PEPTIDE BOND FORMATION OF POLYPEPTIDES AND PROTEIN

What is a peptide bond and how it is formed?

A peptide bond is a chemical bond formed between two molecules when the
carboxyl group of one molecule reacts with the amino group of the other
molecule, releasing a molecule of water (H2O). This is a dehydration synthesis
reaction (also known as a condensation reaction), and usually occurs between amino
acids.
How are peptide bonds formed in proteins?

Peptide bonds are formed by a biochemical reaction that extracts a water molecule
as it joins the amino group of one amino acid to the carboxyl group of a
neighboring amino acid. The linear sequence of amino acids within a protein is
considered the primary structure of the protein.
What is the relationship between polypeptides and proteins?
A protein molecule is made from a long chain of these amino acids, each linked to its
neighbor through a covalent peptide bond (Figure 3-1). Proteins are therefore also
known as polypeptides. Each type of protein has a unique sequence of amino acids,
exactly the same from one molecule to the next.

What is the formation of polypeptide?

Polypeptide chains are formed by dehydration between the amino group of a L-
amino acid4 with the carboxyl group of another. One hundred or more amino acids
are linked together with covalent peptide bonds in various specific sequences in the
polypeptide chain with polypeptide chains combining to form a protein.

Amino acids are the building blocks for proteins. All amino acids contain an amino or
NH2 group and a carboxyl (acid) or COOH group. There are 20 different amino acids
commonly found in proteins and often 300 or more amino acids per protein molecule.
Each amino acid differs in terms of its "R" group. The "R" group of an amino acid is
the remainder of the molecule, that is, the portion other than the amino group, the acid
group, and the central carbon. Each different amino acid has a unique "R" group and
the unique chemical properties of an amino acid depend on that of its "R" group
(Figure 19.1.119.1.1).
 Figure 19.1.119.1.1: Amino Acids. Structure of an amino
acid.

To form polypeptides and proteins, amino acids are joined together by peptide bonds,
in which the amino or NH2 of one amino acid bonds to the carboxyl (acid) or COOH

group of another amino acid as shown in

(Figure 19.1.219.1.2 and Figure 19.1.319.1.3).

Figure 19.1.219.1.2: Peptide Bonds.
A peptide bond forms when the amino group of one amino acid bonds to the carboxyl group of
another amino acid.

A peptide is two or more amino acids joined together by peptide bonds, and a
polypeptide is a chain of many amino acids. A protein contains one or
more polypeptides. Therefore, proteins are long chains of amino acids held together by
peptide bonds.
 Figure 19.1.319.1.3: Formatio
n of a Peptide Bond. A peptide bond forms when the amino group of one amino acid bonds to the
carboxyl group of another amino acid.

The actual order of the amino acids in the protein is called its primary structure
(Figure 19.1.419.1.4) and is determined by DNA. As will be seen later in this unit, DNA
is divided into functional units called genes. A gene is a sequence
of deoxyribonucleotide bases along one strand of DNA that codes for a functional
product - a specific molecule of messenger RNA, transfer RNA, or ribosomal RNA. The
product is usually messenger RNA (mRNA) and mRNA ultimately results in the synthesis
of a polypeptide or a protein. Therefore, it is commonly said that the order
of deoxyribonucleotide bases in a gene determines the amino acid sequence of a
particular protein. Since certain amino acids can interact with other amino acids in the
same protein, this primary structure ultimately determines the final shape and therefore
the chemical and physical properties of the protein.

Figure 19.1.419.1.4: Primar
y Structure of a Protein or Polypeptide. The primary structure of a protein or polypeptide is the
actual sequence of its amino acids. Primary structure is determined by the order of the
deoxyribonucleotide bases in genes.

The secondary structure of the protein is due to hydrogen bonds that form between the
oxygen atom of one amino acid and the nitrogen atom of another. This gives the
protein or polypeptide the two-dimensional form of an alpha-helix or a beta-pleated
sheet (Figure 19.1.519.1.5).
 Figure 19.1.
519.1.5: Secondary Structure of a Protein or Polypeptide. (left) The secondary structure of a
protein or polypeptide is due to hydrogen bonds forming between an oxygen atom of one amino
acid and a nitrogen atom of another. There are two possible types of secondary structure: an
alpha helix and a beta sheet. In the case of an alpha helix, the hydrogen bonding causes the
polypeptide to twist into a helix. With a beta sheet the hydrogen bonding enables the polypeptide
to fold back and forth upon itself like a pleated sheet. (right) The secondary structure of a protein
or polypeptide is due to hydrogen bonds forming between an oxygen atom of one amino acid and
a nitrogen atom of another. There are two possible types of secondary structure: an alpha helix
and a beta sheet. In the case of an alpha helix, the hydrogen bonding causes the polypeptide to
twist into a helix. With a beta sheet the hydrogen bonding enables the polypeptide to fold back
and forth upon itself like a pleated sheet.

In globular proteins such as enzymes, the long chain of amino acids becomes folded

into a three-dimensional functional shape or tertiary structure. This is because certain

amino acids with sulfhydryl or SH groups form disulfide (S-S) bonds with other amino
acids in the same chain. Other interactions between R groups of amino acids such as
hydrogen bonds, ionic bonds, covalent bonds, and hydrophobic interactions also
contribute to the tertiary structure (Figure 19.1.619.1.6). In some proteins, such as
antibody molecules and hemoglobin, several polypeptides may bond together to form a
quaternary structure (Figure 19.1.719.1.7).
 Figure 19.1.619.1.6: Tertiary Structure
of a Protein or Polypeptide. In globular proteins such as enzymes, the long chain of amino acids
becomes folded into a three-dimensional functional shape or tertiary structure. This is because
certain amino acids with sulfhydryl or SH groups form disulfide (S-S) bonds with other amino
acids in the same chain. Other interactions between R groups of amino acids such as hydrogen
bonds, ionic bonds, covalent bonds, and hydrophobic interactions also contribute to the tertiary
structure.

As will be seen later in this unit, during protein synthesis, the order of nucleotide bases
along a gene gets transcribed into a complementary strand of mRNA which is then
translated by tRNA into the correct order of amino acids for that polypeptide or protein.
Therefore, the order of deoxyribonucleotide bases along the DNA determines the order
of amino acids in the proteins. Because certain amino acids can interact with other
amino acids, the order of amino acids for each protein determines its final three-
dimensional shape, which in turn determines the function of that protein (e.g., what
substrate an enzyme will react with, what epitopes the Fab of an antibody will combine
with, what receptors a cytokine will bind to).
 Figure 19.1.719.1.7: Quaternary
Structure of a Protein. The quaternary structure of a protein is due to several polypeptides joining
together, as in the case of antibody molecules. Schematic diagram of the basic unit of
immunoglobulin (antibody) Fab Fc heavy chain (consist of VH, CH1, hinge, CH2 and CH3
regions: from N-term) light chain (consist of VL and CL regions: from N-term) antigen binding
site hinge regions (*) -S-S- mean disulfide bonds. (CC-SA-BY 3.0; Y_tambe).
Summary
1. Amino acids are the building blocks for proteins. There are 20 different amino
acids commonly found in proteins and often 300 or more amino acids per protein
molecule.
2. All amino acids contain an amino or NH2 group and a carboxyl (acid) or COOH
group.
3. To form polypeptides and proteins, amino acids are joined together by peptide
bonds, in which the amino or NH2 of one amino acid bonds to the carboxyl (acid)
or COOH group of another amino acid.
4. A peptide is two or more amino acids joined together by peptide bonds; a
polypeptide is a chain of many amino acids; and a protein contains one or more
polypeptides. Therefore, proteins are long chains of amino acids held together by
peptide bonds.
5. The actual order of the amino acids in the protein is called its primary structure
and is determined by DNA.
6. The order of deoxyribonucleotide bases in a gene determines the amino acid
sequence of a particular protein. Since certain amino acids can interact with
other amino acids in the same protein, this primary structure ultimately
 determines the final shape and therefore the chemical and physical properties of
the protein.
7. The secondary structure of the protein is due to hydrogen bonds that form
between the oxygen atom of one amino acid and the nitrogen atom of another
and gives the protein or polypeptide the two-dimensional form of an alpha-helix
or a beta-pleated sheet.
8. In globular proteins such as enzymes, the long chain of amino acids becomes
folded into a three-dimensional functional shape or tertiary structure. This is
because certain amino acids with sulfhydryl or SH groups form disulfide (S-S)
bonds with other amino acids in the same chain. Other interactions between R
groups of amino acids such as hydrogen bonds, ionic bonds, covalent bonds, and
hydrophobic interactions also contribute to the tertiary structure.
9. In some proteins, such as antibody molecules, several polypeptides may bond
together to form a quaternary structure.

What is denaturing and how does it happen? A protein becomes denatured when its normal
shape gets deformed because some of the hydrogen bonds are broken. Weak hydrogen
bonds break when too much heat is applied or when they are exposed to an acid (like citric acid
from lemon juice).

What happens in protein denaturation?

During the denaturation of proteins, the secondary and tertiary structures get

destroyed and only the primary structure is retained. Covalent bonds are broken
and interaction between amino-acid chains gets disrupted. This results in the loss of
biological activity of the proteins.

hat are 3 main causes of protein denaturation?

The process that causes a protein to lose its shape is known as denaturation.
Denaturation is usually caused by external stress on the protein, such as solvents,
inorganic salts, exposure to acids or bases, and by heat.Oct 12, 2021

What are 4 ways to denature a protein?

Denaturation refers to the physical changes that take place in a protein exposed to
abnormal conditions in the environment. Heat, acid, high salt concentrations,
alcohol, and mechanical agitation can cause proteins to denature.

What happens when a protein is denatured example?

Denaturation of proteins occurs when the secondary and tertiary structure of a protein is
altered and the protein is no longer capable of performing its function. Examples of
denaturing that occur in everyday life include cooking eggs and meat, digestion, and
the use of alcohol for disinfection.

What is the process of denaturation?

denaturation, in biology, process modifying the molecular structure of a protein.
Denaturation involves the breaking of many of the weak linkages, or bonds (e.g.,
hydrogen bonds), within a protein molecule that are responsible for the highly ordered
structure of the protein in its natural (native) state. Oct 6, 2022

Denaturation is the major change in protein or nucleic acid structure by application of some external stress for
example, treatment of proteins with strong acids or bases, high concentrations of inorganic salts or organic solvents
(e.g., alcohol or chloroform), heat, which results in improper functioning of cell activity. Denatured proteins can exhibit
a wide range of characteristics, from loss of solubility to communal aggregation. Proteins are very long strands of
amino acids linked together in specific sequences.

Additional recommended knowledge

Daily Sensitivity Test

 
 How to quickly check pipettes?

Daily Visual Balance Check

Contents

 1 Common examples
 2 Protein denaturation
o 2.1 Background
o 2.2 How denaturation occurs at levels of protein structure
2.2.1 Loss of function
2.2.2 Reversibility and irreversibility
 3 Nucleic acid denaturation
 4 See also

Common examples
When food is cooked, some of its proteins become denatured. This is why boiled eggs become hard and cooked
meat becomes firm.

A classic example of denaturing in proteins comes from egg whites, which are largely egg albumins in water. Fresh
from the eggs, egg whites are transparent and liquid. But by cooking they are turned opaque and white, and form an
interconnected solid mass. The same transformation can be effected with a denaturing chemical. Pouring egg whites
into a beaker of acetone will also turn egg whites opaque and solid. The skin which forms on curdled milk is another
common example of denatured protein. And the traditional Peruvian cold appetizer known as ceviche is prepared by
chemically "cooking" raw fish and shellfish in an acidic citrus marinade, without heat.
 Although denaturation can be irreversible, an example of reversible denaturing in proteins is the modern permanent
wave technique for curling or straightening hair.

Protein denaturation
Denatured proteins can exhibit a wide range of characteristics, from loss of solubility to communal aggregation.

Background

Proteins are very long strands of amino acids linked together in specific sequences. A protein is created
by ribosomes that "read" mRNA that is encoded by codons in the gene and assemble the requisite amino acid
combination from the genetic instruction, in a process known as translation. The newly created protein strand then
undergoes posttranslational modification, in which additional atoms or molecules are added, for
example copper, zinc or iron. Once this post-translational modification process has been completed, the protein
begins to fold (spontaneously, and sometimes with enzymatic assistance), curling up on itself so that hydrophobic
elements of the protein are buried deep inside the structure and hydrophilic elements end up on the outside. The final
shape of a protein determines how it interacts with its environment.

When a protein is denatured, the secondary and tertiary structures are altered but the peptide bonds between the
amino acids are left intact. Since the structure of the protein determines its function, the protein can no longer perform
its function once it has been denatured. This is in contrast to intrinsically unstructured proteins, which are unfolded in
their native state, but still functionally active.

How denaturation occurs at levels of protein structure

See also: Protein structure

 In quaternary structure denaturation, protein sub-units are dissociated and/or the spatial arrangement of protein
subunits is disrupted.
 Tertiary structure denaturation involves the disruption of:
 Covalent interactions between amino acid side chains (such as disulfide bridges between cysteine groups)
 Noncovalent dipole-dipole interactions between polar amino acid side chains (and the surrounding solvent)
 Van der Waals (induced dipole) interactions between nonpolar amino acid side chains.
 In secondary structure denaturation, proteins lose all regular repeating patterns such as alpha-helices and beta-
pleated sheets, and adopt a random coil configuration.
 Primary structure, such as the sequence of amino acids held together by covalent peptide bonds, is not disrupted
by denaturation.

Loss of function

Most biological proteins lose their biological function when denatured. For example, enzymes lose their catalytic
activity, because the substrates can no longer bind to the active site, and because amino acid residues involved in
stabilizing substrates' transition states are no longer positioned to be able to do so.

Reversibility and irreversibility

In many proteins (unlike egg whites), denaturation is reversible (the proteins can regain their native state when the
denaturing influence is removed). This was important historically, as it led to the notion that all the information needed
for proteins to assume their native state was encoded in the primary structure of the protein, and hence in
the DNA that codes for the protein.

Nucleic acid denaturation

The denaturation of nucleic acids such as DNA due to high temperatures, is the separation of a double strand into
two single strands, which occurs when the hydrogen bonds between the strands are broken. This may occur
during polymerase chain reaction. Nucleic acid strands realign when "normal" conditions are restored during
annealing. If the conditions are restored too quickly, the nucleic acid strands may realign imperfectly.