The genetic code refers to the sequence of DNA that codes for genes and proteins in the body. The genetic code is composed of three-nucleotide codons, each used to recruit an amino acid during translation and protein synthesis. Each codon codes for one and only one amino acid, making the code unambiguous; however, some amino acids have more than one codon that can be used to recruit them. This feature of the genetic code is known as degeneracy. Finally, the genetic code is universal. All living organisms use the same genetic material (DNA) in their cells and produce proteins through transcription and translation. Though the processes may change slightly between organisms, the general genetic code is universal to all cells.

The genetic code is not overlapping, meaning that the code is linear. Transcription of DNA has a fixed starting point and proceeds in a linear fashion, as does translation of mRNA. There is no overlapping or reverse reading of the genetic code.

These bonds are specifically referring to the invariable portions of the amino acid and, thus, do not involve the R group (functional group).

This is more of a definition-based answer. The phi angle refers to the bond between the amine nitrogen and the alpha carbon, while the psi angle refers to the bond between the alpha carbon and the carbonyl carbon of the carboxylic acid. These bonds play important roles in determining possible protein structures.

Amino acid sequences with a lot of alanine (A) residues are higly likely to form alpha-helices. Glycine (G) and proline (P) residues often cap alpha-helices, though glycine can sometimes be found inside alpha-helices as well.

Proline is never found inside an alpha-helix due to the conformational hindrance caused by the hydrogen bonding within the residue. Proline is usually found in bends in a protein structure.

Histidine has the following pK_a values:

COOH - 1.82

R-group - 6.00

NH₃ - 9.17

Any pH below the pK_a will cause the molecule to be protonated, while any pH above the pKa will cause the molecule to deprotonate. At a pH of 7, the COOH group to deprotonate, but the NH₃ and R-group will remain protonated.

Tertiary structure of a protein is determined by interactions between the R-groups of the amino acids that make up that protein. The secondary structure of a protein is mediated by the backbone atoms of the polypeptide chain which includes the carboxyl and amine groups. The alpha carbon are what the R-groups are attached to an do not directly contribute to any level of protein structure.

Hydrogen bonds between repeating units of the polypeptide backbone (namely the amino groups and carboxyl groups) mediate secondary structure in proteins.

Primary structure simply describes the order of amino acids in a polypeptide chain. Tertiary structures describe global folding of the entire chain, which may be made up of a multitude of secondary structures like alpha helices or beta sheets. Quaternary structure describes the position of numerous subunits in a protein complex comprised of two or more smaller protein. Huge multiunit proteins are ordered by supramolecular structure.