A biomolecule is a chemical compound that naturally occurs in living organisms. Biomolecules consist primarily of carbon and hydrogen, along with nitrogen, oxygen, phosphorus and sulfur. Other elements sometimes are incorporated but these are much less common.
Biomolecules are necessary for the existence of all known forms of life. For example, humans possess skin and hair. The main component of hair is keratin, an agglomeration of proteins which are themselves polymers built from amino acids. Amino acids are some of the most important building blocks used, in nature, to construct larger molecules. Another type of building block is the nucleotides, each of which consists of three components: a purine or pyrimidine base, a pentose sugar and a phosphate group. These nucleotides, mainly, form the nucleic acids.
The fundamental building blocks of living cells are biomolecules which provide the bedrock of life and now pose a research frontier for theoretical physics. All life forms can be considered to be self-organized systems assembled from these building blocks. Even though one can subdivide life into substructures like cell organelles, the entire cell, tissues, multi-cellular organisms, and even societies, biomolecules make their basic role felt across the entire hierarchy of biological order: pheromones link male and females in disperse societies, drugs treat diseases in individuals, cells are guided in their development through hormones, and every process in cells is directly linked to biomolecules. So naturally, the quest for a theory of living systems starts with the fundamental building blocks - biomolecules. But much as the physics of innate matter has derived its successes from the recognition of scales that subdivide the innate world, e.g., quarks, nuclei, molecules, so life appears to be governed by its own system of scales that provide a staircase to the ultimate goal of understanding human life.
The characterization of biological systems at the molecular level is now slowly reaching a precision that compares well with that to which the physical sciences have been accustomed. This is particularly true at the biomolecular level that ultimately is the foundation for all of life. The new data, like numerous high resolution structures of biomolecules or single molecule recordings, pose a challenge to the life sciences that can be largely met through the conceptual and methodological approaches of theoretical physics. Condensed matter physics and materials science have successfully linked experiment and theory for inorganic matter, often of macroscopic scale; their culture of the combination of experiment and theory can likely benefit living matter when the challenge posed by the inherent finite size and complexity of living matter systems is met.
One of the key functions of certain classes of biomolecules is to either induce or transfer charge carriers of various types (electrons, protons, excitons, etc). Currently the details of the mechanisms of charge separation and subsequent transport, and transduction are poorly understood. To enhance our understanding of these important classes of biomolecular problems, will require new quantum mechanical tools (e.g., advances in density functional theory, quantum chemistry, and quantum Monte Carlo techniques for understanding of charged and excited states), as well as a more detailed understanding of the coupling of the biomolecule to its immediate environment. This is an area whose implications feed back into nanotechnology. Specifically, there is considerable hope in the community for new biomolecular electronic devices and biosensors. Issues likely to be important here are the coupling of biomolecules to inorganic materials leading to new classes of Biomolecular ElectroMechanical Systems (BEMS).
The simplest molecular electronic elements are memory, switch or logic devices, but advances using biomolecules can lead to elements that mimic processes in photosynthesis or respiration. Electrical conduction, or electron transfer, through biomolecules is not as simple to understand or model as in metals and semiconductors, and this complexity presents new challenges for theoretical techniques and technique development. For short molecules, the electron transfer process often is quantum mechanical tunneling. The quantum mechanical nature of the problem can lead to new discoveries and interesting effects such as the Coulomb blockade. The strong electron-vibrational coupling leads to important vibronic effects producing polarons and electron hopping between localized sites. The effects of water, pH, and ions in solution are fundamental topics that have a large effect of the electronic properties of biomolecules, and will surely play important roles in understanding the full potential of devices in bio-environments. There are many opportunities for the further development of the quantum mechanics and many body physics occurring in these areas. The field is just emerging, and there is a need to produce clear successful examples of theory coupled to experiment which produce guideposts for further development.
Recently, the long-standing problem of which biophysical mechanism underlies the physiological compass of birds has been solved, dramatically demonstrating that molecular level calculations can be used to predict animal behavior. Physical theory yields accurate predictions about the effects of weak magnetic fields through different possible magneto-receptor molecules, in particular that very weak oscillating fields in the radiofrequency range will disrupt a compass based on a chemical reaction, but not a compass based on magnetite particles. This prediction has been tested in an experiment, whose results indicate that a chemical mechanism first postulated by theory underlies the magnetic compass.
There are different types of biomolecules. Some of them are-
Carbohydrates are polyhydroxyaldehydes, or polyhydroxyketones, and their derivatives. Carbohydrates are chemical compounds that act as the primary biological means of storing or consuming energy, other forms being fat and protein. Relatively complex carbohydrates are known as polysaccharides. Carbohydrates are naturally produced by plants and animals. Sugars and starches are carbohydrates.
Pure carbohydrates contain carbon, hydrogen, and oxygen atoms, in a 1:2:1 molar ratio, giving the general formula CnH2nOn.
Classification of Carbohydrates:
Carbohydrates are mainly classified as:
Monosaccharides are carbohydrates in the form of simple sugars. Monosaccharides, crystalline, water soluble and sweet tasting. In solution they rotate plane polarized light.
Monosaccharides are classified by the number of carbon atoms they contain (triose, tetrose, pentose, hexose and heptose) and by the active group, which is either an aldehyde or a ketone. These are then combined, e.g. aldohexoses, ketotrioses.
The monosaccharides are classified according to the D or L form of their isomerism as:
A triose is a monosaccharide containing three carbon atoms. There are only two trioses, an aldotriose (Glyceraldehyde) and a ketotriose (Dihydroxyacetone).Trioses are important in respiration.
Glyceraldehyde is a triose carbohydrate with the chemical formula C3H6O3. It is the simplest of all aldoses. It is a sweet colorless crystalline solid that is an intermediate compound in carbohydrate metabolism. The word comes from combining glycerine and aldehyde, as glyceraldehyde is merely glycerine with one hydroxide changed to an aldehyde. Glyceraldehyde has a chiral centre and therefore exists in D- and L- forms.
It may be prepared, along with dihydroxyacetone, by the mild oxidation of glycerol.
Fischer Projection of D-glyceraldehyde:
Dihydroxyacetone is a triose carbohydrate with the chemical formula C3H6O3. It is the simplest of all ketoses and, having no chiral centre, is the only one that has no optical activity.
It may be prepared, along with glyceraldehyde, by the mild oxidation of glycerol, for example with hydrogen peroxide and a ferrous salt as catalyst.
Dihydroxyacetone is used in the cosmetics industry as a tanning substance.
Fischer Projection of Dihydroxyacetone:
A tetrose is a monosaccharide with 4 carbon atoms.
They either have an aldehyde functional group in position 1 (aldotetroses) or a ketone functional group in position 2 (ketotetroses).
The naturally occurring aldotetroses are:
D-erythrose is a tetrose carbohydrate with the chemical formula C4H8O4. It has one aldehyde group and so is part of the aldose family.
Fischer Projection of D-erythrose:
D-threose is a tetrose carbohydrate with the chemical formula C4H8O4. It has one aldehyde group and so is part of the aldose family.
Fischer Projection of D-threose:
The naturally occurring ketotetrose is D-Erythrulose.
D-erythrulose is a tetrose carbohydrate with the chemical formula C4H8O4. It has one ketone group and so is part of the ketose family. It is used in some self-tanning cosmetics.
Fischer Projection of D-erythrulose:
A pentose is a monosaccharide with five carbon atoms.
They either have an aldehyde functional group in position 1 (aldopentoses), or a ketone functional group in position 2 (ketopentoses).
The aldopentoses have three chiral centres.
The 4 D-aldopentoses are:-
Ribose is a five carbon sugar (pentose) that is critical to living creatures. It is a component of the RNA that is used for genetic transcription, and is related to deoxyribose which is a component of DNA. It is also a component of ATP, NADH, and several other chemicals that are critical to the metabolic process.
Haworth Structure of D-Ribose:
Arabinose is a sugar, one of the pentose series of carbohydrates.
Fischer Projection of D-Arabinose:
Xylose is an aldopentose. It is a simple sugar containing five carbon atoms, and including an aldehyde functional group.
It is found in the embryos of most edible plants.
The ketopentoses have 2 chiral centres and therefore 4 possible stereoisomers - ribulose (L- and D- form) and xylulose (L- and D- form).
The aldehyde and ketone functional groups in these carbohydrates react with neighboring hydroxyl functional groups to form intramolecular hemiacetals or hemiketals, respectively. The resulting ring structure is related to furan, and is termed a furanose. The ring spontaneously opens and closes, allowing rotation to occur about the bond between the carbonyl group and the neighboring carbon atom - yielding two distinct configurations (α and β). This process is termed mutarotation.
Ribulose is a sugar or carbohydrate. It is a monosaccharide or pentose and belongs to the series of keto-pentoses. There are two isomers such as D-ribulose (D-erythro-pentulose) and L-ribulose (L-erythro-pentulose).
D-ribulose is a intermediate in the fungal pathway for D-arabitol production.
Xylulose is a sugar. It's a keto-pentose.In nature it occurs in the L- and D- form.
L-xylulose is accumulated in the urin of pentosuria patients. L-xylulose is a reducing sugar like D-glucose.
A hexose is a monosaccharide with six carbon atoms.
They either have an aldehyde functional group in position 1 (aldohexoses), or a ketone functional group in position 2 (ketohexoses).
The aldohexoses have four chiral centres. 16 different stereoisomers are possible. Of these, only 3 occur in nature - D-glucose, D-galactose and D-mannose. There are eight aldohexoses.
Glucose, a simple monosaccharide sugar, is one of the most important carbohydrates and is used as a source of energy in animals and plants. Glucose is one of the main products of photosynthesis and starts respiration. The natural form (D-glucose) is also referred to as dextrose.
Glucose (C6H12O6, molecular weight 180.18) is a hexose—a monosaccharide containing six carbon atoms. Glucose is an aldehyde. Five of the carbons plus an oxygen atom form a loop called a "pyranose ring", the most stable form for six-carbon aldoses. In this ring, each carbon is linked to hydroxyl and hydrogen side groups with the exception of the fifth atom, which links to a 6th carbon atom outside the ring, forming a CH2OH group.
Isomerism of Glucose:
There are two enantiomers of the sugar, D-glucose and L-glucose, but in living organisms, only the D-isomer is found. If the hydroxyl group is to the right in the Fischer projection, then the ring form will be the D enantiomer, if it is to the left, it will be the L enantiomer. D is for "dextro," which is a Latin root for "right," where as L is for "levo" which comes from the Latin root for "left." The ring structure itself may form in two additionally different ways, yielding α (alpha) glucose and β (beta) glucose. The α form has the hydroxyl group "below" the hydrogen, while the β form has the hydroxyl group "above" the hydrogen. These two forms interconvert over a timescale of hours in aqueous solution, to a final stable ratio of α:β 36:64, in a process called mutarotation.
Preparation of Glucose:
Glucose is prepared commercially via the enzymatic hydrolysis of starch.
This enzymatic process has two stages. In the first step, liquefaction, starch slurry is partially hydrolyzed into shorter glucose polymers by a combination of heat and bacterial enzymes. The most common process uses the enzyme α-amylase from the bacteria Bacillus licheniformis or Bacillus stearothermophilus. Over the course of 1-2 hours near 100 °C, these enzymes hydrolyze starch into smaller carbohydrates containing on average 5-10 glucose units each. In the second step, saccharification, the partially hydrolyzed starch is completely hydrolyzed to glucose using the glucoamylase enzyme from the fungus Aspergillus niger. The resulting glucose solution is then purified by filtration and concentrated in a multiple-effect evaporator. Solid D-glucose is then produced by repeated crystallizations.
The Chain form of Glucose:
Haworth Structure of Glucose:
Mannose is a sugar. Mannose enters the carbohydrate metabolism stream by phosphorylation and conversion to fructose-6-phosphate. D-Mannose may prevent adhesion of bacteria to tissues of the urinary tract and bladder.
Mannose can be formed by the oxidation of mannitol.
Ring Structure of D-Mannose:
Fischer Structure of D-Mannose:
Galactose (also called brain sugar) is a type of sugar found in dairy products, in sugar beets and other gums and mucilages. It is also synthesized by the body, where it forms part of glycolipids and glycoproteins in several tissues. It is considered a nutritive sweetener because it has food energy.
The hydrolysis of lactose to glucose and galactose is catalyzed by the enzyme beta-galactosidase, a lactase. In the human body, glucose is changed into galactose in order to enable the mammary glands to secrete lactose.
Fischer Projection of Galactose:
Haworth Structure of Galactose:
The ketohexoses have 3 chiral centers and there are 8 possible stereoisomers. Of these, only the 4 D-isomers are known to occur naturally:
Fructose is a simple sugar. Fructose is derived from the digestion of sucrose, a disaccharide consisting of glucose and fructose which is broken down by enzymes during digestion.
Structure of Fructose:
Fructose, or levulose, is a levorotatory monosaccharide. Fructose is a hexose (6 carbon atoms), it generally exists as a 5-membered hemiketal ring (a furanose).
Structure of Alpha-D-fructose:
Structure of Alpha-L-Fructose:
Structure of Beta-D-Fructose:
Structure of Beta-L-Fructose:
Sorbose is a ketose belonging to the group of sugars known as monosaccharides. The commercial production of vitamin C (ascorbic acid) often begins with sorbose.
Fischer Projection of L-Sorbose:
Tagatose is a functional sweetener. It is a naturally occurring monosaccharide, specifically a hexose.
Tagatose is present in only small amounts in dairy products. It can be produced commercially from lactose, which is first hydrolyzed to glucose and galactose. The galactose is isomerized under alkaline conditions to D-tagatose by calcium hydroxide. The resulting mixture can then be purified and solid tagatose produced by crystallization.
A heptose is a monosaccharide with seven carbon atoms.
They either have an aldehyde functional group in position 1 (aldoheptoses), or a ketone functional group in position 2 (ketoheptoses).
Sedoheptulose is a keto-heptose - a simple sugar with seven carbon atoms and a ketone functional group.
Structure of D-Sedoheptulose:
An oligosaccharide is a saccharide polymer containing a small number (typically three to six) of component sugars, also known as simple sugars. They are generally found either O- or N-linked to compatible amino acid side chains in proteins or to lipid moieties.
They are classsified as:
A disaccharide is a sugar composed of two monosaccharides.
The two monosaccharides are bonded via a condensation reaction. This bond can be between the 1, 4 or 6 carbon on each component monosaccharide.
They are crystalline, water soluble, and sweet tasting.
Some of the common disaccharides are:
Sucrose is the common chemical name for table sugar. Sucrose is a disaccharide; each molecule of sucrose consists of two "simple sugars".
Composition of Sucrose:
In sucrose, a glucose residue and a fructose residue are linked by an 1→2-α,β-glycosidic bond. Sucrose's empirical formula is C12H22O11, and its systematic name is α-D-glucopyranosyl-(1→2)-β-D-fructofuranoside.
Haworth Structure of Sucrose:
Production of Sucrose:
Sucrose is a covalently bonded compound. Sucrose is generally extracted from sugar cane or sugar beet and then purified and crystallized.
Sucrose is broken down in the gut by acidic hydrolysis into its component sugars fructose and glucose.
Properties of Sucrose:
Solubility in water: about 2.1 g sucrose in 1 g water (at 25 °C).
Refractive index of 10% solution:
Melting point: 186 °C
Energy density: 17 kJ/g
Lactose is the sugar making up around 2-8% of the solids in milk. Lactose is a disaccharide consisting of two subunits, a galactose and a glucose linked together. Its empirical formula is C12H22O11 and its molecular weight is 342.3.
Maltose (known as malt sugar) is a disaccharide (sometimes called di-glucose). It is formed from two glucose molecules joined together at carbons one and four by a glycosidic bond. Maltose has a molecular formula of C12H22O11, and the systematic name for maltose is α-D-glucopyranosyl-(1→4)-β-D-glucopyranose. It is broken down by the enzyme maltase.
Trehalose also known as mycose is a 1-alpha (disaccharide) sugar.
Trehalose is a non-reducing sugar formed from two glucose units joined by a 1-1 alpha bond. The bonding makes Trehalose very resistant to acid hydrolysis, and therefore stable in solution at high temperatures even under acidic conditions. The enzyme trehalase, breaks it into two glucose molecules which can then be readily absorbed in the gut. Trehalose has about 45% the sweetness of sucrose. Trehalose is metabolized by a number of bacteria, including streptococcus mutans the common oral bacteria responsible for oral plaque.
Polysaccharides are relatively complex carbohydrates. They are polymers made up of many monosaccharides joined together by glycosidic linkages. They tend to be amorphous, insoluble in water, and have no sweet taste.
When all the constituent monosaccharides are of the same type they are termed homopolysaccharides; when more than one type of monosaccharide is present they are termed heteropolysaccharides.
Examples include storage polysaccharides such as starch and glycogen and structural polysaccharides such as cellulose.
Starches are polymers of glucose in which glucopyranose units are bonded by alpha-linkages. Amylose consists of a linear chain of several hundred glucose molecules. Amylopectine is a branched molecule made of several thousand of glucose units.
Starches are insoluble in water. They can be digested by hydrolysis catalyzed by enzymes called amylases, which can break the alpha-linkages. Humans and other animals have amylases, so they can digest starches.
Glycogen is the storage form of glucose in animals. It is a branched polymer of glucose. Glycogen can be broken down to form substrates for respiration, through the process of glycogenolysis. This involves the breaking of most of the C-O-C bonds between the glucose molecules by the addition of a phosphate.
The structural components of plants are formed primarily from cellulose. Wood is largely cellulose and lignin, while paper and cotton are nearly pure cellulose. Cellulose is a polymer made with repeated glucose units bonded together by beta-linkages. Humans and many other animals lack an enzyme to break the beta-linkages, so they do not digest cellulose. Certain animals can digest cellulose, because bacteria possessing the enzyme are present in their gut.
A protein is a complex, high molecular weight organic compound that consists of amino acids joined by peptide bonds. Proteins are essential to the structure and function of all living cells and viruses. Many proteins are enzymes or subunits of enzymes. In nutrition, proteins serve as the source of amino acids for organisms that do not synthesize those amino acids natively. Proteins are one of the classes of bio-macromolecules, which make up the primary constituents of living things and were discovered by Jöns Jakob Berzelius, in 1838.
Most natural proteins are encoded by DNA. DNA is transcribed to yield RNA, which serves as a template for translation by ribosomes.
3-D Structure of Myoglobin showing colored alpha-helices:
Structures of Protein:
Proteins are amino acid chains that fold into unique 3-dimensional structures. The shape into which a protein naturally folds is known as its native state, which is determined by its sequence of amino acids.
The amino acid sequence. The primary structure is held together by covalent peptide bonds, which are made during the process of translation. The process by which the higher structures form is called protein folding and is a consequence of the primary structure.
They are highly patterned sub-structures—alpha helix and beta sheet—or segments of chain that assume no stable shape. The secondary structures are held together by hydrogen bonds.
A hormone is a chemical messenger from one cell (or group of cells) to another.They are those produced by endocrine glands. Hormone molecules are secreted directly into the bloodstream, other body fluids, or into adjacent tissues. They move by circulation or diffusion to their target cells, which may be nearby cells (paracrine action) in the same tissue or cells of a distant organ of the body. The function of hormones is to serve as a signal to the target cells; the action of hormones is determined by the pattern of secretion and the signal transduction of the receiving tissue.
Hormone actions vary widely, but can include stimulation or inhibition of growth, induction or suppression of apoptosis, activation or inhibition of the immune system, regulating metabolism and preparation for a new activity or a phase of life. In many cases, one hormone may regulate the production and release of other hormones. Hormones also control the reproductive cycle of virtually all multicellular organisms.
Classification of hormones:
Vertebrate hormones fall into four chemical classes:
1. Amine-Derived Hormones.
2. Peptide Hormones.
3. Steroid Hormones.
4. Lipid and Phospholipid Hormones.
1. AMINE-DERIVED HORMONES:
They are derivatives of the amino acids tyrosine and tryptophan. Examples are catecholamines and thyroxine
The thyroid hormone, thyroxine (T4) is a tyrosine-based hormone produced by the thyroid gland. It acts on the body to increase the basal metabolic rate, affect protein synthesis and increase the body's sensitivity to catecholamines (such as adrenaline). An important component in the synthesis is iodine.The thyroid hormones are essential to proper development and differentiation of all cells of human body. To various extents they regulate protein, fat and carbohydrate metabolism.
Structure of Thryoxine:
Thyroxine contains four iodine atoms.
2. PEPTIDE HORMONES:
They consist of chains of amino acids. Examples of small peptide hormones are TRH and vasopressin. Peptides composed of scores or hundreds of amino acids are referred to as proteins. Examples of protein hormones include insulin and growth hormone.
Insulin is a polypeptide hormone that regulates carbohydrate metabolism. It is the primary effector in carbohydrate homeostasis and it also takes part in the metabolism of fat (triglycerides) and proteins - it has anabolic properties. It also affects other tissues. Insulin is used medically in some forms of diabetes mellitus. Insulin has the empirical formula C254H377N65O75S6.
Structure of Insulin:
Red: carbon; green: oxygen; blue: nitrogen; pink: sulfur. The blue/purple ribbons denote the skeleton [-N-C-C-]n in the protein's amino acid sequence H-[-NH-CHR-CO-]n-OH where R is the part protruding from the skeleton in each amino acid.
3. STEROID HORMONES:
They are derived from cholesterol. The adrenal cortex and the gonads are primary sources. Examples of steroid hormones are testosterone and cortisol. Sterol hormones such as calcitriol are a homologous system.
Testosterone is a steroid hormone from the androgen group. It is the principal male sex hormone and the "original" anabolic steroid.The effects of testosterone in humans and other vertebrates occur by way of two main mechanisms: by activation of the androgen receptor (directly or as DHT), and by conversion to estradiol and activation of certain estrogen receptors. Testosterone (T) is transported into the cytoplasm of target tissue cells, where it can bind to the androgen receptor, or can be reduced to 5α-dihydrotestosterone (DHT) by the cytoplasmic enzyme 5α-reductase.
Structure of Testosterone:
3. LIPID AND PHOSPHOLIPID HORMONES:
They are derived from lipids such as linoleic acid and phospholipids such as arachidonic acid. The main class is the eicosanoids, which includes the widely studied prostaglandins.
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