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Chemistry is the study of the molecular and atomic structure of matter and the composition of substances. Any kind of mass-energy that moves with velocities less than the velocity of light is called matter. Substances are defined as the different kinds of matter with reasonably definite compositions. There are four major and traditional branches of Chemistry: Analytical Chemistry, Inorganic Chemistry, Organic Chemistry and Physical Chemistry which are still the basic and important courses for chemistry majors in colleges. Since 1960’s, many new sub-fields of chemistry have appeared, for example, Polymer Chemistry, Colloid Chemistry, Solid State Chemistry, Organometallic Chemistry, Nuclear Chemistry, Biochemistry, Combinatorial Chemistry and Computational Chemistry, part of reasons is that these new branches cannot be properly classified into any of above four traditional fields of chemistry. Freshmen of science majors are usually required to take a course called General Chemistry which describes the chemical and physical properties of substances and the basic theories of atomic and molecular structure, quantum mechanics, statistical mechanics and thermodynamics.

There are various categories of chemical science including:

Analytical chemistry-the science that determines composition of materials in terms of elements and compounds.

Inorganic chemistry–the study of the properties and reactions of all elements and their compounds except hydrocarbons, but including simple carbon compounds such as CO2, CO and HCN.

Organic chemistry–the branch of chemistry studying both natural and synthetic hydrocarbons and their derivatives.

Physical chemistry–study of chemical behavior by physical theories including fundamental laws and mathematical formulas.

Physiological or Biochemistry–study of the chemistry of living things and the chemical changes that occur in metabolism. Because this site is a member of the ALtruis Biomedical Network, the information will be focused on biochemistry.

Fundamental Concepts
Biological molecules usually contain atoms joined by covalent bonds formed by sharing pairs of electrons. Each atom can form a fixed number of covalent bonds in a definite spatial arrangement. Single and double covalent bonds are routinely seen. The most prevalent atoms of concern in biochemistry are carbon, hydrogen, oxygen, and nitrogen.

Osmosis is the movement of water across a semipermeable membrane toward a solution of greater ionic concentration. The molecules and ions within a solution are said to exert an osmotic pressure that draws the water from a less concentrated solution on one side of a membrane (impermeable to the ions) to the other. In a similar fashion, if the membrane allowed free passage of ions, they would move down their concentration gradient to an area of lesser concentration in a process called diffusion. Isotonic solutions have identical solute concentrations and are osmotically balanced.

An acid is a molecule that releases a proton (H+ ion) in solution. A base is a molecule that accepts a proton in solution. Water molecules themselves have a tendency to dissociate into H+ and OH ions in a limited way. The hydrogen ion concentration of pure water is 1 x 10-7 giving pure water a pH measurement of 7. pH is the measurement of the hydrogen ion concentration. Acids have a pH less than 7 and bases have a pH greater than 7. Solutions of weak acids and their conjugate bases (neither exists in completely dissociated form) exhibit the capability to buffer incoming acid or base. A buffered solution will resist a change in pH more so than pure water when an acid or a base is added to it.

Chemistry of Water
Water is the principle component of the human body making up about 60-70% of the body weight. In living cells, biochemicals exist in an aqueous environment and water actively participates in many biochemical reactions. Water, as it surrounds different molecules, helps to determine many biochemical properties of macromolecules.

Water freezes at 0º C (32º F) and boils at 100º C (212º F). Water is tasteless, odorless, an almost universal solvent, has unique thermodynamic properties that enable the body to regulate and maintain temperature and has a high surface tension.

Water (H2O) molecules have a non uniform electrical charge giving them a dipole nature. This means that electrons are unequally distributed within the molecular structure giving the molecule positive and negative poles. This dipole nature allows water molecules to transiently associate with one another via hydrogen bonds in the liquid form. Hydrogen bonds form by the attraction of the negatively charged oxygen nucleus of one water molecule with the positively charged hydrogen of another water molecule. Hydrogen bonds are weak bonds that have only about 1/20th the strength of covalent bonds and they are not limited to water molecules. They are very important in physiological chemistry.

Molecules that themselves are polar or can fit into the hydrogen bonding scheme of water without disrupting it are said to be hydrophilic. Nonpolar molecules interrupt the hydrogen bonding of water and are therefore both hydrophobic and insoluble.

Amino acids, Peptides & Proteins
Proteins and peptides are made of amino acids that are joined by a covalent bonds called peptide bonds. Some 300 amino acids occur in nature but only 20 of these are relevant to protein synthesis in living things.

Amino acids have functional groups attached to a central carbon atom. One of these groups is always a carboxyl group (COOH) and another is an amino group (NH2). A third functional group gives the particular amino acid its particular properties (R group) and the fourth atom bound to the central carbon maybe a hydrogen ion. Amino acids may be basic, acidic, nonpolar or polar dependent on the attached third functional group.

A few amino acids have hydrophobic R groups that are hidden within the protein’s three dimensional structure. Charged R groups of the basic and acidic amino acids help to stabilize the 3-D structure of proteins by the formation of electrostatic bonds.

Amino acids are colorless and with the exception of a very few do not absorb light at all. Those few absorb in the ultraviolet range which is exploited to detect the presence of proteins in some experimental methods.

A peptide bond is formed by the removal of water from the two participating amino acids. H+ is removed from the amino group of one and an OH is removed from the carboxyl group of the other. Peptides consist of two or more amino acids linked by peptide bonds. Polypeptides are chains of more than ten amino acids. All proteins are polypeptides, but they may contain other non-amino acid functional structures such as a vitamin derivative, mineral, lipid or carbohydrate.

Primary structure of peptides and proteins is the linear sequence of amino acids that are bound together by peptide bonds. Change in a single amino acid in a critical area of the protein or peptide can alter biologic function as is the case in sickle cell disease and many inherited metabolic disorders. Disulfide bonds between cysteine (sulfur containing amino acid) residues of the peptide chain stabilize the protein structure. The primary structure specifies the secondary, tertiary and quaternary structure of the peptide or protein.

Secondary structure of peptides and proteins may be organized into regular structures such as an alpha helix or a pleated sheet that may repeat or the chain may organize itself randomly. The individual characteristics of the amino acid R groups and placement of disulfide bonds determine the secondary structure. Hydrogen bonding stabilizes the secondary structure.

Tertiary structure of proteins and peptides is the overall 3-D conformation of the complete protein. Tertiary structure is that which is most thermodynamically stable for a given environment. If the functional protein consists of several subunits, the quaternary structure consists of the conformation of all the subunits bound together by electrostatic and hydrogen bonds. Multisubunit proteins are called oligomers and the various component parts are each monomers or subunits.

With the completion of the Human Genome Project, the emphasis is shifting to the protein compliment of the human organism. This has given rise to the science of proteomics, the study of all the proteins produced by cell type and organism. The future of biotechnology and medicine will be impacted greatly by proteomics.

Carbohydrates
Plants manufacture the structural carbohydrate cellulose and the storage form starch from the energy captured during photosynthesis. In animals, the carbohydrates glucose and glycogen are sources of energy. Carbohydrates are aldehyde or ketone derivatives of alcohols having more than one OH group.

The simple sugars (monosaccharides) are the simplest form of carbohydrate and include the pentose, ribose and the hexoses, glucose (blood sugar) and fructose (fruit sugar). Pentose sugars are important parts of nucleotides and nucleic acids. The hexoses, glucose, galactose, fructose and mannose are most important physiologically. Disaccharides are two monosaccharides bound together. Examples are lactose (milk sugar) and sucrose (table sugar). Oligosaccharides have 3-6 monosaccharide units and polysaccharides have 6 or more monosaccharide units. Polysaccharides may be branched or linear and are known as starches and dextrins.

Starch is made of long chains (branching and unbranched) of glucose subunits that render natural starch insoluble in water. Glycogen is the storage form of carbohydrate in animals. Cellulose is a structural protein of plants making up the cell walls. Cellulose cannot be digested by many mammals because of the lack of an enzyme to breakdown the chemical bonds binding the sugars together. Herbivores, such as cattle, and some insects have protozoa in their gut that help them digest the cellulose. The exoskeleton of some insects is made of the complex carbohydrate, chitin. Special complex carbohydrates called mucopolysaccharides and mucoproteins are essential elements of connective tissues such as those in tendons, ligaments, cartilage, bone and ground substance between cells and tissues. They act to hold water and provide lubrication and cushioning.

Nucleic Acids
Nucleic acids, DNA and RNA are composed of linear strands of nucleotide residues that are a combination of a sugar, phosphate and one of four bases. In DNA, the sugar is deoxyribose and the bases are adenine, cytosine, guanine, and thymine. Nucleotide residues in RNA contain ribose, phosphate and the same bases except that thymine is replaced by uracil. Nucleotides are also important in cell function in the molecule ATP (adenosine triphosphate) which is a high energy currency fueling cellular functions. Adenosine and guanine are also important in cellular communication in the molecules cAMP and cGMP (cyclic adenosine and guanine monophosphate, respectively). Adenosine containing metabolic coenzymes NAD (contains the vitamin niacin) and FAD (contains the vitamin riboflavin are essential to the extraction of energy in cellular reactions.

Pyrimidine bases have one six-member ring structure containing two nitrogen atoms and are cytosine, thymine and uracil. Purine bases have a two ring structure with a six-member and a five member ring sharing two carbon atoms. Each ring in the purine bases has two nitrogen atoms. The purine bases seen most often in living systems are adenine and guanine. Other purine bases of interest are the methylxanthines, caffeine (coffee), theophylline (tea), and theobromine (cocoa).

Synthetic derivatives of nucleotide bases are used in clinical medicine in treatment of gout, viral infections, to prevent organ transplant rejection and in chemotherapy. These synthetic analogs may interfere with cellular growth and division as they are integrated into cellular DNA and RNA where they disrupt translation and or transcription. Others may become toxic to the cell when they are incorporated into other cellular constituents. Some of the analogs act to disrupt metabolic enzyme activity.

Lipids
Lipids include fats, oils, and waxes. Molecules classified as lipids are relatively insoluble in water and are soluble in nonpolar solvents like ether or chloroform. Dietary lipids have a high energy content and are important sources of fat soluble vitamins and essential fatty acids. In cellular structures, lipids form substantial portions of all membranes. Lipids are stored in adipose tissues that act as insulation, both thermal and electrical, and support and cushion internal organs.

Fats are compounds composed of fatty acids bound to glycerol. The side chains or R groups of fatty acids usually contain an even number of carbon atoms in a straight chain. The carbon atoms may be joined by single (saturated) or double bonds (unsaturated).

The physical properties of fats depend on the length of the carbon chains and degree of saturation of their constituent fatty acids. Increasing chain length increases the melting point and unsaturation decreases melting point. Naturally occurring lipids are tailored to their function. For instance, membrane lipids must be more fluid so the fatty acids are more unsaturated than those of storage lipids found in adipose cells. Unsaturated oils can be converted to margarine by the hydrogenation of the double bonds present in the long chain fatty acids thus increasing the saturation level and hardening the fat at room temperature or below.

Steroids are found in association with fats. All steroids have a similar multi-ring structure. The most biologically significant steroids are the sex steroids, estrogen and testosterone. Other steroids of importance are the bile acids, adrenocorticosteroids, and vitamin D.