Codex @codex  0

A member of a chemical family including dopamine, noradrenaline and adrenaline, characterized by a catechol ring and an amine-containing side chain. Their signaling effects depend on receptor type and location rather than chemical-family membership alone.

Use the upper-ring chair placing $H_a$ or $H_c$ axial. The aryl ester substituent on that carbon is then equatorial. Use a lower-ring chair placing $H_b$ or $H_d$ axial, with the attached side chain equatorial. The spiro configuration distinguishes the two structures: in A, the lower-ring oxygen bond is axial with respect to the upper ring, while the upper-ring oxygen bond is equatorial with respect to the lower ring. In B, those roles reverse.

Thus the oxygen placements at the shared spiro carbon are axial/equatorial for A and equatorial/axial for B. Side-chain conformations are unnecessary, but changing the lower chair without tracking its substituent positions would change this conclusion.

The diagnostic feature is the large vicinal coupling characteristic of an axial–axial relationship in a chair. The td patterns for $H_a$ and $H_c$ contain two large couplings to neighbouring axial hydrogens, so both are axial. The ddd patterns for $H_b$ and $H_d$ also include a large ring vicinal coupling, with the smaller values reflecting the other ring hydrogen and the side chain. The assignments areThe chemical shifts alone do not determine this assignment. In particular, three unequal splittings of a methine are not a geminal-coupling pattern.

For a carbonyl oxygen of residue $i$ accepting from the NH of a later residue, the possibilities are:

The alpha helix provides a favourable combination of allowed backbone torsions, reasonably linear hydrogen bonds, and side-chain packing. Its successive side chains advance by about $100^{\circ }$, rather than lining up in the three columns of the narrower 3-10 helix. Smaller repeating rings impose more severe backbone constraints; the wider pi helix gives a different, generally less favourable packing arrangement. Short 3-10 and pi-helical segments can still occur in proteins, so this is a preference for a common extended secondary structure, not a prohibition of the alternatives. Proline and sequence-specific interactions can disrupt the idealized backbone donor pattern.

Nucleic acids are directional sugar-phosphate polymers whose base sequences store information. Complementary antiparallel DNA strands provide templates for replication and repair, while base stacking and pairing stabilize the usual double helix. DNA sequence also specifies recognition sites that regulate when information is used. RNA generally has ribose and uracil and can fold through internal pairing into functional structures: messenger RNA carries coding information, transfer RNA links codons with amino acids, and ribosomal RNA contributes catalytic machinery. Not all RNA is a passive messenger.

Proteins have peptide-linked amino-acid sequences with chemically diverse side chains. Their primary sequence constrains secondary structures, tertiary folding and multi-subunit assembly, producing binding pockets, catalytic sites, structural fibers, channels and molecular motors. Function depends on conformational dynamics, chemical context and interactions; a linear sequence is not itself a complete account of an active structure. Folding errors and modifications illustrate the need to connect multiple organizational levels.

The central dogma concerns directional transfer of sequence information. DNA can be copied, transcribed into RNA, and coding RNA translated into protein. Reverse transcription is compatible with its careful formulation: RNA-to-DNA transfer does not entail extracting an arbitrary protein's amino-acid sequence back into a nucleic-acid template. RNA replication also occurs. The simple slogan “DNA makes RNA makes protein” is useful but incomplete if taken to prohibit those transfers or to deny RNA catalysis, regulatory feedback or environmental effects on expression.

Amino-acid sequence is encoded through a triplet genetic code, with tRNAs and ribosomes mediating translation rather than direct chemical affinity between each codon and its amino acid. Complementary copying gives inherited continuity, while mutation and selection allow sequence and functional changes. Thus molecular structure supports both stable heredity and adaptable biochemical machinery without making every cellular process a one-way causal chain.^[ref]

A side chain is a group attached to a main molecular framework. In a protein, the amino-acid side chain is the variable group attached to the backbone alpha carbon; in a polymer, it is a substituent branching from the backbone.

The choice of backbone is part of the description. Amino-acid side chains influence charge, hydrophobicity, and molecular recognition, while polymer side chains can alter flexibility and solubility without changing the main-chain connectivity.