Chapter 27 - Amino Acids and Proteins

Amino acids are substances that have an amino group as well as a carboxyl group.
  * With the exception of glycine, all amino acids produced from proteins are chiral.
  * All of the 20 typically occurring amino acids are l-amino acids according to the d,l convention.
  * It should be noted that this identification is based on a structural analogy to l-glyceraldehyde, not on the optical activity of amino acid samples.
  * 18 amino acids are (S)-amino acids in the R,S convention.
Despite having the same absolute configuration as cysteine, it is a (R)-amino acid due to the way the sulfur atom affects the assignment about its tetrahedral chiral center.
  * A second chiral center is found in isoleucine and threonine.
  * ^^The 20 protein-derived amino acids are typically classified into four groups: those with nonpolar side chains, those with polar but unionized side chains, those with acidic side chains, and those with basic side chains.^^
  * Because the amino group is protonated and positively charged, while the carboxyl group is deprotonated and negatively charged, amino acids exist as zwitterions at neutral pH.
  * Because of the electron-inductive drawing's impact!
  * More acidic than acetic acid are the NH3 1 group, amino acid carboxyl groups.
  * The a-amino group has a lower basicity than a main aliphatic amine.
$An amino acid's, polypeptide's, or protein's isoelectric point, pI, is the pH at which it has no net charge.$
  * Electrophoresis is the technique of separating substances in an electric field based on their charge.
  * Compounds with a high charge density travel faster than those with a low charge density.
  * The amide link produced between a-amino acids is known as a peptide bond.
A polypeptide is a biological macromolecule made up of numerous amino acids that are linked together by peptide bonds.
  * By convention, the amino acid sequence of a polypeptide is written from the N-terminal amino acid to the C-terminal amino acid.
  * A polypeptide's primary (1°) structure is the sequence of amino acids in the polypeptide chain.
  * The amino acid analysis process is used to determine the relative amino acid makeup of a protein.
  * All of the amide bonds are hydrolyzed in acid, and the individual amino acids present are separated and quantified using chromatography.
  * This method yields no sequence information.
%%A polypeptide or protein's main structure can be identified directly by fragmenting the protein using cyanogen bromide and enzymes, followed by amino acid sequencing of the resultant fragments.%%
* Treatment with cyanogen bromide cleaves proteins at the carboxyl group of methionine residues.
* Protein-cleaving enzymes like trypsin and chymotrypsin break between certain amino acids, resulting in specific pieces.
The Edman degradation removes and identifies the N-terminal amino acid of peptides or proteins using phenyl isothiocyanate.
  * The Edman degradation can be repeated and automated to identify the sequence of up to 20 to 30 N-terminal amino acids.
  * The reconstruction of a protein's full sequence is possible thanks to the sequencing of overlapping regions.
  * Today, mass spectrometry of a protein or nucleic acid sequencing of its gene are the primary approaches for determining a protein's amino acid sequence.
Peptide synthesis necessitates the protection of the amino group of one amino acid and the carboxyl group of the other so that only the necessary coupling occurs.
  * Carbamates, such as the Z (benzyloxycarbonyl) or BOC (tert-butyloxycarbonyl) groups that are eliminated in acid, are the most frequent amino-protecting groups.
  * Carboxyl groups are protected in solution as esters or during solid phase synthesis as esters by attachment to the solid support.
  * Peptide bonds are formed by activating a carboxyl group for nucleophilic attack by an amino group with reagents such as carbodiimides.
In solid-phase synthesis, or polymer-supported synthesis of polypeptides, the C-terminal amino acid is joined to a chloromethylated polystyrene resin as a benzyl ester.
  * %%After then, the polypeptide chain is expanded by one amino acid.%%
  * The fundamental benefit of solid-phase synthesis is that all of the reagent exchange and washing processes are accomplished by simple filtration, and the entire process is automated.
  * When the synthesis is finished, the polypeptide chain is freed from the solid support by benzyl ester linkage cleavage.
A peptide bond is planar, which means that the four atoms of the amide and the two a-carbons of the peptide bond are in the same plane.
  * The planarity is caused by resonance with the amide N atom.
  * The bond angles between the amide nitrogen and the amide carbonyl carbon are around 120°.
  * The hydrophobic effect is the aggregation of hydrophobic groups inside proteins produced by their exclusion from water.
The organization of polypeptide monomers into a noncovalently bound aggregate is known as quaternary (4°) structure.
  * The hydrophobic effect, in which complementary hydrophobic patches on each interacting partner contact each other, is a major factor stabilizing the ordered assembly of proteins into specific quaternary structures, providing a driving force for assembly by relieving unfavorable contacts of the hydrophobic patches with water.
  * Secondary (2°) structure refers to the orderly arrangement (conformations) of amino acids in\slocalized sections of a polypeptide or protein.
  * The a-helix and the b-pleated sheet are the two most common kinds of secondary structure.
Tertiary (3°) structure is the overall folding pattern and spatial arrangement of all atoms in a single polypeptide chain.
  * The solvation of amino acid side chains is critical for protein folding, because hydrophobic side chains are found in the hydrophobic interior of a protein.
  * Because of the hydrophobic effect, the hydrophilic side chains tend to be on the surface, exposed to the aquatic environment.
  * ^^The hydrophobic effect is the aggregation of hydrophobic groups inside proteins.^^