Essential introduction of Biomolecules
This blog discusses Biomolecules, Nucleic acid, carbohydrates, Cell membrane, Lipids, Enzymes, Vitamins, Proteins, Alpha helix, and Beta sheets.
In the previous blog, we have summarized the detailed composition of the cell membrane. The contents of plasms membrane, their structure, function, and their chemical composition. In Which contains lipids, carbohydrates, and proteins. Biochemistry is the branch of science which deals with all these molecules, and it is BIOMOLECULES. These are carbon-based organic compounds that are produced from living organisms.
Today we will take a brief view of all these biomolecules, their function, and their structures. There are more than 25 chemical elements naturally found in biomolecules. Still, it primarily comprises carbon, oxygen, nitrogen, hydrogen, phosphorus, and Sulphur.
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Among all these elements, carbon, hydrogen, oxygen, and nitrogen cover 96% of the total cell. The 3% part is covered with Sulphur, phosphorus, calcium, and potassium. The remaining 1% is covered by the rest of the elements. Biomolecules include both large and small molecules. Here large and small are decided on the basis of molecular weight, small is with a low molecular weight that is less than 1000, and large are comes under molecular weight more than 1000.
These biomolecules can divide into two parts viz; low molecular weight compounds like vitamins, sugars, hormones, fatty acids, nucleotides, etc.; are termed as MICROMOLECULES, where on the other hand high molecular weight compounds like proteins, carbohydrates, nucleic acids are known as MACROMOLECULES. These macromolecules are polymers of micro molecules.
BIOMOLECULES: AMINO ACIDS AND PROTEINS
Amino acids contain carbon, oxygen, hydrogen, and nitrogen it serves as a building block of protein. It contains both amino and carboxyl acid groups. The differentiation of the various amino acids is from the side chain present on it. The functional group attached to the carbon is known as alpha carbon. Other than alpha carbon, there are beta, gamma, delta, epsilon, etc., continue till the last Greek alphabet omega depending upon the location of carbon to which amino group is attached.
The primary functional group is the carboxylic acid (COOH) group. A total of 20 amino acids were found. Nine are essential amino acids that we take from the diet. Five are non-essential amino acids synthesized in the body. Among all the 20 amino acids, Proline is the only amino acid secondary as it possesses secondary amino acid, also known as imino acid. Amino acids can be polar, non-polar, essential, non-essential, semi-essential, ketogenic, and gluconeogenic.
Two or more amino acids combine together and form a compound called a peptide. When two amino acids combine, they are attached via a peptide bond which is rigid and planar, and forms dipeptide similarly; when three amino acids combine, they form tripeptide. Always remember when two amino acids combine, they are connected through one peptide bond and removal of one water molecule. When many amino acids combine, they form a polypeptide.
The average molecular weight of standard amino acids is about 138. Peptides and polypeptides are linear and mostly unbranched polymers of amino acids. The peptide bond is polar; it forms between C – N. The bond has a partial double bond character. The H atom of the NH2 group possesses a partial positive charge. In contrast, the O atom of the carboxyl group has a partial negative charge. Dihedral angles present in the structure of amino acids viz.
- C – N – Ω
- C – Calpha– Ψ
- N – Calpha – Φ
Φ and Ψ have a value between +180o to -180o, while Ω is 180 o in trans conformation and 0o at cis conformation.
Structure of protein
As we know, amino acids are the building blocks of proteins. They are arranged in a specific manner to form a protein structure. These protein structures are present in the primary, secondary, tertiary, and quaternary forms. A protein’s secondary structure is taken as a functional form that can be present in 3 forms, for example, alpha-helix, beta-sheet, and turns or loops. The distance between two amino acids is almost 1.5 A0. These proteins can be fibrous proteins, such as collagen, keratin present in nails, hairs, fibroin present in silk, and globular proteins, such as hemoglobin in RBCs and myoglobin.
NUCLEIC ACID AS BIOMOLECULES
First, it was discovered by Friedrich Miescher from the pus cells nuclei that is from leucocytes of pus cell on surgical bandages and called it nuclein. Its nucleoprotein. After this, Richard Altman, in 1889, obtain material which is first protein-free material, which he named nucleic acid. It is a polymer of nucleotides hence also called polynucleotides.
Two types of nucleic acids are there viz . Deoxyribonucleic Acid (DNA)Ribonucleic Acid (RNA)
A nucleotide is a monomeric unit of nucleic acid; it is a phosphate ester of a nucleoside. It contains three components
- Nitrogenous base
- A five-carbon sugar and
- Phosphate group
Nitrogenous bases can be purine or pyrimidine. Among these purines contain adenine and guanine, while cytosine, thymine, uracil comes under pyrimidine. A five-carbon sugar contains beta D- ribose sugar, a part of RNA, and beta D-2-deoxyribose sugar, a part of DNA in which the 2′ OH group of ribose sugar is replaced by Hydrogen (H). formation of energy currency that is ATP, GTP is one of the functions performed by the nucleic acids. It is also acting as a precursor for many important coenzymes, for example, NAD+, NADP+, FAD, etc., detail about all these enzymes, coenzymes, DNA, RNA we will discuss in upcoming blogs.
CARBOHYDRATES AS BIOMOLECULES
Carbohydrates are polyhydroxy aldehydes or polyhydroxy ketones. Carbohydrates are also called hydrates of carbon. The majority of it contains an equal proportion of H and O. These are getting classify based on their dissociation product number after hydrolysis. For example
- Monosaccharides – these contain a single polyhydroxy aldehyde or polyhydroxy ketone unit. These are simple sugars with the formula CnH2nOn. These are colorless and crystalline solids insoluble in non-polar solvents and easily soluble in polar solvents like water. It classified as
Aldoses – monosaccharides with an aldehyde group. For example – Glyceraldehyde
Ketoses –monosaccharide with ketone group. For example – Dihydroxyacetone
Suffix’-oses’ is an indication of the presence of carbohydrates. The prefix’ tri-, tetr-, pent- ‘Indicates the number of carbon atoms.
- Oligosaccharides – these are polymers made up of two to ten monosaccharides. These can be classified based on several monosaccharides present, viz. disaccharides, trisaccharide, tetrasaccharide. Most abundant is a disaccharide with two monosaccharide units.
- Polysaccharides – are polymers with hundreds or thousands of monosaccharide units. Polysaccharides are not sweet in taste, so they are also called non-sugars.
Various derivatives of these monosaccharides, oligosaccharides, and polysaccharides are present. And various compounds consisting of carbohydrates as it is the most abundant biomolecule on earth. Glycoproteins are the compounds in which carbohydrates are covalently linked with non-carbohydrates compounds. Carbohydrates, when reacts with an oxidizing agent it is classified as reducing sugar, and when react with a reducing agent known as a non-reducing sugar.
LIPIDS
As in the previous blog, we have covered the detailed structure and composition of lipids. As we know, it is insoluble in polar solvent or poorly soluble in water and readily soluble in a non-polar solvent, for example, ether, chloroform, etc. lipid hydrophobicity is due to the presence of hydrocarbon chains (–CH2 – CH2 – CH2 – ) in its structure.
The special fact about lipid is it not a polymer like protein and carbohydrates. The transport and storage function for fuel requires in all the metabolic activity is serves by lipid molecules. It provides structural integrity to the cell membrane. Apart from its normal routine function biologically, it works as a pigment, hormones, cofactor like vitamin K, signaling molecule like eicosanoids, and detergent.
A fatty acid is the simplest form of lipid and constitutes many complex structures. It is a long chain hydrocarbon around 4 to 36 carbon long with one carboxyl group. Fatty acids are also amphipathic in nature that is having both polar and non-polar ends. The most common fatty acids are 16 to 18 carbon-containing. These fatty acids can be SATURATED and UNSATURATED.
SATURATED FATTY ACIDS – these type of fatty acids does not have any double bond in its structure
UNSATURATED FATTY ACIDS – these types of fatty acids contain one or more double bonds in their structure.
VITAMINS
To perform the specific cellular function, our body needs some special organic compounds which are not synthesized in our body. These are known as vitamins. The requirement of vitamins is different for different organisms, and it is mainly classified on the basis of its function and solubility.
The requirement of vitamins is accomplished through diet. Among all vitamins, nine vitamins viz thiamine(B1), riboflavin(B2), niacin(B3), biotin, folic acid, cobalamin(B12), ascorbic acid(C), pantothenic acid(B5), and pyridoxine(B6) are water-soluble, whereas four vitamins that are vitamin. Retinol(A), cholecalciferol/calciol(D), K, and E you can remember it as “Dr. Adke” are fat-soluble. All water-soluble vitamins are precursors of coenzymes, except vitamin C.
Vitamins serve various functions, for example, vit K as an anticoagulant for blood, Vit A has a role in vision, growth, and various diseases, vit D regulates calcium and phosphate metabolism, Vit E and C as antioxidants, etc.;
ENZYMES AS BIOMOLECULES
Enzymes are like a guide for every reaction that happens in our body; these are works as biocatalysts. They increase the rate of reaction without affecting themselves through overall reaction. The various properties of enzymes make them unique and important biomolecules. Most enzymes are proteins, but not all. These are highly specific biomolecules with a high degree of specificity. These proteinaceous enzymes get divided into two classes, viz simple enzymes, and conjugated enzymes.
Simple enzymes contain amino acids, while conjugated amino acids contain protein as well as non-protein components. This non-protein part is known as a cofactor, while without cofactor there is only the protein part will be left, which is known as apoenzyme. A cofactor is the most active part of the conjugated enzyme, which is required for the biological reaction, while an apoenzyme is biologically inactive. Cofactor plus apoenzyme is combinedly referred to as holoenzyme. On the basis of enzyme functions, they are classified into various classes, and they are numbered as EC (Enzyme Commission) viz.
Classification of enzymes
| Enzyme name | Function | Examples |
| EC 1 Oxidoreductase | Catalyze oxidation reaction | Oxidases, oxygenases, dehydrogenases etc. |
| EC 2 Transferases | Transfer of group from one molecule to another | Kinases, transaminases etc. |
| EC 3 Hydrolases | Cleavage of bond by adding water | Phosphatases, peptidases |
| EC 4 Lyases | Catalyze breaking of bonds | Synthases, aldolases etc. |
| EC 5 Ligases | Catalyze formation of bond | Carboxylases |
| EC 6 Isomerases | Catalyze intramolecular rearrangements | Epimerases, mutases etc. |
I hope all your questions related to the fundamentals of biochemistry will clear after reading this huge blog. Stay connected for more such interesting facts.
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