Structural Biochemistry/Nonmetals

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Nonmetals are generally dull and brittle. They are poor conductors of electricity. Compared to metals, they have lower densities, melting points, boiling points, and higher electronegativity.


Carbon is one of element in the earth, which has symbol C and atomic number 6. Its electron configuration is [He]2s2 2p2. Carbon is a very useful element mainly due to its bonding abilities. It is able to form single, double, and triple bonds to other elements (usually Hydrogen). All living organisms contain carbon, including humans who have about 18% carbon by weight.

Carbon has 12 isotopes, which from C8 to C19. C12 and C13 are stable; all other isotopes are radioactive. Carbon is very stable under room temperature. it is not soluble in water, organic solution, or low concentration acid or base.Carbon can react with oxygen in high temperature; in all halogen, only fluorine can react with carbon directly; carbon is very reducible element, which can reduce other metals.

Common uses of carbon include diamonds, gasoline, kerosene, smoke detectors, radiocarbon dating, and graphite used for cooking and artwork. The most major organic compound in nature is soot.

In plants, carbon dioxide and water combine to form simple sugars called buffer carbohydrates . The process of this formation is called photosynthesis and the driving force that provides energy is the sun.


Nitrogen is an element in group (V) of period table which has symbol N and atomic number 7, discovered in 1772 by Scottish physician Daniel Rutherford.

Nitrogen has 17 isotopes. N14 and N15 are stable.

At standard conditions, nitrogen is a colorless, odorless, tasteless inert diatomic gas. It occurs in all living organisms and is a constituent in amino acids, which make up proteins, which make up nucleic acids(DNA and RNA). Nitrogen also plays an important role in plant growing and fruit maturing. Increasing the percentage of Nitrogen in the soil can improve the production of farm plant.

Nitrogen is the largest constituent of the Earth's atmosphere, occupied 78% volume. It makes up about 4% of dry weight of plant matter, about 3% of weight of the human body, and 0.0046% in Earth's shell.


Oxygen is one of elements in group (VI) of period table, which has symbol O, atomic number 8 and electron configuration 1s2 2s2 2p4, discovered in 1774. At standard condition, Oxygen is a colorless, odorless, and tasteless diatomic gas. Oxygen has second highest electronegativity in all elements and is a strong oxidizing agent. So, all elements except inert gases can form compound with Oxygen.Oxygen has 3 stable isotopes: O16, O17 and O18.

Oxygen is the most abundant element in Earth's shell, occupied 48.6%. The Oxygen gas also makes up 23% in the air.

All major structural molecules in living organisms (i.e. proteins, carbohydrates , lipids,amino acid, etc.) contain oxygen. It is used in both photosynthesis as well as cellular respiration in order to sustain life. The overall formula for photosynthesis is 6 CO2 + 6 H2O+ sunlight --> C6H12O6 + 6 O2

It also makes up the ozone layer in the form of O3, which protects the earth from UV rays radiating from the sun.


Picture of natural sulfur crystals

Sulfur is one of elements in group (VI) of period table, which has symbol S, atomic number 16 and electron configuration [Ne] 3s2 3p4. At room temperature, elemental sulfur is a bright yellow crystalline solid formed by cyclic octatomic molecules with formula S8. Sulfur can oxidize most metals and several nonmetals; it also can reduce several strong oxidants, such as oxygen and fluorine. As sulfur burns, a blue flame shows with formation of sulfur dioxide. Sulfur is insoluble in water but solve in some nonpolar solvent, such as carbon disulfide and benzene.

Sulfur has 18 isotopes. Four of them are most stable: S-32 (95.02%), S-33 (0.75%), S-34 (4.21%) and S-36 (0.02%).

Some amino acids contain sulfur in their structure, which form Disulfide bonds, playing very significant roles in proteins.


Phosphorus is an element in group (V) of period table which has symbol P, atomic number 15, and electron configuration [Ne] 3s2 3p3, discovered in 1669 (white phosphorus) by a German businessman whose name is Henning Brand. Phosphorus has high reactivity and is toxic. There is no free element phosphorus found in earth.

The major role of phosphorus is fertilizers. Phosphorus also build detergents, pesticides and nerve agents, and matches. In biology, phosphorus is a component of DNA, RNA, ATP and also forms phospholipids in all membranes.

There are four forms of phosphorus existing in the world:

White phosphorus consists of tetrahedral P4 molecules, in which each atom is bound to the other three atoms by a single bond. When temperature raises to 800 °C, P4 molecules decompose to P2 molecules, forming liquid and gaseous phosphorus. There are 2 forms of solid White phosphorus, which at low temperature is β form and high temperature is α form.White phosphorus is the least stable, the most reactive, more volatile, less dense, and more toxic than the other form of phosphorus. White phosphorus doesn’t dissolve in water, but dissolve in Benzene and ether, stored in water.

Picture of white Phosphorus

Red phosphorus is viewed as one bond in P4 broke and formed single bond with P on neighboring P4 molecule. Red phosphorus is red powder and nontoxic, formed by white phosphorus at 250 °C .

Picture of red Phosphorus

Structure of red Phosphorus:

Black phosphorus is least reactive form of phosphorus, which is stable at temperature below 550 °C. Known as β-metallic phosphorus, it also has a similar structure as graphite. High pressure is required to form black phosphorus.

Structure of black Phosphorus:

Violet phosphorus is formed by red phosphorus above 550 °C.

Nitric Oxide[edit]

Some physical properties for nitric oxide: 1)exists as a gaseous form in nature 2)has limited water solubility 3)has diverse oxidation chemistry and shifted biological concentration

Some previous techniques that involved to develop nitric oxide’s structure such as electron paramagnetic resonance spectroscopy has disadvantage of determining its biological selectivity, sensitivity and toxicity. Comparing to previous methods, optical tools to detect Nitric Oxide was more accurate to discover the forms of Nitric Oxide.

Ratiometric fluorescent probe is the technique to detect the biological structure of nitric oxide using light to provide a high spatial and temporal resolution of the structure.

Fluorescence imaging of biological analytes act as excellent tools to monitor biological processes in real time with a relatively high resolution and accurate detection.

There are three strategies that can be used to recognize the accurate structure of Nitric Oxide. The first strategy is using organic probes. This method involves an oxidation product of Nitric Oxide, such as Dinitrogen trioxide, to react with a functional group to regulate the fluorescence. This reaction results in bright emission enhancement with the presence of Nitric Oxide under the existence of oxygen, the aerobic condition. The second strategy associates with transition metals to mediate reactivity of an emissive dye with Nitric Oxide. With this technique, a paramagnetic Copper ion carrying a secondary amine emission of the fluorophore reacts with Nitric Oxide in coordination. During the reaction, the Cooper ion is being reduced with deprotonation, more positive charges were released, and also the secondary amine with nitrosation. Therefore, the diminishing paramagnetic electric technique in the N-nitrosated product was than produced. In this strategy, the Copper mediated reactivity does not depend on the presence of oxygen. Without the requirement of oxygen gas, the technique with probes is conceivably useful to resolve the imaging Nitric Oxide in hypoxic situation. Some advantages with this method are: faster reaction with Nitric Oxide due to metal medicated reactivity; directly offers a circumstance for devising reversible probes to determine Nitric Oxide. One weakness of this strategy is less bright compared to pure organic probes in term of the on-and-off state. The last technique to encounter the Nitric Oxide formation is to encode probes genetically. It involves the use of encoding of Nitric Oxide reactive proteins with transition metal genetically to further identify the biological formula of Nitric Oxide gas in nature under light. One example using the technique implies two mutant fluorescent proteins connect to an MT domain-charge, react with Nitric Oxide, which than can therefore provide a clear result of formation. [1]

The figure below illustrates the fluorescence probe with emission of light:

Fluorescence probe.jpg