Unit - 1

Amino Acids, Peptides and Proteins

Q1) What is Protein?

A1) Proteins, whose name comes from the Greek word proteios, which means "first," are a type of organic compound found in and essential to all living cells. Proteins hold together, protect, and structure the body of a multicellular organism in the form of skin, hair, callus, cartilage, muscles, tendons, and ligaments. They catalyse, regulate, and protect the body chemistry in the forms of enzymes, hormones, antibodies, and globulins. They influence the transport of oxygen and other substances within an organism as haemoglobin, myoglobin, and various lipoproteins.

Proteins are widely regarded as beneficial and are an essential component of all animals' diets. If humans do not consume enough suitable protein, they can become seriously ill; the disease kwashiorkor is an extreme form of protein deficiency. Antibiotics and vaccines based on protein help to fight disease, and we warm and protect our bodies with clothing and shoes that are frequently made of protein (e.g., wool, silk and leather).

Protein toxins and venoms are less well known for their lethal properties. Botulinum toxin A, produced by Clostridium botulinum, is the most potent poison ever discovered. A teaspoon of this toxin would be enough to kill a fifth of the world's population, according to toxicology studies. Tetanus and diphtheria microorganisms produce toxins that are nearly as poisonous. The venoms of many snakes, as well as ricin, a toxic protein found in castor beans, would be included on a list of highly toxic proteins or peptides.

Despite their diverse physiological functions and physical properties— Proteins are sufficiently similar in molecular structure to be treated as a single chemical family, despite the fact that silk is a flexible fibre, horn is a tough rigid solid, and pepsin is a water soluble crystal. Proteins are fundamentally different from carbohydrates and lipids in terms of composition. Lipids are mostly made up of hydrocarbons, which account for 75 to 85 percent of their mass. Carbohydrates are roughly half-oxygen and, like lipids, usually contain less than 5% nitrogen (often none at all). Proteins and peptides, on the other hand, contain 15 to 25% nitrogen and roughly the same amount of oxygen. The size difference between proteins and peptides is significant. Peptides, with molecular weights less than 10,000, are small proteins.

Q2) What is Natural α-Amino Acids?

A2) When proteins are hydrolyzed in aqueous acid or base, small molecules known as -aminocarboxylic acids are produced. The most common of these components have been isolated, and they are listed in the table below. Because they are not synthesised by human metabolic processes, the amino acids with green names are essential diet components. Protein is the best source of these nutrients, but not all proteins are created equal. Peanuts, for example, have a higher protein content by weight than fish or eggs, but peanut protein contains only a third of the essential amino acids found in the other two sources. Each amino acid is given a one or three letter abbreviation for reasons that will become clear when discussing the structures of proteins and peptides. There are a few things to keep in mind about these amino acids. They are all 1o-amines with the exception of proline, and they are all chiral with the exception of glycine. When written as a Fischer projection formula, the configurations of the chiral amino acids are the same, as shown in the diagram on the right, and this was dubbed the L-configuration by Fischer. The remaining structural component that varies from one amino acid to the next is the R-substituent, which in proline is a three-carbon chain that connects the nitrogen to the alpha-carbon in a five-membered ring. With the exception of cysteine, all of these natural chiral amino acids have an S-configuration according to the Cahn-Ingold-Prelog notation.

The R-substituent in the first seven compounds in the left column is a hydrocarbon. The last three amino acids in the left column have hydroxyl functional groups, while the first two in the right column have thiol and sulphide functional groups, respectively. Histidine and tryptophan have less basic nitrogen heterocyclic rings as substituents than lysine and arginine, which have basic amine functions in their side chains. Finally, carboxylic acid side-chains are substituents on aspartic and glutamic acid, and the last two compounds in the right column are their corresponding amides.

The amino acid formulas above are simple covalent bond representations based on prior knowledge of mono-functional analogues. In reality, the formulas are incorrect. A comparison of the physical properties listed in the following table demonstrates this. The four compounds in the table are all of similar size and have moderate to excellent water solubility. Simple carboxylic acids make up the first two, while an amino alcohol makes up the third. Each of the three compounds is soluble in organic solvents (such as ether) and has a low melting point. The carboxylic acids have pKa values around 4.5, while the amine's conjugate acid has a pKa of 10. The last entry is alanine, a simple amino acid. It has a high melting point (with decomposition), is insoluble in organic solvents, and is a million times weaker as an acid than regular carboxylic acids.

Q3) Why does the chain terminus attracts the negatively charged carboxylate?

A3) The alanine zwitterion has a high melting point, is insoluble in nonpolar solvents, and has the acid strength of a 1o-ammonium ion, as expected given its ionic character. A Jmol representation of a L-amino acid is shown to the right. By pressing the appropriate button beneath the display, the model will change to its zwitterionic state. A few specific amino acids can be seen in their preferred neutral zwitterionic form as well. It's worth noting that the amine function closest to the carboxyl group in lysine is more basic than the alpha-amine. As a result, the positively charged ammonium moiety at the chain terminus attracts the negatively charged carboxylate, forming a coiled conformation.

Because amino acids, peptides, and proteins contain both acidic and basic functional groups, the predominant molecular species present in an aqueous solution is determined by its pH. The Henderson - Hasselbalch Equation, written below, is used to determine the nature of the molecular and ionic species present in aqueous solutions at various pHs. The pKa here denotes the acidity of a particular conjugate acid function (HA).

Q4) Write a short note on Natural α-Amino Acids.

A4) It should be obvious that the pH of the matrix buffer has a significant impact on the outcome of this experiment. If we repeated the electrophoresis of these compounds at a pH of 3.80, the aspartic acid would stay put, while the other amino acids would move toward the cathode. Arginine would move twice as fast as alanine and isoleucine, ignoring differences in molecular size and shape, because its solute molecules would have a double positive charge on average.

The titration curves of simple amino acids have two inflection points, one for the strongly acidic carboxyl group (pKa1 = 1.8 to 2.4) and the other for the less acidic ammonium function (pKa2 = 8.8 to 9.7), as previously mentioned. The pKa2 of the 2o-amino acid proline is 10.6, indicating that 2o-amines are more basic.
The side chains of some amino acids have additional acidic or basic functions. In the table to the right, you'll find a list of these compounds. The extra function's acidity or basicity is represented by a third pKa in the table's fourth column. These amino acids' pIs (last column) are frequently very different from those of the simpler members. As can be seen in the titration curves of arginine and aspartic acid shown below, such compounds have three inflection points in their titration curves. There are four possible charged species for each of these compounds, one of which has no overall charge. The formulas for these species, as well as the pH at which each is expected to predominate, are written to the right of the titration curves. The very high pH required to remove the last acidic proton from arginine reflects the exceptionally high basicity of the guanidine moiety at the end.

Q5) What is The Isoelectric Point?

A5) The isoelectric point, pI, is the pH of an aqueous solution of an amino acid (or peptide) at which the molecules have no net charge on average, as defined above. In other words, the negatively charged groups balance out the positively charged groups perfectly. The pI of simple amino acids like alanine is calculated by adding the pKas of the carboxyl (2.34) and ammonium (9.69) groups. Thus, the experimentally determined pI for alanine is calculated as (2.34 + 9.69)/2 = 6.02. The pI is the average of the pKas of the two most similar acids if additional acidic or basic groups are present as side-chain functions. We define two classes of acids to aid in determining similarity. The first group consists of acids that are protonated to be neutral (e.g. CO2H & SH). Acids that are positively charged in their protonated state (e.g. -NH3+) fall into the second category. The alpha-carboxyl function (pKa = 2.1) and the side-chain carboxyl function (pKa = 3.9) are similar acids in aspartic acid, so pI = (2.1 + 3.9)/2 = 3.0. For arginine, the similar acids are the guanidinium species on the side-chain (pKa = 12.5) and the alpha-ammonium function (pKa = 9.0), so the calculated pI = (12.5 + 9.0)/2 = 10.75.

Q6) State the Carboxylic Acid Esterification.

A6) If the pH is set to an appropriate level, amino acids go through the majority of the chemical reactions that are characteristic of each function. As shown in the two equations below, carboxylic acid esterification is usually carried out under acidic conditions. Amine functions are converted to their ammonium salts under these conditions, but carboxylic acids are not dissociated. The first equation is a typical methanol Fischer esterification. A stable ammonium salt is the first product. Due to acylation of the amine by the ester function, the amino ester formed by neutralisation of this salt is unstable.

The second reaction uses p-toluenesulfonic acid as an acid catalyst to benzylate aspartic acid's two carboxylic acid functions. Zwitterionic species are no longer possible once the carboxyl function is esterified, and the product behaves like any other 1o-amine.

Q7) Define the Ninhydrin Reaction.

A7) Except for proline, common alpha-amino acids undergo a unique reaction with the triketohydrindene hydrate known as ninhydrin in addition to these common amine-carboxylic acid reactions. A purple coloured amino derivative is one of the products of this unusual reaction (shown on the left below), which serves as a useful colour test for these amino acids, which are mostly colourless. The ninhydrin test is frequently used to visualise amino acids in paper chromatography. Samples of amino acids or mixtures of amino acids are applied along a line near the bottom of a rectangular sheet of paper, as shown in the diagram on the right (the baseline). The paper's bottom edge is immersed in an aqueous buffer, which slowly climbs toward the top edge. The compounds in each sample are carried along at a rate that is characteristic of their functionality, size, and interaction with the cellulose matrix of the paper as the solvent front passes through the sample spots. Some compounds move quickly up the paper, while others move very slowly. The retardation (or retention) factor Rf is defined as the ratio of the distance a compound moves from the baseline to the distance the solvent front moves from the baseline. Under ideal conditions, different amino acids have different Rfs. The three sample compounds (1, 2 & 3) in the example on the right have Rf values of 0.54, 0.36, and 0.78, respectively.

Q8) Write a short note on Amino Acids.

A8) Proteins are made up of amino acids, which are organic compounds that combine to form proteins. The building blocks of life are amino acids and proteins.

Amino acids are left over after proteins are digested or broken down. Amino acids are used by the human body to make proteins that aid in the following functions:

•         Break down food

•         Grow

•         Repair body tissue

•         Perform many other body functions

Amino acids can also be used as a source of energy by the body.

Amino acids are classified into three groups:

•         Essential amino acids

•         Nonessential amino acids

•         Conditional amino acids

ESSENTIAL AMINO ACIDS

•         Essential amino acids cannot be made by the body. As a result, they must come from food.

•         The 9 essential amino acids are: histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine.

NONESSENTIAL AMINO ACIDS

The term "non-essential" refers to the fact that our bodies can make an amino acid even if we don't get it from food. Alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, proline, serine, and tyrosine are non-essential amino acids

Q9) State the Building blocks of proteins.

A9) Proteins are critical for life on Earth to continue to function properly. The vast majority of chemical reactions in the cell are catalysed by proteins. They provide many of a cell's structural elements and aid in the fusion of cells into tissues. To allow movement, some proteins act as contractile elements. Others are in charge of transporting vital materials from the cell's exterior ("extracellular") to its interior ("intracellular"). Proteins protect animals from disease in the form of antibodies, and interferon mounts an intracellular attack against viruses that have eluded destruction by antibodies and other immune system defences. Many hormones are proteins. Last but certainly not least, proteins control the activity of genes (“gene expression”).

The incredible diversity of known proteins, which differ significantly in size, shape, and charge, reflects this wide range of critical functions. Scientists realised by the end of the nineteenth century that, while there are many different types of proteins in nature, all proteins hydrolyze to a class of simpler compounds called amino acids, which are the building blocks of proteins. Glycine is the most basic amino acid, named after its sweet taste (glyco, "sugar"). It was isolated from the protein gelatin in 1820 and was one of the first amino acids to be identified. Scientists working on elucidating the relationship between proteins and genes agreed in the mid-1950s that 20 amino acids (known as standard or common amino acids) should be considered the essential building blocks of all proteins. Threonine, the last of these to be discovered, was discovered in 1935.

Q10) Explain Acid-base properties.

A10) The presence of both a basic and an acidic group at the -carbon is another important feature of free amino acids. Amino acids, for example, are amphoteric compounds because they can act as both an acid and a base. The pKa of the basic amino group is usually between 9 and 10, while the pKa of the acidic -carboxyl group is usually around 2. (a very low value for carboxyls). The pH value at which the protonated group's concentration equals that of the unprotonated group is known as the group's pKa. At physiological pH (around 7–7.4), free amino acids mostly exist as dipolar ions, or "zwitterions" (German for "hybrid ions"; a zwitterion has an equal number of positively and negatively charged groups). Any free amino acid, as well as any protein, will exist in the form of a zwitterion at a specific pH. When exposed to changes in pH, all amino acids and proteins pass through a state in which the number of positive and negative charges on the molecule is equal. The isoelectric point (or isoelectric pH) is the pH at which this occurs, and it is denoted as pI. All amino acids and proteins are predominantly in their isoelectric form when dissolved in water. In other words, there is a pH (isoelectric point) at which the molecule has a net zero charge (equal number of positive and negative charges), but no pH at which the molecule has an absolute zero charge (complete absence of positive and negative charges). Amino acids and proteins, in other words, are always in the form of ions and carry charged groups. This fact is critical when studying the biochemistry of amino acids and proteins in depth.

Q11)  Enlist and explains the Groups of Standard amino acids.

A11) Group I: Nonpolar amino acids

Glycine, alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, and tryptophan are all members of Group I amino acids. These amino acids have either aliphatic or aromatic groups in their R groups. This makes them hydrophobic (afraid of water). Globular proteins fold into a three-dimensional shape in aqueous solutions to bury these hydrophobic side chains in the protein interior. Isoleucine is a chiral isomer of leucine that contains two carbon atoms. Proline is the only amino acid in the standard amino acid family that lacks both free -amino and free -carboxyl groups. Instead, the nitrogen atom of proline is linked to two carbon atoms, forming a cyclic structure in its side chain. (In strict terms, this means that proline is a -imino acid rather than an amino acid.) Phenylalanine is made up of a phenyl group attached to alanine, as the name suggests. . Methionine is one of the two sulfur-containing amino acids. Methionine is almost always the initiating amino acid in protein biosynthesis (translation), so it plays a crucial role. Methionine also serves as a source of methyl groups for metabolism. An indole ring is attached to the alanyl side chain in tryptophan.

Group II: Polar, uncharged amino acids

Serine, cysteine, threonine, tyrosine, asparagine, and glutamine are all members of Group II amino acids. This group's side chains have a wide range of functional groups. Most, however, have at least one atom with electron pairs available for hydrogen bonding to water and other molecules (nitrogen, oxygen, or sulphur). Serine and threonine are two amino acids that contain aliphatic hydroxyl groups (an oxygen atom bonded to a hydrogen atom, represented as OH). Tyrosine is a phenol derivative because it has a hydroxyl group in the aromatic ring. The hydroxyl groups in these three amino acids are phosphorylated, which is a common type of posttranslational modification (see Nonstandard amino acids). Cysteine, like methionine, has a sulphur atom. However, unlike methionine's sulphur atom, cysteine's sulphur atom is chemically reactive (see Cysteine oxidation below). Both asparagine and glutamine, which were first isolated from asparagus, have amide R groups. The amino group (NH2) can act as a hydrogen bond donor, while the carbonyl group can act as a hydrogen bond acceptor.

Group III: Acidic amino acids

Aspartic acid and glutamic acid are the two amino acids in this group. Each one has a carboxylic acid on its side chain, which makes it acidic (proton-donating). All three functional groups on these amino acids will ionise in an aqueous solution at physiological pH, resulting in an overall charge of 1. Aspartate and glutamate are the ionic forms of the amino acids. Aspartate and glutamate side chains can form ionic bonds (also known as "salt bridges") and act as hydrogen bond acceptors. Metal-binding sites containing aspartate or glutamate side chains, or both, are found in many proteins that bind metal ions for structural or functional reasons. The amino acid metabolism is dominated by free glutamate and glutamine. In the central nervous system, glutamate is the most abundant excitatory neurotransmitter.

Group IV: Basic amino acids

Arginine, histidine, and lysine are the three amino acids that make up this group. Each side chain is fundamental (i.e., can accept a proton). At physiological pH, both lysine and arginine have an overall charge of +1. The guanidino group in the side chain of arginine is the most fundamental of all R groups (a fact reflected in its pKa value of 12.5). Ionic bonds form between the side chains of arginine and lysine, just as they do with aspartate and glutamate. Histidine's imidazole side chain allows it to work in both acid and base catalysis at physiological pH levels. This is a chemical property that none of the other standard amino acids have. As a result, histidine is a common amino acid found in the active sites of protein enzymes.

Q12)  Define the Cysteine oxidation.

A12) Cysteine's thiol (sulfur-containing) group is extremely reactive. This group's most common reaction is a reversible oxidation that produces a disulfide. The oxidation of two cysteine molecules produces cystine, a molecule with a disulfide bond. A disulfide bridge is formed when two cysteine residues in a protein form such a bond. Disulfide bridges are a common way for many proteins to be stabilised in nature. Extracellular proteins that are secreted from cells frequently contain disulfide bridges. The endoplasmic reticulum, an organelle in eukaryotic organisms, is where disulfide bridges are formed.

The sulfhydryl groups of cysteine are rapidly oxidised to form cystine in extracellular fluids (such as blood). There is a defect in cystinuria, a genetic disorder that causes excessive cystine excretion in the urine. Because cystine is the least soluble of the amino acids, crystallisation of excreted cystine causes calculi (also known as "stones") to form in the kidney, ureter, or urinary bladder. Intense pain, infection, and blood in the urine are all possible side effects of kidney stones. The use of D-penicillamine as a medical intervention is common. Penicillamine works by forming a 50-fold more water-soluble complex with cystine than cystine alone. In summary, a protein's shape and biological function, as well as its physical and chemical properties, are determined by its amino acid sequence. Proteins are polymers of 20 different kinds of amino acids, which gives them their functional diversity. The hormone insulin, for example, is a "simple" protein with 51 amino acids. With 20 amino acids to choose from at each of these 51 positions, a total of 2051, or roughly 1066, different proteins could theoretically be created.

Q13) What are the functions of Define the Cysteine oxidation?

A13) Amino acids are the building blocks for a wide range of complex nitrogen-containing molecules. The nitrogenous base components of nucleotides and nucleic acids (DNA and RNA) are prominent among these. Cofactors derived from complex amino acids, such as heme and chlorophyll, are also present. Heme is an iron-containing organic group that is required for the biological activity of proteins like haemoglobin, which transports oxygen, and cytochrome c, which transports electrons. Photosynthesis requires the pigment chlorophyll. Deoxyribonucleic acid polynucleotide chain portion (DNA). The corresponding pentose sugar and pyrimidine base in ribonucleic acid are shown in the inset (RNA).

Chemical messengers include several -amino acids (or their derivatives). Neurotransmitters include -aminobutyric acid (GABA; a glutamic acid derivative), serotonin and melatonin (tryptophan derivatives), and histamine (histidine derivative). Hormones include thyroxine (a tyrosine derivative produced in the thyroid gland of animals) and indole acetic acid (a tryptophan derivative found in plants).

Several amino acids, both standard and nonstandard, are frequently used as metabolic intermediates. The amino acids arginine, citrulline, and ornithine, which are all part of the urea cycle, are good examples of this. The main mechanism for removing nitrogenous waste is the synthesis of urea.

Q14) Explain the Synthesis of α-Amino Acids.

A14)

1) The following equation illustrates a simple method for preparing alpha-aminocarboxylic acids by amination of alpha-bromocarboxylic acids. Bromoacids, on the other hand, are easily made from carboxylic acids by reacting them with Br2 + PCl3. Although this direct method produced mediocre results when used to make simple amines from alkyl halides, it is more effective when used to make amino acids because the nitrogen atom in the product has a lower nucleophilicity. However, for amino acid synthesis, more complex procedures with high yields of pure compounds are frequently used.

2) The proclivity of amines to undergo multiple substitutions is removed by modifying the nitrogen as a phthalimide salt, resulting in a single clean substitution reaction of 1o- and many 2o-alkylhalides. As shown in the upper equation of the following scheme, this procedure, known as the Gabriel synthesis, can be used to aminate bromomalonic esters. This intermediate can be converted to an ambident anion and alkylated because the phthalimide substituted malonic ester has an acidic hydrogen (coloured orange) that is activated by the two ester groups. Finally, acidification and thermal decarboxylation of the phthalimide moiety and esters, followed by base catalysed hydrolysis of the phthalimide moiety and esters, yields an amino acid and phthalic acid.

3) The Strecker synthesis assembles an alpha-amino acid from ammonia (the amine precursor), cyanide (the carboxyl precursor), and an aldehyde in an elegant manner. This reaction is essentially an imino analogue of cyanohydrin formation (shown below). The resulting alpha-amino nitrile can then be hydrolyzed to an amino acid using acid or base catalysis.

4) Resolution Racemic amino acid products are produced by the three synthetic procedures described above, as well as many others that can be imagined. It is necessary to resolve these racemic mixtures if pure L or D enantiomers are desired. Diastereomeric salt formation with a pure chiral acid or base is a common method of resolving racemates. The following diagram depicts this for a generic amino acid. Keep an eye out for charge symbols, which are shown in coloured circles, and optical rotation signs, which are shown in parenthesis.The carboxylic acid function contributes to the formation of diastereomeric salts in the initial display. To remove the basic character of the amino group, the racemic amino acid is first converted to a benzamide derivative. The carboxylic acid is then combined with an optically pure amine, such as brucine, to form an ammonium salt (a relative of strychnine). Because it is not a critical factor in the logical progression of steps, the structure of this amine is not shown. An equimolar mixture of diastereomeric salts is formed when the amino acid moiety is racemic and the base is a single enantiomer (levorotatory in this case) (drawn in the green shaded box). Diastereomers can be separated using crystallisation, chromatography, or other physical methods, allowing one of the isomers to be isolated for further treatment; in this case, the (+):(-) diastereomer. Finally, the salt is broken down with acid, yielding the resolved (+)-amino acid derivative and the resolving agent (the optically active amine).

Q15) What are ionic compounds?

A15) A transfer of electrons usually occurs when an element composed of atoms that readily lose electrons (a metal) reacts with an element composed of atoms that readily gain electrons (a nonmetal), resulting in ions. The electrostatic attractions (ionic bonds) between the ions of opposite charge present in the compound stabilise the compound formed by this transfer. When each sodium atom in a sample of sodium metal (group 1) gives up one electron to form a sodium cation, Na+, and each chlorine atom in a sample of chlorine gas (group 17) accepts one electron to form a chloride anion, Cl, the resulting compound, NaCl, is made up of sodium ions and chloride ions in the ratio of one Na+ ion to each Cl ion. Similarly, each calcium atom (group 2) can give up two electrons and transfer one to each of two chlorine atoms to form CaCl2, which is made up of Ca2+ and Cl ions in a one-to-two ratio.

An ionic compound is one that contains ions and is held together by ionic bonds. Many of the ionic compounds can be identified using the periodic table: The compound is usually ionic when a metal is combined with one or more nonmetals. For most of the compounds encountered in an introductory chemistry course, this guideline works well for predicting ionic compound formation. However, this isn't always the case (for example, aluminium chloride, AlCl3, is not ionic).

Because of their properties, ionic compounds are easily identifiable. Ionic compounds are solids that melt at high temperatures and boil at temperatures even higher. Sodium chloride, for example, melts at 801°C and boils at 1413°C. (By comparison, the molecular compound water melts at 0 degrees Celsius and boils at 100 degrees Celsius.) Because its ions are unable to flow in solid form, an ionic compound is not electrically conductive (“electricity” is the flow of charged particles). However, when molten, it can conduct electricity because its ions can freely move through the liquid.

Q16) Write down the Properties of Ionic Compound.

A16) Melting Points

Ionic crystal lattices are extremely strong due to the numerous simultaneous attractions between cations and anions that occur. In order to break all of the ionic bonds in an ionic compound, large amounts of energy must be added during the melting process. The melting point of sodium chloride, for example, is around 800°C.

Shattering

Ionic compounds are hard but brittle in general. What is the reason for this? To force one layer of ions to shift relative to its neighbour, a large amount of mechanical force is required, such as striking a crystal with a hammer. When this happens, however, it brings ions with the same charge together (see Figure below). The crystal shatters due to the repulsive forces between like-charged ions. Because of the regular arrangement of the ions, when an ionic crystal breaks, it tends to do so along smooth planes.

(A) The sodium chloride crystal is shown in two dimensions. (B) When struck by a hammer, the negatively-charged chloride ions are forced near each other and the repulsive force causes the crystal to shatter.

Conductivity

The electrical conductivity of ionic compounds is another distinguishing feature. Three experiments are shown below, in which two electrodes connected to a light bulb are placed in beakers with three different substances.

(A) Distilled water is not an electrical conductor. (B) A solid ionic compound, on the other hand, does not conduct. (C) An ionic compound in water conducts electricity well.

Because water is a molecular compound, it does not conduct a current in the first beaker. Solid sodium chloride in the second beaker also does not conduct a current. The solid crystal lattice, despite being ionic and thus composed of charged particles, prevents the ions from moving between the electrodes. For the circuit to be complete and the light bulb to turn on, mobile charged particles are required. The NaCl has been dissolved in the distilled water in the third beaker.  The crystal lattice has now been broken apart, allowing the positive and negative ions to move freely. The movement of cations to one electrode and anions to the other allows electricity to flow (see Figure below). When an ionic compound is melted, the ions become free to conduct a current. When melted or dissolved in water, ionic compounds produce an electric current.

Q17) Write the Chemical Reactions of Ionic Compound.

A17) Chemical reactions play an important role in biology at all levels. A reaction, in its most basic form, necessitates reactants and products. The atoms or molecules that are involved in the change are known as reactants, and the changed atoms or molecules are known as products. Enzymes act as catalysts in most biological reactions, speeding up the process. When reactants are combined to form a product with different chemical properties than the original reactants, this is known as a chemical reaction. An energy change and a change in the electron configuration around the original atoms are always involved. A chemical reaction occurs when electrons redistribute their orbitals to include two or more atomic nuclei, as in a covalent bond, or donate or accept electrons, as in an ionic bond. During chemical reactions, two types of bonds form: covalent and ionic.

Ionic bonds are formed when an atom's outermost, or valence, electrons are given or received in association with another atom. Because the electrons are now orbiting the receiving atom rather than their original atom, the receiving atom's number of protons and electrons is now imbalanced, and it becomes a negatively charged ion. The donating atom has a proton-electron imbalance as well, and as a result of losing a negatively charged electron while maintaining the same number of protons, it becomes a positively charged ion. The properties of the resulting molecule differ from those of the original atoms. It's important to remember that the resulting ionic compounds have partial charges due to the unequal electron distribution around the reacting atoms. This significance is discussed in more depth in Specialized Cell Structure and Function, but it explains why water can dissolve any substance with a partial charge. The joining of a sodium atom that donates an electron to a chlorine atom that accepts the electron to form sodium chloride, also known as table salt, is an example of an ionic bond.

When two or more atoms share their electrons, they form covalent bonds. Instead of being donated or accepted, the electrons incorporate their orbitals to form an electron cloud around all of the participating atoms. When electrons are evenly distributed among all reacting nuclei, the resulting molecule has no partial charge, as when carbon covalently bonds with itself. However, in some cases, such as polar covalent bonds, the electrons are not evenly distributed, resulting in partial charges.

Many bonds, in reality, are a hybrid of ionic and covalent bonds, with characteristics of both types. Atoms with polar covalent bonds share their electrons unevenly (covalent characteristic) and give one end of the molecule a slight positive (+) charge and the other end a slight negative (-) charge. Because the oxygen atom has more protons acting as electron magnets, the electrons spend more time around it, making water a polar covalent molecule. Because the electrons spend more time orbiting around the oxygen atom due to this unequal sharing of electrons, the oxygen end of the molecule has a slight negative charge, while the hydrogen end has a partial positive charge. There is a partial positive and partial negative end to the molecule as a whole.

Q18) Explain the Isoelectric Point Separations of Peptides and Proteins.

A18) The separation of biomolecules, particularly proteins, in the presence of an electric field (e.g., electrophoresis) has spawned a slew of methodologies for reducing sample complexity and probing the physiochemical properties of these biomolecules. Electrophoretic methods are used to investigate proteins and peptides, which are possibly the most studied class of molecules. Electrophoresis on agarose and polyacrylamide gels, two-dimensional gel electrophoresis (2DE), capillary electrophoresis, isotachophoresis, and other methods are among them.

Isoelectric focusing (IEF) is an electrophoretic technique that separates ampholytic components, or molecules that act as weak acids and bases, according to their isoelectric points. In IEF, ampholytes travel according to their charge in the presence of a pH gradient, under the influence of an electric field, until the molecule's net charge is zero (e.g., isoelectric point, pI). When it comes to peptides and proteins, the separation is determined by the amino acid composition and exposed charged residues that act as weak acids and bases (Figure 1). The migration of ampholytic species will follow basic electrophoresis principles; however, in the presence of a pH gradient, mobility will change, with migration slowing at values close to the pI value. Ampholytes as simple as amino acids can create a pH gradient and act as an isoelectric buffer.

Q19) Write Classification of AMPs Based on Sources.

A19) According to statistical data in APD3, the sources of AMPs are mammals (human host defence peptides account for a large proportion), amphibians, microorganisms, and insects. The AMPs discovered in oceans have also gotten a lot of attention.

*  Mammalian Antimicrobial Peptides

Humans, sheep, cattle, and other vertebrates all have antimicrobial peptides. Cathelicidins and defensins are the two most common AMP families. Defensins are classified as -, -, or -defensins, depending on where the disulfide bonds are located (Reddy et al., 2004). HDPs (human host defence peptides) can protect humans from microbial infections, but they have different expressions at different stages of life. Cathelicidin LL-37, a well-known AMP derived from the human body, is commonly found in the skin of newborn infants, whereas human beta-defensin 2 (hBD-2) is frequently expressed in the elderly rather than the young (Gschwandtner et al., 2014). HDPs can be found in the skin, eyes, ears, mouth, respiratory tract, lung, intestine, and urethra, among other places. Furthermore, AMPs in human breast milk play an important role in breastfeeding by lowering the morbidity and mortality of breast-fed infants (Field, 2005). Casein201 (peptide derived from -Casein 201–220 aa), which has been identified in colostrum, is found in preterm and term human colostrums at different levels (Zhang et al., 2017). Dairy is a significant source of AMPs, which are produced by the enzymatic hydrolysis of milk. Several AMPs have been discovered in -lactalbumin, -lactoglobulin, lactoferrin, and casein fractions, with lactoferricin B (LfcinB) being the most well-known (Sibel Akaln, 2014). Furthermore, it will be interesting to see if AMPs derived from dairy products can be used to preserve dairy products.

HDPs, such as cathelicidins and defensins, affect immune regulation, apoptosis, and wound healing in addition to antimicrobial activity (Wang, 2014).

*  Amphibian-Derived Antimicrobial Peptides

Amphibian antimicrobial peptides are important in protecting amphibians from pathogens that have caused a global decline in amphibian populations (Rollins-Smith, 2009). The most well-known amphibian AMP is magainin, which is found in the skin secretions of frogs from the genera Xenopus, Silurana, Hymenochirus, and Pseudhymenochirus, all of which belong to the Pipidae family (Conlon and Mechkarska, 2014). Cancrin, whose amino acid sequence is GSAQPYKQLHKVVNWDPYG, has also been identified as the first AMP discovered in the sea amphibian Rana cancrivora (Lu et al., 2008). This indicates a larger source of amphibian AMPs.

*  Insect-Derived Antimicrobial Peptides

Antimicrobial peptides are primarily synthesised in insects' fat bodies and blood cells, which is one of the primary reasons for their high adaptability to survival (Vilcinskas, 2013). Cecropin is the most well-known family of insect AMPs, and it's found in guppy silkworm, bees, and Drosophila. Cecropin A has been shown to have anti-inflammatory and anti-cancer properties. The number of AMPs varies significantly between species; for example, the invasive harlequin ladybird (Harmonia axyridis) and black soldier fly (Hermetia illucens) have up to 50 AMPs, whereas the pea aphid (Acyrthosiphon pisum) has none. Jellein, a peptide derived from bee royal jelly, has antibacterial and antifungal properties, and its lauric acid-conjugated form inhibits the parasite Leishmania major.

*  Microorganisms-Derived Antimicrobial Peptides

Antimicrobial peptides can be extracted from bacteria and fungi, and some well-known peptides include nisin and gramicidin from Lactococcus lactis, Bacillus subtilis, and Bacillus brevis, among others (Cao et al., 2018). Biological expression has received increased attention as a result of the high cost of chemical synthesis of AMPs. Expression systems have been used in Pichia pastoris, Saccharomyces cerevisiae, and bacteria such as Escherichia coli, B. Subtilis, and plants, but it should be noted that AMPs are difficult to produce in E. Coli due to toxicity, proteolytic degradation, and purification, which is required to take advantage of fusion.

Furthermore, a variety of AMPs have been extracted and isolated from plant stems, seeds, and leaves, and they are divided into several groups, including thionins, defensins, and snakins. More marine-derived AMPs have been reported to have contributed to people's increasing value for marine resources. Several of the reported marine AMPs have shown promising results in vivo, for example, As-CATH4 has an immunity-stimulating effect in vivo and can enhance the anti-infective capability of drugs used in combination with it. Myticusin-beta is an immune-related AMP produced by Mytilus coruscus that could be used instead of antibiotics. Furthermore, GE33, also known as pardaxin, is a marine AMP, and a vaccine based on it has been shown to improve antitumor immunity in mice.

Q20) Explain the Structure of Protein.

A20) Protein, All living organisms contain this highly complex substance. Proteins have a high nutritional value and play a direct role in the chemical processes that keep life going. Proteins were recognised as important by chemists in the early nineteenth century, including Swedish chemist Jöns Jacob Berzelius, who coined the term protein in 1838, a word derived from the Greek prteios, which means "first place." Proteins are species-specific, which means that proteins from one species differ from proteins from another. They are also organ-specific; for example, muscle proteins differ from brain and liver proteins within a single organism.

A protein molecule is much larger than a sugar or salt molecule, and it is made up of many amino acids linked together in long chains, much like beads on a string. Proteins contain about 20 different amino acids that occur naturally. Amino acid composition and sequence are similar in proteins with similar functions. Although it is not yet possible to deduce all of a protein's functions from its amino acid sequence, the properties of the amino acids that make up proteins have been linked to established correlations between structure and function.

Animal organs typically have a much higher protein content than blood plasma. Muscles, for example, contain about 30% protein, while the liver contains 20% to 30% and red blood cells contain 30%. Hair, bones, and other organs and tissues with a low water content contain higher percentages of protein. In animals, the amount of free amino acids and peptides is much lower than the amount of protein; protein molecules are made in cells by stepwise alignment of amino acids and released into the body fluids only after synthesis is completed.

The high protein content of some organs does not imply that protein importance is proportional to their quantity in an organism or tissue; on the contrary, some of the most important proteins, such as enzymes and hormones, are found in minute quantities. Proteins' significance stems primarily from their function. So far, all enzymes discovered have been proteins. Enzymes are the catalysts for all metabolic reactions, allowing an organism to build up the chemical substances required for life—proteins, nucleic acids, carbohydrates, and lipids—convert them to other substances, and degrade them. It is impossible to live without enzymes. There are a number of protein hormones that play important regulatory roles. The respiratory protein haemoglobin serves as an oxygen carrier in the blood, transporting oxygen from the lungs to body organs and tissues in all vertebrates. The structure of the animal body is maintained and protected by a large group of structural proteins.