DEPARTMENT OF BIOCHEMISTRY AND MOLECULAR BIOLOGY

FACULTY OF LIFE SCIENCE

FEDERAL UNIVERSITY DUTSIN-MA, KATSINA STATE

Lecture Note On Bch 431 (2 Credit Units)

Course Lecturer; Sabiu Umar Abdullahi

INTRODUCTION

Bioinorganic chemistry deals with the chemical reactivity of metal ions in biological
environments. Chemists, biochemists, spectroscopists and molecular biologists meet at the
frontiers of chemistry and biology to try and elucidate the underlying principles of bioinorganic
systems.

Elements, in the context of chemistry, refer to the fundamental substances that make up all
matter. Each element is composed of atoms that have the same number of protons in their atomic
nuclei. The periodic table of elements is a tabular arrangement of these elements based on their
atomic number, electron configuration, and recurring chemical properties.

Elements can be broadly categorized into several groups:

1. Metals: These elements are typically shiny, conductive, and have a metallic luster.
Examples include iron, copper, and gold.
2. Non-metals: Non-metals are generally poor conductors of heat and electricity. They can
be found in various forms, such as gases (like oxygen and nitrogen), solids (such as
carbon and sulfur), or brittle solids (like phosphorus).
 3. Metalloids: Metalloids possess characteristics of both metals and non-metals. They
exhibit intermediate properties and can behave as semiconductors. Examples include
silicon, arsenic, and germanium.
4. Noble gases: Noble gases are chemically inert and have low reactivity. They exist as
gases at room temperature and include helium, neon, argon, krypton, xenon, and radon.
5. Rare Earth elements: The rare earth elements consist of a group of chemically similar
elements located in the lanthanide series of the periodic table. They include elements
such as lanthanum, cerium, and europium.

Each element has unique physical and chemical properties, and they combine to form
compounds and molecules that make up the vast diversity of materials found in the universe.

Indeed, the human body is made up of 99.9% of just 11 elements, 4 of which (hydrogen, oxygen,
carbon and nitrogen) account for 99% of the total (62.8%, 25.4%, 9.4% and 1.4%, respectively).
Why we require as many as 25 elements in total from the periodic table and would become
clearer as we advance in this course, but one thing shines out, namely that these elements have
been selected on the basis of their suitability for the functions that they are called upon to play, in
what is predominantly an aqueous environment.

When it comes to discussing elements in the context of nutrition and biology, there are two main
categories: macro and micro elements. Additionally, elements can be further categorized as
essential or non-essential;

1. Macro and Micro elements

a. Macro elements: These are elements that are required in relatively large quantities by the
living organisms. They play crucial roles in various biological processes. The major
macro elements for most living organisms include carbon (C), hydrogen (H), oxygen (O),
nitrogen (N), phosphorus (P), and sulfur (S). These elements are present in large amounts
in biological molecules like carbohydrates, lipids, proteins, and nucleic acids.
b. Micro elements (also known as trace elements): These are elements that are required in
very small quantities by living organisms. Although they are needed in smaller amounts,
they still play essential roles in various biological processes. Examples of micro elements
include iron (Fe), zinc (Zn), copper (Cu), manganese (Mn), iodine (I), selenium (Se), and
 molybdenum (Mo). These elements are often cofactors for enzymes or are involved in
specific biochemical reactions.
2. Essential and Non-Essential Elements:
a. Essential elements: These are elements that are necessary for the normal growth,
development, and functioning of living organisms. Essential elements vary depending on
specific organism, but they are typically required for basic physiological processes. For
example, humans require essential elements such as calcium (Ca) for bone health,
potassium (K) for nerve function, and magnesium (Mg) for energy production.
b. Non-essential elements: These are elements that are not necessary for normal growth or
functioning of an organism. It doesn't mean that non-essential elements are not present or
have no physiological role; rather, they are not considered essential because they can be
synthesized or obtained from other sources. An example of a non-essential element for
humans is gold (Au). While gold has no known biological function in humans, it can be
used in certain medical treatments or as a marker in research studies.

It's important to note that the essentiality of elements can vary across different organisms. What
may be essential for one organism may not be essential for another. The classification of
elements as essential or non-essential is based on their importance for a particular organism's
biological processes and survival.

ROLES OF THE ELEMENTS IN BIOCHEMISTRY;

1. Regulatory action is exercised by Na +, K+, Mg2+ and Ca2+. The flux of these ions
through cell membranes and other boundary layers send signals that turn metabolic
reactions on and off.
a) Cofactors for Enzymes: Metal ions often function as cofactors for enzymes involved in
metabolic pathways. They can bind to enzymes and participate in catalytic reactions. For
example, zinc ions are required for the activity of many metalloenzymes involved in
carbohydrate, lipid, and protein metabolism.
b) Enzyme Activation/Inhibition: Metal ions can directly activate or inhibit enzyme activity.
They can bind to specific sites on enzymes and induce conformational changes that either
enhance or suppress their catalytic activity. For instance, magnesium ions are crucial for
 the activity of enzymes involved in ATP-dependent reactions, while heavy metal ions
like lead or mercury can inhibit various metabolic enzymes.
c) Gene Expression: Metal ions can regulate gene expression by binding to specific DNA
sequences or transcription factors. They can act as transcriptional activators or repressors,
modulating the expression of genes involved in metabolic pathways. For example, iron-
responsive elements (IREs) are specific RNA sequences that bind iron-regulatory
proteins (IRPs) and control the expression of genes involved in iron metabolism.
d) Signal Transduction: Metal ions can participate in signal transduction pathways,
transmitting signals from the cell surface to the nucleus and regulating metabolic
responses. For instance, calcium ions act as second messengers in various signaling
cascades, including those involved in glucose metabolism, by binding to and activating
downstream signaling proteins.
e) Transport and Homeostasis: Metal ions are transported across cell membranes by specific
transporters. These transporters play a crucial role in maintaining the intracellular
concentration of metal ions, which is essential for proper metabolic function. For
example, the divalent metal transporter 1 (DMT1) is responsible for iron uptake into
cells, ensuring the availability of iron for heme synthesis and other metabolic processes.
f) Oxidative Stress and Antioxidant Defense: Metal ions can generate reactive oxygen
species (ROS) through redox reactions. Excessive ROS production can lead to oxidative
stress and damage cellular components, including metabolic enzymes. To counteract this,
metal ions such as copper, zinc, and manganese are required as cofactors for antioxidant
enzymes like superoxide dismutase (SOD) and catalase, which help neutralize ROS and
protect metabolic pathways from oxidative damage.
2. Structural role – calcium in bones and teeth [as Ca10(PO 4) 6X2; X = F, Cl, OH] is
well known. Many proteins owe their structural integrity to the presence of metal ions
such as Ca2+, Zn2+, Mg2+.
a) Calcium: Calcium is the most abundant mineral in both bones and teeth. In bones, it
combines with phosphate ions to form hydroxyapatite, a crystalline mineral that provides
rigidity and hardness. In teeth, calcium is present in the form of enamel, which is the
outermost layer and the hardest tissue in the human body.
b) Phosphorus: Phosphorus is another critical mineral found in bones and teeth. It combines
with calcium ions to form hydroxyapatite crystals. Phosphorus helps to regulate the
deposition and resorption of calcium, ensuring the maintenance of bone density and
strength.
c) Magnesium: Magnesium is a metal that is present in small amounts in bones and teeth. It
plays a role in the structural integrity of bone by binding to the surface of hydroxyapatite
crystals. Magnesium also influences the activity of enzymes involved in bone
metabolism.
d) Zinc: Zinc is a trace metal that contributes to the formation and mineralization of bone. It
is involved in the synthesis of collagen, a key protein in the organic matrix of bones. Zinc
deficiency can impair bone development and increase the risk of fractures.
e) Copper: Copper is another trace metal required for the synthesis and maintenance of bone
tissue. It is involved in the formation of collagen and elastin, which provide flexibility
and resilience to bones. Copper deficiency can lead to bone abnormalities.
f) Iron: Iron is necessary for the proper formation and functioning of bone cells, including
osteoblasts (bone-forming cells) and osteoclasts (cells involved in bone resorption). Iron
deficiency can impair bone cell function and contribute to bone loss.
g) Silicon: Although not a metal, silicon is a mineral that is important for bone and tooth
health. It contributes to the mineralization of bone by enhancing the deposition of
calcium and other minerals.
3. Electron transfer – metal-containing electron transfer agents such as ferrodoxins (Fe)
and many copper-containing “blue proteins” are involved in electron transfer
chemistry that goes on in the biological systems.
a) Enzymatic reactions: Many metal-containing enzymes, such as superoxide dismutase
(SOD), catalase, and peroxidases, are involved in the metabolism and detoxification of
ROS. For example, SOD uses metal ions like copper, zinc, or manganese to convert
superoxide radicals into less harmful hydrogen peroxide.
b) Electron transfer: Transition metals, such as iron and copper, participate in electron
transfer reactions in redox enzymes and cofactors. These reactions are essential for
energy production and metabolic processes. However, the same metals can also generate
 ROS via Fenton and Haber-Weiss reactions, where they react with hydrogen peroxide to
form highly reactive hydroxyl radicals.
c) Oxygen transport and storage: Iron, in the form of heme, is a critical component of
hemoglobin and myoglobin, which transport and store oxygen in the body. During
oxygen transport, small amounts of oxygen can be converted to superoxide radicals,
contributing to oxidative stress.
d) Metalloproteins and cofactors: Several metal ions, including iron, copper, zinc, and
manganese, serve as cofactors in metalloproteins. These proteins participate in redox
reactions and are involved in various biological processes, such as DNA repair,
antioxidant defense, and metabolism. However, improper handling or regulation of these
metals can lead to ROS generation and oxidative damage.
e) Redox signaling: Metal ions, particularly copper and iron, can act as redox-active
signaling molecules. They participate in redox reactions that regulate cellular processes,
including cell growth, differentiation, and apoptosis. However, dysregulation of metal
homeostasis can disrupt redox signaling and contribute to oxidative stress-related
diseases.
4. Metalloenzymes and metallocoenzymes have metal ions at their active sites.
Examples of metalloenzymes are as follows: superoxide dismutase (Cu, Zn), urease
(Ni), alcohol dehydrogenase (Zn), cytochrome P-450 (Fe), etc. The best known
coenzyme is vitamin B12 which contains cobalt (Co).
a) Catalysis: Metals can act as cofactors for enzymes, facilitating catalytic reactions. They
can provide a suitable environment for the reaction to occur, participate directly in the
chemical transformation, or stabilize reaction intermediates. For example, zinc ions in
carbonic anhydrase facilitate the hydration of carbon dioxide, while iron ions in the heme
group of cytochrome P450 enzymes are involved in oxygenation reactions.
b) Electron transfer: Metals in metalloenzymes and metallocoenzymes can transfer electrons
during enzymatic reactions. They can serve as electron acceptors or donors, facilitating
electron transfer within the enzyme or between the enzyme and other molecules.
Examples include iron-sulfur clusters in electron transport chains and copper ions in
copper-containing enzymes like cytochrome c oxidase.
c) Structural stability: Metals can contribute to the structural stability of metalloenzymes
and metallocoenzymes. They can form coordination bonds with specific amino acid
residues, providing structural integrity and maintaining the overall protein fold. Metal
ions can help stabilize the active site of the enzyme, ensuring proper substrate binding
and catalysis. Examples include the role of zinc ions in stabilizing the structure of zinc
finger motifs in transcription factors.
d) Regulation: Metals can also play a regulatory role in metalloenzymes. They can control
enzyme activity by binding to specific regulatory sites, modulating the enzyme's
conformation or catalytic properties. For example, the binding of calcium ions to
calmodulin regulates the activity of various enzymes involved in calcium signaling
pathways.
e) Cofactor regeneration: In some cases, metallocoenzymes are involved in the regeneration
of other coenzymes. The metal ion acts as a cofactor, facilitating the transfer of functional
groups or electrons between the coenzyme and the substrate. An example is the role of
zinc in alcohol dehydrogenase, where it assists in the oxidation of alcohols by
transferring hydride ions to the coenzyme NAD+.
5. Oxygen carriers -all mammals contain hemoglobins (Fe) that carry oxygen from the
lungs to the tissue where it is used in oxidative processes that generate energy.
a) Hemoglobin: Hemoglobin is a protein found in red blood cells that binds to oxygen and
carries it from the lungs to the tissues throughout the body. The iron atom at the center of
each heme group in hemoglobin binds to oxygen, allowing for efficient oxygen transport.
b) Myoglobin: Myoglobin is a similar protein found in muscle cells that also binds to
oxygen. It stores oxygen in muscle tissues, allowing for its availability during periods of
increased activity or low oxygen supply. Like hemoglobin, myoglobin contains an iron
atom that binds to oxygen.
c) Cytochromes: Cytochromes are a class of proteins that contain heme groups with iron
atoms. They are involved in electron transport chains in various cellular processes,
including cellular respiration. Cytochromes facilitate the transfer of electrons, which is
essential for the production of ATP, the energy currency of cells.
d) Oxygenases: Some enzymes called oxygenases utilize metal ions, such as iron or copper,
to incorporate oxygen into organic molecules. These reactions are involved in various
metabolic pathways, including the breakdown of toxins and drugs in the liver.
e) Oxygen-binding proteins: Apart from hemoglobin and myoglobin, there are other
oxygen-binding proteins that use metals as oxygen carriers. For example, hemocyanins,
found in certain invertebrates like mollusks and arthropods, contain copper atoms that
reversibly bind oxygen for respiratory purposes.

FUNDAMENTALS OF INORGANIC CHEMISTRY

1. Oxidation states
 The alkali, alkaline and main group elements tend to adopt an oxidation state that
corresponds to a noble gas configuration e.g. Na+, Mg2+, Al3+, O2-, Cl-.
 The chemistry of the first-row (3d) transition metal ions is dominated by low or
moderate oxidation states e.g. Ni2+, Cu2+, Co2+, Fe2+, Ni2+, Zn2+, etc.
 The second-(4d) and third-row (5d) transition metal ions prefer higher oxidation
states (e.g. Mo(VI)), and require electronegative ligands for stability (hard ligands
such as F-or O2-).
2. Coordination numbers and preferred geometries Coordination compounds consist of a
central atom or ion, such as Co 3+, surrounded by electron-rich groups (ligands), such as
NH3. The ligands are directly bound (coordinated to) to the central atom or ion; they are
usually between 2 and 9 in number and may be single atoms, ions or molecules. The
ligands directly bound to the metal are said to be in the inner coordination sphere, and the
counter-ions that balance out the charge are said to be outer sphere ions. Coordination
compounds are usually referred to as complexes; they can be charged or uncharged and
their structure is defined by the coordination number (the number of ligand atoms bonded
to the central atom) and their coordination geometry (the geometrical arrangement of the
ligands and the symmetry of the entire complex). The central ion can be in any oxidation
state, which remains unchanged in the coordination complex. Coordination preferences of
the transition metals depend on the sizes of the metal ion and the ligands surrounding the
metal ion. Small cations can accommodate fewer ligands in their inner coordination
sphere and tend to adopt a tetrahedral geometry (less steric and electrostatic repulsion).
Many proteins fold in a manner that defines a cavity that selectively binds metal ions of a
particular size. For example, Fe in haemoglobin is housed in a pentacoordinate environment with
four planar pyrrole nitrogen atoms of the porphyrin ring in the square plane, and a nitrogen atom
of the imidazole group of a histidine residue of the polypeptide on the proximal side. Trans to the
latter nitrogen at the distal side of the porphyrin ring (6th position) is another nitrogen of a
histidine.

The diagram above is the representation of one of the sub-units of hemoglobin. The
continuous black band represents the peptide chain and the various sections of the helix. Dots
on the helical chain represent a-carbon atoms. The heme group is near the top of the diagram,
with the iron atom represented by a large dot. The coordinated histidine is labelled F8,
meaning the 8th residue of the F helix.

3. Ligand preference (based on hard-soft acid-base (HSAB) theory) Hard metal ions (e.g.
Fe3+, Mn2+, Na+, K+, Mg2+, Ca2+, Cr3+, Co3+) can be selectively ligated by small hard
anions, of which alkoxide (RO-) derivatives (e.g. tyrosinates, hydroxamates, and
catecholates) are the only reasonable candidates at biological pH. Softer metal ions (e.g.
 Cu2+, Ni2+,Co2+, Zn2+, Fe2+) are preferred by the soft ligands such as imidazole and thiolate
ligands.

Classification of biologically important metal ions and ligands according to the ‘hard–soft
acid–base’ concept and their general characteristics

In general ‘hard’ acids prefer ‘hard’ ligands whereas ‘intermediate’ and ‘soft’ acids form
more stable complexes with ‘soft’ bases. Hard–hard interactions will be primarily ionic in
nature whereas soft–soft interactions will be governed by ‘orbital’ interactions. If a hard
metal is combined with a soft ligand, the metal does not readily accept the electron density
being offered by the ligand, and so the resulting complex is less stable since both partners are
incompatible. As a general rule, the affinity of a donor atom in a ligand for a hard metal ion
varies as follows: F > O > N > Cl > Br > I > C ~ S. This order is reversed for soft metals.

4. Influence of pH Competition between metal ions and the protons is active, particularly
when ligands derive from ionized functionality. However, at neutral pH, the formation
constants of transition metals are usually greater than the acidity constants (Ka) that
correspond to the affinity of a ligand for a proton. In some intracellular compartments,
the pH can be lowered from the normal physiological level of 7.4 to a pH of 5.5, and it is
used to facilitate the release of iron from transferrin (iron transporting protein).
5. Ligand field stabilization energy Metal ions may derive extra stability when bound by
ligands as a result of the orbital splitting. The sum total of the contributions from all d-
electrons is termed the ligand field stabilization energy (LFSE). For example, a low spin
 d6 system (Fe2+) results in a large LFSE in octahedral environments, as well as the d3
system (Cr3+).
6. Kinetics and mechanisms of reactions involving metal complexes In biology, the ligand
environments of metal ions are often in a state of change. For example, the activation of
the protein calmodulin by Ca2+ requires the replacement of calcium-bound water
molecules by protein ligands. The exchange of ligands at metal centers plays a role in the
regulation of cellular metabolism. For example, the rapid ligand exchange rates of Ca 2+
(Kex ~ 109 s-1) relative to Mg 2+ (Kex ~ 105 s-1) explains the selection of the former as a
secondary messenger system. The knowledge of the reaction mechanisms for substitution
of metal bound ligands is essential for proper understanding of inorganic biochemistry.
Interchange mechanisms may be termed dissociative (Id) or associative (Ia), where the
coordination numbers of the metal center formally decrease or increase, respectively.
7. Electron transfer reactions; In biological redox chemistry, a substrate molecule usually
binds directly to the metal centre. For example, the reduction of nitrate to nitrite by the
molydoenzyme, nitrate reductase, proceeds via transfer of electrons from Mo(IV) to
nitrate after the latter binds to the former.

FUNDAMENTALS OF BIOCHEMISTRY

a. Biological ligands Proteins constitute one of the basic functional units in biology. The
proteins are built-up of amino acids, and the terminal groups (side chains) provide the
ligating atoms. There are 20 common amino acids, and a protein backbone is formed
from a basic set of amino acids by formation of amide links between the amino and
carboxylic acid functionality (revise under BCH201 along with how peptides are
formed).
The metal-binding domain of Ca2+-activated enzyme (phospholipase A2) showing coordination
of a chelating carboxylate, two water molecules, and three backbone carbonyls.

b. Polynucleotide Structure RNA and DNA are constructed from nucleic acids as building
blocks, which are derived from five bases, adenine, guanine, cytosine, thyamine or uracil,
and are attached to a ribose sugar (RNA) or deoxyribose (DNA) ring by an N-glycosidic
linkage, and a phosphate group is attached to the sugar. DNA typically exists in a form of
a double-stranded structure formed by hydrogen bond formation between specific base
pairs (Revise under BCH201).
Left-Structural units of nucleic acids. Middle-A single and a double-stranded DNA. Right
Specific hydrogen bond patterns formed between complementary base pairs.

The negatively charged sugar-phosphate backbone of the major and minor grooves of DNA play
host to a variety of charged species (e.g. metals, ligands and protein side chains). Alkali and
alkaline earth metals tend to coordinate to the oxyligands (phosphate, sugar hydroxyls, and
carbonyl functionality), whereas softer transition metals preferentially coordinate to the
heteroatoms N and O on the base units. The principal metal-binding domains on nucleotides are
illustrated in the following: