Biochemistry of Minerals Biological forms of minerals in living systems NaKCaMg P Cl CNHOS...

Biochemistry of Minerals

Biological forms of minerals in living systems

Na K Ca Mg

P

Cl

C NH O S

Fe Zn Cu Mn Se

V Si As Mo I

Co

Br F

Favored Oxidation state

+1 +2 +2 Variable, more than one state

Stability of complex

Very low Low to medium

High High (medium for Mn2+ and Fe2+)

Favored donor atoms

Oxygen Oxygen Sulfur or nitrogen

Sulfur or nitrogen (oxygen for Mn and Fe)

Mobility in biological media

Very mobile Semi mobile Static Static, semi mobile for Mn2+ and Fe2+

Na+, K+ Mg2+,Ca2+ Zn2+, Ni2+ Fe, Cu, Co, Mo, Mn

Characteristics of Biochemical Ion Complexes

After Frausto de Silva and Williams

Glucose

intestine

Glucose

Na+

liver

Mg2+

Mn2+

K+

Ca2+

PO43-

mitochondria

Hemoglobin

O2

Fe2+

H2O

Fe2+

PO43-

Mg2+

Cu2+

Inorganic Enzyme Cofactors(one-third of all enzymes require a metal ion for catalytic function)

Inorganic Cofactor Function Enzyme Class

Magnesium substrate binding kinasesCalcium substrate activation hydrolasesPotassium structure stabilization pyruvate kinase

Iron oxygen binding, electron transport cytochromesZinc substrate binding, structure stability DNA bindingCopper dioxygen activation oxidasesManganese dioxygen activation oxidasesCobalt group transfer mutases (with B12)Selenium peroxidation peroxidases

Metalloenzymes vs Metal Activated Enzymes

Metal Activated

1. Metal in equilibrium

Metalloenzyme

Metal firmly affixed to protein

2. Activated by adding metal ion Adding metal has minimal effect

3. Metal lost on isolation Metal stays bound, removable by chelators

4. No stoichiometry with protein Integral number per protein

5. Electrostatic bonding Coordinate covalent bonding

6. Multiple metal binding sites Limited number, generally one

7. Binding sites, angles irregular Binding sites exhibit specific geometry

8. Mostly group IA and IIA metals Na+, K+, Mg2+. Ca2+

Mostly 3d transition metalsZn2+, Fe2+. Cu2+, Co2+

Zinc (over 300)

DehydrogenasesRNA, DNA polymeraseCarbonic anhydraseCarboxypeptidaseAmino peptidase

Copper

Superoxide dismutaseTyrosinaseCytochrome oxidase (with Fe)Lysyl oxidasePeptide amidating Dopamine beta hydroxylase

Iron

Ribonucleotide reductaseCytochrome oxidase (with Cu)

Manganese

ArginaseWater splitting enzymePyruvate carboxylase

Cobalt (with B12)

Methylmalonyl CoA mutaseHomocysteine transmethylase

Molybdenum

NitrogenaseXanthine oxidase

Calcium

Thermolysin

NickelUrease

Examples of Metalloenzymes

Na+, K+, Cl-

Osmotic controlElectrolyte equilibriaIon currentsGated channels

Mg2+

Phosphate metabolism

Ca2+

Muscle contractionCell signalingEnzyme cofactorBlood clottingMineralizationMorphogenesisGene regualtion

Zn2+

Lewis acidEnzyme cofactorProtein structureHormone activatorNeurotransmitterGenetic expression regulator

Fe2+, Fe3+

Heme ironElectron transportOxygen activatorOxygen carrier

Cu+, Cu2+

Enzyme cofactorOxygen carrierOxygen activatorIron metabolism

Quick Overview of Mineral Functions

Quick Overview (cont.)

Se

Redox reactionsAntioxidant

Mo2+

Enzyme cofactorNitrogen activator

HPO4=, Si

Acid-base non metalsBiomineralization

Co3+

Vitamin b12

Ni2+

CoenzymeRemnant of early life

Cr3+

Insulin mimeticGlucose metabolism

Mn2+

Enzyme cofactor (limited)

Examples of Metalloproteins

1. Metallothionein

Function

Cu, Zn, Cd storage, heavy metal buffer

2. Ferritin Iron storage, iron buffer

3. Calmodulin Ca binding, allosteric regulator

4. Transferrin Iron transport

5. Selenoprotein W Selenium transport

6. Calbindin Calcium transport

Biomineralization

Calcium and phosphate

Bones and Teeth

Leg bone of a horse showing the trebecular (spongy) bone and the cortical (solid) bone. This bone is able to withstand forces generated by this 1,500 lb animal

Trebecular bone of the lower spine. Changes with aging.

Cortical bone with Halversion system (a series of channels supplying nutrients). Black dots are osteocytes

Cross section through trebecular and cortical bone revealing the internal architecture surrounded by marrow tissue.

Demineralized bone: Shown is he organic matrix consisting mostly of collagen upon which the bone crystals are laid.

Hydroxyapatite (crystal structure) Ca10(PO4)6 OH2

Ca P O H

Zinc Function• 300 enzymes require zinc

– DNA, RNA polymerases

• numerous hormones require zinc– insulin– EGF

• transcription factors (zinc finger proteins)• membrane stability• myelination• skeletal development

Metal Ions in Catalysis- One third of all enzymes require a metal ion for catalysis

His –Zn2+

His

His

O

H

CO

O

H2O

Zn 2+Polarizes H2O, making it a better

nucleophile

Zn 2+Polarizes H2O, making it a better

nucleophile

His –Zn2+

His

His

O

H

..+ C

O

O

His –Zn2+

His

His

O

H

..+ H+ + H O C

O

O

Bicarbonate

Displaces HCO3-

Biochemical Iron • Hemoglobin- oxygen carrier in the blood• Myoglobin- O2 carrier in cells (mostly in muscle)• Cytochromes- electron carriers in membranes• Catalase- enzyme that destroys H2O2 (hydrogen

peroxide)• Cytochrome oxidase- electron transport, ATP

synthesis in mitochondria• Cytochrome P450- detoxifying enzyme• Nitrogenase- nitrogen fixation• Ferritin- iron storage in cells, plasma• Transferrin- iron transport in blood• Iron-sulfur electron proteins- electron carriers• Tyrosine and phenylalanine hydroxylase-

enzymes that synthesizes L-DOPA and tyrosine, respectively

• Ribonucleotide reductase- enzyme that forms deoxyribose from ribose

Function• Oxygen Transport & Storage

– Hemoglobin– Myoglobin

• Electron Transport & Energy Metabolism– Cytochromes – Fe-S proteins

• Substrate Oxidation & Reduction – Iron dependent enzyme-

– Ribonucleotide reductase– Amino acid oxidases– Fatty acid desaturases– Nitric oxide synthetase– Peroxidases All use O2 as a substrate

Examples of Iron-dependent Enzymes

L-tyrptophan + BH4 + O2 5 OH L-tryptophan + BH2 + H2O

Fatty Acid desaturase

Aldehyde Oxidase

R-CHO + O2 RCOOH + H-O-O-H

Tryptophan 5-monooxygenase

Stearoyl-CoA + NADH + H+ + O2 Oleoyl-CoA + NAD+ + 2H2O

Peroxidase

2H2O2 2H2O + O2

(O2 is either incorporated into the product or reduced by electrons)

Electron Transport Complexes

• Membranes bound heme proteins or “cytochromes”

• Iron-Sulfur proteins..high reducing potential

• Mobile electron carriers– Coenzyme Q– Cytochrome c

Transport Mechanism

NADH

NAD+

FMN

FMNH2 CoQ

CoQH2

Cyt b(Fe3+)

Cyt b(Fe2+)

Cyt c1

(Fe3+)

Cyt c1

(Fe2+)Cyt c(Fe3+)

Cyt c(Fe2+)

Cyt a+a3

(Fe3+)

Cyt a+a3

(Fe2+) O2

H2O

A bucket-brigade

Reduced Oxidized

..

..

..

..

..

..

..

..

-0.32 volts + 0.82 volts

M o

M o - H

M o - H

H

M o - H

H

H -

N = N

H 2H - M o = N = N

F d - e -

F d

R

R e -

A TP A D P

H - M o = N - N H 2

0 . 2 9

F d - e -

F d

R

R e -

A T P A D P

0 . 4 0

F d - e -

F d

R

R e -

A TP A D P

M o = N

N H 3

N H 3

M o

A c t iv a t e d

Electron Transfer “Pump” Dinitrogenase

Dinitrogenase Reductase

e + H+

e + H+

e + H+

Iron and Molybdenum in Nitrogenase

Fe

N2 + 3H2 2NH3