Download 8/28 A brief introduction to biologically important elements and their

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9/1/08
EAS 3030
A brief introduction to biologically important elements and their uses
Twenty five elements are known to be essential for living organisms, and several more
may be biochemically significant (Frausto da Silva and Willams, The Biological
Chemistry of the Elements, 1991). After the major constituents of organic substances (C,
O, H), several groups of elements may be distinguished.
Alkalis, alkaline earths, halides
The alkali metals sodium, potassium (Group IA in the Periodic Table)
and the halide chlorine (Group VIIB) are essential for a number of processes, including
ion transport, electrical signaling, and electrolyte balance. The alkaline earths calcium
and magnesium (Group IIA) play different roles. Mg is critically linked to phosphate
biochemistry, as it binds to ATP and kinases, enzymes which control ATP activity. It is
also important in many enzymes, and plays the central photo-capture role in chlorophyll.
Calcium is important for cell wall structure, the contraction of muscle (and other) fibers,
and the acquisition and transport of phosphate. It is involved in cell division and other
reproductive processes. Ca is a main component of common biomineralization structures
including oxalates (in the worst case, kidney stones), phosphates (such as bone and teeth)
and calcium carbonate shells.
Transition metals
Most of the first row transition metals are important for enzymes. They have one or both
of two important properties – some readily change oxidation state, acting as critical redox
couples. Several have high charge density, making them good candidates for reaction
centers. Vanadium and molybdenum (the only second row transition element that
appears to be essential for life, and not for all organisms) play central roles in the
nitrogen fixation reaction through both of those properties. The Mo-nitrogenase enzyme
is the most important source of fixed nitrogen. Nitrate reductase is also a Mo-enzyme.
Manganese is critical to oxygen metabolism, occurring in superoxide dismutase enzymes
(needed to destroy these very reactive free radicals) in both chloroplasts and
mitochondria. Iron has many roles, in redox chemistry as cytochromes, ferridoxins, and
superoxide disumtases. A related function is the transport of oxygen in haem groups,
such as hemoglobin. Iron-sulfur clusters are important for Photosystem I, and in concert
with Mo for nitrogenase. Cobalt and nickel are found in several important compounds,
including vitamin B12. They are important in reactions involving reduced species such
as H2 (hydrogenases), CH4 and H2S, and so are abundant in microbes such as archea that
inhabit anoxic environments. Copper (both valence states I and II) has high affinity for
organic molecules, and can readily change redox state. It is involved in a number of
oxidase enzymes, and in enzymes needed for the reduction of nitrite and nitrous oxide
during denitrification. It is part of some important extracellular enzymes, i.e. enzymes
secreted by cells to act on substrates outside the cell, possibly to prepare them for cellular
uptake. Zinc is common in cytoplasmic enzymes, and in eukaryotes Zn-enzymes regulate
DNA activity. It also is used in extracellular enzymes for digestion.
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Semi-metals
The biochemical role of silicon (group IVA) is uncertain, but may be involved in
reducing aluminum toxicity. As a skeletal component, silicon is essential for two classes
of phytoplankton, radiolarians and diatoms. Silicon is present in many higher plant
leaves, and is abundant in grasses, providing structural rigidity and defense against
grazing.
Non-metals
Sulfur (Group VIA) has many uses, given its many possible oxidation states. Both
oxidized and reduced sulfur are used as substrates with which to metabolize carbon by
bacteria. In other organisms, sulfur groups occur in protein-cleaving enzymes, and make
important transition metal complexes with V, Fe, Ni, Zn and Mo (as noted above). Sulfur
bonds determine the higher structure (tertiary and quaternary of proteins), and sulfur is
part of some amino like acids cysteine and methionine. Another Group VIB element,
selenium, is less common but is important in peroxidases (enzymes which destroy
peroxide radicals). Like sulfur, it occurs directly in an amino acid (selenomethionine).
Phosphorous and Nitrogen
These elements are the focus of much biogeochemical research, because in many
environments, the availability of one or the other appears to “limit” production by
primary producers. As we will see, the cycles of these elements are linked to each other,
and to carbon, oxygen, and sulfur. The understanding of linkages between some of the
less abundant metals and the N or P cycles has grown considerably in recent years,
another topic we will consider.
Phosphorous
This group VA element is critical to all organisms and has many uses. Phosphate-bearing
molecules ATP, NAD, and NADP are central to the most basic metabolic functions of
respiration and photosynthesis. Phospholipids are essential part of cell membranes.
Ester-bound phosphate links the bases in DNA and RNA. Calcium phosphate is an
important skeletal material (bone, teeth). Phosphate transport across cell walls is linked
to cation transport, particularly Ca++.
Nitrogen
Also from group VA, nitrogen is part of all nucleotides and amino acids. N transport is
commonly as glutamine, pyridoxal, and as lysine. In organisms N is almost exclusively
found in amine (-NH2) groups. Nitrogen present in the environment as ammonium or
nitrate must be transformed, and the reduction of nitrate to amine-bound N is an
important pathway for many organisms. Most N in the environment exists as the very
inert triple-bonded N2 in the atmosphere – only a small group of microorganisms has the
capacity to “fix” or reduce N2 into biologically available forms. Thus organisms are
faced with a paradox – there is a huge reservoir of nitrogen as N2, but it is quite
unavailable to all but a handful.
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Other elements known to be active biologically are either less commonly used, or less
well understood. Several others are used skeletally by a few organisms but have no
known biochemical role. The reference cited above (Frausto da Silva and Williams,
1991) is an excellent source for more information on this general topic.
Metabolism and Energetics
Organisms have two basic kinds of functions. They process metabolites (chemical
compounds that undergo metabolic reactions) to obtain energy necessary to maintain life
functions, and they expend energy to acquire materials from the environment and
synthesize new biomass to grow and reproduce. For convenience we can view these as
separate processes, although they of course are not.
1) energy metabolism, also known as dissimilatory or catabolic metabolism
2) growth, also known as assimilatory or anabolic metabolism
Biological energy yielding reactions are almost all redox reactions. Thus elements that
have readily accessible multiple redox states at Earth surface temperatures are critical for
life. These include C, N, O, S, Fe, and Mn, plus a few others that play minor roles.
Recall that oxidation-reduction reactions are electron transfer reactions. Thus every time
a substance is “reduced” (i.e. electrons added), the other half of the redox couple must be
“oxidized” (i.e. lose electrons). These can take several forms.
Respiration can be aerobic or anaerobic, but in either case an outside “electron acceptor”
must be used. In other words, as a carbon (energy) source is taken up by cells and
oxidized to release energy, another compound from outside the cell must be reduced, or
“accept” electrons
Aerobic respiration uses di-oxygen as the oxidant, and we can schematically write
1.
CH2O + O2 ⇒ CO2 + H2O
Carbon is oxidized and O2 is reduced (accepts electrons). This pathway generally has the
highest energy yield of all the catabolic reactions, and it is exclusively used by animals,
who are all obligate aerobes.
Anaerobic respiration can use a number of other redox elements as the electron acceptor.
They include nitrate (NO3-), sulfate (SO4=), ferric iron (Fe3+) and manganese (Mn4+ or 3+),
all of which oxidize carbon and are reduced in the process. An example is dissimilatory
sulfate reduction (DSR), one version of which operates on acetate:
2.
2 H+ + CH3COO- + SO4= ⇒ 2 CO2 + 2 H2O + HS-
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Here the sulfur is reduced all the way from +6 to -2, i.e. accepts 8 e-. The term
dissimilatory refers to a chemical process that produces an inorganic product from an
organic reactant(s).
Fermentation is an anaerobic process that yields energy by changing the oxidation state
of a substrate both “up” and “down”, i.e. parties reduced and part is oxidized. As long as
there is a net energy yield (i,e. ∆Grxn < 0) bacteria can profit from this kind of reaction. A
well-known example is the formation of ethanol from sucrose:
3.
C6H12O6 ⇒ 2 C2H5OH + 2 CO2
In this case the carbon in the sucrose was in the zero oxidation state C0, but two carbons
are reduced to C-2 during the production of the alcohol, while one is oxidized to C+4 in the
carbon dioxide. Charge balance is conserved, but energy is yielded. No “outside”
oxidant or reductant is introduced for the reaction to take place.
Methanogenesis is related to fermentation, but is sufficiently different in a biochemical
sense that it can be considered separately. Methanogenic bacteria have a couple of basic
pathways. The first reaction is a type of fermentation. In this reaction one carbon from
the acetic acid is reduced and the other oxidized.
4.
CH3COOH ⇒ CO2 + CH4
The second type of reaction uses hydrogen to reduce carbon and make methane
5.
4 H2 + CO2 ⇒ CH4 + 2 H2O
Hydrogen can be produced in a number of ways, both biologically and also by the
reduction of water by reaction with metals or minerals. It is likely that some of the
earliest forms of metabolism involved reactions like 5 using H2 produced by mineralwater reactions at elevated T (hydrothermal reactions).
The energy yields of fermentation and methanogenesis are low compared to respiration.
Energy-yielding reactions commonly, but not always involve carbon. One that does not
has been found to occur in anaerobic marine muds:
6.
4 S0 + 4 H2O ⇒ SO4= + 3 H2S + 2 H+
In this reaction elemental sulfur is disproportionated into sulfate and sulfide. A
disproportionation reaction is one in which an element is simultaneously reduced and
oxidized to form two different products.
While the use of terms like disproportionation and dissimilatory may seem like
unnecessary jargon, for better or worse they are common in the scientific literature and
it’s quite useful to know what they mean.