Download amino acids

Proteins are large organic compounds made of amino acids arranged in a linear
chain and joined together by peptide bonds between the carboxyl and amino groups
of adjacent amino acid residues.
Metalloprotein is a generic term for a protein that contains a metal cofactor.
Metalloproteins function in O2 transport, electron transfer, and the regulation of gene
expression (for example).
amino acids: molecule containing both amine and carboxyl functional groups. In
biochemistry, this term refers to alpha-amino acids with the amino and carboxylate
groups are attached to the same carbon (α–carbon).
primary structure
secondary structure
tertiary structure (or folding)
Secondary
Primary
Tertiary
quaternary structure
Ligand
Coordinate covalent bond
Proteins as ligands: The most common amino acid groups that function as
ligands are the thiolate of cysteine, the imidazole of histidine, the
carboxylates of glutamic and aspartic acids and the phenolate group of
tyrosine.
Proteins as ligands: The most common amino acid groups that function as
ligands are the thiolate of cysteine, the imidazole of histidine, the
carboxylates of glutamic and aspartic acids and the phenolate group of
tyrosine.
tuning of redox potentials and electron transfer: electron transfer reactions are
sensitive to both the ligand donor atoms and the stereochemistry at the metal
centre.
Example: Cu(I) adopts tetrahedral or trigonal geometries and prefers soft donor
atoms. Cu(II) adopts square planar (or square pyramidal or octahedral) geometry
and prefers harder donor atoms. By changing the ligand environment of a Cu(II)
centre so that it is forced to distort into a near Td geometry through use of bulky
ligands, or by introducing soft-ligand donors, Cu(II) can be more readily reduced to
Cu(I) resulting in higher redox potentials.
Ligand exchange rates: The anticancer drug cis-[Pt(NH3)2Cl2] (cisplatin)
undergoes a ligand exchange process to lose a Cl- ligand and ultimately binds to
DNA so strongly that only strong platinum binding agents, like CN- can displace
the Pt-DNA bond. Subsequently, the platinum cross-links two bases via
displacement of the other chloride ligand.
Inner-sphere vs. outer-sphere electron transfer
Myoglobin and Hemoglobin
Porphyrin
MbO2 and HbO2 adducts are Fe(III) complexes with the superoxide ligand, O2-.
Coordination of dioxygen to deoxy Hb or Mb is accompanied by electron
transfer to form O2-, which is stabilized by hydrogen bonding to a distal
imidazole (His) proton, and coupling between O2- and Fe(III) leads to a
diamagnetic, S = 0, ground state.
Allosteric Effect
proximal histidine
Allosteric Effect
The Fe-O-O bond angle is 115o, therefore the bond is “bent”.
Allosteric Effect
X-ray (and for myoglobin) neutron diffraction studies indicate the formation
of a hydrogen bond between the coordinated dioxygen molecule and the N-H
proton of the distal histidine residue.
Allosteric Effect
Three primary methods for synthesizing Fe model complexes are:
1. Synthesizing porphyrins that are sterically crowded on the distal side
2. Coordination of a sterically hindered axial base as a mimic for the T-state.
3. Attaching the five-coordinate system to a surface, like silica gel, to reduce its
mobility and ability to add a sixth ligand.
Cytochrome: Any of a class of iron-containing proteins important in cell respiration
as catalysts of oxidation-reduction reactions.
Cytochrome P450: one of a large group of iron-containing oyxgenases that utilize
atmospheric dioxygen to functionalize molecules using cofactors such as flavins
or NAD(P)H, as well as non-heme iron or copper and other metalloporphyrin
complexes.
Structure and Function:
There are two main functional roles for these oxygenases.
1. The metabolism of xenobiotics (compounds exogenous to the organism).
2. The biosynthesis of critical signaling molecules used for control of development
and homeostasis.
Cytochrome c (Cyt c): can be defined as electron transfer proteins having one or
several heme c groups, bound to the protein by one or two thioether bonds
involving cysteine residues. The fifth, axial heme iron ligand is always provided
by a histidine residue. Cyt c possess a wide range of properties and function in
a large number of different redox processes.
Iron-sulfur proteins: characterized by the presence of iron-sulfur clusters
containing two, three or four iron centres that are sulfide-linked with variable
oxidation states.
The Fe centres are generally tetrahedral.
The thiolato sulfur centers are from cysteinyl residues.
The sulfide groups are either two- or three-coordinate.
Rubredoxin: low-molecular-weight iron-containing proteins found in sulfurmetabolizing bacteria and archaea; electron transfer between [Fe(III)(Cys)4]1- and
[Fe(II)(Cys)4]2-.
Aconitase: metalloenzyme that catalyses the stereo-specific isomerization of
citrate to isocitrate via cis-aconitase in the second step of the citric acid (Krebs)
cycle, a non-redox-active process (proceeds by the elimination or addition of
water). Aconitase has an active [Fe4S4]2+ cluster, which may convert to an
inactive [Fe3S4]+ form.
ferredoxin: iron-sulfur proteins that mediate electron transfer in a range of
metabolic reactions. The metallo-sites can be of the form Fe2S2, Fe3S4 or Fe4S4.
Nitrogenase: complex enzyme composed of two components. The MoFe protein
contains all of the machinery to perform the reaction, but requires a steady
source of electrons. The reaction requires the addition of six electrons for each
nitrogen molecule that is split into two ammonia molecules. The Fe protein uses
the breakage of ATP to pump these electrons into the MoFe protein.
Ferritins: act in metal storage.
Transferrin: acts in metal transport.
Superoxide Dismutase (SOD): enzymes that disproportionate the biologically
harmful superoxide ions that leak from respiratory enzymes and are harmful to
cells.
M(n+1)+SOD + O2− → Mn+SOD + O2
Mn+SOD + O2− + 2H+ → M(n+1)+SOD + H2O2
2O2- + 2H+  H2O2 + O2
CuZnSOD
Plastocyanin: a copper-containing mobile electron-carrier protein involved in
electron-transfer between photosystem II and I in higher plants and some algae.
Azurin: small copper containing metalloenzyme involved in photosynthetic and
respiratory electron transfer.
Hemocyanin: large, multisubunit proteins capable of transporting oxygen, found in
various arthropods and mollusks
O2 + 2Cu(I) O22- + 2Cu(II)
Ascorbate oxidase: a homodimeric, copper-containing enzyme which catalyzes the
redox reaction between ascorbate and oxygen in plants and bacteria.
Carbonic anhydrases: a family of zinc-containing metalloenzymes that catalyze the
rapid conversion of carbon dioxide to bicarbonate and protons in tissues where
there is a high CO2 concentration.
Carboxypeptidase A: zinc-containing metalloenzyme that hydrolyzes the peptide
bond adjacent to the C-terminal end of a polypeptide chain.
Cisplatin: cis-diamminedichloridoplatinum(II); platinum-based chemotherapy drug
Vitamin B12: cobalt and corrin ring containing molecules involved in DNA
synthesis and regulation, fatty acid synthesis and energy production.