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Wiley Series in Protein and Peptide Science

Vladimir N. Uversky, Series Editor

Metalloproteomics • Eugene A. Permyakov

Instrumental Analysis of Intrinsically Disordered Proteins: Assessing Structure and Conformation • Vladimir Uversky and Sonia Longhi

Protein Misfolding Diseases: Current and Emerging Principles and Therapies • Marina Ramirez-Alvarado, Jeffery W. Kelly, and Christopher M. Dobson

Calcium Binding Proteins • Eugene A. Permyakov and Robert H. Kretsinger

Protein Chaperones and Protection from Neurodegenerative Diseases • Stephan Witt

Transmembrane Dynamics of Lipids • Philippe Devaux and Andreas Herrmann

Flexible Viruses: Structural Disorder in Viral Proteins • Vladimir Uversky and Sonia Longhi

Protein Families: Relating Protein Sequence, Structure, and Function • Christine A. Orengo and Alex Bateman

Chemistry of Metalloproteins: Problems and Solutions in Bioinorganic Chemistry • Joseph J. Stephanos and Anthony W. Addison

Chemistry of Metalloproteins

Problems and Solutions in Bioinorganic Chemistry

Joseph J. Stephanos

Anthony W. Addison

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Preface

This book is an attempt to reveal the chemical concepts that rule the biological action of metalloproteins. The emphasis is on building up an understanding of basic ideas and familiarization with basic techniques. Enough background information is provided to introduce the field from both chemical and biological areas. It is hoped that the book may be of interest to workers in biological sciences, and so, primarily for this purpose, a brief survey of relevant properties of transition metals is presented.

The book is intended for undergraduates and postgraduates taking courses in coordination chemistry and students in biology and medicine. It should also be a value to research workers who would like an introduction to this area of inorganic chemistry. It is very suitable for self-study; the range covered is so extensive that the book can serve as a student's companion throughout his or her university career. At the same time, teachers can turn to it for ideas and inspirations.

The book is divided into seven chapters and covers a full range of topics in bioinorganic chemistry. It is well-illustrated and each chapter contains suggestions for further reading, providing access to important review articles and papers of relevance. A reference list is also included, so that the interested reader can readily consult the literature cited in the text.

It is hoped that the present book will provide the basis for a more advanced study in this field.

Joseph J. Stephanos

Anthony W. Addison

1
Introduction

The discipline of bioinorganic chemistry is concerned with the function of metallic and most of nonmetallic elements in biological processes. Also, it is the study of the chemistry, structure, and reactions of the metalloprotein molecules belonging to the living cell.

The precise concentrations of different ions, for instance, in blood plasma indicate the importance of these ions for biological processes, (Table 1-1).

Table 1-1 Ion Concentration in Extracellular Blood Plasma

Ion mM Ion mM
Na+ 138 SO42− 1
Cl 100 Fe 0.02
K+ 4 Zn2+ 0.02
Ca2+ 3 Cu2+ 0.015
Mg2+ 1 Co2+ 0.002
HPO42− 1 Ni2+ 0

Such elements fall into four broad classifications: the polluting, contaminating, beneficial, and essential elements.

img

Figure 1-1 Distribution of elements essential for life (Cotton and Wilkinson, 1980).

Twenty-five elements are currently thought to be essential to warm-blooded animals (Table 1-2).

Table 1-2 Percentage Composition of Essential Elements in Human Body

Element Percentage (by Weight) Element Percentage (by Weight)
Oxygen 53.6 img Silicon 0.04
Carbon 16.0 Iron, fluorine 0.005
Hydrogen 13.4 Zinc 0.003
Nitrogen 2.4 Copper, bromine 2 × 10−4
Sodium, potassium, sulfur 0.10 Selenium, manganese, arsenic, nickel 2 × 10−5
Chlorine 0.09 Lead, cobalt 9 × 10−6

Essentiality has been defined according to certain criteria:

Every essential element follows a dose–response curve, shown in Fig. 1-2. At lowest dosages the organism does not survive, whereas in deficiency regions the organism exists with less than optimal function.

img

Figure 1-2 The dose-response curves of selenium and fluoride.

The ten ions classified as trace metal are Fe, Cu, Mn, Zn, Co, Mo, Cr, Sn, V, and Ni, and the four classified as bulk metals are Na, K, Mg, and Ca. The nonmetallic elements are H, B, C, N, O, F, Si, P, S, Cl, Se, and I.

Biological Roles of Metal Ions

What are the general roles of metal ions in biological systems?

The general roles of metal ions in biological systems are summarized in Table 1-3.

Table 1-3 Role of Metal Ions and Examples

Metal Functions and Examples
Na+, K+ Charge transfer, osmotic balance, nerve impulses
Mg2+ Structure in hydrolases, isomerases, phosphate transfer, and trigger reactions
Ca2+ Structure, charge carrier, phosphate transfer, trigger reactions
Zn2+ (tetrahedral) Structure in zinc finger, gene regulation, anhydnase, dehydrogenase
Zn2+ (square pyramidal) Structure in hydrolases, peptidases
Mn2+ (octahedral) Structure in oxidases, photosynthesis
Mn3+ (tetragonal) Structure in oxidase, photosynthesis
Fe2+ Electron transfer, nitrogen fixation in nitrogenase, dioxygen transport in hemoglobin and myoglobin
Fe3+ Electron transfer in oxidases
Cu+, Cu2+ Electron transfer in type I blue copper proteins, oxidases and hydroxylases in type II blue copper proteins, hydroxylases in type III blue copper proteins, dioxygen transport in hemocyanin
Co2+ (tetrahedral) Alkyl group transfer, oxidases
Co+, Co2+, Co3+ (octahedral) Alkyl group transfer in B12
Ni2+ (square planar) Hydrogenase, hydrolases
Mo4+, Mo5+, Mo6+ Nitrogen fixation in nitrogenose, oxo transfer in oxidases

Metals in biological systems function in a number of different ways:

  • Groups 1 and 2 metals operate as structural elements or in the maintenance of charge, osmotic balance, or nerve impulses.
  • Transition metal ions that exist in single oxidation states, such as zinc (II), function as structural elements in superoxide dismutase and zinc fingers or as triggers for protein activity, e.g., calcium ions in calmodulin or troponin C.
  • Transition metals that exist in multiple oxidation states serve as electron carriers, e.g., iron ions in cytochromes or in iron–sulfur clusters of the enzyme nitrogenase or copper ions in azurin and plastocyanin.
  • As facilitators of oxygen transport, e.g., iron ions in hemoglobin or copper ions in hemocyanin.
  • As sites at which enzyme catalysis occurs, e.g., copper ions in superoxide dismutase or iron and molybdenum ions in nitrogenase.
  • Metal ions may serve multiple functions, depending on their location within the biological system, so that the classifications in Table 1-3 are somewhat arbitrary and/or overlapping.

Proteins: Formation, Structures, and Metalloproteins

This section is designed to introduce the chemistry of proteins. The text broadly includes where and how the proteins are formed, along with the structure and formation of metalloproteins.

Following the introduction of organelles and their functions within the cell, the discussion will be concerned with the general structure of deoxyribonucleic acid (DNA) and how the nucleus maintains its control of cell growth, division, and formation of [messenger, transfer, and ribosomal ribonucleic acid (mRNA, tRNA, rRNA)]. This is followed by how mRNA and tRNA master the formation of proteins within a cell. Then, primary, secondary, tertiary, and quaternary structures of the formed proteins and the factors that control each of these structures are discussed.

Specific points about the ligation of various metal ions to different amino acids within the proteins are made, and the binding stabilities of various metal ions toward different amino acids are arranged.

The general formulas, side chains, and corresponding names of the common natural α-amino acids, the formation of the peptide chain from the amino acids, and the physiological roles of proteins are described.

The chemistry of the prosthetic and cofactors is explored. Enough basic biochemistry is presented to enable the student to understand the discussions that follow.

Organelles and Their Functions

Identify the organelles and their functions within the cell.

  • Cells are the building blocks of all living things.
  • There are similarities in the appearance, chemical constituents, and activities of all cells (Fig. 1-3).
    img

    Figure 1-3 (a) Animal cell and (b) plant cell.

  • Different structures within the cell are called organelles.
  • Each organelle has an important, specific function in the cell.
  • The mitochondria are responsible for conversion of food into usable energy (metabolism):
    • They contain enzymes for cell metabolism.
    • More than 50% of the energy produced by mitochondrial oxidation of carbohydrates is recaptured as adenosine diphosphate (ADP) and converted into adenosine triphosphate (ATP).
    • The derived energy is trapped in ATP molecules (Scheme 1-1).
      img

      Scheme 1-1 Derived energy is trapped in adenosine triphosphate molecules (ATP).

    • ATP can diffuse rapidly throughout the cell, delivering energy to sites where it is required for cellular processes.
  • In green plants, chloroplasts contain chlorophyll molecules and other pigments.
    • Chlorophyll and other pigments in chloroplasts absorb light energy from the sun and use it to produce ATP, glucose, and oxygen.
  • Ribosomes are round particles (mRNA) that are sent by the nucleus to activate protein synthesis.
    • The mRNA causes a specific protein molecule to be synthesized from the pool of amino acids present in the cell cytoplasm.
  • The nucleus, or command station, contains information for the development and operation of the cell.
    • This information is stored chemically in long molecular strands called DNA. A combination of DNA and protein forms fine strands of chromatin. When a cell is about to divide, the chromatin strands coil up and become densely packed, forming chromosomes.
    • The number of chromosomes varies with the species: Humans have 23, the fruit fly has 4, corn has 10, and the mosquito has 3.
Structure of DNA

What is the general structure of deoxyribonucleic acids, DNA?

  • Polymerization of nucleoside phosphates produces the nucleic acids, DNA and RNA.
    img
  • DNA is a giant molecule with molecular weight of order 1 billion or more.
  • The information is chemically stored by nitrogen-base molecules that are bonded to the sugar residues of the sugar–phosphate chain.
  • There are four nitrogen bases:
    1. Two purines, which are bicyclic molecules:
      img
    2. Two pyrimidines, which are monocyclic:
      img
  • The order in which they appear on the chain makes up the molecular message (Fig. 1-4).
    img

    Figure 1-4 Order of N bases on chain.

  • The DNA molecule is also capable of duplicating itself and dividing.
  • Under a microscope we can see the duplicated chromosomes divide equally as the cell divides.
  • The DNA double strand forms when the bases on the two adjacent single strands form hydrogen bonds:
    img
  • Adenine and thymine form a hydrogen bonded pair, or complementary base pair.
  • Cytosine and guanine also form a complementary base pair (Fig. 1-5).
    img

    Figure 1-5 DNA double strand.

  • These complementary base pairs are conformed by the base ratios: G/C = 1 and A/T = 1 (Table 1-4).

Table 1-4 Nitrogen-Base Content of DNA from Different Organisms

Species Tissue Source Calf Thymus Crab All tissue Algea (Euglcna) Chloroplast Virus (Coliphaga ×174) Replicative Form
A 29.0 47.3 38.2 26.3
T 28.5 47.3 38.1 26.4
A/T 1.01 1.00 1.00 1.00
G 21.2 2.7 12.3 22.3
C 21.2 2.7 11.3 22.3
G/C 1.00 1.00 1.09 1.00
Note: Data in mole percent.
Cell Growth and Division

How does the nucleus maintain its control of cell growth and division?

  • During ordinary cell division called mitosis, two new cells result from a single parent.
  • Each daughter has the same number of chromosomes as the parent.
  • If DNA is the molecular stuff of the chromosome, it must be able to reproduce itself.
  • The DNA double helix rewinds and separates into two single strands (Fig. 1-6).
  • As the unwinding occurs, the single strands act as templates for synthesis of new complementary strands.
  • When the parent DNA double helix has completed its unwinding, two new DNA double-stranded molecules are formed.
  • The process by which new DNA is formed is called replication.
img

Figure 1-6 DNA double helix rewinds and separates into two single strands.

Protein Synthesis

How can proteins be synthesized in cells?

  • The order of the N bases on the DNA molecule determines the order of amino acids in the protein molecule.
  • While DNA is in the nucleus, the proteins are synthesized on ribosomes outside the nucleus as follows:
    • As the DNA double helix unwinds, the N base segment becomes exposed.
    • The DNA molecule serves as template for the synthesis of mRNA molecule.
    • The synthesis of mRNA is analogous to the replication synthesis of DNA (Fig. 1-7).
      img

      Figure 1-7 Synthesis of mRNA.

    • mRNA has structure similar to DNA but contains:
      • Ribose instead of deoxyribose
      • N-base uracil instead of thymine:
        img
  • After mRNA is synthesized, it is transported out of the nucleus and becomes attached to the ribosomes, where the protein syntheses begin (Fig. 1-8).
    img

    Figure 1-8 Protein synthesis.

  • At the ribosomes, the order of the bases on the mRNA determines the amino acid sequence in the protein molecule.
  • The amino acid sequence is determined by a triplet code on the mRNA molecule.
  • A group of three N bases represents a code for signifying a single amino acid (Scheme 1-2).
    img

    Scheme 1-2 Genetic codes.

  • The amino acids are brought to the mRNA at the ribosomes by much smaller RNA molecules called tRNA.
  • Each tRNA has a triplet of bases, which is complementary to an amino acid code on mRNA.
  • The tRNA molecules bring the amino acids to the ribosomes as they move along the mRNA strand, and the amino acids are knit into the growing protein chain.
  • After the tRNA has discharged its amino acid passenger, it moves out into the cytoplasm, finds another amino acid, and returns to the ribosome surface.
Common Natural α-Amino Acids

Give the general formula, side chain, and corresponding name of the common natural α -amino acids.

  • There are 20 common natural amino acids.
  • The general formula for an α-amino acids is
    img
  • They are summarized in Table 1-5.

    Table 1-5 L-α-amino Acids

    Name Side Chain (R at pH = 7) pKa Nature
    Glycine, Gly, G —H 2.35, 9.78 Structural, spacer
    Alanine, Ala, A —CH3 2.35, 9.87 Hydrophobic
    Valine, Val, V
    img
    2.29, 9.74 Hydrophobic
    Leucine, Leu, L
    img
    2.33, 9.74 Hydrophobic
    Isoluecine, Ile, I
    img
    2.32, 9.76 Hydrophobic
    Phenylalanine, Phe, F
    img
    2.16, 9.18 Hydrophobic
    Proline, Pro, P
    img
    1.95, 10.64 Hydrophobic, structural
    Tryptophan, Trp, W
    img
    2.43, 9.44 Hydrophobic
    Serine, Ser, S
    img
    2.19, 9.21 Ambivalent
    Threonine, Thr, T
    img
    2.09, 9.11 Hydrophobic
    Methionine, Met, M
    img
    2.13, 9.28 Hydrophobic but weak Lewis base, soft
    Tyrosine, Tyr, T
    img
    ∼10 Hydrophobic, but strong Lewis base, only when deprotonated
    Aspartic, Asp, D
    img
    ∼5 Hydrophobic, Lewis base, anion
    Asparagine, Asn, N
    img
    2.1, 8.84 Lewis base, anion
    Glutamine, Gln, Q
    img
    1.99, 3.90, 9.90 Polar, neutral
    Glutamic, Glu, E
    img
    2.16, 4.27, 9.36 Lewis base, anion
    Histidine, His, H
    img
    1.80, 6.04, 9.33 Hydrophobic, Lewis base
    Cysteine, Cys, C
    img
    1.92, 8.35, 10.46 Lewis base, anion, soft
    Lysine, Lys, K
    img
    2.16, 9.18, 10.79 Polar, cationic, protonated
    Arginine, Arg, R
    img
    1.82, 8.99, 12.48 Polar, cationic, protonated
Peptide Chain Formation

How can the peptide chain be formed from the amino acids?

  • Linear polymerization by condensation to yield amide peptide linkage (Scheme 1-3).
  • All proteins are polypeptides.
img

Scheme 1-3 Polypeptide formation.

Protein physiological functions

What are the physiological roles of proteins?

  • The physiological roles of proteins are:
    • Structural: finger nails, hair, and skin
    • Transport: oxygen, electrons, and iron
    • Catalysis: enzymes responsible for all synthesis of proteins, DNA, and organics
Structural Features of Proteins

Define: primary, secondary, tertiary, and quaternary structures. And what are the factors that control each of these structures?

  • The properties and functions of a particular protein depend on the sequence of the amino acids in the protein, or the primary structure.
    • The primary structure determines higher levels of structures.
    • These structural details are crucial to the biological role of a protein.
  • The secondary structure arises from the relative disposition of atoms in the polypeptide “backbone”:
    img

    The groups of four gray-shaded atoms are coplanar. Free rotation occurs about the bond connecting the carbon with the carbonyl and the nitrogen. Therefore, the extended polypeptide chain is a semirigid structure with two-thirds of the atoms of the backbone held in a fixed plane.

    • Examples of secondary structures:
      1. random coil
      2. α–helix (Fig. 1-9)
      3. β–pleated (Fig. 1-10), associated as (i) parallel and (ii) antiparallel
      4. reverse turns (Fig. 1-11)
      5. omega loops (Fig. 1-12)
    img

    Figure 1-9 α-Helix structure of protein.

    img

    Figure 1-10 β-Pleated structure.

    img

    Figure 1-11 Reverse turn.

    img

    Figure 1-12 Omega loop.

    Both reverse turns and omega loops appear at the outer surface of the molecules.

  • A Tertiary structure refers to the folding of the already secondary structured amino acids to form a three-dimensional (3D) structure. The overall 3D architecture of the polypeptide backbone:
    • Fibrous proteins: coils (Fig. 1-13).
      img

      Figure 1-13 Fibrous oligomers, PDB 1G6U (Ogihara et al., 2001).

    • Globular proteins: compact, ellipsoidal, spherical, until denatured. The folded tertiary, globular, structure of myoglobins is imposed over the helical secondary structure. Structures from X-ray diffraction are shown in Fig. 1-14.
    • Synthetic polypeptides have random or simply repetitive structures.
img

Figure 1-14 Tertiary structure of oxymyoglobin at 1.6 Å resolution, PDB 1MBO (Phillips, 1980).

Causes of Polypeptide Chain Folding
  • Disulfide linkages (cysteine) (Fig. 1-15)
    • Disulfide linkage is a redox reaction:
      equation
    • To a large extent, various folding factors rely on “correct” positioning to relevant residues by other contributing folding factors, i.e., there is cooperativity, which causes an entropy gain.
  • H-bonding
    • Hydrogen bonds within proteins are constant in time, whereas in fluid media, they are constantly breaking and re-forming.
    • Again, groups are in correct proximity (Fig. 1-15).
      img

      Figure 1-15 Disulfide linkages and H bonding.

  • A hydrophobic interaction arises from the unfavorable nature of interactions between water and nonpolar solutes (Fig. 1-16).
    img

    Figure 1-16 Hydrophobic interaction and solvent entropy.

    • There is a common tertiary structure among proteins from diverse species. Similar folding conformations of distantly related cytochromes (Figs. 1-17 to 1-19) are noticed.
      img

      Figure 1-17 Cytochrome c, tuna, PDB 3CYT (Takano and Dickerson, 1980).

      img

      Figure 1-18 Cytochrome c553, Bacillus pasteurii, PDB 1C75 (Benini et al., 2000).

      img

      Figure 1-19 Cytochrome c2, Rhodobacter sphaeroides, PDB 1CXC (Axelrod et al., 1994).

    • The interior packing is composed of generally dense, van Der Waals interactions, although voids are found (Scheme 1-4).
      img

      Scheme 1-4 External, ambivalent, and internal amino acids.

    • Ionized groups occur:
      1. On the outer surface (majority, 100%)
      2. In clefts or inner sites, where they have a particular/special role in the protein's function
  • Unfolding is caused by:
    1. Conformational entropy—more orientations accessible
    2. Strain in folded state
  • Quaternary structure refers to the aggregation of polypeptide chains into larger assemblies such as in hemoglobin (Fig. 1-20), and hemerythrin. In hemerythrin
    8He img He8
    Subunits (13,500) Octamer (108,000)

    There are two types:

    1. Isologous: img
    2. Heterologous: img
      img
  • Aggregation is driven by:
    1. Hydrogen bonding
    2. Hydrophobic interaction
    3. Salt bridges: Lys+, Arg+ vs. Glu, Asp
      img
  • Ionic moieties brought together, Coulombic attraction, so ΔH < 0, solvent H2O released, so ΔS > 0. For example, the association of the four subunits of Hb4 has Standard Gibbs free energy, img.
img

Figure 1-20 Quaternary structure of human oxyhemoglobin at 2.1 Å resolution, PDB 1HHO (Shaanan, 1983).

Metal Amino Acid Complexes

Arrange the binding stabilities of various metal ions toward different amino acids.

  • Mn+ binding group are:
    equation

    Define:

    1. Enzymes
    2. Metalloenzymes
    3. Coenzymes
    4. Cofactors
  • Enzymes:
    • Catalyze biological processes
    • Control rates of reactions
    • Promote certain geometries in the transition state, which lowers the activation energy for the formation of one product rather than the other
  • Matalloenzymes are composed of:
    • A protein structure (called apoprotein/apoenzyme)
    • Small prosthetic group
    • Prosthetic groups that are a simple metal ion, a complex metal ion, or an organic compound
  • Coenzyme reversibly combines with the enzyme for a particular reaction and then is released to combine with another.
  • Cofactors are the prosthetic groups and the coenzymes.
    • Provide ability to transfer molecular groups or radicals that polypeptides cannot (e, phosphate, alkyl group, etc.), in enzyme-catalyzed reactions
    • Provide ability to bind and transfer molecules that polypeptide cannot (e, O2)
    • Simple cofactors: Mg2+, Fe2+, Zn2+, etc.
    • Several are nucleotide derivatives of ATP
      1. Nicotinamide adenine dinucleotide (NADH) (Scheme 1-5): a mild source of H as NADH. Note pervasive presence of phosphate ester links.
        img

        Scheme 1-5 Nicotinamide adenine dinucleotide.

      2. Ubiquinone (coenzyme-Q), CoQ6, CoQ10 (Scheme 1-6).
        img

        Scheme 1-6 CoQ6 and CoQ10.

      3. Flavins, i.e., flavin mononucleotide (FMN) (riboflavin phosphate) (Scheme 1-7):
        img

        Scheme 1-7 Flavin mononucleotide.

        c01uf001

        See also flavin adenine dinucleotide (FAD).

      4. Tetrapyrrolic cofactors:
        c01uf001
      5. Phosphates
  • Suitable as noncarbon “universal” component
  • Carbon-based esters subjected to hydrolysis by digestive enzymes
  • Must be readily available in environment, so G° is not wasted in hunting and concentrating
  • Used in presence of Cys–SH, so cannot be oxidized or reduced
  • Used for persistent structures, so should be inert (slow reacting)
  • Kinetic consideration:
    c01uf001
    1. P5+ used as ester
    2. Rate of hydrolysis depends on rate of P–O bond scissions
Comparison of P–O versus M–O Bond Scission Rates for Row 3 Elements

Compare M–O bond scission rates for row-3 elements in group-oxidation states in H2O, and show the advantages of P–O.

  • Use O17or O18 isotopes as tags [(e.g. O17, nuclear magnetic resonance (NMR)]:
    c01uf001
    • t1/2 for O exchange at room temperature in seconds:
      Na+ Mg2+ Al3+ Si4+ P5+
      10−9 10−5 100 103 1010

      Therefore, phosphates are better than silicate.

  • Relative exchange rates: Na+ > Mg2+ > Al3+ > Si4+ > P5+
    equation
    • Exchange rates (↓) decrease as q/r (↑) increase as well as the ionic potential gets higher.
    • High ionic potential polarizes ligand, e.g., H2O, and introduces covalency.
      c01uf001

      Consequently, H+ is released, as increases of q/r lead to decreasing pKa:

      c01uf001
Redox Advantages: Sulfur versus Phosphorus

Consider all S and P possible anions, which will be the strongest oxidizing agent? And which will be the strongest reducing agent?

  • Comparison of P and S:
    2 SO42− + 4H+ + e S2O62− + 2 H2O E° (mV) = −220
    S6+ + e S5+
    2 SO32− + 4H+ + 2e S2O2− + 2 H2O E° (mV) = −86
    S4+ + 2 e S2+
    S + 2H++2e H2S E° (mV) = +142
    S0 + 2 e S2−
    SO42− + 2H+ + 2e SO32−+ H2O E° (mV) = +172
    cS6+ + 2e S4+
    SO42− + 8H+ + 6e S + 4H2O E° (mV) = +35
    S6+ + 6e S0
    S2O62− + 4H+ + 2e 2 SO3−2 + 4H2O E° (mV) = +564
    S5+ + 2e S4+
    PO33− + 2H+ + 2e PO23− + H2O E° (mV) = −499
    P3+ + 2e P+
    PO23− + 4H+ + e P + 2H2O E° (mV) = −508
    P+ + e P0
    PO43− + 2H+ + 2e PO33− + H2O E° (mV) = −276
    P+5 + 2e P3+
    P + 3H+ + 3e PH3 E° (mV) = −63
    P0 + 3e P3−
  • Hot, concentrated H2SO4 is a strong oxidizing agent; dilute H2SO4 is not an oxidizing acid.
    1. SO32−, sulfite ion is mild reducing agent
    2. HSO3, hydrogen sulfite ion is mild reducing agent
    3. SO42−, sulfate ion is oxidizing agent only in concentrated acid
  • H3PO4, is not oxidizing agent
    1. H2PO3, dihydrogen phosphite ion is reducing agent in H+ or OH
    2. HPO32−, hydrogen phosphite ion is reducing agent in H+ or OH
Bioenergetic Phosphate Derivatives

Give examples of the phosphate adducts that are bioenergetically important.

  • Other PO33− adducts are bioenergetically important:
    img
  • ATP acts as G – currency of bioenergetics:
    equation

    Corresponds to free energy available from transferring PO3 unit to H2O.

References

  1. H. L. Axelrod, G. Feher, J. P. Allen, A. J. Chirino, M. W. Day, B. T. Hsu, and D. C. Rees, Acta Crystallogr., Sect. D, 50, 596–602 (1994).
  2. S. Benini, A. Gonzalez, W. R. Rypniewski, K. S. Wilson, J. J. Van Beeumen, and S. Ciurli, Biochemistry, 39, 13115–13126 (2000).
  3. F. A. Cotton and G. Wilkinson, in Advanced Inorganic Chemistry, 4th ed., Wiley, p. 1311, Hoboken, NJ (1980).
  4. N. L. Ogihara, G. Ghirlanda, J. W. Bryson, M. Gingery, W. F. DeGrado, and D. Eisenberg, Proc. Natl. Acad. Sci. USA, 98, 1404–1409 (2001).
  5. S. E. Phillips, J. Mol. Biol., 142, 531–554 (1980).
  6. B. Shaanan, J. Mol. Biol., 171, 31–59 (1983).
  7. T. Takano and R. Dickerson, Proc. Natl. Acad. Sci. USA, 77, 6371–6375 (1980).

Suggestions for Further Reading

Texts on Biochemistry

  1. 1. J. J. R. F. da Silva and R. J. P. Williams, Biological Chemistry of Elements, Oxford University Press, New York (1991).
  2. 2. L. Stryer, Biochemistry, Freeman, New York (1995).
  3. 3. D. Voet and J. G. Voet, Biochemistry, Wiley, New York (1995).
  4. 4. Advances in Protein Chemistry, Academic Press, New York.
  5. 5. P. D. Boyer, Ed., The Enzymes, 3rd ed., Academic, New York (1970–1986).
  6. 6. H. Neurath, Ed., The Proteins, 2nd ed., Academic, New York, vol. I to vol. V.

Texts on Bioinorganic Chemistry

  1. 7. I. Bertini, H. B. Gary, E. I. Stiefel, and J. S. Valentine, in Biological Inorganic Chemistry, University Science Books Sausalito, CA, (2007).
  2. 8. H-B. Kraatz and N. Metzler-Nolte, in Concepts and Models in Bioinorganic Chemistry, Wiley, Hoboken, NJ (2006).
  3. 9. W. Kaim and B. Schwederski, in Bioinorganic Chemistry: Inorganic Elements in the Chemistry of Life, Wiley, New York (1994).
  4. 10. E-I. Ochaia, in Bioinorganic Chemistry: A Survey, Elsevier, San Diego, CA (2008, 2011).
  5. 11. R. M. Roat-Malone, in Bioinorganic Chemistry: A Short Course, Wiley-Interscience, Hoboken, NJ (2002).
  6. 12. S. J. Lippard and J. M. Berg, in Principles of Bioinorganic Chemistry, University Science Books, Mill Valley, CA (1994).
  7. 13. L. Que, Jr., Ed., Physical Methods in Bioinorganic Chemistry, University Science Books, Mill Valley, CA (2001).
  8. 14. R. B. King, Ed., Encyclopedia of Inorganic Chemistry, Wiley, New York, (1994).
  9. 15. J. E. Macintyre, A. Exec. Ed., in Dictionary of Inorganic Compounds, Chapman and Hall, London (1992).
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