A biomolecule is any organic Organic Chemistry is a discipline within chemistry that involves the scientific study of the structure, properties, composition, reactions, and preparation of hydrocarbons and their derivatives. These compounds may contain any number of other elements, including hydrogen, nitrogen, oxygen, the halogens as well as phosphorus, silicon and sulfur. molecule A molecule is defined as an electrically neutral group of at least two atoms in a definite arrangement held together by very strong chemical bonds. Molecules are distinguished from polyatomic ions in this strict sense. In organic chemistry and biochemistry, the term molecule is used less strictly and also is applied to charged organic molecules that is produced by a living organism The term "organism" first appeared in the English language in 1701 and took on its current definition by 1834 (Oxford English Dictionary), including large polymeric A polymer is a large molecule composed of repeating structural units typically connected by covalent chemical bonds. While polymer in popular usage suggests plastic, the term actually refers to a large class of natural and synthetic materials with a variety of properties molecules such as proteins Proteins are organic compounds made of amino acids arranged in a linear chain and folded into a globular form. The amino acids in a polymer are joined together by the peptide bonds between the carboxyl and amino groups of adjacent amino acid residues. The sequence of amino acids in a protein is defined by the sequence of a gene, which is encoded, polysaccharides Polysaccharides are polymeric carbohydrate structures, formed of repeating units joined together by glycosidic bonds. These structures are often linear, but may contain various degrees of branching. Polysaccharides are often quite heterogeneous, containing slight modifications of the repeating unit. Depending on the structure, these macromolecules, and nucleic acids A nucleic acid is a macromolecule composed of chains of monomeric nucleotides. In biochemistry these molecules carry genetic information or form structures within cells. The most common nucleic acids are deoxyribonucleic acid and ribonucleic acid (RNA). Nucleic acids are universal in living things, as they are found in all cells and viruses as well as small molecules In the fields of pharmacology and biochemistry, a small molecule is a low molecular weight organic compound which is by definition not a polymer. The term small molecule, especially within the field of pharmacology, is usually restricted to a molecule that also binds with high affinity to a biopolymer such as protein, nucleic acid, or such as primary metabolites Metabolites are the intermediates and products of metabolism. The term metabolite is usually restricted to small molecules. A primary metabolite is directly involved in normal growth, development, and reproduction. A secondary metabolite is not directly involved in those processes, but usually has an important ecological function. Examples include, secondary metabolites Secondary metabolites are organic compounds that are not directly involved in the normal growth, development, or reproduction of organisms. Unlike primary metabolites, absence of secondary metabolities does not result in immediate death, but rather in long-term impairment of the organism's survivability, fecundity, or aesthetics, or perhaps in no, and natural products A natural product is a chemical compound or substance produced by a living organism - found in nature that usually has a pharmacological or biological activity for use in pharmaceutical drug discovery and drug design. A natural product can be considered as such even if it can be prepared by total synthesis.
As organic molecules, biomolecules consist primarily of carbon Carbon is the chemical element with symbol C and atomic number 6. As a member of group 14 on the periodic table, it is nonmetallic and tetravalent—making four electrons available to form covalent chemical bonds. There are three naturally occurring isotopes, with 12C and 13C being stable, while 14C is radioactive, decaying with a half-life of and hydrogen Hydrogen is the chemical element with atomic number 1. It is represented by the symbol H. With an atomic weight of 1.00794 u, hydrogen is the lightest and most abundant chemical element, constituting roughly 75 % of the Universe's elemental mass. Stars in the main sequence are mainly composed of hydrogen in its plasma state. Naturally occurring, nitrogen Nitrogen is a chemical element that has the symbol N, the atomic number of 7 and an atomic mass 14.00674 u. Elemental nitrogen is a colorless, odorless, tasteless and mostly inert diatomic gas at standard conditions, constituting 78% by volume of Earth's atmosphere, and oxygen Oxygen (pronounced /ˈɒksɨdʒɨn/, OK-si-jin, from the Greek roots ὀξύς (acid, literally "sharp", from the taste of acids) and -γενής (-genēs) (producer, literally begetter) is the element with atomic number 8 and represented by the symbol O. It is a member of the chalcogen group on the periodic table, and is a highly, and, to a smaller extent, phosphorus Phosphorus is the chemical element that has the symbol P and atomic number 15. A multivalent nonmetal of the nitrogen group, phosphorus is commonly found in inorganic phosphate rocks. Elemental phosphorus exists in two major forms - white phosphorus and red phosphorus. Although the term "phosphorescence", meaning glow after illumination, and sulfur Sulfur or sulphur is the chemical element that has the atomic number 16. It is denoted with the symbol S. It is an abundant, multivalent non-metal. Sulfur, in its native form, is a bright yellow crystalline solid. In nature, it can be found as the pure element and as sulfide and sulfate minerals. It is an essential element for life and is found in. Other elements sometimes are incorporated but are much less common.
Contents |
Types of biomolecules
A diverse range of biomolecules exist, including:
- Small molecules In the fields of pharmacology and biochemistry, a small molecule is a low molecular weight organic compound which is by definition not a polymer. The term small molecule, especially within the field of pharmacology, is usually restricted to a molecule that also binds with high affinity to a biopolymer such as protein, nucleic acid, or:
- Lipids Lipids are a broad group of naturally-occurring molecules which includes fats, waxes, sterols, fat-soluble vitamins , monoglycerides, diglycerides, phospholipids, and others. The main biological functions of lipids include energy storage, as structural components of cell membranes, and as important signaling molecules, phospholipids Phospholipids are a class of lipids and are a major component of all cell membranes as they can form lipid bilayers. Most phospholipids contain a diglyceride, a phosphate group, and a simple organic molecule such as choline; one exception to this rule is sphingomyelin, which is derived from sphingosine instead of glycerol, glycolipids Glycolipids are carbohydrate-attached lipids. Their role is to provide energy and also serve as markers for cellular recognition, sterols Sterols are an important class of organic molecules. They occur naturally in plants, animals and fungi, with the most familiar type of animal sterol being cholesterol. Cholesterol is vital to cellular function, and a precursor to fat-soluable vitamins and steroid hormones, glycerolipids
- Carbohydrates A carbohydrate is an organic compound with general formula Cmn, that is, consisting only of carbon, hydrogen and oxygen, the last two in the 2:1 atom ratio. Carbohydrates can be viewed as hydrates of carbon, hence their name, sugars Sugar is an informal term for class of edible crystalline substances, mainly sucrose, lactose, and fructose. They have characteristically a sweet flavor. In food, sugar almost exclusively refers to sucrose, which primarily comes from sugar cane and sugar beet. Excessive consumption of sucrose has been associated with increased incidences of type 2
- Vitamins A vitamin is an organic compound required as a nutrient in tiny amounts by an organism. The term 'vitamin' first became popular in the early 1800s as a contraction of the words 'vital' and 'mineral', though the actual meaning of the word has developed somewhat since that time. A compound is called a vitamin when it cannot be synthesized in
- Hormones A hormone is a chemical released by one or more cells that affects cells in other parts of the organism. Only a small amount of hormone is required to alter cell metabolism. It is essentially a chemical messenger that transports a signal from one cell to another. All multicellular organisms produce hormones; plant hormones are also called, neurotransmitters Neurotransmitters are endogenous chemicals which relay, amplify, and modulate signals between a neuron and another cell. Neurotransmitters are packaged into synaptic vesicles that cluster beneath the membrane on the presynaptic side of a synapse, and are released into the synaptic cleft, where they bind to receptors in the membrane on the
- Metabolites Metabolites are the intermediates and products of metabolism. The term metabolite is usually restricted to small molecules. A primary metabolite is directly involved in normal growth, development, and reproduction. A secondary metabolite is not directly involved in those processes, but usually has an important ecological function. Examples include
- Monomers A monomer is a small molecule that may become chemically bonded to other monomers to form a polymer. The most common natural monomer is glucose, which is linked by glycosidic bonds into polymers such as cellulose and starch, and is over 76% of the weight of all plant matter:
- Amino acids Amino acids are molecules containing an amine group, a carboxylic acid group and a side chain that varies between different amino acids. These molecules are particularly important in biochemistry, where this term refers to alpha-amino acids with the general formula H2NCHRCOOH, where R is an organic substituent. In the alpha amino acids, the amino
- Nucleotides Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides play central roles in metabolism. In that capacity, they serve as sources of chemical energy , participate in cellular signaling (cyclic guanosine monophosphate and cyclic adenosine monophosphate), and are incorporated into
- Monosaccharides Monosaccharides are the most basic units of biologically important carbohydrates. They are the simplest form of sugar and are usually colorless, water-soluble, crystalline solids. Some monosaccharides have a sweet taste. Examples of monosaccharides include glucose (dextrose), fructose (levulose), galactose, xylose and ribose. Monosaccharides are
- Polymers A polymer is a large molecule composed of repeating structural units typically connected by covalent chemical bonds. While polymer in popular usage suggests plastic, the term actually refers to a large class of natural and synthetic materials with a variety of properties:
- Peptides Peptides are short polymers formed from the linking, in a defined order, of α-amino acids. The link between one amino acid residue and the next is called an amide bond or a peptide bond, oligopeptides, polypeptides Peptides are short polymers formed from the linking, in a defined order, of α-amino acids. The link between one amino acid residue and the next is called an amide bond or a peptide bond, proteins Proteins are organic compounds made of amino acids arranged in a linear chain and folded into a globular form. The amino acids in a polymer are joined together by the peptide bonds between the carboxyl and amino groups of adjacent amino acid residues. The sequence of amino acids in a protein is defined by the sequence of a gene, which is encoded
- Nucleic acids A nucleic acid is a macromolecule composed of chains of monomeric nucleotides. In biochemistry these molecules carry genetic information or form structures within cells. The most common nucleic acids are deoxyribonucleic acid and ribonucleic acid (RNA). Nucleic acids are universal in living things, as they are found in all cells and viruses, DNA Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms and some viruses. The main role of DNA molecules is the long-term storage of information. DNA is often compared to a set of blueprints or a recipe, or a code, since it contains the instructions needed, RNA Ribonucleic acid is a biologically important type of molecule that consists of a long chain of nucleotide units. Each nucleotide consists of a nitrogenous base, a ribose sugar, and a phosphate. RNA is very similar to DNA, but differs in a few important structural details: in the cell, RNA is usually single-stranded, while DNA is usually double-
- Oligosaccharides An oligosaccharide is a saccharide polymer containing a small number of component sugars, also known as simple sugars. The name is derived from the Greek word oligos, meaning "a few", and from the Latin/Greek word sacchar which means "sugar". Oligosaccharides can have many functions for example, they are commonly found on the, polysaccharides Polysaccharides are polymeric carbohydrate structures, formed of repeating units joined together by glycosidic bonds. These structures are often linear, but may contain various degrees of branching. Polysaccharides are often quite heterogeneous, containing slight modifications of the repeating unit. Depending on the structure, these macromolecules (including cellulose Cellulose is an organic compound with the formula n, a polysaccharide consisting of a linear chain of several hundred to over ten thousand β(1→4) linked D-glucose units)
- Cellulose Cellulose is an organic compound with the formula n, a polysaccharide consisting of a linear chain of several hundred to over ten thousand β(1→4) linked D-glucose units, lignin Lignin or lignen is a complex chemical compound most commonly derived from wood, and an integral part of the secondary cell walls of plants and some algae. The term was introduced in 1819 by de Candolle and is derived from the Latin word lignum, meaning wood. It is one of the most abundant organic polymers on Earth, exceeded only by cellulose,
- Hemoglobin Hemoglobin is the iron-containing oxygen-transport metalloprotein in the red blood cells of vertebrates, and the tissues of some invertebrates
Nucleosides and nucleotides
Main articles: Nucleosides Nucleosides are glycosylamines consisting of a nucleobase bound to a ribose or deoxyribose sugar. Examples of these include cytidine, uridine, adenosine, guanosine, thymidine and inosine and Nucleotides Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides play central roles in metabolism. In that capacity, they serve as sources of chemical energy , participate in cellular signaling (cyclic guanosine monophosphate and cyclic adenosine monophosphate), and are incorporated intoNucleosides are molecules formed by attaching a nucleobase Nucleobases are the parts of DNA and RNA that may be involved in pairing (see also base pairs). The main ones are cytosine, guanine, adenine (DNA and RNA), thymine (DNA) and uracil (RNA), abbreviated as C, G, A, T, and U, respectively. They are usually simply called bases in genetics. Because A, G, C, and T appear in the DNA, these molecules are to a ribose Ribose, is an organic compound with formula C5H10O5; specifically, a monosaccharide with linear form H-(C=O)-(CHOH)4-H, which has all the hydroxyl groups on the same side in the Fischer projection ring. Examples of these include cytidine Cytidine is a nucleoside molecule that is formed when cytosine is attached to a ribose ring via a β-N1-glycosidic bond. Cytidine is a component of RNA, uridine, adenosine, guanosine, thymidine and inosine.
Nucleosides can be phosphorylated by specific kinases in the cell, producing nucleotides. Both DNA and RNA are polymers, consisting of long, linear molecules. The repeating structural units, or monomers, of the nucleic acids are called nucleotides.[1]
Each nucleotide is made of an acyclic nitrogenous base, a pentose and one to three phosphate groups. They contain carbon, nitrogen, oxygen, hydrogen and phosphorus. They serve as sources of chemical energy (adenosine triphosphate and guanosine triphosphate), participate in cellular signaling (cyclic guanosine monophosphate and cyclic adenosine monophosphate), and are incorporated into important cofactors of enzymatic reactions (coenzyme A, flavin adenine dinucleotide, flavin mononucleotide, and nicotinamide adenine dinucleotide phosphate).[2]
Saccharides
Monosaccharides are the simplest form of carbohydrates with only one simple sugar. They essentially contain an aldehyde or ketone group in their structure.[3] The presence of an aldehyde group in a monosaccharide is indicated by the prefix aldo-. Similarly, a ketone group is denoted by the prefix keto-.[1] Examples of monosaccharides are the hexoses glucose, fructose, and galactose and pentoses, ribose, and deoxyribose Consumed fructose and glucose have different rates of gastric emptying, are differentially absorbed and have different metabolic fates, providing multiple opportunities for 2 different saccharides to differentially affect food intake.[3]
Disaccharides are formed when two monosaccharides, or two single simple sugars, form a bond with removal of water. They can be hydrolyzed to yield their monosaccharide building blocks by boiling with dilute acid or reacting them with appropriate enzymes.[1] Examples of disaccharides include sucrose, maltose, and lactose.
Polysaccharides are polymerized monosaccharides, complex, carbohydrates. They have multiple simple sugars. Examples are starch, cellulose, and glycogen. They are generally large and often have a complex branched connectivity. Because of their size, polysaccharides are not water-soluble, but their many hydroxy groups become hydrated individually when exposed to water, and some polysaccharides form thick colloidal dispersions when heated in water.[1] Shorter polysaccharides, with 2 - 10 monomers, are called oligosaccharides.[4] A fluorescent indicator-displacement molecular imprinting sensor was developed for discriminating saccharides. It successfully discriminated three brands of orange juice beverage.[5] The change in fluorescence intensity of the sensing films resulting is directly related to the saccharide concentration.[6]
Lignin
Lignin is a random polymer composed mainly of aromatic rings with short (up to three) aliphatic carbons chains connecting the rings. Lignin is the second most common biopolymer (after cellulose) and is one of the primary structural components of most plants. It contains subunits derived from p-coumaryl alcohol, coniferyl alcohol, and sinapyl alcohol[7] and is unusual among biomolecules in that it is racemic i.e. it is not optically active. The lack of optical activity is because the polymerization of lignin occurs via free radical coupling reactions in which there is no preference for either configuration at a chiral center.
Lipids
Lipids are chiefly fatty acid esters, and are the basic building blocks of biological membranes. Another biological role is energy storage (e.g., triglycerides). Most lipids consist of a polar or hydrophilic head (typically glycerol) and one to three nonpolar or hydrophobic fatty acid tails, and therefore they are amphiphilic. Fatty acids consist of unbranched chains of carbon atoms that are connected by single bonds alone (saturated fatty acids) or by both single and double bonds (unsaturated fatty acids). The chains are usually 14-24 carbon groups long, but it is always an even number.
For lipids present in biological membranes, the hydrophilic head is from one of three classes:
- Glycolipids, whose heads contain an oligosaccharide with 1-15 saccharide residues.
- Phospholipids, whose heads contain a positively charged group that is linked to the tail by a negatively charged phosphate group.
- Sterols, whose heads contain a planar steroid ring, for example, cholesterol.
Other lipids include prostaglandins and leukotrienes which are both 20-carbon fatty acyl units synthesized from arachidonic acid. They are also known as fatty acids
Amino acids
Amino acids contain both amino and carboxylic acid functional groups. (In biochemistry, the term amino acid is used when referring to those amino acids in which the amino and carboxylate functionalities are attached to the same carbon, plus proline which is not actually an amino acid).
Amino acids are the building blocks of long polymer chains. With 2-10 amino acids such chains are called peptides, with 10-100 they are often called polypeptides, and longer chains are known as proteins. These protein structures have many structural and enzymatic roles in organisms.
There are twenty amino acids that are encoded by the standard genetic code, but there are more than 500 natural amino acids. When amino acids other than the set of twenty are observed in proteins, this is usually the result of modification after translation (protein synthesis). Only two amino acids other than the standard twenty are known to be incorporated into proteins during translation, in certain organisms:
- Selenocysteine is incorporated into some proteins at a UGA codon, which is normally a stop codon.
- Pyrrolysine is incorporated into some proteins at a UAG codon. For instance, in some methanogens in enzymes that are used to produce methane.
Besides those used in protein synthesis, other biologically important amino acids include carnitine (used in lipid transport within a cell), ornithine, GABA and taurine.
Protein structure
The particular series of amino acids that form a protein is known as that protein's primary structure. This sequence is determined by the genetic makeup of the individual. Proteins have several, well-classified, elements of local structure formed by intermolecular attraction, this forms the secondary structure of protein. They are broadly divided in two, alpha helix and beta sheet, also called beta pleated sheets. Alpha helices are formed of coiling of protein due to attraction between amine group of one amino acid with carboxylic acid group of other. The coil contains about 3.6 amino acids per turn and the alkyl group of amino acid lie outside the plane of coil. Beta pleated sheets are formed by strong continuous hydrogen bond over the length of protein chain. Bonding may be parallel or antiparallel in nature. Structurally, natural silk is formed of beta pleated sheets. Usually, a protein is formed by action of both these structures in variable ratios. Coiling may also be random. The overall 3D structure of a protein is termed its tertiary structure. It is formed as result of various forces like hydrogen bonding, disulfide bridges, hydrophobic interactions, hydrophilic interactions, van der Waals force etc. When two or more different polypeptide chains cluster to form a protein, quaternary structure of protein is formed. Quaternary structure is a unique attribute of polymeric and heteromeric proteins like hemoglobin, which consists of two alpha and two beta peptide chains.
Apoenzymes
An apoenzyme is the inactive storage and generally secretory form of a protein. This is required to protect the secretory cell from the activity of that protein. Apoenzymes becomes active enzyme on addition of a cofactor. Cofactors can be either inorganic (e.g., metal ions and iron-sulfur clusters) or organic compounds, (e.g., flavin and heme). Organic cofactors can be either prosthetic groups, which are tightly bound to an enzyme, or coenzymes, which are released from the enzyme's active site during the reaction.
Isoenzymes
Isoenzymes are enzymes with similar function but different structure. They are products of different genes. They are produced in different organs to perform the same function. LDH are examples of such enzymes. Their varied levels in blood are used to determine any deformity in the organ of secretion.
Vitamins
A vitamin is a compound that is generally not synthesized by a given organism but is nonetheless vital to its survival or health (for example coenzymes). These compounds must be absorbed, or eaten, but typically only in trace quantities. When originally proposed by Casimir Funk, a Polish biochemist, he believed them to all be basic and therefore named them vital amines. The "l" was later dropped to form the word vitamines.
See also
References
- ^ a b c d Slabaugh, Michael R.; Seager, Spencer L. (2007). Organic and Biochemistry for Today (6th ed.). Pacific Grove: Brooks Cole. ISBN 0-495-11280-1.
- ^ Alberts B, Johnson A, Lewis J, Raff M, Roberts K & Wlater P (2002). Molecular biology of the cell (4th ed.). New York: Garland Science. pp. 120–1. ISBN 0-8153-3218-1. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mboc4.TOC&depth=2.
- ^ a b Peng, Bo, and Yu Qin (June 2009). "Fructose and Satiety". Journal of Nutrition: 6137–42.
- ^ Pigman, W.; D. Horton (1972). The Carbohydrates. 1A. San Diego: Academic Press. p. 3. ISBN 68-26647.
- ^ Jin, Tan, Wang He-Fang, and Yan Xiu-Ping (2009). "Discrimination of Saccharides with a Fluorescent Molecular Imprinting Sensor Array Based on Phenylboronic Acid Functionalized Mesoporous Silica". Anal. Chem. 81 (13): 5273–80. doi:10.1021/ac900484x.
- ^ Bo Peng and Yu Qin (2008). "Lipophilic Polymer Membrane Optical Sensor with a Synthetic Receptor for Saccharide Detection". Anal. Chem. 80 (15): 6137–41. doi:10.1021/ac800946p.
- ^ K. Freudenberg & A.C. Nash (eds) (1968). Constitution and Biosynthesis of Lignin. Berlin: Springer-Verlag.
|
|||||
Categories: Biomolecules | Molecules | Biochemistry | Organic compounds
<<Table of Contents | Show All>>
|
