Inorganic Biochemistry
Lecture A: acid base catalysis
Cellular organisation
Genome: genetic information
Proteome: translation of genetic info via ribosomes into proteins
Metallome: collection of metals that the cell contains
Compartmentalization → metals are (mostly) stored in specific compartments as there is either their
site of action (catalysis/structural) or to avoid toxicity or disturbance of functions (such as Ca2+ that
is a signalling molecule).
The human body consists of Hydrogen, Oxygen, Carbon, Nitrogen, Calcium, Phosphorus, Sulfur,
Sodium, Potassium, Chloride, Magnesium, Silicon, Iron, Zinc, Copper, Iodine, Manganese, Fluor,
Chromium, Selenium, Molybdenum, and Cobalt.
The most important roles of metals I biological catalysis are to
• act as a Lewis acid
• to polarize bonds in a substrate
• electron transfer
• binding and activation of small molecules
• being involved in electrostatic potential differences
• being involved in signaling
,The genome is the genetic information in a cell. The proteins in the cell are called the proteome and
similar the metals that are present in a cell are called the metallome.
Passive diffusion → concentration gradient. For water, ions, and large molecules special channels are
needed, these are called gated channels → physical (potential) or chemical (hormone) stimulus
Calcium, Potassium and Sodium → high exchange rates → signalling
Magnesium is more comparable to transition metals in complex stability.
A lot of the Calcium in biology → hydroxyapatite: bone, tooth.
Ca2+ mainly outside cell Ca2+-ATPase (Na+/Ca2+ exchange)
Ca2+ high in ER/SR, Golgi apparatus and mitochondria SERCA (sarco(endo)plasmic reticulum ATP-
ase)
Ca2+ intracellular second messenger → binding to calmodulin
• large flexible (irregular) coordination sphere
• coordination to seven oxygen atoms: 5 from the amino acid
side chains (including a bidentate carboxylate), one from the
peptide backbone, and one of H2O
• fast exchange rates
• short lived strong signal → Ca2+ binding to calmodulin → EF-hand
conformation to activate kinases + activation of nitric oxide synthases
• nitric oxide: cellular messenger for widening of blood vessels
NADPH H + Arg + O2 → citrulline + H2O + NO
Cofactors: one or more inorganic ions, such as Mg, K, V, Fe, Ni, Cu, Zn, Mo, W
and/ or a coenzyme.
Coenzyme: an organometallic/coordination complex.
Prosthetic group: a firmly or covalently bound coenzyme to a protein.
Holoenzyme: the complete enzyme
Apoenzyme: the protein part of an enzyme
Vitamin: essential component of nutrition
A metal ion can be incorporated in a protein by binding to a negatively charged amino acid (Glu, Asp,
Tyr or Cys) or oppositely charged ones → protein can be regarded as an oil drop such that charge
insertion energy has to be compensated by opposite charges
,Hard lewis acids/bases
• low polarizability (of electrons)
• high oxidation states (acids)
• high electronegativity’s (bases) → no easy electron donation
soft lewis acids/bases
• easy polarizability
• low oxidation states
• low electronegativity’s
lewis acid: electron acceptor/ proton donor
lewis base: electron donor/ proton acceptor
• hard acids with hard bases and soft acids with soft bases
Transcription factors: bind to DNA and control the transcription into mRNA. Some of these factors
have Zn-induced protein folds (zinc fingers).
Thioneins: cysteine-rich proteins that are produced in liver and kidney when Cu+, Zn2+, Hg2+ or Cd2+
are present and form metallothioneins with them.
Metallothioneins: unharmful sequestration of excess Cu and Zn
Detoxification and safe transport of Hg and Cd out of body
Iron is the most important d-block element in biological systems. 70% of the iron in man is found
in hemoglobin in the erythrocytes where it’s involved in the binding of oxygen. Furthermore it plays a
role in electron transfer in the FeS proteins and the cytochromes and is found in the active site of a
number of redox and other enzymes.
Most important ion pairs in tissues
Blood: Na+ Cl-
Muscle: K+ HPO4 2-
Stomach: H+ Cl-
Seawater: Na+ Cl-
Clear concentration gradients: signalling, energy storing
Blood → osmosis: avoids red blood cells from bursting/shrinking → maintenance of gradient for
nerval signalling
Muscle → compartmentalization → signalling for muscle contraction/waste from respiration
Stomach → acidity: killing microbes, facilitate uptake of nutrients
, Potential = RT/z ln([in]/[out])
Concentration gradients/compartmentalization maintained by homeostasis
Ions can’t pass cell membrane → ion channels and transporters
• active/ passive transport (depends on electrochemical gradient)
• gated ion channels: chemical/physical/mechanical stimulus for opening
• channels are selective: due to selectivity filter
selectivity filter principle (example: K+ transporter)
• ions pass through selectivity filter into aqueous cavity
• passage only possible if ions can be dehydrated and stabilized → ions should
have both suitable ionic radius + suitable charge (Zeff/r)
dehydration enthalpy very positive → compensation of this increase in G by coordination to amino
acid side chains in selectivity filter
K+ selectivity filter
• K+ equatorially stabilized by coordination to
four carbonyls and axially by two H2O
• Strongly conserved TVGYG region
• Rates close to diffusion
• Passive transport
Na+/K+ -ATPase
• Homeostasis of Na+ and K+
• Na+ outside cells (in blood), K+ inside cells
• After action potential restoration of gradient → active
transport (unfavourable) ATP-driven
Lecture A: acid base catalysis
Cellular organisation
Genome: genetic information
Proteome: translation of genetic info via ribosomes into proteins
Metallome: collection of metals that the cell contains
Compartmentalization → metals are (mostly) stored in specific compartments as there is either their
site of action (catalysis/structural) or to avoid toxicity or disturbance of functions (such as Ca2+ that
is a signalling molecule).
The human body consists of Hydrogen, Oxygen, Carbon, Nitrogen, Calcium, Phosphorus, Sulfur,
Sodium, Potassium, Chloride, Magnesium, Silicon, Iron, Zinc, Copper, Iodine, Manganese, Fluor,
Chromium, Selenium, Molybdenum, and Cobalt.
The most important roles of metals I biological catalysis are to
• act as a Lewis acid
• to polarize bonds in a substrate
• electron transfer
• binding and activation of small molecules
• being involved in electrostatic potential differences
• being involved in signaling
,The genome is the genetic information in a cell. The proteins in the cell are called the proteome and
similar the metals that are present in a cell are called the metallome.
Passive diffusion → concentration gradient. For water, ions, and large molecules special channels are
needed, these are called gated channels → physical (potential) or chemical (hormone) stimulus
Calcium, Potassium and Sodium → high exchange rates → signalling
Magnesium is more comparable to transition metals in complex stability.
A lot of the Calcium in biology → hydroxyapatite: bone, tooth.
Ca2+ mainly outside cell Ca2+-ATPase (Na+/Ca2+ exchange)
Ca2+ high in ER/SR, Golgi apparatus and mitochondria SERCA (sarco(endo)plasmic reticulum ATP-
ase)
Ca2+ intracellular second messenger → binding to calmodulin
• large flexible (irregular) coordination sphere
• coordination to seven oxygen atoms: 5 from the amino acid
side chains (including a bidentate carboxylate), one from the
peptide backbone, and one of H2O
• fast exchange rates
• short lived strong signal → Ca2+ binding to calmodulin → EF-hand
conformation to activate kinases + activation of nitric oxide synthases
• nitric oxide: cellular messenger for widening of blood vessels
NADPH H + Arg + O2 → citrulline + H2O + NO
Cofactors: one or more inorganic ions, such as Mg, K, V, Fe, Ni, Cu, Zn, Mo, W
and/ or a coenzyme.
Coenzyme: an organometallic/coordination complex.
Prosthetic group: a firmly or covalently bound coenzyme to a protein.
Holoenzyme: the complete enzyme
Apoenzyme: the protein part of an enzyme
Vitamin: essential component of nutrition
A metal ion can be incorporated in a protein by binding to a negatively charged amino acid (Glu, Asp,
Tyr or Cys) or oppositely charged ones → protein can be regarded as an oil drop such that charge
insertion energy has to be compensated by opposite charges
,Hard lewis acids/bases
• low polarizability (of electrons)
• high oxidation states (acids)
• high electronegativity’s (bases) → no easy electron donation
soft lewis acids/bases
• easy polarizability
• low oxidation states
• low electronegativity’s
lewis acid: electron acceptor/ proton donor
lewis base: electron donor/ proton acceptor
• hard acids with hard bases and soft acids with soft bases
Transcription factors: bind to DNA and control the transcription into mRNA. Some of these factors
have Zn-induced protein folds (zinc fingers).
Thioneins: cysteine-rich proteins that are produced in liver and kidney when Cu+, Zn2+, Hg2+ or Cd2+
are present and form metallothioneins with them.
Metallothioneins: unharmful sequestration of excess Cu and Zn
Detoxification and safe transport of Hg and Cd out of body
Iron is the most important d-block element in biological systems. 70% of the iron in man is found
in hemoglobin in the erythrocytes where it’s involved in the binding of oxygen. Furthermore it plays a
role in electron transfer in the FeS proteins and the cytochromes and is found in the active site of a
number of redox and other enzymes.
Most important ion pairs in tissues
Blood: Na+ Cl-
Muscle: K+ HPO4 2-
Stomach: H+ Cl-
Seawater: Na+ Cl-
Clear concentration gradients: signalling, energy storing
Blood → osmosis: avoids red blood cells from bursting/shrinking → maintenance of gradient for
nerval signalling
Muscle → compartmentalization → signalling for muscle contraction/waste from respiration
Stomach → acidity: killing microbes, facilitate uptake of nutrients
, Potential = RT/z ln([in]/[out])
Concentration gradients/compartmentalization maintained by homeostasis
Ions can’t pass cell membrane → ion channels and transporters
• active/ passive transport (depends on electrochemical gradient)
• gated ion channels: chemical/physical/mechanical stimulus for opening
• channels are selective: due to selectivity filter
selectivity filter principle (example: K+ transporter)
• ions pass through selectivity filter into aqueous cavity
• passage only possible if ions can be dehydrated and stabilized → ions should
have both suitable ionic radius + suitable charge (Zeff/r)
dehydration enthalpy very positive → compensation of this increase in G by coordination to amino
acid side chains in selectivity filter
K+ selectivity filter
• K+ equatorially stabilized by coordination to
four carbonyls and axially by two H2O
• Strongly conserved TVGYG region
• Rates close to diffusion
• Passive transport
Na+/K+ -ATPase
• Homeostasis of Na+ and K+
• Na+ outside cells (in blood), K+ inside cells
• After action potential restoration of gradient → active
transport (unfavourable) ATP-driven
