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The group $\mathrm{C}{\mathrm{H}}_2=\mathrm{CHC}{\mathrm{H}}_2-$, attached through the saturated carbon adjacent to the double bond.

An alpha-amino acid has amino functionality on the carbon next to its carboxyl carbon. The skeleton in amino acid shows this adjacency explicitly. Numbering the carboxyl carbon as C1 makes the adjacent position C2, also called the alpha position. ^[ref]

A 1,2-carbon migration interconverts adjacent tertiary alpha-hydroxy carbonyl compounds. Formation of a new carbonyl at the original carbinol carbon accompanies conversion of the original carbonyl into an alcohol. Unlike dehydration, the net process preserves both oxygens.

An ambident nucleophile can form a bond through more than one atom. An enolate can attack through carbon or oxygen; these give distinct products, although its resonance contributors describe the same ion.

Here an amide means a carbonyl group whose carbon is bonded directly to nitrogen; each of $R$, $R^{\prime }$ and $R^{\prime \prime }$ may be hydrogen or a group attached through carbon. A peptide bond contains this linkage. Chemical resonance distinguishes its nitrogen from that of an amine. ^[ref] and ^[ref]

A simple neutral amine has nitrogen bonded to one, two, or three groups attached through carbon, with hydrogen filling the remaining positions in the neutral three-bond form. These are the primary, secondary, and tertiary forms respectively. An amide has different connectivity to a carbonyl group. ^[ref]

An amino acid combines carboxylic acid and amine functionality in the same molecule; the name alone does not specify their separation. An alpha-amino acid has its amino nitrogen attached to the carbon immediately adjacent to the carboxyl carbon, the amino acid alpha carbon. For example, ${\mathrm{H}}_2\mathrm{N}-\mathrm{C}{\mathrm{H}}_2-\mathrm{COOH}$ is glycine, whereas ${\mathrm{H}}_2\mathrm{N}-\mathrm{C}{\mathrm{H}}_2-\mathrm{C}{\mathrm{H}}_2-\mathrm{COOH}$ has an extra intervening carbon and is not an alpha-amino acid. These chemical formulas describe connectivity, not the predominant protonation state in water.

Most common proteinogenic amino acids share the skeleton ${\mathrm{H}}_2\mathrm{N}-\mathrm{CH}(R)-\mathrm{COOH}$, with $R$ the amino acid side chain. In glycine, $R$ is hydrogen; in alanine, $R=\mathrm{C}{\mathrm{H}}_3$. Proline is a useful exception to the displayed primary-amine skeleton: its amino nitrogen is part of a ring and has a second carbon substituent. The shared backbone permits assembly into polypeptides, while different amino acid side chains give the resulting proteins diverse chemistry. ^[ref]

In a chemical solution, protonation changes the electric charges without changing this backbone. Free glycine near neutral pH is predominantly ${\mathrm{H}}_3{\mathrm{N}}^{+}-\mathrm{C}{\mathrm{H}}_2-\mathrm{CO}{\mathrm{O}}^{-}$, a zwitterion. Its positive and negative groups are joined within one molecule; zero net electric charge does not mean absence of local electric charges, nor does it mean the uncharged drawing ${\mathrm{H}}_2\mathrm{N}-\mathrm{C}{\mathrm{H}}_2-\mathrm{COOH}$ predominates. Glycine protonation explains how lowering or raising pH changes the balance. ^[ref]

Building a protein joins the carboxyl carbon of one amino acid to the amino nitrogen of another through a peptide bond, an amide linkage. The formal net condensation loses the elements of water; cellular translation uses activated substrates at a ribosome, rather than simply mixing free amino acids in water. Incorporated units are amino acid residues. The interior amide groups no longer have the same acid/base behavior as the two free terminal groups of glycine, so its free-molecule glycine titration cannot be copied independently at every chain position. ^[ref]

Chirality distinguishes most common proteinogenic amino acids from glycine. The other nineteen members of the conventional twenty have a stereocenter at their amino acid alpha carbon; ordinary translation incorporates their L forms. Glycine's two identical hydrogen substituents make it achiral. Thus being an amino acid, or even an alpha-amino acid, does not by itself imply chirality. ^[ref]

The amino acid alpha carbon is the backbone carbon carrying the amino acid side chain in the usual protein amino acid residue. Marking successive amino acid alpha carbons is a useful way to trace a polypeptide chain, but omits intervening backbone chemical atoms. See Clark, Douglas and Choi: the central alpha carbon.

An amino acid side chain is the variable group attached to an amino acid alpha carbon, conventionally denoted $R$. For alanine it is $\mathrm{C}{\mathrm{H}}_3$: a carbon bonded to three hydrogen chemical atoms. In a beta strand, successive amino acid side chains alternate between the two faces in the idealized arrangement. See Clark, Douglas and Choi: amino-acid R groups.

Research author on planetary thermal and carbon evolution.

The anomeric carbon is the former carbonyl group carbon that becomes a stereocenter on ring closure: C1 of glucose. It is an existing chemical atom, not an added one.

Anoxygenic photosynthesis captures light without producing molecular oxygen. It occurs in some bacteria and uses electron sources other than water. Whether carbon fixation accompanies this light capture depends on the organism and conditions; photosynthesis does not imply one universal carbon-assimilation pathway. See Alberts et al.: chloroplasts and photosynthetic bacteria.

An addition whose regiochemical outcome is opposite to the conventional Markovnikov orientation. hydroboration followed by oxidation places OH at the less substituted alkene carbon.

A carbon substituent opposite the activated N–O leaving group migrates onto nitrogen as the N–O bond cleaves. The oxime geometry therefore determines which bond is replaced by a carbon–nitrogen bond.

Aromatic oxazolination introduces an oxazolinyl group at an aromatic C–H position. Activating 2-Oxazolidinone with triflic anhydride supplies an electrophilic carbon that an electron-rich arene can attack.

An organohalide with the halogen attached directly to an aromatic ring carbon. Its substitution chemistry differs from an alkyl halide because the C–halogen bond is attached to an sp2 carbon.

The atomic number $Z$ is the number of protons in an atomic nucleus, and fixes the chemical element. It is a count, with no units. An atomic nucleus with six protons is always carbon, regardless of how many neutrons accompany them or how many electrons surround it. See the IUPAC Gold Book, atomic number.

Three independent bookkeeping questions become easy once their symbols are kept separate. Let $N$ count neutrons, $n_e$ count electrons, $A$ be the mass number, and $Q$ be the net electric charge. A proton carries electric charge $+e$ and an electron carries $-e$, where $e$ is the positive elementary charge; a neutron carries zero net electric charge. HenceThe reasoning is just counting: add protons and neutrons for $A$, and subtract negative electron contributions from positive proton contributions for $Q$. A neutral chemical atom has $Q=0$, so $n_e=Z$. For a positively charged ion, fewer electrons remain. Notation ${}_Z^A\mathrm{X}$ gives the mass number at upper left and atomic number at lower left, with $\mathrm{X}$ standing for the chemical element; a right superscript such as $+$ specifies the electric charge in units of $e$. See Flowers et al., Chemistry 2e, atomic structure and symbolism.

For neutral carbon-12, ${}_6^{12}\mathrm{C}$, the atomic number gives six protons, the subtraction $N=12-6=6$ gives six neutrons, and neutrality gives six electrons. Neutral carbon-13, ${}_6^{13}\mathrm{C}$, instead has $N=13-6=7$ neutrons, with the same six protons and six electrons. Thus these two isotopes occupy the same carbon box in the periodic table.

For neutral sodium of mass number $23$, ${}_{11}^{23}\mathrm{Na}$, the counts are eleven protons, $23-11=12$ neutrons, and eleven electrons. Removing one electron gives the ion ${}_{11}^{23}{\mathrm{Na}}^{+}$: $Q/e=1$, so $n_e=11-1=10$. Both its atomic number and its twelve neutrons stay unchanged. This is ionization, not conversion into the chemical element neon, even though a neutral neon chemical atom also has ten electrons.

This bookkeeping is useful whenever a symbol must be translated into a physical inventory. Mass number answers how many protons plus neutrons there are; electric charge answers the imbalance between protons and electrons; atomic number alone answers which chemical element it is. Keeping those questions distinct prevents an isotope or an ion from being mistaken for a different chemical element.

Assigning the origin and destination of atoms through a synthetic route. carbon counts and the positions of surviving carbonyls expose chain-length and ring-connectivity errors.

An allene has a $\mathrm{C}=\mathrm{C}=\mathrm{C}$ unit whose terminal substituents lie in perpendicular planes. In $\mathrm{abC}=\mathrm{C}=\mathrm{Ccd}$, with $a\ne b$ and $c\ne d$, the two terminal pairs can define enantiomers without any tetrahedral carbon stereocenter. The groups need be different within each end pair, not all four mutually different. This is axial chirality.^[ref]

A neighbouring tertiary amine displaces a leaving group to form a three-membered ammonium ring; attack at the original ring carbon cleaves its old C–N bond and incorporates the side-chain carbon into an expanded nitrogen ring.