In this section, we will continue our discussion in radicals and we will discuss about the radicals in our life. In this case, we will see how radicals play prominent roles in antioxidant and immune system of body, and also in the atmosphere as it affects the climate of the Earth.
To begin with, we will start from one of the important ingredients of life which is oxygen. In the context of cells, oxygen is toxic to cells (cytotoxic) and as it has capability to oxidise important parts of cell to make it malfunction. Therefore, aerobes only survive by developing anti-oxidant and it was thought this factor was the driving force of evolutions into multicellular system. Furthermore, as we acknowledge that living things need to use oxygen for respiration.
There are several mechanism of antioxidant defences in our body to make the cell survive in the oxygen environment. The first one is catalytic removal of radicals by using certain enzymes such as superoxide dismutase, superoxide reductase, catalase, or peroxidase. In this enzymatic process, it destroy oxygen rich species. Besides that, the cells can also decrease the concentration of reactive species or radicals to reduce the possibility of oxidation. Another defence mechanism from radicals is by using proteins non-enzymatic to protect against oxidation and this protein is a sacrificial materials-type. Radicals can also be prevented by using a quencher which is a small molecules to destroy radicals. In the other sides, the cell can replace a part which are sensitive molecules by the other molecules which are resistant to radicals. Lastly is a sacrificial agents in almost the same as proteins non-enzymatic antioxidants defence mechanism.
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| The structure of SOD |
One of the important enzymes in radicals defence mechanism is superoxide dismutase (SOD) which destroys the superoxide (O2−) radicals. The superoxide ion radical is perhaps the most important oxidant in nature and if we examine closely it is a charged radicals which is quite rare as in our first discussion radicals are mostly uncharged single electron species. In the other hands, SOD is a Cu/Zn based enzymes that dismutate O2−; furthermore Mn and Fe SODs are also found. The SOD adopts dismutation, which is a single reactant produces two products, to destroy the radicals. The mechanism of O2− dismutation in SOD is the O2− reacts with the Cu2+ in SOD to produce O2 and Cu+ in SOD. Then, Cu+ in SOD reacts with O2− and the aids of H+ to produce H2O2 and regenerate the enzymes.
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| Cu-based SOD dismutation mechanism |
However, H2O2 generates OH radicals which is also a problem and there are two main defence mechanism to overcome this problem. The mechanism is catalase converts
H2O2 into
H2O and
O2, or peroxidase converts into
H2O molecules through sacrificial oxidation mechanism. The glutathione peroxidase scavange
H2O2 to disulphide bridge as shown below.
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| Glutathione peroxidase quenching mechanism |
As mentioned earlier, Cu is essential for SOD activity but in higher concentration it can produce radicals from thiols,
H2O2, ascorbic acid, etc. Besides that, Fe is also essential for SOD as well as for respiration but it can also be dangerous in higher concentration because it can generate radicals from
H2O2, HOCl, adrenalin, etc. Therefore, the control of metal ions is very important.
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| Ascorbic acid quenching mechanism |
Vitamin C or ascorbic acid can also be a quencher of radicals by using its acidic protons to quench radicals. Ascorbic acid is commonly a quencher for OH, HOO, and
H2O2 radicals, the quenching mechanism is shown below.
In our body, radicals can also be used as a defence mechanism in from foreign bodies such as bacteria and the cells of the immune system adopt defence and removal system. This mechanism is one of the role of phagocytotic cell which is a large cell that kill and destroy a foreign body and it is produced at lymph gland and contained in blood. This defence mechanism is started by recognising process of bacteria or foreign body and "label it" as a foreign body by macrophages. There are two types of macrophages which are neutrophils and monocytes, and they are not a phagocytotic cell. Then, after the bacterium is marked, then phagocytosis engulfs the bacterium to kill and destroy it. The killing mechanism of a bacterium by phagocytes is varies and one of the mechanism is superoxide mediated. The mechanism is
O2 reacts with NADPH to form
O2− radicals which then could react either with NO radicals to form ONO
O− or with SOD to form
H2O2.
H2O2 can cross bacterial wall membranes and kill the bacteria as OH radicals are produced inside the bacteria because bacteria do not have material that could change
H2O2 into less harmful substance. Therefore, the OH radicals burst the bacteria and this process is called oxidation burst.
Then, we move from our body to the upper atmosphere to see the radical chemistry in the atmosphere. Firstly that we need to know is atmospheric science is a complex area include chemistry, air circulation, 2D and 3D currents, physics of flows (fluid dynamics), etc. Then, the atmospheric chemistry asks about certain questions such as the pollutants, the effect of natural processes, and how the process fits together. Besides that, the atmospheric chemistry is much more complex than the chemistry in the lab because of certain factors. Those factors such as:
- concentrations generally much lower in the atmosphere;
- multiple components and multiple rates;
- water vapour always present;
- high UV and possibly cosmic rays;
- chemistry changes with depth as the pressure changes;
- dust present that can give catalytic and transport effect;
- air currents are closed laminar flows.
Furthermore, from the atmospheric chemistry that causes some changes into more environmentally friendly products such as solvent less coatings (paints), fine chemical and pharmaceuticals, transportation, and energy.
One of the important component in atmospheric chemistry is water as it gives very important effect but variable and always below saturation level. Another measurement of water content in atmosphere is called relative humidity can be calculated by using equation below and this relative humidity valid at certain temperature.
In fact, about 1/4 of all the solar radiation on the earth is used to evaporate water, and water has a good solvent properties with the average of residence time of 10 days. Therefore, water transport pollutants in the form of gas, liquid, and solid. Furthermore, the water circulation on the earth is shown below.
Another component in atmosphere is methane, C
H4, which is produced from the reduction of C
O2 by microorganisms (rumants). Methane is also exist with another hydrocarbon at the upper atmosphere and the figure below show the concentration of hydrocarbon in the upper atmosphere. For your information, methane is a more powerful greenhouse gas than C
O2.
Meanwhile, nitrogen compounds such as N
2O and N
H3 are produced by bacteria, and sulphur compounds such as C
H3SSC
H3, C
H3SH, COS, C
S2 and are mainly from the oceans and produced by phytoplankton such as
Phaecoystis pouchetti. Surprisingly, halomethane such as C
H3Cl and C
H3Br which are the most abundant source of atmospheric halocarbon are produced from oceanic biological processes.
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| Mount Etna Eruption 2013 |
Geochemical activity which is mainly from local and erratic volcanoes (e.g. Mt. Etna) emits more S
O2 than the whole Europe's combined industries but normally only small amounts are produced. Besides that, fires from forest fires contribute half of all the emitted CO, C
H3Cl, HCN, C (soot), and other compounds such as dioxans. Furthermore, lightening can also produce nitrogen compounds.
Many reactions in the atmosphere are photochemical and it is iniated by adsorption of a photon rather than thermal collisions through the Norrish I mechanism. One of the examples is the reaction of NO
2 and by adsorbing the wavelength at less than 410 nm it produces NO and O radicals. Besides that, in sunlight the reaction is:
However, the reaction is not that simple and the reactions are shown below.
As shown on the reaction above, one of the components is ozone which is very important in the atmosphere with two major reactions. The first reaction is shown below.
Another reaction is where both carbonyl oxides and ozone act like diradicals as demonstrated below.
As mentioned earlier, in the atmosphere has lower concentration and water always present which distinguish the reaction in the atmosphere with in the lab. The reaction is shown below.
Meanwhile, in higher concentration of water (i.e. in the lab), we could get the reaction
or another reaction as shown below and it depends on the R group.
Besides that, we could also get an oligomers of the carbonyl oxide.
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| Formation of oligomers of carbonyl oxide |
Furthermore, all of these reactions are not relevant in the atmosphere.
OH radical is one of the prominent radicals in the upper atmosphere as it produces mainly from ozone as discussed earlier. The most important about OH radicals is it generates many atmospheric reactions which produce several other radicals as demonstrated below,
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| OH radicals reactions |
Where M is metals. In general, OH, H, or OOH radicals abstract H or X, or add to alkenes to degrades itself for example in isoprene as demonstrated below.
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| Isoprene degradation |
Besides that, C
H4 can also be formed instead of C
H3 radicals because it is more stable, but C
H4 is degraded into another compound such as CO, C
O2, and
H2O.
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| Methane degradation |
In our body, radicals can also be used as a defence mechanism in from foreign bodies such as bacteria and the cells of the immune system adopt defence and removal system. This mechanism is one of the role of phagocytotic cell which is a large cell that kill and destroy a foreign body and it is produced at lymph gland and contained in blood. This defence mechanism is started by recognising process of bacteria or foreign body and "label it" as a foreign body by macrophages. There are two types of macrophages which are neutrophils and monocytes, and they are not a phagocytotic cell. Then, after the bacterium is marked, then phagocytosis engulfs the bacterium to kill and destroy it. The killing mechanism of a bacterium by phagocytes is varies and one of the mechanism is superoxide mediated. The mechanism is O2 reacts with NADPH to form O2− radicals which then could react either with NO radicals to form ONOO− or with SOD to form H2O2. H2O2 can cross bacterial wall membranes and kill the bacteria as OH radicals are produced inside the bacteria because bacteria do not have material that could change H2O2 into less harmful substance. Therefore, the OH radicals burst the bacteria and this process is called oxidation burst.
In fact, about 1/4 of all the solar radiation on the earth is used to evaporate water, and water has a good solvent properties with the average of residence time of 10 days. Therefore, water transport pollutants in the form of gas, liquid, and solid. Furthermore, the water circulation on the earth is shown below.
However, the reaction is not that simple and the reactions are shown below.
Another reaction is where both carbonyl oxides and ozone act like diradicals as demonstrated below.
or another reaction as shown below and it depends on the R group.
Besides that, we could also get an oligomers of the carbonyl oxide.
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