2.13.1 Structural Conformations in Proteins

Definition: A linear polypeptide with a specific sequence and number of amino acids is called the primary structure.

• It is shown by all proteins at the time of their synthesis on the 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).

Levels of Protein Structure:

• A linear polypeptide with a specific sequence and number of amino acids.
• Shown by all proteins at the time of their synthesis on the ribosomal surface.

• A helical (α-helix) or flattened sheets (β-pleated sheet) like structures.
• Established by H-bonding between opposite charge-bearing groups of different amino acids.

• In some proteins, the linear polypeptide is changed into α-helix.
• Then α-helix folds again and again by ionic bonds and disulfide bridges to form a globular shaped structure.
• This is called the tertiary structure.

• Some proteins exist in very complex structures.
• More than one globule is attached together by hydrophobic interaction.
• Such structures are called quaternary structures.

Intermediate Level

Amino Acids in Detail

General Structure:

\beginarrayc H \\ | \\ H₂N - C - COOH \\ | \\ R \endarray

• α-carbon – central carbon
• -NH₂ – amino group
• -COOH – carboxyl group
• -R – variable group (side chain)
• -H – hydrogen atom

• Different in each of the 20 amino acids.
• Determines the chemical properties of the amino acid.
• Can be:
• Nonpolar (hydrophobic)
• Polar (hydrophilic)
• Charged (acidic or basic)
• Aromatic

Examples of Amino Acids:

Essential and Non-Essential Amino Acids

Peptide Bond Formation

• Two amino acids come close together.
• The -OH from the carboxyl group of one amino acid and the -H from the amino group of the other amino acid are removed.
• They form a water molecule.
• A peptide bond is formed between the C of the carboxyl group and the N of the amino group.

• Product of two amino acids.
• Has two ends:
• Amino end (-N terminal)
• Carboxyl end (-C terminal)

Polypeptide: - Formed when several amino acids are linked together by many peptide bonds.

Protein Structure Levels

Functions of Proteins

Important Points

• 1. Proteins are polymers of amino acids or polypeptide chains.
• 2. A protein may consist of a single polypeptide or more than one polypeptide.
• 3. Proteins play most of the critical roles in the cells and are required for the structure, functioning, maintenance, and regulation of the body systems.
• 4. Proteins are the main structural components of the cell.
• 5. All proteins contain C, H, O, and N, while some contain P, S.
• 6. Few proteins have Fe, I, and Mg incorporated into the molecule.
• 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
• - A hydrogen atom
• - An amino group (-NH₂)
• - A carboxyl group (-COOH)
• - A variable group known as the -R group
• 10. The R group has a different structure in each of the 20 biologically important amino acids and determines their individual chemical properties.
• 11. Essential amino acids are those amino acids which cannot be produced by our bodies and they should essentially be acquired through our diet.
• 12. Nine essential amino acids: Lysine, Leucine, Isoleucine, Histidine, Methionine, Phenylalanine, Threonine, Valine, Tryptophan.
• 13. Non-essential amino acids can be synthesized in the human body by modifying other amino acids and other food components.
• 14. Eleven non-essential amino acids: Alanine, Arginine, Asparagine, Aspartic acid, Cysteine, Glutamic acid, Glutamine, Glycine, Proline, Serine, Tyrosine.
• 15. Peptide bond is formed when two or more amino acids bind with each other to form a condensed molecule.
• 16. Dipeptide = product of two amino acids.
• 17. Polypeptide = when several amino acids are linked together by many peptide bonds.
• 18. Protein structure levels:
• - Primary – Sequence of amino acids
• - Secondary – α-helix or β-pleated sheet
• - Tertiary – Globular 3D structure
• - Quaternary – More than one globule

Remember

• - Proteins = polymers of amino acids
• - Amino acids = building blocks of proteins
• - 20 amino acids commonly found in proteins
• - α-carbon = central carbon
• - **-NH₂** = amino group
• - -COOH = carboxyl group
• - **-R** = variable group
• - Essential amino acids = 9; cannot be made by the body
• - Non-essential amino acids = 11; can be made by the body
• - Peptide bond = bond between two amino acids
• - Dipeptide = two amino acids
• - Polypeptide = many amino acids
• - Protein structure levels: Primary, Secondary, Tertiary, Quaternary
• - Primary = sequence of amino acids
• - Secondary = α-helix or β-pleated sheet
• - Tertiary = globular 3D structure
• - Quaternary = more than one globule

Common Mistakes

• 1. Confusing amino acids and proteins – Amino acids are the building blocks; proteins are the polymers.
• 2. Thinking all amino acids are essential – Only 9 are essential; 11 are non-essential.
• 3. Confusing essential and non-essential amino acids – Essential = cannot be made by the body; Non-essential = can be made by the body.
• 4. Thinking the R group is the same in all amino acids – The R group is different in each of the 20 amino acids.
• 5. Confusing peptide bond and glycosidic bond – Peptide bond = between amino acids; Glycosidic bond = between sugars.
• 6. Thinking proteins have only one level of structure – Proteins have four levels: primary, secondary, tertiary, quaternary.
• 7. Confusing primary and secondary structure – Primary = sequence of amino acids; Secondary = α-helix or β-pleated sheet.
• 8. Thinking tertiary structure is held by peptide bonds – Tertiary structure is held by ionic bonds, disulfide bridges, and hydrophobic interactions.
• 9. Confusing dipeptide and polypeptide – Dipeptide = 2 amino acids; Polypeptide = many amino acids.
• 10. Thinking all proteins are enzymes – Enzymes are proteins, but not all proteins are enzymes.
• 11. Forgetting that proteins contain nitrogen – All proteins contain C, H, O, and N.
• 12. Thinking denaturation breaks peptide bonds – Denaturation disrupts secondary, tertiary, and quaternary structure but not primary structure (peptide bonds remain intact).

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.
• 2.12.1 Structure of Proteins:
• 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 are shown in figure 2.26.
• 2.12.3 Essential and non-essential Amino acids:
• Amino acids are categorized into two groups:
• 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, glut