Ch.09  Biomolecules

Analysis of Chemical Composition: For this, a living tissue is taken. The tissue is ground in trichloroacetic acid (Cl3CCOOH); by using pestle and mortar. The slurry is then filtered through a cloth. The filtrate contains acid-soluble pool and the retentate contains acid-insoluble fraction. Organic compounds are found in the acid-soluble pool, while inorganic substances are found in acid-insoluble fraction.

Biomolecules: All the carbon compounds which are obtained from living tissues are called biomolecules.

AMINO ACIDS

Amino acids are organic compounds which contain an amino group and an acidic group as substituents on the same carbon, i.e. α-carbon. Due to this, they are called α-amino acids. The amino acids are substituted methanes. There are four substituent groups which occupy the four valency positions. These groups are; hydrogen, carboxyl group, amino group and a variable group; called R group. The nature of the R-group governs a amino acid.

However, there are only 21 types of amino acids which occur in proteins. The R-group in these proteinaceous amino acids could be of various types. The amino, carboxyl and the R functional groups decide the chemical and physical properties of an amino acid.

Amino acid with a hydrogen is called glycine, one with a methyl group is called alanine, one with hydroxyl methyl group is called serine, etc. Based on the number of amino and carboxyl group, the amino acids can be acidic, basic or neutral. A feature of amino acid is the ionizable nature of –NH2 and –COOH groups. Hence, structure of amino acids changes in solutions of different pH.

LIPIDS

• Lipids are usually insolub le in water. Lipids can be simple fatty acids and some lipids have phosphorous and phosphorylated organic compounds in them. Lipids; containing phosphorus; are called phospholipids. A fatty acid has a carboxyl group attached to an R group. The R group can be a methyl or ethyl or higher number of CH2 group (1 carbon to 19 carbons).

• Fatty acids could be saturated or unsaturated. Many lipids have both glycerol and fatty acids. In this case, the fatty acids are found esterified with glycerol. They can be monoglycerides, diglycerides and triglycerides. Based on melting points, they can be termed as fats and oils. Oils have lower melting points while fats have higher melting points.

• There are several carbon compounds; with heterocyclic rings; found in living organisms. Some of them are nitrogenous bases, e.g. adenine, guanine, cytosine, uracil and thymine. When a nitrogenous base is attached to a sugar, it is called a nucleoside, e.g. adenosine, guanosine, thymidine, uridine and cytidine. If a phosphate group is also found esterified to the sugar then they are called nucleotides, e.g. adenylic acid, thymidylic acid, guanylic acid, uridylic acid and cytidylic acid.

• Primary Metabolites: Metabolites which have identifiable functions are called primary metabolites. They play known key roles in normal physiological processes. All the primary metabolites are found in animal cells.

• Secondary Metabolites: There are certain metabolites about which we do not have enough information to suggest their role in physiological processes. Such metabolites are called secondary metabolites. Secondary metabolites are not found in animal cells.

Mircomolecules: Biomolecules with molecular eights less than one thousand Dalton are called micromolecules or simple as biomolecules.

Biomacromolecules: Biomolecules with molecular weights more than one thousand Dalton are called biomacromolecules. These are found in the acid-insoluble fraction.

PROTEINS

• Protein is a polymer of amino acids. Based on similar or different monomers repeating in a protein, it is classified as homopolymer and heteropolymer. When same monomer is repeated in the protein, it is called homopolymer. When different monomers are present in the protein, it is called heteropolymer.

• Essential Amino Acids: Some amino acids are essential for our health. But our body does not make them and they need to be supplemented through diet. Such amino acids are called essential amino acids. Collagen is the most abundant protein in the animal world. Ribulose biphosphate Carboxylase-Oxygenase (RUBISCO) is the most abundant protein in the whole biosphere.

POLYSACCHARIDES

• The long chains of sugars are called polysachharides. If a polysaccharide is made up of similar monosaccharides, it is called homopolymer, e.g. cellulose. If a polysaccharide is made up of different monosaccharides, it is called heteropolymer.

• The right end of a polysaccharide chain is called the reducing end and the left end is called the non-reducing end.

• Starch forms helical secondary structures. Starch can hold I2 (iodine) molecules in helical portion. Cellulose does not contain complex helices and hence cannot hold I2.

• In a polysaccharide chain, the right end is called the reducing end and the left end is called the non-reducing end. Starch forms helical secondary structures. In fact, starch can hold I2 molecules in the helical portion.

NUCLEIC ACIDS

• A nucleic acid is composed of nucleotide. There are three chemically distinct components in a nucleotide. One of them is a heterocyclic compound, the second is a monosaccharide and the third is phosphoric acid or phosphate.

• The heterocyclic compounds; present in nucleic acids are the nitrogenous bases, viz. adenine, guanine, uracil, cytosil and thymine. Adenine and Guanine are substituted purines, while uracil, cytosil and thymine are substituted pyrimidines.

• Based on the presence of purine or pyrimidine, the heterocyclic ring is called purine and pyrimidine. Polynucleotides contain either ribose sugar or 2’ deoxyribose sugar. If ribose sugar is present, then the nucleic acid is called ribonucleic acid (RNA). If deoxyribose sugar is present, then the nucleic acid is called deoxyribose nucleic acid (DNA).

STRUCTURE OF PROTEINS​

• Primary Structure: The sequence of amino acids is called the primary structure of a protein. The left end is represented by the first amino acid, while the right end is represented by the last amino acid. The first amino acid is also called N-terminal amino acid. The last amino acid is called C-terminal amino acid.

• Secondary Structure: The protein is not a linear chain of amino acids rather the chain would bend at some places and even form helices. Regularly repeating local structures gives secondary structure to protein.

• Tertiary Structure: The overall shape of a protein molecule; and the spatial relationship of the secondary structures to one another; is called tertiary structure of protein. In other words, the various folds which give three dimensional appearances to protein form its tertiary structure.

• Quaternary Structure: The way the individual folded polypeptides are arranged with respect to each other is called quaternary structure of protein.

Nature of Bonds linking monomers​

• Glycosidic Bond: Certain type of functional group which joins a sugar molecule to another group is called glycosidic bond. Another group may or may not be another carbohydrate.nd is the linkage between the 3’ carbon atom of one sugar molecule and the 5’ carbon atom of another.

• Peptide Bond: A chemical bond formed between two molecules; when the carboxyl group of one molecule reacts with the amine group of another molecule; is called peptide bond (amide bond). A molecule of water is released during this reaction. This is a dehydration synthesis reaction and usually occurs between two amino acids. This is also known as a condensation reaction. The resulting CO – NH bond is called a peptide bond. The resulting molecule is called an amide. The four-atom functional group – C (=O) NH – is called an amide group or a peptide group.

• Phospho-diester Bond: A group of strong covalent bonds between a phosphate group and two other molecules over two ester bonds is called a phosphor-diester bond. Phosphodiester bonds make the backbone of the strands of DNA and hence are central to all life on Earth. In DNA and RNA, the phosphodiester bonds

DYNAMIC STATE OF BODY CONSTITUENTS – CONCEPT OF METABOLISM​

• Metabolism: All the biomolecules are constantly being changed into some other biomolecules and made from some other biomolecules. The turnover of biomolecules takes place continuously. All these reactions are together called metabolism.

• Anabolism: When a complex biomolecule is synthesized from simple biomolecules through a biological process, the process is called anabolism. Energy is utilized during anabolism.

• Catabolism: When a complex biomolecule is disintegrated to produce simple biomolecules through a biological process, the process is called catabolism. Energy is released during catabolism.

• Metabolic Pathway: Metabolites are converted into each other in a series of linked reactions. Such a series of linked reactions is called metabolic pathway. Every chemical reaction in the metabolic pathways is a catalyzed reaction. The metabolic pathways are either linear or circular. These pathways crisscross each other; which means there are traffic junctions. But the interlinked metabolic traffic is very smooth and no single mishap has been reported for healthy conditions.

• The Living State: All living organisms exist in a steady state; characterized by concentrations of each of the biomolecules. The steady state is a non-equilibrium state. It can be said that the living process is a constant effort to prevent falling into equilibrium. Without metabolism, there cannot be a living state.

ENZYMES​

• An enzyme is a catalyst which is utilized in metabolic reactions. Almost all enzymes are proteins.

• "Lock and Key" Model: The lock and key model was suggested by Emil Fischer in 1894. Emil Fischer postulated that both the enzyme and the substrate possess specific complementary geometric shapes that fit exactly into one another. This model explains the specificity of enzyme. But this model fails to explain the stabilization of the transition state which an enzyme achieves.

• Induced Fit Model: This is the most accepted model and is a modification over the lock and key model. The induced fit model was proposed by Daniel Koshland in 1958. Per this model, since enzymes are rather flexible structures; the active site is continually reshaped by interactions with the substrate when the substrate interacts with the enzyme. In some cases, the substrate molecule also changes shape slightly when it enters the active site. The active site continues to change until the substrate is completely bound. The final shape and charge is determined at this point of enzyme-substrate reaction.

• There are many differences between enzyme catalysts and inorganic catalysts. Inorganic catalysts work efficiently at high temperatures and high pressures, enzymes get damaged at high temperatures (above 40°C). But enzymes which are isolated from thermophilic organisms show thermal stability.

Mechanisms of Enzymatic Actions

• Enzyme lowers the activation energy by creating an environment in which the transition state is stabilized.

• Enzyme lowers the energy of the transition state by creating an environment with the opposite charge distribution to that of the transition state. But an enzyme does this without distorting the substrate.

• Enzyme provides an alternative pathway.

• Enzyme reduces the reaction entropy charge by bringing substrates together in the correct orientation to react.

• Increase in temperatures speeds up reactions. But if the enzyme is heated too much, its shape deteriorates and it regains it shape only when the temperature comes back to normal. Some enzymes work best at low temperatures, e.g. thermolabile.

• The catalytic cycle of an enzyme action can be described in the following steps:

• The substrate binds to the active site of the enzyme, fitting into the active site.

• The binding of the substrate induces the enzyme to alter its shape, fitting more tightly around the substrate.

• The active site of the enzyme breaks the chemical bonds of the substrate and the new enzyme- product complex is formed.

• The enzyme releases the products of the reaction and the free enzyme is ready to bind to another molecule of the substrate.

Factors Affecting Enzyme Activity

• Temperature and pH: Enzymes usually function in a narrow range of temperature and pH. Each enzyme shows its highest activity at optimum temperature and optimum pH. Beyond that range, the activity declines. Low temperature preserves the enzyme temporarily in inactive state, while high temperature destroys the enzyme.

• Concentration of Substrate: The velocity of enzymatic action at first rises with an increase in substrate concentration. But the velocity of reaction does not rise once it reaches a maximum velocity (Vmax). This happens because there are fewer molecules of enzyme and no free enzyme molecule is left to bind with the additional substrate molecules.

• Effect of Inhibitor: When the inhibitor closely resembles the substrate, and inhibits the activity of an enzyme, it is known as competitive inhibitor. Because of its close structural similarity with the substrate, the inhibitor competes with the substrate for the binding site on the enzyme. Such competitive inhibitors are often used in the control of bacterial pathogens.

Classification and Nomenclature of Enzymes

Enzymes are divided into 6 classes each with 4-13 subclasses and named accordingly by a four-digit number.

1. Oxidoreductases/dehydrogenases: Enzymes which catalyze oxidoreduction between two substrates S and S’.

2. Transferases: Enzymes catalyzing a transfer of a group, G (other than hydrogen) between a pair of substrate S and S’.

3. Hydrolases: Enzymes catalyzing hydrolysis of ester, ether, peptide, glycosidic, C-C, C-halide or P-N bonds.

4. Lyases: Enzymes that catalyze removal of groups from substrates by mechanisms other than hydrolysis leaving double bonds.

5. Isomerases: Includes all enzymes catalyzing inter-conversion of optical, geometric or positional isomers.

6. Ligases: Enzymes catalyzing the linking together of 2 compounds, e.g., enzymes which catalyze joining of C-O, C-S, C-N, P-O etc. bonds.

Co-factors

• In many cases, non-protein constituents are bound to the enzyme which makes the enzyme catalytically inactive. Such non-protein constituents are called cofactors. In such cases, the protein portion of the enzyme is called the apoenzyme. There are three kinds of cofactors, viz. prosthetic groups, co-enzymes and metal ions.

• Prosthetic Groups: Prosthetic groups are organic compounds. They are distinguished from other cofactors in that they are tightly bound to the apoenzyme. For example, in peroxidase and catalase, which catalyze the breakdown of hydrogen peroxide to water and oxygen, haem is the prosthetic group and it is a part of the active site of the enzyme.

Co-enzymes:​

• Co-enzymes are also organic compounds but their association with the apoenzyme is only transient. A co-enzyme’s association; with apoenzyme; usually occurs during catalysis. Moreover, co-enzymes serve as co-factors in several different enzyme catalyzed reactions. The essential chemical components of many coenzymes are vitamins, e.g., coenzyme nicotinamide adenine dinucleotide (NAD) and NADP contain the vitamin niacin.

• Metal Ions: Several enzymes require metal ions for their activity. Such metal ions form coordination bonds with side chains at the active site and at the same time form one or

• more coordination bonds with the substrate, e.g., zinc is a cofactor for the proteolytic enzyme carboxypeptidase. Catalytic activity is lost when the co-factor is removed from the enzyme which proves that they play a crucial role in the catalytic activity of the enzyme.