Inorganic chemistryB.Sc III

Bioinorganic chemistry

– Bulk Elements: O, C, H, N, Ca, S, P,

Na, K, Cl, Mg, etc.• Trace Elements: Mo, Mn, Fe, Co, Cu, Zn, I, Si, etc.• Ultra-trace Elements: V, Cr, Se, Br, Sn, F, etc.

Inorganic Elements in Biological Systems

Porphyrins and Related Complexes in Bioinorganic Molecules

• A porphine ring has a square planar geometry with a “pocket” in the center.

• A metalloporphyrin complex can result by incorporating a metal atom into the pocket (look at heme from Rasmol).– Axial sites are available for other ligands.

• Structure, specificity, and reactivity are changed by differing the side chains, metal ions, and surrounding species.

Porphyrins

Metalloporphyrin complex

Heme B group of hemoglobin. An iron (Fe) atom in the middle is shown in red, complexed to four interior nitrogen atoms shown in blue.

Hemoglobin and Myoglobin

• Oxygen transfer and storage agents in the blood and muscle tissue.– Hemoglobin transports oxygen (O2) from the

lungs/gills to tissues and muscles.– Myoglobin stores oxygen (O2) in the muscles and

tissues.Oxygen commonly transfers from the hemoglobin to

the myoglobin for later use.

Hemoglobin (I)

• Made up of four globin protein subunits ( and ).– Each protein partially encloses a heme group.

• Each heme group is in a porphyrin pocket.– One axial position of the iron is bound to an imidazole

nitrogen from the protein.– One axial position is available/vacant or has H2O bound

to it.• Dissolved O2 can bind reversibly to this axial position.

http://www.umass.edu/microbio/chime/hemoglob/

Hemoglobin (II)

• In hemoglobin, the Fe(II) does not become oxidized to Fe(III) or Fe(IV).– Occurs readily in simpler systems (see Figure on the

next page).• There needs to be reversible binding of the O2

without oxidation. A free heme also oxidizes in an aqueous environment.– Why doesn’t oxidation occur in hemoglobin by O2

or H2O?

Hemoglobin (Figures)

Hemoglobin (III)

• In nonoxygenated hemoglobin, the Fe(II) is about 70 pm out of the plane of the porphyrin nitrogens (show with Chime).

• Bonding O2 or CO in the sixth position causes the iron to be come planar.– Fe(II) becomes diamagnetic

• Oxygen bonds at an angle of ~130 degrees (show with Chime).

Explain these structural changes upon bonding.

Hemoglobin(IV)

• There is a considerable amount of backbonding from the metal to the O2.– Can be described as Fe(III)-O2

-

• Why is the O2 bent? The energy changes very little with this angle.– suggestions

Hemoglobin (V)

• Cooperativity– The function of hemoglobin is to bind O2 at high oxygen

pressure and carry it through the blood to needed areas (and myoglobin for storage).

Hb + 4O2 Hb(O2)4

Hb(O2)4 + 4Mb 4Mb(O2) + Hb

• As one iron binds an oxygen molecule in Hb, the molecular shape changes to make binding of additional oxygen molecules easier. In a similar fashion, initial removal of oxygen triggers the release of the remaining oxygens.

Hemoglobin

• At low partial pressures of O2, Mb has a much greater affinity for O2.

• The Bohr effect.– Increased acidity favors the

release of O2 from Hb(O2)4

]O][Mb[

)]O(Mb[K

2

2Mb

8.22

42Hb ]O][Hb[

])O(Hb[K

Sodium is important in the body, as it helps maintain body fluid homeostasis.

People with disorders that do not have enough sodium in the body can take

medication such as serum sodium in order to maintain a healthy amount of

sodium in the body. Sodium is also crucial in osmotic pressure, as the body

adjusts to when there is too little or too much sodium in the body. Sodium is

also the main cation in outside cells containing fluid in mammalian bodies,

and very little sodium inside the cells, consisting of approximately 90% of the

body's total sodium content.

Biological Role of Sodium

Magnesium and calcium are ubiquitous and essential to all known living organisms.

They are involved in more than one role, with, for example, Mg/Ca ion pumps

playing a role in some cellular processes, magnesium functioning as the active

center in some enzymes, and calcium salts taking a structural role

Biological Role of Magnesium and calcium

Nitrogen Fixation

• The growth of all organisms depend on the availability of Nitrogen (e.g. amino acids)

• Nitrogen in the form of Dinitrogen (N2) makes up 80% of the air we breathe but is essentially inert due to the triple bond (NN)

• In order for nitrogen to be used for growth it must be "fixed" (combined) in the form of ammonium (NH4) or nitrate (NO3) ions.

Nitrogen Fixation

• The nitrogen molecule (N2) is quite inert. To break it apart so that its atoms can combine with other atoms requires the input of substantial amounts of energy.

• Three processes are responsible for most of the nitrogen fixation in the biosphere:

• atmospheric fixation

• biological fixation

• industrial fixation

Biological Fixation cont.• Biological nitrogen fixation requires a complex set of enzymes and a huge

expenditure of ATP.

• Although the first stable product of the process is ammonia, this is quickly incorporated into protein and other organic nitrogen compounds.

• Scientist estimate that biological fixation globally adds approximately 140 million metric tons of nitrogen to ecosystems every year.

Some nitrogen fixing organisms

• Free living aerobic bacteria– Azotobacter– Beijerinckia– Klebsiella– Cyanobacteria (lichens)

• Free living anaerobic bacteria– Clostridium– Desulfovibrio– Purple sulphur bacteria– Purple non-sulphur bacteria– Green sulphur bacteria

• Free living associative bacteria– Azospirillum

• Symbionts– Rhizobium (legumes)– Frankia (alden trees)

Some nitrogen fixing organisms

Leguminous Non Heterotrophs Phototrophs Heterotrophs Phototrophs plants leguminous plantsAzotobacter spp. Various Clostridium spp Chromatium soybeans, Alnus, MyricaKlebsiella Cyanobacteria Desulfovibrio Chloribium clover, CeanthusBeijerinck ia Disulfoto- Rhodospirillum locust, etc ComptoriniaBacillus maculum Rhodopseudo- In association Casurina polymyxa monas with a bacterium in assocationMycobacterium Rhodo- of the genus with flavum microbium Rhizobium or actinomycetesAzospirillium Rhodobacter Bradyrhizobium of the genus lipoferum Heliobacterium Frank iaCitrobacter freundiiSome Methylotrophs

Free living SymbioticAerobes Anaerobes

Nitrogen Fixation

• All nitrogen fixing bacteria use highly conserved enzyme complex called Nitrogenase

• Nitrogenase is composed of of two subunits: an iron-sulfur protein and a molybdenum-iron-sulfur protein

• Aerobic organisms face special challenges to nitrogen fixation because nitrogenase is inactivated when oxygen reacts with the iron component of the proteins

Nitrogenase

FeMo Cofactor

N2 + 8H+

2NH3 + H2

8e-

4C2H2 + 8H+ 4C2H2

DinitrogenaseDinitrogenase

reductase

Fd(red)

Fd(ox)

nMgATP

nMgADP + nPi

N2 + 8H+ + 8e- + 16 MgATP 2NH3 + H2 + 16MgADP

Nitrogenase

Types of Biological Nitrogen Fixation

Free-living (asymbiotic)• Cyanobacteria• Azotobacter

Associative• Rhizosphere–Azospirillum• Lichens–cyanobacteria• Leaf nodules

Symbiotic• Legume-rhizobia• Actinorhizal-Frankia