Biomolecules: Peptide Bonds: Formation and Cleavage

_______ is a specific cleavage of the peptide bond with the help of a special protein, an enzyme called _______.

Proteolysis; protease

What is hydrolysis?

A chemical reaction that breaks bonds between two molecules by the addition of water; functions in disassembly of polymers to monomers.

What is a polypeptide?

A polymer (chain) of many amino acids linked together by peptide bonds.

Why is proteolytic cleavage a specific process?

Because "you" can choose which peptide bonds "you" cleave because proteases are very selective about where they cut, and many of them will only cleave peptide bonds between certain specific amino acids.

How are peptide bonds formed?

By the nucleophilic addition-elimination reaction between the carboxyl group of one amino acid and the amino group of another amino acid. The result is a newly-formed dipeptide. This is a condensation reaction, and gives off a water molecule in the process.

The end of the backbone to a polypeptide chain that starts with a carbonyl carbon is called the _______.

C terminal

Describe the nature of a peptide bond.

It is an amide bond formed between two amino acids. It is a rigid and planar bond stabilized by resonance delocalization of a nitrogen's electrons to a carbonyl's oxygen.

Explain how the protease trypsin functions.

It only cleaves on the carboxyl side of basic of basic amino acids, like arginine and lysine.

With the addition of trypsin, where would this polypeptide chain be cleaved: N term-Thr-Arg-His-Pro-Lys-Val-C term?

N term-Thr-Arg/-His-Pro-Lys/-Val-C term (3 different fragments)

Due to the double-bond-like character of a peptide bond, is the entire polypeptide chain necessarily a rigid-like structure?

No, because even though there isn't much rotation about the peptide bond, there still exists free rotation about the alpha carbon atoms.

Explain this pattern: N-C-C-N-C-C-N-C-C-N-C-C-N-C-C-...

The backbone of a polypeptide chain, where each set (nitrogen atom, alpha carbon, carbonyl carbon) represents an amino acid. It always starts with a nitrogen atom and ends with the carbonyl carbon.

What is a peptide bond?

The chemical bond that forms between the carboxyl group of one amino acid and the amino group of another amino acid.

What is the nature of the valence electrons located on a peptide bond of an amino acid?

The double bond formations, being part of resonance structures, may shift (resonance delocalization of electrons). The negative and positive charges then accord with the ideas of polarity. Due to this double-bond-like character, the peptide bond is a very rigid and planar one.

What are the components of an amino acid?

The term amino acid is short for "α-amino [alpha-amino] carboxylic acid." Each molecule contains a central carbon (C) atom, termed the α-carbon (or alpha carbon), to which both an amino and a carboxyl group are attached. The remaining two bonds of the α-carbon atom are generally satisfied by a hydrogen (H) atom and the R group.

When strong acids are used in the splitting of molecular bonds, it is known as _______.

acid hydrolysis

The end of the backbone to a polypeptide chain that starts with a nitrogen atom is called the _______.

amino or N terminal

Acid hydrolysis, when combined with heat, is a _______ of cleaving peptide bonds because each of the peptide bonds gets cleaved.

nonspecific way

Within a polypeptide chain, each amino acid is called a _______.

residue

Two common means by which the hydrolysis of a peptide bond is helped are by the usage of _______ or by _______

strong acids; proteolytic enzymes