Metals in Biochemistry: Amino Acids and pH

The tendency of an acid to donate a proton (H+). A low pKa indicates a strong acid, meaning it readily releases a proton.

A carboxylic acid side chain with a pKa below 7 will be deprotonated at physiological pH, becoming COO-. This makes it an effective ligand for metal ions.

The side chain of histidine has an imidazole group with a pKa of 6.00. It will be present as NH at physiological pH, donating its electron pair for coordination with metal ions, not the NH2+ form.

While cysteine and tyrosine have pKas above 7, indicating they should be protonated at physiological pH, the presence of a metal ion increases their acidity. This makes them ligands for metals.

Lysine's side chain amino group (pKa 10.79) and arginine's guanidinium group (pKa 12.48) remain protonated at physiological pH. They are unlikely to act as ligands for metal ions.

A molecule with a central metal atom surrounded by organic rings, found in hemoglobin and chlorophyll.

A type of porphyrin with iron at its center, essential for oxygen transport in red blood cells.

A modified porphyrin molecule containing magnesium, found in chlorophyll, crucial for photosynthesis.

An amino acid with a sulfur-containing side chain, often involved in metal binding.

An amino acid with a nitrogen-containing imidazole ring, commonly used in metal coordination.

An amino acid with a carboxyl group (-COOH) in its side chain, capable of binding to metals.

An amino acid similar to glutamic acid, also possessing a carboxyl group in its side chain.

An amino acid with a phenolic hydroxyl group (-OH) in its side chain, sometimes involved in metal coordination.

The side chains of amino acids that directly bind to metal ions in biological systems.

The ability of a molecule or ion to bind to a metal atom.

The twenty common amino acids are the building blocks of proteins. Each amino acid has a unique side chain that gives it specific chemical properties. These properties determine the structure and function of proteins. For example, some amino acids have charged side chains that can form ionic bonds, while others have hydrophobic side chains that can contribute to the structure of membranes

The Henderson-Hasselbalch equation is used to calculate the pH of a solution containing a weak acid and its conjugate base. It relates the pH of the solution to the pKa of the acid, which is a measure of its acidity, and the ratio of the concentrations of the acid and its conjugate base. The equation is essential for understanding acid-base chemistry and its application in biological systems, such as blood pH regulation.

The conjugate base of an acid is formed when the acid loses a proton (H+). For example, the conjugate base of hydrochloric acid (HCl) is chloride ion (Cl-). The conjugate base is essential for understanding the chemical behavior of acids and is involved in many reactions in biological systems.

The concentration of an acid refers to the amount of acid present in a given volume of solution. The higher the concentration, the more acid is present. The concentration of an acid is important in determining its acidity and its ability to participate in chemical reactions

The concentration of the conjugate base is defined as the amount of conjugate base present in a given volume of solution. This concentration is essential for understanding the pH of a solution and how the acid-base equilibrium is affected.

The concept of acid dissociation is the process by which an acid separates into its ions. This often occurs when an acid is dissolved in water. The extent of dissociation determines the strength of an acid, with stronger acids dissociating more readily.

A cobalt(II) ion surrounded by a porphyrin ring, a benzimidazole ring, and a 5,6-dimethylbenzimidazole group. This complex is the active component of vitamin B-12, essential for several metabolic pathways.

A molybdenum ion complexed with a pterin ring. This complex is crucial for various oxo transfer proteins, which catalyze reactions involving oxygen atom transfer.

A nickel(II) ion bound to a hydroporphyrin ring. This complex is the active component of Factor F430, an essential cofactor in methanogenesis.

Amino acid residues involved in coordination with metal ions in metalloproteins. These residues contribute to the overall structure and function of the protein.

A functional group in which a sulfur atom is attached to two carbon atoms. This group is found in amino acids such as methionine and cysteine.

The sequence of amino acids in a protein chain, connected by peptide bonds.

The three-dimensional shape of a protein, formed by hydrogen bonds between amino acid residues.

The overall three-dimensional structure of a protein, including all its folds, twists, loops, and interactions.

The arrangement of multiple protein subunits, each with its own tertiary structure, into a larger complex.

A type of secondary structure in proteins characterized by a helical shape, stabilized by hydrogen bonds.

A type of secondary structure in proteins characterized by a sheet-like arrangement, stabilized by hydrogen bonds.

Iron-binding molecules produced by bacteria. They can remove iron from the host, making it difficult for the host to fight infections.

The bonds that link amino acids together to form proteins. They involve the carboxyl group of one amino acid and the amino group of the next.

A right-handed helical structure formed by hydrogen bonds between the backbone N-H and C=O groups of the amino acids, with every turn containing 3.6 amino acids and the side chains pointing outward.

A structural motif in proteins formed by hydrogen bonds between the backbone N-H and C=O groups of adjacent β-strands, which can be arranged in parallel or anti-parallel orientations.

The overall three-dimensional shape of a protein, determined by interactions between the side chains of its amino acids.

The sequence of amino acids in a protein chain. This is the primary level of protein structure.

The local folding patterns of the polypeptide chain, including α-helices and β-sheets.

A structural motif found in proteins where two or more polypeptide chains associate with each other.

The process of protein folding, where the polypeptide chain folds into its three-dimensional shape.