Learning Objectives: What are Proteins? How Proteins are Formed? What is Peptide Bond? Peptide vs Protein, C-Terminal and N-Terminal of Proteins, pI of Proteins, Sub-units of Proteins and Characteristics of Peptide Bond
What are Proteins?
Ø Proteins are the polymers of amino acids (specifically the polymers of L-α- amino acids).
Ø During protein synthesis (translation), the amino acids are joined one by one covalently through the peptide bond.
Ø The sequence of amino acids in a protein is determined by the genetic sequence which is encoded in the genetic code.
Ø The size of the protein ranges from three to thousands of amino acids (see the table below)
Ø Proteins are the most abundant organic molecules in the living system.
Ø Proteins occur in every part of the cell and they constitute about 50% of the cellular dry weight.
Ø Protein is one among the four macro-molecules (Carbohydrates, Lipids, Proteins and Nucleic Acids) of the cells and they form the fundamental basis of the structure and function of life.
Ø Protein was first described by Gerardus Johannes Mulder and the term was coined by Jöns Jacob Berzelius in 1838.
Ø The term PROTEIN was derived from the Greek word ‘proteios‘ meaning ‘holding the first place’ highlighting the prime importance of proteins in the living system.
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Ø Mulder used the term proteins for the high molecular weight nitrogen-rich and most abundant substances present in animals and plants.
Dipeptide, Tripeptide, Oligopeptide, Polypeptide
Ø TWO amino acids joined through ONE peptide bond to form a DIPEPTIDE.
Ø THREE amino acids joined through TWO peptide bonds to form a TRIPEPTIDE.
Ø A few amino acids are joined to form an OLIGOPEPTIDE.
Ø Many amino acids are joined to form a POLYPEPTIDE.
Ø The amino acid molecules in a peptide are called residues.
Peptide vs Protein
Ø Word polypeptide and peptide are a little ambiguous and can overlap in meaning.
Ø Protein is generally used to refer to the complete biological molecule in a stable conformation.
Ø Whereas peptide is generally reserved for a short amino acid oligomer often lacking a stable 3D structure.
Ø The boundary between the two is not well defined and usually lies near 20–30 residues
Ø A polypeptide can refer to any single linear chain of amino acids, usually regardless of length, but often implies an absence of a defined conformation and function.
What is Peptide Bond?
Ø Definition: A peptide bond is a covalent bond joining the α-amino group of one amino acid to the carboxyl group of another with the loss of a water molecule.
Ø In proteins, the amino acids are covalently joined through a substituted amide linkage called PEPTIDE BOND.
Ø The peptide bond is formed by the removal of ONE molecule of water from the α –COOH of one amino acid and α –NH2 of another amino acid.
Ø Peptide bond formation is an example of a condensation reaction (a very common reaction in the living system).
N – Terminal and C – Terminal of Protein
Ø Proteins are usually open chain forms and possess two ends called terminals on either side.
Ø In a peptide, the amino acid residue at the end with a free α amino group is called the amino terminal or N – TERMINAL.
Ø The residue at the other end which has a free α- carboxyl group is called carboxyl terminal or C – TERMINAL.
The pI of Proteins
Ø Amino groups and carboxyl groups of all non-terminal amino acids in a protein are involved in peptide bonds.
Ø These amino acids which are involved in peptide bonds do NOT ionize. Thus, they do NOT contribute to the total acid or base properties of a polypeptide.
Ø However, each polypeptide has one free carboxyl group and one amino group at their C-terminal and N-terminal respectively.
Ø These ends can ionize as free amino acids.
Ø Some amino acids in proteins have ionizable side chains (R groups) such as basic amino acids (Lysine, arginine and histidine) and acidic amino acids (glutamic acid and aspartic acid).
Ø The ionizable groups in the side chain (R groups) contribute to the overall acid or base properties of a protein.
Ø Thus, like amino acids, a polypeptide also has an isoelectric pH (pI).
Ø At pI the proteins do NOT move in the electric field.
Ø This principle is used in the protein purification technique called isoelectric focusing.
Sub-units of Protein
Ø Some protein consists of a single polypeptide chain.
Ø Some others contain multi-subunits having many peptides.
Ø The individual peptides in a functional protein may be identical or different.
Ø Example: Hemoglobin has FOUR polypeptide chains, TWO identical α chains and TWO identical β chains.
Characteristics of Peptide Bond
Ø The peptide bond is an amide linkage and it is rigid and planar.
Ø The peptide bond is a SINGLE bond but it has a partial double bond character.
Ø Due to the partial double bond character, free rotation is NOT permitted around the peptide bond.
Ø The α carbon atom in adjacent amino acid residues is separated by three covalent bonds, arranged as Cα – C – N – Cα.
Ø The peptide C – N bond is shorter than the C – N bonds in simple amines.
Ø Also, atoms associated with the peptide bond are co-planar.
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Ø There is a resonance or partial sharing of two pairs of electrons between the carbonyl oxygen and the amide nitrogen in the peptide bond.
Ø The oxygen has a partial negative charge and the nitrogen has a partial positive charge resulting in a small eclectic dipole.
Ø Thus, the C – N bond is unable to rotate freely because of its partial double bond character.
Ø Rotation is permitted only at N – Cα and Cα – C bonds.
Ø The SIX atoms associated with the peptide bond are in a single plane with the oxygen atom of the carbonyl group and the hydrogen atom of the amide nitrogen trans to each other.
Summary: Proteins are the polymers of amino acids. Amino acids are joined through a special type of covalent bond called the peptide bond. The peptide bond is a substituted amide linkage formed between the amino group of one amino acid and the carboxylic group of the second amino acid. The peptide bond has a partial double bond character hence free rotation is not permitted around the peptide bond even if it is a single bond.
Try this QUIZ on Peptide Bond
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Reference:
David, L., Nelson, D.L., Cox, M.M., Stiedemann, L., McGlynn Jr, M.E. and Fay, M.R., 2000. Lehninger principles of biochemistry.
Voet, D. and Voet, J.G., 2010. Biochemistry. John Wiley & Sons.
Key Questions on Proteins and Peptide Bond
- What are proteins?
- Difference between Peptide and Protein
- How peptide bond is formed?
- What are the N-terminal and C-terminal of a Protein?
- Do proteins have pI (isoelectric pH)?
- What are the characteristics of peptide bonds?
- What is the reason for the partial double bond character of peptide bonds?
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