Peptide Bond Formation

The macromolecules of biological organisms fall into five main groups: peptide, proteins, carbohydrates, nucleic acids, and lipids (nonpolymeric-nonpolar materials soluble in organic solvents, such as fats and oils). Proteins-peptides and nucleic acids, and many carbohydrates, are biopolymers. In this article, we will limit our discussion to peptide bond formation. Proteins are the basic constituents of living organisms, But peptide bonds formation is essential for the building of proteins.

Peptides

Peptides are biological macromolecules of small molecules called amino acids. Their unit of amino acids ranges from about 2  to less than 200 amino acid units, so peptides can be very large biomacromolecules. Many peptides make a complex with non-amino-acid components such as metal ions (for example, Fe 2+ , Zn 2+ , Cu + , and Mg 2+ ) or certain complex organic molecules usually derived from vitamins. (Vitamins are organic molecules necessary in verysmall quantities for normal cell structure and metabolism.)

Peptides are very important molecules in cells function and organisms metabolism, playing both Complex structural and functional roles. The proteins of bone and connective tissue, for example, are of major structural importance than any other part. 

Some Peptides are enzymes, catalyzing or inhibiting specific biochemical reactions; some transport materials in the bloodstream or across biological membranes to the cell; and some (hormones) carry chemical messages to coordinate the body’s activities. Insulin and glucagon, for example, are peptide hormones made in the pancreas and secreted to regulate the body’s blood-sugar level.

Basic Unit of Peptides: Amino Acids

An amino acid is an organic compound containing an amino group ( – NH 2 ) in one terminal and a carboxyl group (- COOH) in the other terminal. The building blocks of peptides are alpha-amino acids (a-amino acids). An a-amino acid has the general structure(R is an H atom.).

Peptide bond Formation

What is Chirality in amino acid?

All amino acids contain a chiral carbon center. This chiral center is optically active in nature. When you send plane-polarized light in the dilute solution of amino acid. The optically active molecule rotates the plane-polarized light.

 It is possible either clockwise or counterclockwise. Alpha-amino acids rotate the plane-polarized light counterclockwise. All living systems contain alpha-amino acid or l- amino acids. Then the final peptide molecules also follow levo rotation. 

Peptide bond Formation

The carbon atom next to the carboxyl carbon is called the chiral carbon atom. In an alpha-amino acid, the amino group is attached to the same chiral carbon atom. Glycine, NH 2-CH 2-COOH is the simplest and first most alpha-amino acid. R is a hydrogen atom in the glycine amino acid. 

This lists the 20 amino acids from which most proteins are composed in nature (check in our previous blog post). Under the name of each alpha-amino acid, its common three-letter abbreviation is shown in the table (previous post). For instance, the abbreviation for glycine amino acid  is gly.

Each alpha-amino acid has a different R group, or side chain. The side chains of the alpha-amino acids in a protein determine the protein’s physical and chemical properties. Nine of the alpha-amino acids have nonpolar molecular fragments, or hydrocarbon fragments, side chains. The remaining 11 amino acids have polar molecular fragment side chains, capable of ionizing or forming hydrogen bonds with other amino acids or with water.

Zwitterions of amino acids:

At the near-neutral pH of a biological system in the aqueous solution, the alpha-amino acid groups in a protein are generally in the form of zwitterions, which are species having both a

positive and a negative charge. The carboxyl group is acidic, so its proton ionizes and dissociates from carboxylic group:

Peptide bond Formation

The amino group is basic in nature, so it has the capacity to pick up a proton and becomes protonated amine group:

Peptide bond Formation

At neutral pH in the aqueous medium, the net result is that the carboxyl group loses H + to the amino group of alpha-amino acids, yielding the zwitterion:

Peptide bond Formation

Except for the simplest alpha-amino acid, glycine, NH 2-CH 2-COOH, the alpha-amino acids exist as enantiomers, or optical isomers. Such isomers are mirror images. But glycine is not optically active molecule. Any molecule having one tetrahedral carbon atom bonded to four different groups of atoms exhibit optical isomerism. The mirror-image of these isomers are referred to as the levo or l -isomer and the detox or d -isomer; their three-dimensional molecular structures are illustrated here:

In these three-dimensional molecular perspective formulas, a solid wedge is a bond pointing outward from the blog post page, the hatched wedge is a bond pointing backward from the blog post page, and the straight line is a bond lying in the plane of the page of this blog post. 

For instance, in the l -amino acid (general molecular structure), the -COOH group and H 2N- groups are in the plane, the R- group points toward you from the blog post page, and the H- atom points backward from the blog post page. 

All of the amino acids that occur naturally in proteins are l -amino acids in nature. The alpha-amino acids in a protein are linked together by peptide bond formation. A peptide (or amide) bond is the -CO-NH- bond resulting from a condensation reaction between

the carboxyl group of one alpha-amino acid and the amino group of a second alpha-amino acid:

The product out of peptide bond formation in this example is a dipeptide, a molecule formed by linking together two alpha-amino acids. Similarly, a tripeptide is formed by linking together three alpha-amino acids.

A polypeptide is a biopolymer formed by the linking of many amino acids by many peptide bond formation. It may or may not have a biological functional activity. A protein is a polypeptide that has a biological functional activity. 

Peptide bond Formation

If the protein catalyzes the biological reaction, then the protein is called an enzyme. It makes chemical bonds. But in other words, there are some proteins, which only change at the physical level. 

Peptide bond formation: Introduction

A peptide bond, also known as a eupeptide bond, is created when the carboxyl group of one amino acid is joined to the amino group of another amino acid. A peptide bond is a form of covalent chemical link that is an amide functional group in nature. This bond connects two successive alpha-amino acids, starting with C1 (carbon number one) and ending with N2 (nitrogen number two). A peptide or protein chain contains this connection.

Water (H2O) molecules are released during the peptide bond formation. A peptide link is usually a covalent bond (-CO-NH- bond), and the removal of the water molecule is referred to as dehydration chemical reaction. 

In most cases, this action happens between the amino group and carboxylic group of the alpha-amino acid. A peptide, on the other hand, is a Greek term that means “digested.” A peptide is a short polymer made up of monomers of amino acids joined by an amide bond.

Peptide bond Formation

Peptide Bond Formation: Synthesis

On a molecular level, a peptide bond formation is created through a dehydration synthesis or chemical reaction. This is also known as a condensation reaction of molecules, and it happens most commonly between two or many alpha-amino acids.

Dehydration synthesis bonds two or many alpha-amino acids together to produce a peptide bond formation, as seen in the diagram above. One of the amino acids contributes a carboxyl group(-COOH) to the process while losing a hydroxyl group (hydrogen and oxygen).

The -NH2 or amino group of the other alpha-amino acid is depleted of hydrogen. A peptide bond formation is created when the hydroxyl group is replaced by nitrogen. One of the main reasons that peptide bond formation is referred to as substituted amide connections is this. Covalent bonds exist between the two alpha-amino acids.

The -CO-NH- link formed during the processes is a peptide bond formation, and the final molecule contains an amide functional group. An amide functional group, often known as a peptide functional group, is a four-atom functional group(middle) with the formula -C(=O)NH-.

Characteristics of Peptide Bond formation

  1. Peptide bonds are strong because they have a partial double bond due resonance in that functional group: Heating to high temperature or a high salt content does not break them. Peptide bond can be broken by exposing them to a strong acid or base at a high temperature for an extended period of time. Some specific enzymes are also involved in the biological breaking of peptide bonds (digestive enzymes).
  2. Because peptide bonds are stiff and planar in nature, they help to keep protein structure stable in specific conditions. Partially positive charge groups (polar hydrogen atoms of amino groups of amino acid) and partially negative charge groups make up a peptide bond formation (polar oxygen atoms of carboxyl groups of amino acid).

Different Forms of Peptide Bond formation

Dipeptide = contains 2 amino acid units combined and form one peptide bond formation with the release of one water molecule.

Tripeptide = contains 3 amino acid units combined and forms two peptide bond formations with the release of two water molecules.

Tetrapeptide = contains 4 amino acid units combined and forms three peptide bond formation with the release of three water molecules.

Oligopeptide = contains not more than 10 amino acid units combined and forms not more than nine peptide bond formation with the release of not more than nine water molecules.

Polypeptide = contains more than 10 amino acid units, up to 100 residues combined and forms not more than 99 peptide bond formation with the release of not more than 99 water molecules.

Macropeptides = made up of more than 100 amino acids combined and forms more than 100 peptide bond formation with the release of more than 100 water molecules.

Degradation of Peptide Bond

The degradation of peptide bonds in the peptide molecule is a reaction in which the peptide bonds between molecules are broken. The dissolution of the peptide bond is accomplished through hydrolysis with the help of strong base or strong acid(the addition of water). They will emit Gibbs energy in the range of 8-16 kJ/mol during the process.

However, at a temperature of 25 C, this is an extremely hard and long  process with a half-life of 350 to 600 years per peptide bond. Proteases and other enzymes act as catalysts in this process to break the peptide bond.

Peptide bond Formation

Peptide Bond Structure

The planar, trans, and stiff conformation of a peptide bond formation in the peptide molecules. It also has a character with a partial double bond due to resonance. The resonance or partial sharing of two pairs of electrons between the amide functional group nitrogen atom and carboxyl functional group oxygen atom is referred to as peptide bond coplanarity.

The peptide bond formation atoms C, H, N, and O are in the same plane as the amide functional group’s hydrogen atom and the carboxyl functional group’s oxygen atom, which are trans to each other. This gives extra stability for the peptide bond.

The scientists Linus Pauling and Robert Corey discovered that peptide bonds are stiff and planar in nature.

The polarity of the molecules

The polarity of the molecules are listed as follows

Lewis Structure and Molecular Geometry

Lewis structure and molecular geometry of molecules are listed below

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