonine, valine and tryptophan.
• Non-essential amino acids: The non-essential amino acids can be synthesized in the human body modifying other amino acids and other food components.
• They need not to be part of our diet.
• Chances of their deficiency are rare but due to illness or starvation may lead to their deficiency.
• They are involved in removal or detoxification of toxins, essential in the RBC and WBC synthesis, improve brain and cardiac functioning.
• The eleven non-essential amino acids are: alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, proline, serine and tyrosine.
• 2.13 Synthesis and breakage of peptide linkages:
• When two or more amino acids bind with each other to condensed molecule a bond called peptide bond is formed.
• On hydrolysis of proteins these peptide bonds are broken to release multiple amino acids.
• Peptide bonds are formed when animal and plant cells store extra amino acids as polypeptides or proteins for their structural and functional role.
• Each cell have this reaction of polymerization of amino acids.
• Peptides bonds are vital for the maintenance of primary structure of proteins.
• Dipeptides and polypeptides are formed by the condensation of amino acids on the ribosome under the instructions of mRNA which carry these coded instructions from DNA. This process is known as translation.
• During this process, when an amino acid reacts with another amino acid, the -OH from carboxylic acid group of one amino acid and -H from amino group of other amino acid are liberated and form a water molecule, as a result a bond is established between C of carboxylic acid group and N of amino group of two amino acids called peptide bond.
• Hence, a product of two amino acids is formed which is known as dipeptide.
• A dipeptide has two ends; one is called amino or -N terminal end while other is called carboxylic acid or -C terminal end.
• A new amino acid can be added in this chain from its carboxylic acid or -C terminal end in the same way.
• Thus, a tripeptide (a product of three amino acids) is formed and another water molecule is also released.
• Similarly, when several amino acids are linked together by many peptide bonds, the polypeptide chain is formed.
• Peptide bonds are broken at catabolism of proteins during digestion in gut by the action of protein and polypeptide chain digesting enzymes like pepsin, trypsin erysin etc.
• Peptide bonds of proteins and polypeptides may also break at cellular level by lysosomal enzymes to release amino acids for new protein synthesis or for ATP synthesis.
• 2.13.1 Structural conformations in proteins:
• A linear polypeptide with a specific sequence and number of amino acids is called primary structure.
• It is shown by all proteins at the time of their synthesis on ribosomal surface.
• After synthesis a protein does not remain in its primary structure but can be changed into some other structural conformations (particular form, shape or structure).
• A helical (α-helix) or flattened sheets (β-pleated sheet) like structures which are established by H-bonding between opposite charge bearing groups of different amino acids are called secondary structures.
• In some proteins the linear polypeptide is changed into α-helix, then α-helix fold again and again by ionic bonds and disulfide bridges to form a globular shaped structure, the tertiary structure.
• Some proteins exist in very complex structure in which more than one globule is attached together by hydrophobic interaction.
• Such structures are called quaternary structures.
• 2.14 Significance of amino acid sequence:
• Sequence of amino acid in a polypeptide is a characteristic feature of primary structure of protein which is responsible for proper functioning of protein.
• It is determined by the sequence of nucleotide in DNA.
• Even due to point mutation (change of single or few nucleotides in DNA) the sequence of amino acid in a particular protein (polypeptide) may be disturbed which causes severe defects in the body as it happens in sickle cell anemia, a hereditary disease.
• Normal red blood cells are disc-shaped and look like doughnuts without holes in the centre.
• They move easily through your blood vessels.
• Red blood cells contain an iron-rich protein called haemoglobin.
• This protein carries oxygen from the lungs to the rest of the body.
• Normal haemoglobin (Hbᴀ) contains four polypeptides i.e. two α-chains which consist of 141 amino acids each and two β-chains which consist of 146 amino acids each.
• Sickle cell anemia is a serious disorder in which the body makes sickle or crescent shaped red blood cells.
• Sickle cells contain abnormal hemoglobin called sickle haemoglobin (Hbˢ).
• Sickle haemoglobin causes the cells to develop a sickle, or crescent, shape.
• Sickle cells are stiff and sticky.
• They tend to block blood flow in the blood vessels of the limbs and organs.
• Blocked blood flow can cause pain and organ damage.
• Sickle cell anemia is caused by a point mutation in β-globin gene in which only one nucleotide is replaced by another which causes a change in amino acid sequence of β-chain of haemoglobin.
• Sickle cell haemoglobin (Hbˢ) shows only one difference from Hbᴀ i.e., glutamic acid is replaced by valine at position number six in β-chain.
• 2.15 Classification of proteins:
• Based upon structure and shape proteins can be classified into two groups i.e., fibrous and globular.
• Fibrous proteins: These proteins have fibre or filament like shape. Therefore, they exist in secondary structure during function. These proteins are insoluble in aqueous medium, elastic in nature and cannot be crystalized. Examples are: collagen, fibrinogen, actin, myosin and keratin.
• Globular proteins: These proteins have spherical or globules like shape. Therefore, they exist in tertiary or quaternary structure during function. These proteins are soluble in aqueous medium, inelastic in nature and can be crystalized. Examples are: enzymes, hormones, antibodies, channel proteins.
• 2.16 Role of proteins:
• Proteins are very important molecules in our cells. They are involved in virtually all cell functions.
• Each protein within the body has a specific function.
• Some proteins are involved in support or composition of body parts i.e., structural roles, while others are involved in various physiological activities like bodily movement or in defence against germs i.e., functional roles.
• Table 2.4: List of structural proteins:
• Table 2.5 List of functional proteins:
• STEAM ACTIVITY 2.2: The presence or absence of protein in a given sample can be confirmed by biochemical tests.

60-Second Revision

• Proteins = polymers of amino acids
• Amino acids = building blocks of proteins
• 20 amino acids commonly found in proteins
• Essential amino acids = 9; must be in diet
• Non-essential amino acids = 11; made by body
• Peptide bond = bond between two amino acids
• Dipeptide = two amino acids
• Polypeptide = many amino acids
• Primary structure = sequence of amino acids
• Secondary structure = α-helix or β-pleated sheet
• Tertiary structure = globular shape
• Quaternary structure = more than one globule
• Fibrous proteins = fibre-like; insoluble; structural
• Globular proteins = spherical; soluble; functional
• Sickle cell anemia = point mutation; glutamic acid → valine at position 6 in β-chain
• Warning: Proteins and amino acids are not the same. Not all amino acids are essential. Peptide bonds are different from glycosidic bonds. Fibrous and globular proteins have different properties and functions. Sickle cell anemia is caused by a point mutation, not a large mutation.