Example Chemistry Essay

Oxidation

Oxidation involves an increase in the oxidation number of a species. This involves the addition of oxygen or the loss of hydrogen or electrons. Ultimately the first two can always be viewed as equivalent to loss of electrons. Oxidation always occurs together with reduction as part of a redox reaction. The substance producing the oxidation is termed the oxidant (electron acceptor) and is concomitantly reduced. Likewise the oxidised species (electron donor) can be termed the reductant. (Atkins, 1990)

There are many examples of oxidation reactions in the catabolism of glucose. For example in the first stage of the glycolytic pathway leading from glucose to pyruvate, after the six carbon intermediates are cleaved to generate glyceraldehyde 3-phosphate the enzyme glyceraldehyde phosphate dehydrogenase catalyses the conversion of glyceraldehyde 3-phosphate to 3-phosphoglycerol phosphate (utilizing the cofactor NAD and inorganic phosphate) This oxidation is the first time that reducing potential in the form of NADH is generated in the breakdown of glucose (note the NAD is correspondingly reduced in the process).

Reduction

Reduction is a decrease in the oxidation number of a substance resulting from the gain of electrons as part of a redox reaction. This is often but not necessarily associated with the loss of oxygen or hydrogen. (See oxidation above).

An example of a reduction reaction occurs in the final stage of glycolysis under anaerobic conditions where pyruvate is reduced to lactate catalysed by the enzyme lactate dehydrogenase. The reducing potential for this reaction is provided by NADH and H⁺ and prevents the cells finite supply of NAD being tied up in the reduced form from reactions such as the oxidation example above. Again the reductant NADH is oxidised in the process.

Phosphorylation

Phosphorylation involves the addition of a phosphate (PO₄^2-) or phospho (PO₃^2-) from a donor to receptor molecule usually by a nucleophilic displacement of the phosphorus atom by a lone pair on an electronegative heteroatom (e.g. O or N). (Cox, 2004)

In the first reaction of the catabolism of glucose, the glucose molecule is phosphorylated by the high-energy phosphate compound adenosine triphosphate (ATP) catalysed by the enzyme hexokinase. The hydroxyl group on carbon atom 6 of the glucose nucleophilically attacks the terminal phosphate of ATP displacing a PO₃^2- group, which is added to the glucose releasing ADP. In addition to priming the molecule with energy it keeps the glucose in the cytoplasm, as the glucose transporters are specific for free glucose. (Cox, 2004)

Hydrolysis

Hydrolysis is the reaction of a chemical species (molecule or ion) with water. In biological systems this usually involves addition of the elements of water across a chemical bond to break the bond, resulting in an OH group attached to one atom of the hydrolysed bond and an H atom added to the other atom. This can split the molecule into two separate molecules (see example) or can break a cyclical compound into a linear structure.

The neurochemical transmitter acetylcholine is responsible for conduction of the motor neurone impulse across the synaptic gap. To prevent continuation of the signal and tetanic paralysis of the muscle the acetylcholine is hydrolysed to acetate and choline by the enzyme acetylcholine esterase. This is an uncomplicated ester hydrolysis in which water nucleophilically attacks the carbonyl group of the acetate component of the ester. (Vander, 2001)

Condensation

A condensation reaction occurs when two or more reacting species react to form a single product and eliminate a simple molecule in the process. Where the simple molecule is water the condensation reaction can be thought of as the opposite of the hydrolysis reaction. Likewise the two reacting species can be separated but on the same molecule resulting in a cyclization reaction. (McNaught, 1997)

Peptide synthesis occurring on the ribosome and catalysed by its peptide synthetase activity is an example of a condensation reaction. Condensation takes place between the amino group of the added amino acid and the carboxyl group of the growing peptide chain (activated by an aminoacyl-tRNA linkage) eliminating the elements of water. (Alberts, 1989).

Isomerization

In an isomerization reaction the product of the reaction is an isomer of the reactant. In such a reaction there is no net change in the stoichiometry of the molecular formula between reactants and products (though intermediate steps may involve extra atoms). The isomerization can be the result of molecular or conformational rearrangements (McNaught, 1997)

The second reaction of the glycolytic breakdown of glucose is an example of an isomerization reaction. Glucose-6-phosphate is converted to fructose-6-phosphate by the enzyme glucose phosphate isomerase. This produces a more symmetrical molecule with a second available primary alcohol group for phosphorylation.

Deamination

Deamination is the removal of an amine (NH₂) group from a molecule. The nitrogen is usually removed as ammonia, the extra hydrogen coming from water leaving a ketone group in place of the amine. This reaction also increases the resulting oxidation number of the reacting species and is often termed oxidative deamination. (Cox, 2004)

Oxidative deamination is an important reaction in the degradation of amino acids especially in the liver. Glutamate, produced from other amino acids by transamination, is converted into a-ketoglutarate and ammonia by the enzyme glutamate dehydrogenase in association with the cofactors NAD or NADP. The ammonia is ultimately excreted via the urea cycle. (Cox, 2004)

Carboxylation

Carboxylation is the addition of a carboxylate group to a molecule. This is an important method for increasing the number of carbon atoms in a synthesis. The source of the carbon is typically carbon dioxide for example in the reaction of a carbonated grignard reagent (or the bicarbonate ion in aqueous biological systems).

The fixation of carbon dioxide by green plants is an important example of a carboxylation reaction. In plants that use the Calvin cycle, CO₂ is incorporated into 3-phosphoglycerate by the enzyme ribulose-diphosphate carboxylase. This carboxylates the five-carbon ribulose sugar to produce a six-carbon intermediate, which is then hydrolysed to produce two 3 carbon molecules of 3-phosphoglycerate.