Each sentence will further have many words and each word will have characters. Therefore we have divided a storybook into characters. This is exactly the same case when we take the matter into account. The matter is made up of substances which contain molecules. The molecules, in turn, are made up of groups of atoms.

A molecule is the smallest unit (particle) of a compound having the physical and chemical properties of that compound. This does not mean that molecules can not be broken down into smaller parts, e.g. the atoms from which they are formed or the fragments of the molecule, each consisting of several atoms or parts of atoms.


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A molecule is a collection of two or more atoms that make up the smallest recognisable unit into which a pure material may be split while maintaining its makeup and chemical characteristics. Some examples of molecules are

As atoms come together to form molecules, chemical bonds bind them together. As a consequence of sharing or exchanging electrons between the atoms, these bonds form. It is only the electrons that are ever active in bonding in the outermost shell.

Water is known to be a basic molecule consisting of a few atoms. Basic molecular substances are molecules in which strong covalent bonds bind the atoms. Nevertheless, weak forces bind the molecules together so that they have high melting and boiling points.

Ozone is a molecule made up of three atoms of oxygen. The chemical ozone symbol is O3 as the oxygen atom symbol is O. Most of the ozone present in our atmosphere is produced by a sun-emitted association of oxygen molecules with ultraviolet radiation.

A model of a water molecule, showing the bonds between the hydrogen and oxygen.Most substances on Earth are compounds containing multiple elements. Chemical bonding describes how these atoms attach with each other to form compounds, such as sodium and chlorine combining to form NaCl, common table salt. Compounds that are held together by chemical bonds are called molecules. Water is a compound of hydrogen and oxygen in which two hydrogen atoms are covalently bonded with one oxygen making the water molecule. The oxygen we breathe is formed when one oxygen atom covalently bonds with another oxygen atom to make the molecule O2. The subscript 2 in the chemical formula indicates the molecule contains two atoms of oxygen.

The illustration of the crystalline structure of mica shows the corner O atoms bonded with K, Al, Mg, Fe, and Si atoms, forming polymerized sheets of linked tetrahedra, with an octahedral layer of Fe, Mg, or Al, between them. The yellow potassium ions form Van der Waals bonds (attraction and repulsion between atoms, molecules, and surfaces) and hold the sheets together. Van der Waals bonds differ from covalent and ionic bonds, and exist here between the sandwiches, holding them together into a stack of sandwiches. The Van der Waals bonds are weak compared to the bonds within the sheets, allowing the sandwiches to be separated along the potassium layers. This gives mica its characteristic property of easily cleaving into sheets.

Chemical bonds are generally divided into two fundamentally different types: ionic and covalent. In reality, however, the bonds in most substances are neither purely ionic nor purely covalent, but lie on a spectrum between these extremes. Although purely ionic and purely covalent bonds represent extreme cases that are seldom encountered in any but very simple substances, a brief discussion of these two extremes helps explain why substances with different kinds of chemical bonds have very different properties. Ionic compounds consist of positively and negatively charged ions held together by strong electrostatic forces, whereas covalent compounds generally consist of molecules, which are groups of atoms in which one or more pairs of electrons are shared between bonded atoms. In a covalent bond, atoms are held together by the electrostatic attraction between the positively charged nuclei of the bonded atoms and the negatively charged electrons they share. This chapter will focus on the properties of covalent compounds.

In many molecules, the octet rule would not be satisfied if each pair of bonded atoms shares only two electrons. Consider carbon dioxide (CO2). If each oxygen atom shares one electron with the carbon atom, we get the following:

Some molecules contain triple bonds, covalent bonds in which three pairs of electrons are shared by two atoms. A simple compound that has a triple bond is acetylene (C2H2), whose Lewis diagram is as follows:

Cells are composed of water, inorganic ions, and carbon-containing (organic) molecules. Water is the most abundant molecule in cells, accounting for 70% or more of total cell mass. Consequently, the interactions between water and the other constituents of cells are of central importance in biological chemistry. The critical property of water in this respect is that it is a polar molecule, in which the hydrogen atoms have a slight positive charge and the oxygen has a slight negative charge (Figure 2.1). Because of their polar nature, water molecules can form hydrogen bonds with each other or with other polar molecules, as well as interacting with positively or negatively charged ions. As a result of these interactions, ions and polar molecules are readily soluble in water (hydrophilic). In contrast, nonpolar molecules, which cannot interact with water, are poorly soluble in an aqueous environment (hydrophobic). Consequently, nonpolar molecules tend to minimize their contact with water by associating closely with each other instead. As discussed later in this chapter, such interactions of polar and nonpolar molecules with water and with each other play crucial roles in the formation of biological structures, such as cell membranes.

It is, however, the organic molecules that are the unique constituents of cells. Most of these organic compounds belong to one of four classes of molecules: carbohydrates, lipids, proteins, and nucleic acids. Proteins, nucleic acids, and most carbohydrates (the polysaccharides) are macromolecules formed by the joining (polymerization) of hundreds or thousands of low-molecular-weight precursors: amino acids, nucleotides, and simple sugars, respectively. Such macromolecules constitute 80 to 90% of the dry weight of most cells. Lipids are the other major constituent of cells. The remainder of the cell mass is composed of a variety of small organic molecules, including macromolecular precursors. The basic chemistry of cells can thus be understood in terms of the structures and functions of four major classes of organic molecules.

Phospholipids, the principal components of cell membranes, consist of two fatty acids joined to a polar head group (Figure 2.7). In the glycerol phospholipids, the two fatty acids are bound to carbon atoms in glycerol, as in triacylglycerols. The third carbon of glycerol, however, is bound to a phosphate group, which is in turn frequently attached to another small polar molecule, such as choline, serine, inositol, or ethanolamine. Sphingomyelin, the only nonglycerol phospholipid in cell membranes, contains two hydrocarbon chains linked to a polar head group formed from serine rather than from glycerol. All phospholipids have hydrophobic tails, consisting of the two hydrocarbon chains, and hydrophilic head groups, consisting of the phosphate group and its polar attachments. Consequently, phospholipids are amphipathic molecules, part water-soluble and part water-insoluble. This property of phospholipids is the basis for the formation of biological membranes, as discussed later in this chapter.

The polar, hydrophilic amino acids can be subdivided into three major classes, the polar uncharged-, the acidic-, and the basic- functional groups. Within the polar uncharged class, the side chains contain heteroatoms (O, S, or N) that are capable of forming permanent dipoles within the R-group. These include the hydroxyl- and sulfoxyl-containing amino acids, serine, threonine, and cysteine, and the amide-containing amino acids, glutamine and asparigine. Two amino acids, glutamic acid (glutamate), and aspartic acid (aspartate) constitute the acidic amino acids and contain side chains with carboxylic acid functional groups capable of fully ionizing in solution. The basic amino acids, lysine, arginine, and histidine contain amine functional groups that can be protonated to carry a full charge.

The primary sequence of a protein is linked together using dehydration synthesis (loss of water) that combine the carboxylic acid of the upstream amino acid with the amine functional group of the downstream amino acid to form an amide linkage (Figure 2.10). Similarly, the reverse reaction is hydrolysis and requires the incorporation of a water molecule to separate two amino acids and break the amide bond. Notably, the ribosome serves as the enzyme that mediates the dehydration synthesis reactions required to build protein molecules, whereas a class of enzymes called proteases are required for protein hydrolysis.


The discovery of IDPs has challenged the traditional protein structure paradigm, that protein function depends on a fixed three-dimensional structure. This dogma has been challenged over the last twenty years by increasing evidence from various branches of structural biology, suggesting that protein dynamics may be highly relevant for such systems. Despite their lack of stable structure, IDPs are a very large and functionally important class of proteins. In some cases, IDPs can adopt a fixed three-dimensional structure after binding to other macromolecules. Overall, IDPs are different from structured proteins in many ways and tend to have distinct properties in terms of function, structure, sequence, interactions, evolution and regulation.

Chemistry is the scientific study of the properties and behavior of matter.[1] It is a physical science within the natural sciences that studies the chemical elements that make up matter and compounds made of atoms, molecules and ions: their composition, structure, properties, behavior and the changes they undergo during reactions with other substances.[2][3][4][5] Chemistry also addresses the nature of chemical bonds in chemical compounds. 006ab0faaa

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