In this article we are going to analyze is peptide bond a hydrogen bond or not.
A peptide bond cannot be a Hydrogen bond because a peptide bond formation takes place when two amino acids combine together and form a bond. Based on the number of amino acids coming together or combining peptide bond can be classified as dipeptide bond (combination of 2 amino acids and so on ).
The reason it has trans configuration and not a cis configuration because if it is in cis configuration there will be a steric hindrance or steric interference due to the presence of side chains at the r groups. If all the r groups are present on the same side then there will be a steric hindrance, that is why a peptide bond has a trans configuration and it is uncharged but it is polar, though it is uncharged it has a polarity and this polarity is due to resonance or the delocalization of the electrons.
Why there is a need for us to study hydrogen bond or what is its significance in chemistry, we are going to have a closer approach towards this. We can predict the solubility and boiling point with the help of the concept of hydrogen bonding. So compounds that can form better hydrogen bonding tend to be more soluble in water and have higher boiling point.
Hydrogen bond (has bond energy around 8-42 KJ/mole), is smaller than ionic or covalent bond (having a bond energy greater than 200 KJ/mole) but stronger than Vander Waal force (that has bond energy less than 8KJ/mole).
Consider a covalent bond between A—H having a bond energy of 200 KJ/mole (consider A to be an electronegative atom whose electronegativity is greater or equal to 3. It could be Fluorine, Oxygen and Nitrogen but a special exception in case of organic chemistry it could be Carbon and Chlorine). Atom A being an electronegative atom will attract the electron pair of the covalent bond towards itself. So a (electronegative atom) will develop partial negative charge and H (hydrogen) will develop partial positive charge.
Then consider an atom B having an electron pair (hydrogen has a partial positive charge) , so what B will do is come and bond with the hydrogen of A—H ( which are bonded covalently). So the bond formation between B and H is called hydrogen bonding or hydrogen bonding. B should be an electronegative atom, must have small size and should have a lone pair (Fluorine, Oxygen, Nitrogen and in case of organic chemistry it will be Chlorine).
And the bond energy of the formed hydrogen bond is somewhere between 8-42 KJ/mole (and the bond energy of covalent bond A—H is 200 KJ/mole). So we say covalent bond (A—H ) is a strong bond as compared to hydrogen bond and will have a shorter bond length. H—B being comparatively weaker will have longer bond length.
Most of the time hydrogen bond is weaker then covalent bond wherein bond energy of covalent bond is more then the bond energy of hydrogen bond. But only in one special case bond energy of covalent bond is equal to the bond energy of hydrogen bond i.e. HF2-. The bond energy of both covalent bond and hydrogen bond in HF2- is 200 kJ/mole. But bond energy of covalent bond can never be less than the bond energy of hydrogen bond.
is peptide bond a hydrogen bond
In hydrogen bonding the covalently bonded atom should be electronegative enough. In the above case Fluorine is the most electronegative atom hence will form stronger hydrogen bonding and will have more bond energy or bond strength (F, O, N). We can say bond energy, hydrogen bond strength are directly proportional to the electronegativity of the covalently bonded atom in the hydrogen bonding.
In the above example how can we identify which one will have or form stronger hydrogen bonding? The concept followed here is hydrogen bond strength is inversely proportional to the electronegativity of the atom bonded to hydrogen in the hydrogen bonding process. We know oxygen is more electronegative then Nitrogen, so that means if hydrogen bond strength is inversely proportional to the atom bonded to hydrogen atom (should have less electronegativity), so Nitrogen has less electronegativity and the answer which is appropriate is O–H—N.
The above hydrogen bonding is with homo-molecules meaning with same kind of molecule.
R—O—H (alcohol) and H—O—H (water)
Here hydrogen bonding is within hetero-molecules as two different molecules are involved.
Let’s study the molecule of H3BO3 (Boric acid)
It exists as a dimer ( H3BO3) ,the reason is due to the intermolecular hydrogen bonding between the molecule.
(Chelation-It is the formation of ring)
Intramolecular Hydrogen bonding
In this type of hydrogen bonding the bond will be formed within the same molecule or single molecule.
Consider O-nitrophenol
This is an example of Intramolecular Hydrogen bonding.
Some properties of hydrogen bonding:
Referring to the solubility concept, when alcohol (basically the lower ones) can be soluble in water due to the presence of hydrogen bonding between alcohol (R—O—H) and water (H—O—H) molecule.
Taking into account the volatility of compounds having hydrogen bonding, they have quite high boiling point and hence they are not very less volatile.
When compounds have hydrogen bonding what happens is they occur in association with molecules, so the flow is quite difficult hence they possess quite high surface tension and viscosity.
Peptide bond v/s hydrogen bond
This two types of bond are quite different in nature.
In the section followed we are going to analyze peptide bond and hydrogen bond based on formation of bond, strength and where they are usually found.
Factors
Peptide bond
Hydrogen bond
Formation of bond
A peptide bond is formed when two amino acids combine together and form a bond.
A hydrogen bond is formed when hydrogen atom covalently bonded with another atom also forms a bond with one more electronegative atom (F, O ad N).
StrengthA peptide bond is much more stronger and cannot be easily broken.
A hydrogen bond is much more weaker.
Found in
Peptide bond can be found between amino acids and also in fish, meat , wheat etc.
Hydrogen bond is found in many molecules such as water, ammonia, etc.
Hydrogen Bonds are very important to proteins as they provide stability and rigidity to the proteins. In secondary structure of proteins hydrogen bond is present between the amino acid.
We can see that the hydrogen bond is formed between the hydrogen atom of amino group of one amino acid and with the electronegative atom (oxygen) of the amino group of the one more amino acid. The twisting of linear chain (of the amino acid) to form alpha helical (referred basically as form ) is the result of the phenomenon of hydrogen bonding. So we can say in proteins hydrogen bonding has mostly has got a structural role to play.
Peptides have biological function in the human body and needed for various activities. Here we are going to discuss all possible prospects of peptide bond formation.
Protein is a life-sustainable complex. There is no other compound in the body that contains as much nitrogen as is present in the protein. Generally, a protein compound is composed of H, O, N, C, and S. The word protein is the greek word PROTAS which means Digested.
Proteins were first described by the Dutch chemist Gerardus Johannes Mulder. This article will give a brief about peptide bond formation. The peptide bond has got another name called the Isopeptide bond.
The percentage of protein present in healthy adult males is 14%. The protein is present in Muscle Tissue, Teeth and Bones. Generally, the peptide bonds are formed in the ribosomes in the cell due to protein synthesis.
The formation of peptide bond is one of the important process in cell .There are 100s of peptides in body with different functions.
Peptides are short chains of different amino acids. The bonds between them are known as a peptide bonds. The Peptide bond is also known as Amide bond.
Peptide Bond has two functional groups- 1) Carboxylic group 2) Amino group. Peptides are present in every cell and have a significant role in the Human Body. The amide link is called Peptide. Amino Acids are linked together based on a sequence encoded in DNA. No two proteins are identical in terms of structure and function. Even if the amino acids are present in different proteins, the sequence of amino acids in Polypeptide differs; this makes protein chemically diverse.
What catalyzes Peptide bond formation?
The formation of the peptide bond is catalyzed by peptidyl transferase, it is an RNA- based enzyme.
The proteins are synthesized in ribosomes of the cells. The peptide bond formation is is in between amino acids of P site and A site of a ribosome. When one amino acid combines the carboxyl group of another amino acid, a peptide bond is formed. Proteins should be taken in one’s diet as the protein food helps in solid muscle building and sharp eyesight.
Where does peptide bond formation occur?
The well known answer for synthesis of protein in cell is Ribosome. Hence peptide bond formation also occurs in Ribosomes.
The word Ribosome is also known as Protein factories. These are the main sites of protein synthesis. With the help of the enzyme peptidyl transferase the peptide bond formation is catalyzed. The process of two bringing TRNAs nearby will result in formation of peptide bond with the help of RNA.( also known as Ribozyme)
Peptide bond formation steps:
A peptide bond bonds together in between two amino acids through dehydration.
Degradation of protein into smaller fragments by following steps-
Liberation of Polypeptides
The proteins need to be hydrolyzed into polypeptide units by the presence of Urea/Guanidine HCl
Number of polypeptides
Dansyl Chloride is added to the protein, it specifically binds to n-terminal amino acids to form dansyl peptide.
Breakdown of the polypeptide into fragments-
polypeptides are degraded into smaller dipeptides by two methods-
Chemical Cleavage
This type of cleavage helps in the formation of peptides on hydrolysis like- Cyanogen Bromide(CNBr).
Enzymatic Cleavage
This method is commonly used to hydrolyze the peptide bond containing Lysin or Arginine. Trypsin, Chymotrypsin, pepsin, cleaves the peptide bond.
Types Of Peptides:
There are three different peptides:-
Oligopeptides
The compound formed from less than and equal to 10 amino acids is called Oligopeptide. Example- Ceruletide.
Polypeptides
Polypeptide compound formed from more than ten amino acids. Some examples are Insulin and growth hormones. A single long chain of a polypeptide is called simple protein.
Dipeptides
Two amino acids bonded together is called a dipeptide. For example- artificial sweetener consists of two amino acids, namely aspartic acid and phenylalanine.
Tripeptides– Examples- Glutathione.
It acts as an antioxidant and is necessary for DNA and protein synthesis cell proliferation.
Polypeptide– Ex- Insulin
Oligopeptides and polypeptides are joined by linkages like disulfide linkage build peptide bonds.
Different classes of Peptides-
Milk Protein: Milk proteins act as an enzyme, and it is necessary for the breakdown of digestive enzymes (Cassin). The enzyme that breaks the proteins is called Proteinase.
Peptones: These are derived from animal milk by proteolytic digestion. Peptones are essential for nutrient media preparation. There are some types of peptides like Glutathione, Nisin, Lysine. Ex- Beef, Broccoli, Spinach, Chicken, Potatoes, Tomatoes, Oranges are rich in glutathione. Several strains of streptococcus lactis form nisin.
Characteristics Of Peptide Bonds-
Structure Of Peptide-
CO-NH bond is called a peptide bond. It is a covalent bond. The Peptide is a three-dimensional structure. U.V. absorption bands and I.R. gives Functionality (Functional Groups). The primary purpose of the I.R. linkage is to identify Amide Linkage.
FISCHER AND HOFL MEISTER– They suggested that amino acids in proteins are joined by linear fashion by a peptide linkage. I.R. spectra of the Peptide have shown that bands near 3300 -3100 cm inverse are the characteristic N.H. stretching (N-H) of secondary amines.
U.V.: Spectra of peptides -Proteins show absorption in the 180-200nm region.
X-RAY diffraction studies: It reveals the bond length and bond angles likewise.
The Peptide structure is to be found first hydrolyzed to its constituent amino acids, separated, and identified. Ex- When glycine and Alanine link together, they release water. It need not be the same in all amino acids, and it can be different too. The next step is significant for determining the sequence of various amino acids constituting the Polypeptide.
Biologically Important Peptides-
Some biologically important peptides are –
Neuropeptides act as critical messengers in Neurosecretory cells like Oxytocin, Vasopressin.
1) OXYTOCIN– Oxytocin is also known as Love Drug. It is a non-peptide and contains nine alpha-amino acids. This hormone is needed chiefly in Women. Oxytocin is a peptide, and it is generated in the brain. Oxytocin plays an essential role in Reproduction. Oxytocin stimulates uterine contraction before delivery.
2) VASOPRESSIN– It is also a Nano peptide and contains nine alpha-amino acids. This is secreted from the Pituitary gland, and helps the kidney to retain water from Urine.
4) Gastrointestinal Tract peptides– GASTRIN-(10 amino acids)- It helps in the secretion of Hydrochloric acid in the stomach.
5) GLUCAGON– (10 amino acids)- Pancreatic hormone involved in glucose metabolism. It increases blood pressure and antidiuretic hormone; Sensory pathways mediate vasopressin release. Vasopressin synthesized the hypothalamus and is produced in the posterior pituitary gland. Both men and women produce vasopressin.
The peptide bond is formed when the carboxylic group of one molecule reacts with the amino group of the other molecule. The reaction is continued by Hydrolysis, which removes water, and a peptide bond is formed. The release in water will form an amide bond and is essential for removing toxins. Peptide bond formation is the essential step for formation. This type of reaction is known as a condensation reaction.
The condensation of the acidic and primary groups by eliminating water is called peptide linkage. Peptide linkage has a planar configuration. The peptide formation requires a lot of energy that is an endergonic reaction. A variety of peptides are derived from foods during digestion. They act on Growth factors, Hormone, Antimicrobial Agents and Antioxidants.
There are wide ranges of proteins in the world. They are simple proteins, globular proteins, and conjugated proteins. They exist because of the initial formation of the peptide bond.
The peptide bond formation is spontaneous, but the process is slow, forming and breaking peptide bonds. In nature, there are three hundred amino acids.Among them, only 20 amino acids are used by the proteins. The amino acids bond is a solid covalent bond known as an amide bond. As amino acids are added, the generated bond is a polypeptide. Sangar’s test determines the N-Terminal.
There are wide ranges of proteins in the world. They are simple proteins, globular proteins, and conjugated proteins. They exist because of the initial formation of the peptide bond. The ribosome catalyzes the peptide bond formation because it is the unit for protein synthesis. The peptide bonds can even be denatured or degraded. The method used for degradation is Hydrolysis.
In Hydrolysis, the Polypeptide is broken into small fragments. The protein degradation is prolonged and possible by some enzymes like peptidases. The peptide bond formation is present in all proteins and helps bind amino acids into chains. A Biuret test is one of the necessary tests for identifying a peptide bond.
Ester is a very common functional group, that takes part in variety of organic reactions. The term “ester” was first introduced by a German chemist, Leopold Gmelin, in the first half of 19th century.
Ester is basically a chemical compound derived from parent acid and parent alcohol. In general, an ester bond contains one carbon atom doubly bonded to one oxygen atom and singly bonded to another oxygen molecule, further connected with alkyl or aryl group. Ester is denoted as R-COOR1.
In this article, “ester bond structure” formation, structure with some other detailed facts and some frequently asked questions about ester bond are described briefly.
Ester Bond Formation
Formation of an ester bond is generally a condensation reaction (elimination of water molecule).
Ester bond formation reaction proceed with a parent acid and a parent alcohol as reactant. Acid catalyst must be present to accelerate the forward reaction. Concentrated sulphuric acid (H2SO4) is used as acid catalyst but dry hydrogen chloride in gaseous state may be used in some cases. This method is called Esterification Reaction.
RCOOH+ R1OH ⇌ RCOOR1 + H2O
Alcohols are converted to its corresponding esters in the above reaction. But this esterification reaction is not applicable for that OH group directly attached to the benzene group that is phenol group. Phenols are comparatively more acidic than the alkyl or allyl alcohol. Due to the greater acidity, it reacts with carboxylic acid very slowly and the reaction becomes unstable for the purpose of preparing.
This reaction of forming ester is reversible and relatively slow process because the newly formed ester and water can react to form the corresponding alcohol and acid.
In the esterification reaction, the reactivity of carboxylic acid is enhanced by the presence of acid catalyst which protonates the oxygen doubly bonded with carbon (carbonyl carbon).
Mechanism of Esterification Reaction
Mechanism of esterification is described below-
1.Formation of Cation:
Parent carboxylic acid takes up a proton from the acid catalyst.
2.Nucleophilic attack:
The parent alcohol acts as a nucleophile and attacks the carbon center of acid combined carboxylic acid.
3.Proton Transfer:
Proton (H+) is transferred from the hydroxyl group of acid to the hydroxyl group of alcohol and a good leaving group (OH2) is formed
4. Pi bond formation:
The lone pair of the oxygen comes from the hydroxyl group is donated to make a pi bond with the carbon. Then the good leaving group is eliminated as water molecule (H2O) from the intermediate formed by the combination of carboxylic acid, acid catalyst and alcohol. As a result ester linkage is formed.
Ester bond is generally a covalent bond and very much essential in formation of variety of lipids. In lipid, condensation reaction to form an ester takes place between glycerol and a fatty acid. In phospholipids, one fatty acid present in the triglyceride is substituted by a group containing phosphate (PO43-).
Esters can form hydrogen bonds with their oxygen atom (donor atom) with the hydrogen atom (acceptor atom) of water molecule. Esters are weak electrophilic due to its carbonyl centre. Thus it can participate in nucleophilic substitution or any other nucleophilic chemical reaction. Due to the electrophilic character of carbonyl carbon, the C-H bond adjacent to the carbonyl centre is mild acidic in nature, (pka=25) but it undergoes deprotonation reaction in presence of strong base like NaOH, KOH etc.
Ester linkages have one carbonyl center. It gives rise to bond angle almost 1200 and attain a planar structure and sp2 hybridization. Esters are not structurally rigid group of molecules like amide linkage. Esters are preferred to attain s-cis conformation rather than E or s-trans conformation due to dipole -dipole interaction and hyperconjugation effect.
In ester the bond rotation about C-O-C bond is allowed as this bond possesses low energy barrier.Due to less rigidity, melting point of ester is generally low and volatility is high with comparing to alcohols and ethers having similar molecular weight. Polarity of esters is greater than ethers but lesser than alcohols.
Identification of esters can be done through gas chromatography due to its volatile nature. Vibrational frequency (wave number) of C=O bond (νc=o) is almost 1730-1750 cm-1. This frequency can be changed due to the changing of functional groups attached to it. For example, presence of any group having conjugation with the carbonyl carbon may decrease the wave number almost 30 cm-1.
Though carboxylic acids have some unpleasant bad smell esters have a characteristic pleasant fruity smell. For this smell, esters are used as fragrances in essential oils, perfumes. Esters perform as for a broad array of plastics, resins, plasticizers etc. and one of the well known synthetic lubricants in the commercial market. Polymer of esters that is polyesters are important plastics. Phosphodiester linkage is the back bone of DNA molecule.
The hydrolysis of ester bond takes place in presence of strong bases like Potassium hydroxide (KOH) is called saponification reaction. This reaction is an important formation procedure of soaps, fats and oils etc.
Answer: Esters are mainly neutral compound. In chemical reaction like hydrolysis, “splitting with water” the alkoxide group (OR1) is substituted by another group.
Are esters polar molecule?
Answer: Yes, esters are polar molecule. But their boiling and melting points are lesser than the corresponding carboxylic acids and alcohols.
What can break an ester bond?
Answer: Hydrolysis with a strong base can break ester bond. In hydrolysis, hydroxide ion (OH–), the nucleophile, attacks the carbonyl carbon center and ester bond is cleaved.
Is ester soluble in water?
Answer: Due to the hydrogen bonding with water molecules, esters having low molecular weight are soluble in water, but the solubility is not so high.
Disulfide bond plays a very much important role to form the secondary structure of protein. It is basically a covalent type bond.
Disulfide bond is formed by the oxidation of sulfyhydryl or thiol group (S-H group), present only in Cysteine amino acid (non essential amino acid). It is also known as S-S bond . Disulfide bond is denoted by R-S-S-R1. In which “R” is the amino acid residue.
In this article “disulfide bond structure” basically the type and formation with other detailed facts are explained briefly.
Disulfide Bond Structure And Formation
This chemical bond present in the protein structure.
It is one type of covalent linkage formed between two thiol groups (SH group) present mainly in Cysteine residue. One S-1 coming from one sulfyhydryl group acts as a nucleophile (electron rich) and it attacks another cysteine residue to form the disulfide bond.
The formation reaction of a disulfide bond is-
R-SH + R1-SH + (1/2) O2 ⇌ R-S-S-R1 + H2O
[R denotes the chain residue of a peptide].
This bond forming Cysteine chain residue may come from the same protein or from distinct that is two different protein.
Formation of disulfide bond leads to two electron transfer from the reduced S-H group to oxidized S-S group.
Like the peptide bond, disulfide bond plays an important role to stabilize the tertiary structure of protein. Disulfide bond is generally a covalent linkage formed between two sulfyhydryl group and stronger than similar covalent linkage.
This bond is consisting of two parts. One is polar part or hydrophilic part that is oriented towards the outer surface of the protein and helps to participate in various reaction and attract the solvate molecules.
Another part is non polar part or hydrophobic part oriented mostly towards the inner surface of the protein. This characteristic orientation of non polar part towards the inner surface has a physical significance. It takes part in the bond formation with different amino acid.
Disulfide bonds have their bond dissociation energy approximately 50 Kcal/mol and the S-S bond distance is nearly about 200pm. From this data it can be concluded that disulfide bond is relatively strong and short range bond also.
One of the most important function of disulfide bond is to determine the secondary and tertiary structure of protein.
The main function of disulfide bond is that it provides the extra stabilization to the 3D structure of protein molecule (during protein synthesis). Thus it is called as the building block of tertiary protein structure (Peptide bonds stabilize the primary structure of protein).
It also helps in the folding of the single polypeptide chain or inter protein.
Protein gains this extra stability as the entropy of the denatured state of protein is diminished through formation of the disulfide bond.
In living organisms variety of biological and physiological process is governed by disulfide bond. Thirodoxin, an enzyme that accelerated the electron transfer process from reduced S-H group to oxidized S-S group. In most of the cases disulfide bond is formed in intramolecular way but in some of the special cases intermolecular disulfide bond can also be formed.
Cleavage of disulfide bond can cause a lot of negative impact in a living body as the important biological process will be collapsed and conformation of many important structure will be disrupted and as a result cell growth can be affected.
Breaking of a disulfide bond is not an easy task due to its strong covalent linkage.
Disulfide bond can be cleaved by adding reducing agent. Among them the most common reducing agent used are β- mercaptoethanol or BME and dithiothritol or DTT.
The cleavage reaction of disulfide bond can be accelerated by adding some enzyme, Thioredoxin (TRX) and Glutaredoxin(GRX). These enzymes help to protect the newly incorporated Cysteine residue.
Disulfide bond cannot be broken by applying heat because heat can only break the weak linkages present in the protein structure like the hydrogen bond or nonpolar hydrophobic interactions at its melting temperature (Tm) . The main reason of not breaking the disulfide bond that disulfide bond is much more stronger bond than a hydrogen bond( bond dissociation energy of a hydrogen bond and a disulfide bond is 2.8-7.2 kcal/mol and 60 kcal/mol respectively).
Disulfide bond cannot also cleaved by normal hydrolysis (by reacting with water). The cleavage occurs basically at higher pH (alkaline pH). If only alkaline solution is reacted with disulfide bond, then hydroxyl ion (OH-1) attacks the disulfide bond and as a result a new bond is formed with one of the sulfur atoms. In this way disulfide bond is split.
Some frequently asked questions about disulfide bond are answered below.
Frequently Asked Questions (FAQ)
Do disulfide bonds form spontaneously?
Answer: Disulfide bond can be formed spontaneously in presence of molecular oxygen (O2).
Are disulfide bonds polar?
Answer:The polarity of disulfide bond is not so large. It has less polarity with comparing to two Cysteine residues.
Which peptides can form disulfide bond?
Answer:The amino acids having no sulfyhydryl group (SH group) cannot participate in disulfide bond formation. Thus Cysteine is the only amino acid can form disulfide bond.
Disulfide bond is mainly a covalent linkage between the side chain residues in same protein or may be different protein.
In addition of peptide bond Disulfide bond is a different type of covalent bond, is present in protein molecule. This bond is formed due to oxidation of the sulfyhydryl or thiol group (SH group) come from Cysteine (non essential amino acid) residue. Disulfide bond expressed as R-S-S-R1 and also known as S-S bond.
In this article ” what is a disulfide bond “different facts of Disulfide bond, such as formation procedure, types and functions of disulfide bond are described briefly.
How Disulfide Bonds are Formed?
The formation procedure of disulfide bond is described in this point.
Disulfide linkage is one type of covalent linkage in which two thiol groups (SH group) generated from two Cysteine residue is involved in this bond formation. S– anion coming from one Cysteine acts as a nucleophile and it attacks the other Cysteine side chain residue to from the disulfide bond.
The reaction of formation a disulfide bond is-
R-SH + R1-SH + (1/2) O2 ⇌ R-S-S-R1 + H2O
The formation of disulfide bond involves two electron transfer and this transfer takes place from the reduced sulfyhydryl group (S-H) of Cysteine residue to the Cystine (S-S) the oxidized form.
Disulfide bond is a chemical covalent bond present in the tertiary structure of protein. It is one of the important type of linkage like peptide linkage, hydrogen bonding salt bridge interaction present in protein.
Disulfide Bond In Protein
With the peptide bond, Disulfide linkage is also an very essential bond in peptides or proteins. It is stronger bond than the other bonds contribute in the tertiary structure of protein.
Disulfide bond is present in almost all types of extracellular protein (used in cell structure systems). This linkage is one of the integral component of secondary and tertiary structure of protein (peptide bond is the building block of primary structure).
The disulfide bond usually consist of two parts, one is polar part or hydrophilic part and another is non polar part or hydrophobic part. Among these two part, the hydrophobic part is oriented towards the inner surface of protein, whereas the hydrophilic part is directed towards the outer surface of the bond. This orientation of polar or hydrophilic part helps to form the linkage between two amino acid residue.
The average bond dissociation energy of disulfide bond is approximately 50 kcal/mol and S-S bond length is nearly 2 angstorm. Disulfide linkage is very much strong and very short range bond.
The main activity of disulfide bond is to provide stabilization to the 3D structure of protein and exhibit physiologically appropriate redox procedure. Disulfide bond is an essential part in protein folding and stability. The tertiary structure of protein get stabilization by disulfide interaction.
The disulfide linkage governs the basic biological process in a living organism. The electron transfer process ( two electrons are transferred from Cysteine to Cystine) is accelerated by enzymes, Thirodoxin. Maximum disulfide is formed intramolecular, in some special cases this bond can be formed between two vicinal Cysteine residues and leads the only natural covalent linkage in the polypeptide formation.
Cleavage of disulfide bond in protein can cause the collapse of the conformation of various biological process and failure of formation of disulfide bond properly may be the reason of severe disorders as the protein molecules form aggregates and results the cell death.
Disulfide bond can be broken by oxidation – reduction process and by adding oxidizing and reducing agent. The most widely used reducing agents to prevent the oxidation is the disulfide bond is β- mercaptoethanol known as BME and dithiothritol (DTT).
The oxidation reduction procedure in protein is proceed through in vitro path and it is an exchange reaction between thiol to disulfide. Disulfide bond is generally formed by the oxidation of thiol group (SH) present in
Disulfide bonds are readily oxidized by a various type of oxidants and the rate constants are quite high (105-107 M-1 S-1). The intermediate which is formed in the reaction medium is thiosulfinates [RSS(=O)R.]. This intermediate undergoes further oxidation and at the end of the oxidation, cleavage of disulfide bond is occurred.
Can Disulfide Bond Be Broken By Heat
Disulfide bond can not be broken by applying heat energy. Heat mainly denatures the protein ( proteins become unfolded from folded structure).
The breaking of disulfide bond is basically an irreversible process. Breaking of disulfide bond causes the denaturation of protein at melting temperature (in which protein denatures). This is proceed through disulfide- thiol exchange reaction.
In presence of MTS (methanethiosulphonate) the heat induced exchange reaction from disulfide to thiol is hindered and heat resistance power of protein is improved.
Heat energy disrupts the hydrogen bond and the non polar hydrophobic interactions in protein. Applying heat increases the internal energy as well as kinetic energy within the molecules . Thus molecules start vibrating rapidly and the weak bonds present in the group of molecule is broken.
Disulfide bond is formed by the hydrophobic and hydrophilic interaction. Due to absorbing heat hydrogen bonding and hydrophobic interactions become disrupted and as a result breakage of hydrogen bond occurs.
The bond dissociation energy of hydrogen bond is approximately 12-30 kilojoule / mol and for disulfide bond it is almost 251 KJ/mol. Thus cleavage of disulfide bond does not occur by applying normal heat energy.
Globular proteins basically exist in the equilibrium condition between folded and unfolded states. Under normal condition folded state is mostly favored. Applying heat energy nearly equals to melting temperature (Tm) , the protein is started unfolding, that is denaturation of protein is occurring.
Very precisely it can be predicted that disulfide bond can not be broken by water.
Disulfide bonds are very much strong chemical covalent bond and its bond dissociation energy is also quite high with comparing to other similar covalent bonds. It gives stabilization to the tertiary structure of protein. It is not possible to break a disulfide bond by adding water.
If any alkaline aqueous solution takes part in the reaction with disulfide bond, the hydroxide ions (OH–) attacks the disulfide bond and will form a new bond with one of the sulfur atom from the two sulfur atoms formed disulfide bond. As a result disulfide bond will be cleaved.
The above reaction is known as alkaline hydrolysis of disulfide bond.
Frequently Asked Questions (FAQ)
Some frequently asked questions about the disulfide linkage are answered below.
How formation of disulfide bond can be prevented?
Answer: pH of the sample should be low (at or below pH 3-4). At low pH the thiol groups (SH) are protonated and cannot take part in the bond formation reaction.
How disulfide bonds affect protein stability?
Answer: Disulfide bonds reduce the entropy in the protein molecule in its denatured state.
Do disulfide bonds form spontaneously?
Answer: Yes, disulfide bonds can be formed in a spontaneous process by molecular oxygen.
A peptide bond formation takes place when two amino acids combine together and form a bond, so basically, it is the linking of amino acids.
Based on the number of amino acids coming together or combining peptide bond can be classified as dipeptide bond (two amino acids combine to form a peptide bond), tripeptide (three amino acids come together to form a peptide bond). When many amino acids come together and form bond they are called as polypeptides.
Oligopeptides are the short peptides which consist of less than 10 amino acids. Important point to be noted that the dipeptide should not be confused with number of bonds (‘di’ over here does not mean number of bonds, it simply refers to the number of amino acids combining). As we know that amino acids are the monomers to form a protein and they are considered to be the building blocks of proteins (very essential for protein formation).
There are 20 very important amino acids which form bonds together in various different kinds of combinations to form many different proteins. Namely- alanine (ala), arginine (arg), asparagine (asn), aspartic (asp), cystein (cys), glutamine (gln), glutamic acid (glu), glycine (gly), histidine (his), isoleucine (ile), leucine (leu), lysine (lys), methionine (met), phenylalanine (phe), proline (pro), serine (ser), thereonine (thr), tryptophan (trp), tyrosine (tyr), and valine (val).
The scientists who proposed that amino acids combine together and form peptide bond were Hofmeister and Emile Fischer. The bond formation between two amino acids (peptide bond), or two amino acids join to form peptide bond by dehydration, meaning there is loss of water molecule. Hence it is a condensation reaction.
The steps involved in peptide bond formation are discussed in the section below in detail .
First dehydration (loss of H2O molecule) will take place and then the amino acids will combine. Let us see how this happens. Consider the example of combination of glycine and alanine (amino acids). The N atoms of ammonia (alanine) has partial positive charge. We can also say alpha carbonyl group of glycine and alpha amino group of alanine.
So nitrogen will act as nucleophile and carbon will act as electrophile. Nitrogen will donate its low pair which will result a bond formation between nitrogen and carbon.
The OH and H attached to carbon and nitrogen respectively will be eliminated out as water (H2O) molecule. The linkage between carbon and nitrogen is known as Amide linkage/bond (wherein amino acids combine together). This special type/kind of bond is called peptide bond.
One end free amino group is known as amino terminus or N terminus and other terminal end free carboxylic group is known as carboxy terminus or C terminus. Each amino acid of the polypeptide/dipeptide formed is referred to as residue.
Characteristics of peptide bond
Double bond character of peptide.
It was deduced by linus Pauling and the other co-workers. Consider the figure, you can notice that in a) the first structure. The carbon nitrogen linkage is a double bond where nitrogen has an unshared pair of electrons and carbon-oxygen has a double bond. Now, coming in to b) the second structure, carbon-oxygen is single bond and carbon-nitrogen is a double bond. So, which one will be correct among the structures?
Is carbon nitrogen a single bond or a double bond? The bond length observed for carbon nitrogen single bond is 1.47A and bond length for carbon nitrogen double bond is 1.27 A. But the actual carbon nitrogen bond length in a peptide chain is supposed to be 1.32 A.
So the peptide bond is neither a single bond nor a double bond, the reason for this is because of resonance characteristics or the resonance property of carbon-nitrogen bond that makes it a special bond with 1.32 A and this is restrict rotation because it has a partial double bond character. Hence, it’s neither a single bond nor a double bond, because of this partial double bond character this restrict rotation of the carbon nitrogen bond and thus plays a role in the three dimensional structure of a protein molecule.
A peptide bond due to its partial double bond character is rigid and hence this prevents a free rotation around the carbon nitrogen bond and a peptide bond is planar in nature because all the six atoms that are involved in the peptide bond (starting from C 1 to C 2 they all lie in same plane). Hence a peptide bond is planar. (As all the six atoms lie in the same plane).
The reason it has trans configuration and not a cis configuration because if it is in cis configuration there will be a steric hindrance or steric interference due to the presence of side chains at the r groups. If all the r groups are present on the same side then there will be a steric hindrance, that is why a peptide bond has a trans configuration and it is uncharged but it is polar, though it is uncharged it has a polarity and this polarity is due to resonance or the delocalization of the electrons.
The peptide bond formation mechanism is quite simple one. There are many methods but the one which is convenient is used commonly .
We can see that nitrogen is having a lone pair so it act as a nucleophile in the reaction and carbon of other amino acids acts as an electrophile.
Nitrogen will donate its lone pair (meaning there will be an attack of nucleophile on the electrophile). This leads to a bond formation between atom of one amino acid and N atom of other amino acid.
In this process OH which is attached to carbon and H that is attached to the nitrogen atom are eliminated out as H2O molecule. This is a dehydration/elimination step.
There are many methods but here we shall discuss about the solid phase peptide synthesis method and its mechanism. In short it is known as SPPS and was discovered by Robert Bruce Merrifield (in the year 1962). He prepared/synthesized peptide by taking/using polystyrene solid beads as a support.
So SPPS is one of the repeated cycles of N-Terminal deprotection and coupling reaction. In which deprotection, protection and coupling reaction is carried out. In a simplified way we can say amino acid and resin support is taken, so the amino acid will attach to resin support. Protection of NH2 group has to be carried out, where in protection group is attached to N atom. Then you have to couple with another amino acid. Like this many more amino acids are added which will form a chain of amino acids (cycle is repeated again and again).
After this the attached protected group is removed. After synthesis crude peptide is cleaned from solid support. Solid support is a special type of polystyrene in which there are some aromatic rings that have chloromethyl groups. This polymer is known as Merrifield Resin that is formed by copolymerization of styrene with p-Chloro methyl styrene.
STEP 1:Protection of amino acid using protecting groups.
STEP 5:BOC protecting group is removed as in step 3
NOTE: Step 4 and 5 are repeated to add many amino acids and long peptide chain is formed.
STEP 6: Completed polypeptide is removed from polymer with HF anhydrous addition.
What catalyzes peptide bond formation?
The enzyme that catalyzes peptide bond formation (during the process of synthesis of protein is peptidyl transferase. Peptidyl transferase (aminoacyltransferase) which is responsible in formation of peptide bonds (between the adjacent amino acids) by making use of tRNA. (During the time of process of translation of biosynthesis of proteins).
We know that peptide bond requires a catalyzing enzyme for the reaction to progress .
Peptide bond formation is a hydrolysis reaction.
A hydrous reaction is referred to a chemical reaction where a water molecule breaks chemical bonds (one or more). Most of the times water will act as nucleophile.
A peptide bond formation is not a hydrolysis reaction but a dehydration reaction where during the process of 2 amino acids combining a water molecule is lost/eliminated. Hence dehydration process takes place. It is a condensation reaction of amino acids (one amino acid is of alpha-amino group of the next amino acid.
So generally in a dehydration reaction what happens is one hydroxyl group and one hydrogen atom of other group combine together and form a water molecule and is eliminated. So in the peptide bond formation similar reaction happens. Hence it is dehydration reaction and not a hydrolysis reaction.
Peptide bond formation in amino acids.
Amino acids may be classified based on functional groups (core structural) like alpha, beta, gamma, and delta. Based on their polarities, levels of pH. The types of side chain groups (aliphatic, hydrophobic, aromatic, presence of sores etc.)
The forward reaction is seen to be dehydrolysis reaction as it is thermodynamically unfavorable. This means that to form a peptide bond, there is a need to input energy. Amino acids come together to form peptide bond. Nucleophile attacks on electrophile (N on C) and a bond is formed. Hydroxy group of carbon and hydrogen of N combines and is eliminated as water.
It can be said that peptide bond formation is not a spontaneous process, why not let’s check out.
The formation of peptide bond at a temperature of 25 degrees Celsius in not favorable because of higher enthalpy change (around 1.5 kcal/mol). The reason for this value is as the ionization of free acid and the amine groups takes place at neutral pH. We know that transfer of proton from an acid to the base involves large amount of negative enthalpy change, reversing it to neutralize both will have positive enthalpy change.
As the products are neutral, getting back the energy is not possible. The bond energies (neutral carboxylic acid, amine) are observed to be not that different from water and an amide, hence we can clearly see there is domination of neutralization.
So amide can be formed at a temperature of 60 degrees Celsius as required change of enthalpy can overcome enthalpy change (at that particular temperature).
Where does peptide bond formation occur?
Peptide bond formation is seen to occur in organelle of cell called as ribosome and rRna. It is a chemical bond which occurs between 2 molecules (amino acids).
So, any of the amino acids can come together to form peptide bond and then they form proteins which are very important to us.
We know that almost all our cells in the body are made up of proteins and hence amino acids/peptide bond play a very important role.
Nitrogen atom from the amine group of one amino acid forms the peptide linkage with the carbon atom of carboxylic acid group coming from another amino acid.
Cysteine, having a -SH group in its side chain participates in the disulfide bond formation.
Formation Reaction
Peptide bonds are formed through condensation reaction.
Disulfide Bonds are formed through oxidative folding process.
The formation of disulfide linkage involves a reaction between the thiol groups come from two cysteine residue, in which S– anion can act as nucleophile and attacks the side chain of another cysteine residue to form the disulfide linkage.
Definition of Disulfide Linkage And Peptide Linkage
Disulfide bonds are formed between the side chain sulfhydryl (SH) groups of cysteine residues through the oxidative folding process. This sulfide linkage is key component of secondary and tertiary structure of protein molecules. This is basically a chemical covalent bond, plays an important role in the heat induced gelation of globular proteins. Disulfide linkage (S-S linkage) helps to bind two peptide chain or different parts of any other peptide chain and becomes the structural determinant of protein.
Peptide bond is a chemical covalent bond which is also known as amide (CONH2) linkage present in protein primary structure. This bond is formed by linking two consecutive alpha (α)aminoacid. In this peptide bond formation, amine group (NH2) from one alpha amino acid reacts with the carboxylic acid group (COOH) of another alpha amino acid through the condensation process (elimination of one water molecule).
These disulfide linkages are found in almost all types of extracellular peptides or proteins and it is an integral component of the tertiary structure of protein.
In protein disulphide bridges , that are formed by the coupling of two thiol groups (SH groups) are the backbone of secondary and tertiary structure of protein. This linkage is expressed as “R-S-S-R1”,also familiar as S-S bond.
This linkage usually consist of polar or hydrophilic part and non polar or hydrophilic part. The hydrophilic side chains are often oriented towards the surface, while the non polar or hydrophilic part are mostly pushed inside the protein structure. With the polar groups, accessible on the surface, the proteins are able to link with the other protein or non protein molecules.
Thus disulfide linkage stabilizes the 3D structure of protein and exhibit physiologically appropriate redox activity. This linkages also help to decrease entropic choices that facilitate folding progression towards the improperly folded configuration.
This bond can govern the basic biological processes in living organisms. The formation of the disulfide bondby the linking between the two side chain consisting S atomsleads to twoelectron transfer process from a reduced sulfyhydryl groups of cysteins (S-H) to the oxidized cystine group (S-S).
The above reaction is often accelerated by enzyme catalyst, thioredoxin or protein disulfide isomerases.
Disulfide linkages are basically formed intramolecular, but in some cases it may be formed between two visinal cysteines.
The peptides having no sulfyhydryl groups (SH groups) can not participate in the disulfide bond formation.
There are almost 500 amino acids known to the scientists. Among them only twenty amino acids are there which are the building component of any living organisms. In peptide bond formation almost all these twenty amino acids can participate ,but they all can not take part in disulfide bond formation.
The amino acids only having thiol or sulfuhydryl groups can form the disulfide linkage. In this group cysteine is the only amino acid (non essestial amino acid) which has the capability of this bond formation.
Cysteine is slightly different from the other known amino acids due to its reactive SH group. Thus two cysteine residue can form the disulfide linkage between different parts of the same protein molecules through their oxidisable thiol groups . Even the residues can form this linkage between two separate polypeptide chains also.
Cysteine is very important for collagen and main protein for skin, nails and hair. Cysteine can be mostly found in extracellular domains of membrane proteins and in secretary proteins also.
There is another sulfur containing amino acid , Methionine, can not participate in disulfide linkage formation due to absence of thiol groups .It has methyl group (CH3) attached with sulfur. This attachment makes methionine more hydrophobic, sterically hindered and much less reactive with comparing to cysteine.
The advantage of cysteine over other sulfur containing amino acid in formation of disulfide linkage is that cysteine can be easily oxidized and form the dimer that contains disulfide linkage between two cysteine residue in a poly peptide chain.
In this article ” Peptide Bond vs Ester Bond” the similarities and differences between these two bonds are clarified specifically.
Subject
Peptide Bond
Ester Bond
Connection between
Peptide bonds connect two amino acids
Ester bond connects an alcohol with an carboxylic acid.
Function
Peptide Bond forms protein / polypeptide
Ester linkages are backbone of lipid molecules
Formation
Peptide bond is formed through condensation reaction between two amino acids
Ester bond is also formed between alcohol and acid molecule due to condensation reaction
Participating atoms
Nitrogen atom from one amino acid forms the peptide linkage with the carbon of carboxylic group from another amino acid.
In ester bond, an oxygen atom is bound with the carbon atom of any alkyl or aryl group.
Ester bond is a type of chemical bond, that helps to join alcohol group with carboxylic acid group in the presence of catalyst ,but peptide bond is a type of chemical covalent bond that is formed between the reaction of two successive α amino acid. Similarities and differences between these two bonds are pointed out in this article.
Definition of Ester Linkage and Peptide Linkage
The ester linkage is formed when a carboxylic acid group (COOH) from a molecule and an alcohol group(OH) from another different molecule participate in a reaction in the presence of concentratedacid ( act as catalyst) and eliminate one water (H2O) molecule. One of the important ester linkage present in living organism is formed between the oxygen molecule of glycerol and hydroxyl group comes from fatty acid.
Peptide bond is mainly a covalent chemical bond which is called amide (-CONH2) type bond present in protein. It is formed by linking two consecutive alpha amino acids. In the formation of peptidebond, amine group (NH2) from one amino acid reacts with the carboxylic acid group (COOH) of another amino acid and one water molecule is removed.
One of the most well known lipid in biology is ‘glyceride”.A glyceride consists of glycerol andfatty acid, and these two groups are bound by the ester linkage. Fatty acid is stored in the form of glyceride by reacting with glycerol molecule. Another example of familiar lipid is “phospholipid” ,a group of polar lipids that basically contains a glycerol molecule attached with phosphate group (PO43-) and two “hydrophobic tails”, derived from fatty acids. These groups are joined by alcohl residue (glycerol molecule).
There is a basic different between a peptide bond and an ester bond, discussed below.
Peptide bonds are one type of amide (-CONH2) bond and exclusively primary structure. It basically connects two consecutive amino acids. In formation of a peptide bond nitrogen atom from one amino acid is bonded with the carbon atom from the carboxylic group present in the other amino acid.
Ester bond is one type of intramolecular chemical covalent bond. They are described as a carbon is linked with another three atoms: a sigma bond (single bond) with a carbon, a pi bond (double bond) with an oxygen and a single bond with another oxygen atom. Ester groups or ester bond is derived from parent acid ( carboxylic acid) and parent alcohol. Esters are written as RCOOR in organicchemistry.
In peptide bond, due to delocalization of unshared electron pair, C-N bond possesses partial doublebond character. This bond is not flexible and free rotation about this bond is become restricted. Whereas ester bond contains a carbonyl center (C=O) and the C-C-O and O-C-O bond angle becomes 1200. The unshared pair of electrons from oxygen can not participate in resonancebecause , after sharing the electron pairs oxygen becomes partially positive and it will notbe feasible as oxygen is more electronegative than nitrogen. Thus it behaves as single bond and possesses sp2 hybridization and structurally flexible because of the rotation of C-O-C bond.
Ester bonds are the backbones of lipids and peptide bonds are the key components o protein.
Basically ester bonds are formed due to the condensation reaction between carboxylic acid group (COOH) and hydroxyl groups (OH) of one acid and alcohol. On the other hand, peptide bond is formed due to the condensation reaction between amine (NH2) and carboxyl group (COOH) of two consecutive α amino acid. Therefore both these bonds are formed through condensation reaction.
From the above discussion, it is clearly shown that, peptide bond is totally different from ester bondin structure, geometry, participating atoms.
Is Peptide Bond Stronger Than Phosphodiester Bond?
Peptide bond is stronger than the ester bond.: Why peptide bond is stronger than ester linkage” is discussed clearly in this point.
From the study between these two bonds, it is proved that peptide bondis stronger than ester bond.Peptide bonds have some double bond character due to presence of unshared electron pair but ester bonds are structurally flexible with respect to peptide bond. In ester the C-O-C bond contains lower energy barrier than peptide bond.
The basic difference between these two bonds are C-N bond in peptide linkage is replaced by the C-O linkage in ester. The average bond dissociation energy of C-O bond is 358 KJ/mol and C-N bond is approximately 293 KJ/mol. From the thermodynamic point of view of the hydrolysis of the peptide bond, the Gibbs free energy released is 2-4 kcal/mol (8-16 KJ/mol) and for ester bond it is 5.3 kcal/mol (22.26 KJ/mol).
The hydrolysis reaction of a peptide bond is not favored and the half life is 350-600 years per bond at 298K (250C) due to the presence of partial double bond character in peptide bond.
Peptide bonds and phosphodiester bonds are two important types of chemical bonds found in biological molecules. Peptide bonds are formed between amino acids, linking them together to form proteins. On the other hand, phosphodiester bonds are found in nucleic acids, such as DNA and RNA, connecting the sugar-phosphate backbone. While both bonds involve the joining of molecules, they have distinct structures and functions. To better understand the differences between peptide bonds and phosphodiester bonds, let’s take a look at the following table:
Key Takeaways
Bond Type
Structure
Function
Peptide Bond
Formed between amino acids
Links amino acids to form proteins
Phosphodiester Bond
Found in nucleic acids (DNA, RNA)
Connects sugar-phosphate backbone
Definition of Key Terms
Peptide Bond
A peptide bond is a type of chemical bond that connects two amino acids in a protein chain. It is formed through a condensation reaction, also known as dehydration synthesis, where the carboxyl group of one amino acid reacts with the amino group of another amino acid. This reaction results in the formation of a peptide bond and the release of a water molecule. Peptide bonds play a crucial role in protein synthesis and contribute to the overall structure and function of proteins.
In a polypeptide chain, multiple peptide bonds connect amino acids together, forming a long chain. The sequence and arrangement of amino acids in a polypeptide chain determine the specific structure and function of the protein. The peptide bond provides stability to the protein structure and allows for various interactions between amino acids, such as hydrogen bonding and hydrophobic interactions.
Phosphodiester Bond
A phosphodiester bond is a type of chemical bond that connects nucleotides in nucleic acids, such as DNA and RNA. It is formed through a condensation reaction between the phosphate group of one nucleotide and the hydroxyl group of another nucleotide. This reaction results in the formation of a phosphodiester bond and the release of a water molecule.
In DNA, the phosphodiester bonds connect the sugar-phosphate backbone of the double helix structure. The sequence of nucleotides in DNA is determined by the specific arrangement of phosphodiester bonds. These bonds provide stability to the DNA molecule and play a crucial role in storing and transmitting genetic information.
Phosphodiester bonds in RNA are similar to those in DNA, connecting nucleotides in a single-stranded molecule. RNA molecules play essential roles in protein synthesis, acting as intermediates between DNA and protein. The phosphodiester bonds in RNA allow for the formation of specific base pairs and facilitate the processes of transcription and translation.
To summarize, both peptide bonds and phosphodiester bonds are important chemical bonds in molecular biology. Peptide bonds connect amino acids in proteins, while phosphodiester bonds connect nucleotides in nucleic acids. These bonds play vital roles in the structure, function, and transmission of genetic information in living organisms.
Understanding Peptide Bonds
Peptide bonds play a crucial role in the formation and structure of proteins. These bonds are formed through a process called condensation reaction, which involves the joining of two amino acids. In this article, we will explore the formation of peptide bonds, their role in proteins, their strength, and how they differ from ester bonds.
Formation of Peptide Bonds
Peptide bonds are formed when the carboxyl group of one amino acid reacts with the amino group of another amino acid. This reaction results in the release of a water molecule and the formation of a covalent bond between the two amino acids. The process occurs during protein synthesis, where the genetic information encoded in DNA is transcribed into RNA and then translated into a polypeptide chain.
The formation of peptide bonds is a fundamental step in protein synthesis. It is catalyzed by ribosomes, which act as molecular machines that bring together the amino acids and facilitate the bonding process. Through a series of enzymatic reactions, the ribosome connects the amino acids in the correct sequence to form a polypeptide chain.
Role of Peptide Bonds in Proteins
Peptide bonds are essential for the structure and function of proteins. They link amino acids together, forming the backbone of the protein chain. The sequence of amino acids in a protein determines its unique three-dimensional structure, which is critical for its specific function.
Proteins are involved in a wide range of biological processes, including enzymatic reactions, cell signaling, transport of molecules, and structural support. The peptide bonds provide stability to the protein structure, allowing it to maintain its shape and carry out its designated function.
Strength of Peptide Bonds
Peptide bonds are relatively strong and stable due to the nature of the chemical bond formed between the amino acids. The bond is a covalent bond, which means that the atoms involved share electrons. This sharing of electrons creates a strong connection between the amino acids, making peptide bonds resistant to breaking.
However, under certain conditions, such as extreme pH or the presence of specific enzymes, peptide bonds can be hydrolyzed, resulting in the breakdown of the protein. This process is essential for protein degradation and recycling within the cell.
Peptide Bond vs Ester Bond
Peptide bonds are often compared to ester bonds due to their similar chemical structure. Both bonds involve the connection of two molecules through a condensation reaction. However, there are significant differences between the two.
Peptide bonds connect amino acids in proteins, while ester bonds connect fatty acids to glycerol in lipids. Peptide bonds are more stable and less susceptible to hydrolysis compared to ester bonds. This difference in stability is due to the presence of nitrogen in the peptide bond, which enhances its strength.
In summary, peptide bonds are vital for the formation and structure of proteins. They play a crucial role in protein synthesis, provide stability to the protein structure, and contribute to the diverse functions of proteins in biological systems. Understanding the properties and characteristics of peptide bonds is essential for comprehending the complex world of molecular biology and biochemistry.
Understanding Phosphodiester Bonds
Phosphodiester bonds play a crucial role in the structure and function of nucleic acids, such as DNA and RNA. These bonds are formed between the phosphate group of one nucleotide and the sugar group of another nucleotide, creating a backbone that connects the individual nucleotides together. In this article, we will explore the formation of phosphodiester bonds, their role in DNA and RNA, and their strength.
Phosphodiester bonds are formed through a condensation reaction, also known as a dehydration synthesis. During this process, a water molecule is removed, and the phosphate group of one nucleotide reacts with the hydroxyl group of the sugar group of another nucleotide. This reaction results in the formation of a phosphodiester bond and the release of a water molecule.
The formation of phosphodiester bonds is a crucial step in the synthesis of DNA and RNA. It allows nucleotides to connect in a specific sequence, forming a polynucleotide chain. This chain serves as the backbone of the genetic material, carrying the instructions necessary for protein synthesis and other cellular processes.
Phosphodiester bonds are essential for the stability and integrity of DNA and RNA molecules. In DNA, these bonds connect the sugar-phosphate backbone, while the nitrogenous bases (adenine, thymine, cytosine, and guanine) are connected through hydrogen bonds. The specific sequence of nucleotides, held together by phosphodiester bonds, determines the genetic information encoded in DNA.
In RNA, phosphodiester bonds also connect the sugar-phosphate backbone, but instead of thymine, uracil is present as one of the nitrogenous bases. RNA molecules play a crucial role in protein synthesis, as they carry the genetic information from DNA to the ribosome, where it is translated into a polypeptide chain.
Strength of Phosphodiester Bonds
Phosphodiester bonds are relatively strong, allowing DNA and RNA molecules to maintain their structural integrity. The strength of these bonds is due to the covalent nature of the chemical bond formed between the phosphate and sugar groups. This covalent bond is resistant to hydrolysis, which is the breaking of chemical bonds through the addition of water molecules.
However, it is important to note that phosphodiester bonds can be cleaved through enzymatic reactions, such as those catalyzed by nucleases. These enzymes play a role in DNA repair, replication, and transcription by breaking the phosphodiester bonds at specific sites.
In summary, phosphodiester bonds are vital for the structure and function of DNA and RNA. They connect nucleotides together, forming the backbone of these nucleic acids. The specific sequence of nucleotides, held together by phosphodiester bonds, carries the genetic information necessary for protein synthesis and other cellular processes. These bonds are relatively strong, providing stability to the genetic material, but can be cleaved by specific enzymes when necessary.
Comparing Peptide Bonds and Phosphodiester Bonds
Peptide bonds and phosphodiester bonds are two important types of chemical bonds found in biological molecules. In molecular biology, these bonds play crucial roles in protein synthesis and DNA structure. Let’s explore the similarities and differences between peptide and phosphodiester bonds.
Similarities Between Peptide and Phosphodiester Bonds
Both peptide and phosphodiester bonds are involved in connecting two molecules together. In the case of peptide bonds, they connect amino acids to form a polypeptide chain, which is the building block of proteins. On the other hand, phosphodiester bonds connect nucleotides to form the backbone of nucleic acids like DNA and RNA.
Both peptide and phosphodiester bonds are formed through a condensation reaction, also known as dehydration synthesis. This process involves the removal of a water molecule to form a covalent bond between the molecules. The formation of these bonds is essential for the stability and function of proteins and nucleic acids.
Differences Between Peptide and Phosphodiester Bonds
While both bonds serve similar functions, there are some key differences between peptide and phosphodiester bonds. The main difference lies in the molecules they connect. Peptide bonds connect amino acids, which are the building blocks of proteins, while phosphodiester bonds connect nucleotides, which are the building blocks of nucleic acids.
Another difference is the chemical composition of the bonds. Peptide bonds are formed between the carboxyl group of one amino acid and the amino group of another amino acid. In contrast, phosphodiester bonds are formed between the phosphate group of one nucleotide and the hydroxyl group of another nucleotide.
Is a Peptide Bond a Phosphodiester Bond?
No, a peptide bond is not a phosphodiester bond. As mentioned earlier, peptide bonds connect amino acids to form proteins, while phosphodiester bonds connect nucleotides to form nucleic acids. These two types of bonds have distinct molecular structures and serve different functions in biological processes.
Is a Peptide Bond Stronger Than a Phosphodiester Bond?
The strength of a chemical bond depends on various factors, including the nature of the atoms involved and the surrounding environment. In general, peptide bonds are considered stronger than phosphodiester bonds. This is because peptide bonds involve the sharing of electrons between carbon and nitrogen atoms, which creates a stable covalent bond. Phosphodiester bonds, on the other hand, involve the sharing of electrons between phosphorus and oxygen atoms, which is relatively weaker.
In conclusion, peptide bonds and phosphodiester bonds are both important in molecular biology and biochemistry. While they have some similarities in terms of their formation and function, they also have distinct differences in the molecules they connect and their chemical composition. Understanding these bonds is crucial for comprehending protein synthesis and DNA structure.
Other Relevant Bonds
Glycosidic Bond vs Peptide Bond
In molecular biology and biochemistry, there are various types of chemical bonds that play crucial roles in the structure and function of biological molecules. Two important bonds to consider are the glycosidic bond and the peptide bond.
The glycosidic bond is a type of covalent bond that connects two monosaccharides (sugar molecules) together. It is formed through a condensation reaction, where a hydroxyl group from one sugar molecule reacts with the anomeric carbon of another sugar molecule, resulting in the formation of a glycosidic linkage. This bond is commonly found in carbohydrates, such as starch and cellulose, which are essential for energy storage and structural support in living organisms.
On the other hand, the peptide bond is a special type of covalent bond that connects two amino acids in a polypeptide chain during protein synthesis. It is formed through a condensation reaction between the carboxyl group of one amino acid and the amino group of another amino acid. This process, known as peptide bond formation, occurs on ribosomes during translation. The peptide bond is crucial for the formation of the primary structure of proteins and plays a vital role in determining their overall structure and function.
Although both the glycosidic bond and the peptide bond involve the connection of two molecules through a chemical bond, there are significant differences between them. Here’s a comparison:
Glycosidic Bond
Peptide Bond
Connects two monosaccharides
Connects two amino acids
Found in carbohydrates
Found in proteins
Involves the anomeric carbon of one sugar molecule
Involves the carboxyl group and amino group of two amino acids
Forms glycosidic linkage
Forms peptide linkage
Important for energy storage and structural support
Crucial for protein synthesis and determining protein structure
Isopeptide Bond
Another relevant bond to consider is the isopeptide bond. This bond is formed between the side chains of two amino acids, typically lysine and aspartic or glutamic acid, through an amide linkage. Isopeptide bonds are unique because they are formed through a different mechanism compared to the peptide bond.
Isopeptide bonds play a significant role in various biological processes. For example, they are involved in the formation of cross-links in proteins, which can affect protein stability and function. Additionally, isopeptide bonds are crucial for the conjugation of ubiquitin to target proteins, marking them for degradation by the proteasome.
In summary, understanding the different types of chemical bonds, such as the glycosidic bond, peptide bond, and isopeptide bond, is essential for comprehending molecular biology, protein synthesis, and DNA structure. These bonds contribute to the formation of complex biological molecules, such as carbohydrates, proteins, and nucleic acids, and play vital roles in their structure and function.
Conclusion
In conclusion, peptide bonds and phosphodiester bonds play crucial roles in biological processes. Peptide bonds are responsible for linking amino acids together to form proteins, while phosphodiester bonds connect nucleotides in DNA and RNA molecules.
Peptide bonds are formed through a dehydration synthesis reaction, resulting in a strong and stable bond. They contribute to the three-dimensional structure and function of proteins, determining their folding and interactions.
On the other hand, phosphodiester bonds are essential for the stability and replication of genetic material. They create the backbone of DNA and RNA strands, allowing for the transmission of genetic information.
Both peptide bonds and phosphodiester bonds are vital for life and understanding their differences helps us comprehend the complexity of biological systems.
What are the differences between a Peptide Bond and an Ester Bond?
A comparative analysis of peptide bond and ester bond reveals distinct differences. A peptide bond forms between amino acids, creating proteins, while an ester bond occurs during the formation of esters. Peptide bonds involve the amine and carboxylic acid groups, whereas ester bonds involve the reaction between an alcohol and a carboxylic acid. These dissimilarities result in varied structures and functions of the molecules.
References
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In the field of molecular biology, understanding the intricate processes of protein synthesis and DNA structure is crucial. These processes involve the interaction of various components such as amino acids, nucleotides, and chemical bonds. Biochemistry plays a vital role in unraveling the complexities of these molecular interactions.
One of the fundamental concepts in molecular biology is the formation of polypeptide chains through peptide bond formation. This process involves the connection of amino acids through a series of condensation reactions, resulting in the formation of a polypeptide chain. Similarly, the formation of nucleic acids, such as RNA and DNA, occurs through the formation of phosphodiester bonds.
Chemical bonds, specifically phosphodiester bonds, connect the two nucleotides in a DNA molecule. These bonds play a crucial role in maintaining the stability and integrity of the DNA structure. The molecular structure of DNA is composed of base pairs held together by hydrogen bonds, forming the famous double helix structure.
During protein synthesis, the ribosome plays a central role in the process of transcription and translation. Enzymes facilitate the formation of the polypeptide chain by catalyzing the necessary chemical reactions. The polynucleotide chain of RNA serves as a template for the synthesis of proteins, ensuring the accurate transfer of genetic information.
In summary, the understanding of molecular biology and biochemistry is essential in comprehending the intricate processes involved in protein synthesis, DNA structure, and the formation of chemical bonds. These concepts provide insights into the fundamental mechanisms that govern life at a molecular level.
For more information on these topics, you can refer to the following sources:
What is the relationship between peptide bond formation and the concept of peptide bond vs phosphodiester bond?
The Lambdageeks Guide to Peptide Bond Formation provides a comprehensive understanding of the process involved in the formation of peptide bonds. This concept intersects with the idea of peptide bond vs phosphodiester bond, which refers to the comparison between these two types of chemical bonds. The question arises as to how the formation of peptide bonds relates to the differences between peptide bonds and phosphodiester bonds.
Frequently Asked Questions
What is a peptide bond in the context of molecular biology?
A peptide bond is a covalent bond that forms between two amino acids during protein synthesis. It occurs when the carboxyl group of one amino acid reacts with the amino group of another, releasing a molecule of water in a condensation reaction.
What is the difference between a peptide bond and a phosphodiester bond?
A peptide bond is a covalent bond that forms between two amino acids, while a phosphodiester bond is a covalent bond that forms between two nucleotides in the backbone of DNA and RNA. The key difference lies in the molecules they connect – peptide bonds connect amino acids in proteins, while phosphodiester bonds connect nucleotides in nucleic acids.
How is a peptide bond formed in protein synthesis?
During protein synthesis, a peptide bond is formed in a process called a condensation reaction. This occurs on the ribosome, where the carboxyl group of one amino acid reacts with the amino group of another, releasing a molecule of water and forming a peptide bond.
What is an isopeptide bond?
An isopeptide bond is a type of peptide bond that forms between the carboxyl group of one amino acid and the side chain amino group of another. This bond is not as common as the regular peptide bond, which forms between the carboxyl group and the amino group of the main chain.
How does a phosphodiester bond occur in DNA structure?
A phosphodiester bond occurs in DNA structure when a phosphate group in one nucleotide forms two covalent bonds with the hydroxyl groups of two other nucleotides. This creates the backbone of the DNA molecule, with the phosphodiester bonds linking the sugar of one nucleotide to the phosphate of the next.
What is the difference between a peptide bond and a glycosidic bond?
A peptide bond is a covalent bond that forms between two amino acids in proteins, while a glycosidic bond is a covalent bond that forms between two sugar molecules in carbohydrates. Both bonds are formed through condensation reactions and can be broken by hydrolysis.
What type of bond is a peptide bond?
A peptide bond is a type of covalent bond. It is formed when the carboxyl group of one amino acid reacts with the amino group of another, releasing a molecule of water. This bond links amino acids together to form a polypeptide chain.
How strong is a peptide bond?
A peptide bond is a strong covalent bond. It is resistant to breaking under most physiological conditions, which helps to maintain the structure and function of proteins.
How does a peptide bond compare to an ester bond?
A peptide bond is a covalent bond that forms between two amino acids, while an ester bond is a covalent bond that forms between a carboxyl group and a hydroxyl group. Both bonds are formed through condensation reactions, but they occur in different types of molecules – peptide bonds in proteins and ester bonds in lipids and some carbohydrates.
How does a phosphodiester bond contribute to the structure of nucleic acids?
A phosphodiester bond contributes to the structure of nucleic acids by linking the sugar of one nucleotide to the phosphate of the next, creating the backbone of the DNA or RNA molecule. This bond is strong and resistant to breaking, which helps to maintain the integrity of the genetic material.
In this article, we are going to see is O2 a triple bond, why, how along with its characteristics and facts in detail.
Oxygen has a valency of 6 electrons. In an O2, two oxygen atoms are covalently bonded. Two valence electrons are getting shared by both oxygens to attain a stable electronic configuration. The rest of the electrons act as lone pairs. Hence a triple bond does not form by O2.
Michael Sendivogius isolated Oxygen (1604). Oxygen is an element of a periodic table with atomic number 8 and denoted as O. It belongs to Group 6A. It has 6 valence electrons present in its outermost valence shell. It has two pairs of electrons that are lone pairs. It constitutes 21% of the earth’s atmosphere and considers an essential element.
Triple bond
To find out is O2 a triple bond, let’s understand what is a triple bond.
A triple bond is formed when two atoms share three outermost shell electrons and are combined chemically. As the number of electrons available more bonds get formed which leads to an increase in the bond strength of a molecule. Single bonds and double bonds are weak as compared to triple bonds.
A triple bond is made up of three bonds out of which one is sigma and two pi bonds.
When there is an axial overlapping of orbitals Sigma bond is formed. A pi bond is formed by lateral overlapping of orbitals.
When two same atoms are combined chemically to form a bond then it is term as a diatomic molecule. In an O2 molecule, two identical oxygen atoms form a bond. Both oxygen atoms share two electrons each to form two covalent bonds.
The oxygen atom has a valency of 6 therefore needs 2 electrons for stabilization. By sharing 2 electrons both oxygen atoms attain stable electronic configuration. That’s why O2 is a diatomic molecule.
O2 molecule is formed by bonding two oxygen atoms covalently. There is a valency of six electrons in the valence shell of an oxygen atom. It must have only two electrons to complete the octet state. Both the oxygen atoms share two electrons with each other. Due to this they complete their octet state and get stabilized.
In the O2 molecule both the oxygen atoms attain stabilization by forming two covalent bonds with each other. There is no necessity to share more electrons to form a triple bond. So is O2 a triple bond, No, O2 is not a triple bond.
O2 is a diatomic molecule. When two identical atoms of the same elements combine together chemically to form a molecule, it is termed as diatomic. In the case of O2, two oxygen atoms combined covalently. As we know, the oxygen atom has a valency of six electrons. It wants only two electrons to complete the octet state.
Two oxygen shares two valence electrons to form a bond. By sharing these two electrons both the oxygen atoms fulfill their octet condition and attain stabilization. O2 molecule has two covalent bonds. Hence O2 is an example of a double bond structure.
In an O2 molecule, Oxygen atoms have 6 valence electrons so it shares 2 electrons with other oxygen atom and attains stable electronic configuration. As molecules get stabilized by sharing of two electrons, the formation of two bonds. There is no requirement for further bonding. Hence oxygen does not form 8 bonds.
Question: How many triple bonds does O2 have?
Answer: Zero, O2 does not have a triple bond.
In the O2 molecule both the oxygen atoms attain stabilization by forming two covalent bonds with each other. There is no necessity to share more electrons to form a triple bond. Hence O2 does not have a triple bond.
Question: What bonds are in a triple bond?
Answer: A triple bond includes three bonds.
A triple bond is made up of three bonds out of which one is sigma and two pi bonds. When there is an axial overlapping of orbitals Sigma bond is formed. A pi bond is formed by lateral overlapping of orbitals.
Question: Why is O2 not a triple bond?
Answer: O2 is not a triple bond because,
There are six electrons in the outermost shell of Oxygen. It must have only two electrons to complete the octet state. In the O2 molecule both the oxygen atoms attain stabilization by forming two covalent bonds with each other. There is no necessity to share more electrons to form a triple bond. Therefore O2 is not a triple bond.
In the case of O2, two oxygen atoms combined covalently. The oxygen atom has a valency of six electrons. It must have only two electrons to complete the octet state. Two oxygen shares two valence electrons to form a bond. By sharing these two electrons both the oxygen atoms fulfill their octet condition and attain stabilization. O2 molecule has two covalent bonds. Hence O2 is an example of a double bond.
