Amino acids and polypeptides

• The structure of amino acids consists of a central carbon atom called the α-carbon, which is covalently bonded to an amino group (-NH2), a carboxyl group (-COOH), a hydrogen atom (H), and a side chain group (R).
• The side chain group determines the properties and chemical characteristics of each amino acid.
• Amino acids are organic compounds that are essential building blocks for proteins, and they play a vital role in many biological processes.
• A molecule is said to be chiral if it has a non-superimposable mirror image.
• The isoelectric point (pI) of an amino acid is the pH at which the amino acid has a net charge of zero.
• At low pH values, the amino group is protonated and has a positive charge, while the carboxyl group is also protonated and has a neutral charge.
• A further increase in the pH will result in the amino group losing the proton and thus becoming neutrally charged.
• The pI of an amino acid can be calculated using the following formula: pI = (pKa1 + pKa2) / 2.
• The genetic code is the set of rules that governs how information in the DNA sequence is translated into proteins.
• Universality: The genetic code is essentially the same across all living organisms, from bacteria to plants to animals
• Redundancy: The genetic code is redundant, meaning that more than one codon can code for the same amino acid
• Non-ambiguity: Each codon codes for only one amino acid, and each amino acid is coded for by one or more codons
• Conservation: The genetic code is highly conserved, meaning that it has remained essentially the same over millions of years of evolution
• The genetic code has specific codons that act as start and stop signals for protein synthesis.
• The start codon (AUG) signals the ribosome to begin translation, while the stop codons (UAA, UAG, and UGA) signal the ribosome to stop translation and release the completed protein.
• The term "redundancy of the genetic code" refers to the fact that more than one codon (a sequence of three nucleotides) can code for the same amino acid during the process of protein synthesis.
• This means that there is some flexibility in the genetic code, and that even if a mutation occurs in a codon, it may not necessarily result in a change to the amino acid sequence of the protein.
• Codon bias refers to the tendency of some organisms to preferentially use certain codons to encode for particular amino acids more frequently than other codons that code for the same amino acid.
• Proteins are macromolecules that are essential for many biological processes, such as catalysis, signalling, transport, and structural support.
• The primary structure of a protein is the linear sequence of amino acids that make up the polypeptide chain, determined by the genetic information encoded in the DNA.
• The primary structure of a protein is critical to its function, as it determines the sequence of amino acids and thus the three-dimensional shape of the protein.
• The secondary structure of a protein refers to the local conformation of the polypeptide chain, specifically the arrangement of the backbone atoms.
• The two most common types of secondary structure are alpha-helices and beta-sheets, which are stabilised by hydrogen bonding between backbone atoms.
• The tertiary structure of a protein is stabilized by a variety of interactions, including hydrogen bonding, electrostatic interactions, hydrophobic interactions, and disulfide bonds.
• The quaternary structure of a protein refers to the arrangement of multiple polypeptide chains (subunits) that make up a functional protein.
• The quaternary structure of a protein is stabilized by a variety of interactions, including hydrogen bonding, electrostatic interactions, hydrophobic interactions, and disulfide bonds.
• The primary structure of a protein is typically represented using a one-letter code for the amino acids, with the amino-terminal end (N-terminus) of the protein on the left and the carboxy-terminal end (C-terminus) on the right.
• The peptide bond has a rigid planar structure due to the partial double bond character of the C-N bond.
• The partial double bond character of the peptide bond means that the bond cannot rotate freely, except for rotation around the bond between the C(alpha) atom and the adjacent carbonyl carbon.
• The tertiary structure of a protein refers to the overall three-dimensional conformation of the polypeptide chain, including the arrangement of side chains.
• The partial double bond character of the peptide bond means that the bond cannot rotate freely, except for rotation around the bond between the C(alpha) atom and the adjacent carbonyl carbon.
• The peptide bond has a rigid planar structure due to the partial double bond character of the C-N bond.
• The primary structure of a protein is typically represented using a one-letter code for the amino acids, with the amino-terminal end (N-terminus) of the protein on the left and the carboxy-terminal end (C-terminus) on the right.
• The tertiary structure of a protein is stabilized by a variety of interactions, including hydrogen bonding, electrostatic interactions, hydrophobic interactions, and disulfide bonds.
• The quaternary structure of a protein refers to the arrangement of multiple polypeptide chains (subunits) that make up a functional protein.
• An alpha helix is a right-handed coil or helix structure formed by hydrogen bonding between the carbonyl oxygen of one amino acid residue and the amide hydrogen of an amino.
• A beta sheet is a sheet-like structure formed by hydrogen bonding between adjacent strands of the polypeptide chain.
• The beta sheet can be either parallel, where the strands run in the same direction, or anti-parallel, where the strands run in opposite directions.
• A beta turn is a type of secondary structure that connects two strands of a beta sheet.
• The beta turn is typically composed of four amino acid residues and is characterised by a tight turn in the polypeptide chain.