1) Proteins

• Biochemistry is an interdisciplinary subject that explores the molecular bases of life in its diversity, from viruses to humans.
• The objectives of biochemistry are to understand the compounds that build the living organisms, the composition, structure, and functions of cellular and extracellular components, the reactions and processes that occur in cells and extracellular spaces of the organisms, and the mechanisms and factors that regulate these processes.
• Pathological biochemistry, also known as Pathobiochemistry, is a part of biochemistry that explores the molecular causes and manifestations of the pathological conditions resulting from disorders of biomolecules, biochemical reactions and processes, and their regulation.
• Proteins are the most abundant biological macromolecules, occurring in all cells and all parts of cells, and exhibiting great diversity of biological functions.
• Proteins are the most important final products of the information pathways from DNA through mRNA to proteins.
• Structural functions of proteins include all cellular and extracellular structures, such as membranes, cytoplasm, ribosomes, chromatin, and ECM.
• Catalytic functions of proteins are all enzymes, which are proteins.
• Arginine (Arg) and Histidine (His) are considered conditionally essential amino acids.
• Heteroproteins (heteroenzymes) are protein variants with the same function, but found in different species, often with great homology in the structure due to evolutional connection between species.
• There are 20 a-amino acids that are involved in protein synthesis, known as proteogenic.
• Humans are incapable of synthesizing half of the 20 common amino acids, and these essential amino acids must be provided in the diet: Valine (Val), Leucine (Leu), Isoleucine (Ile), Lysine (Lys), Methionine (Met), Phenylalanine (Phe), Threonine (Thr), Tryptophan (Trp).
• Aloproteins (aloenzymes) are variants of a protein found in different individuals of the same species, often resulting from variant alleles of the gene (polymorphisms, SNPs).
• Several of the proteogenic amino acids also serve functions distinct from the formation of peptides and proteins, such as tyrosine in the formation of thyroid hormones, cateholamines or glutamate acting as a neurotransmitter.
• Several other amino acids are found in the body in free or in combined states, not associated with peptides or proteins.
• Transport roles of proteins include gases like hemoglobin (O2, CO2), myoglobin (O2), mineral cations like transferrin (Fe3+), ceruloplasmin (Cu2+), organic anions and lipids like retinol binding protein (retinol, Vit A), transcortin (also known as corticosteroid-binding protein (cortisol)), and albumin (bilirubin, free fatty acids (FFA)).
• Proteins are composed of amino acids that contain either hydrophilic or hydrophobic R-groups.
• A protein’s conformation is stabilized largely by weak Interactions.
• The hydrophobicity of certain amino acid R-groups tends to drive them away from the exterior of proteins and into the interior.
• This refers to the interaction of ionized R-groups of amino acids with the dipole of the water molecule, too.
• Typical charge-charge interactions that favor protein folding are those between oppositely charged R-groups.
• Substantial for protein folding are the charge-dipole interactions.
• There are both attractive and repulsive van der Waals forces that control protein folding.
• Disulfide bond is important for maintenance of tertiary structure.
• The nature of the interaction of the different R-groups with the aqueous environment plays the major role in shaping protein structure.
• Disulfide bond (bridge) appears between the – SH groups of two cysteine residues of one or different polypeptide chains of a protein.
• Electrostatic forces are mainly of three types; charge-charge, charge-dipole and dipole-dipole.
• The majority of the amino acids found on the exterior surfaces of globular proteins contain charged or polar R-groups.
• Although van der Waals forces are extremely weak – they are huge in number – this makes them significant to the folding of proteins.
• H-bonding occurs not only within and between polypeptide chains but with the surrounding aqueous medium.
• Regulatory functions of proteins include hormones like most of the hormones of the pituitary gland (GH, TSH, FSH, LH), growth factors (FGF, EGF, VEGF, PDGF), and cytokines (ILs, IFNs).
• Defensive functions of proteins include antibodies, lectins, components of complement, and blood-clotting factors.
• Contracting (motor) functions of proteins include actin, myosin, troponin, and tropomyosin.
• Production of energy functions of proteins include proteins of the electron-transport chain.
• Isoproteins, also known as isoenzymes, are variants of a protein found in each individual of the species and have the same functions, but different localization, structure, thermostability, electrical charge, electrophoretic mobility, etc.
• Titin, a constituent of vertebrate muscle, has nearly 27 000 AA residues.
• The environment (water) in which proteins are found also contains H-bond donors and acceptors of the water molecule.
• Insulin is a polypeptide of 51 AA (21 AA of chain A and 30 AA in chain B).
• The reason for the shorter peptide C-N bond is the resonance or partial sharing of two pairs of electrons between the carbonyl oxygen and the amide nitrogen.
• A protein’s conformation is stabilized largely by weak Interactions, including hydrogen bonding.
• Peptide bond is a strong covalent bond, the peptide C-N bond is shorter and appears to be partial double bond in comparison to the C-N bond in a simple amine.