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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]

An amino acid residue is the portion of an amino acid incorporated into a polypeptide chain. For example, the A in the illustrative protein primary structure is an alanine residue, rather than a free alanine molecule floating beside the chain. Counting amino acid residues counts chain positions; repeated letters are separate positions. See IUPAC-IUB, section 3AA-16: symbols for amino-acid residues.

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.

A codon is a three-nucleotide unit read in a specified reading frame during biological translation. For example, GCU specifies alanine in the standard genetic code. Its letters are read $5^{\prime }\to 3^{\prime }$.

The C-terminus is the carboxyl end of a protein or amino acid chain. During biological translation, each new residue is added at this end. The example under gene expression gives N–methionine–alanine–C, placing alanine at the C-terminus; its stop codon supplies no further residue. ^[ref]

Enantiomers are a pair of nonsuperposable mirror-image molecules. The D and L configurations of alanine are an example; glycine has no such pair because its amino acid alpha carbon carries two identical hydrogen chemical atoms. ^[ref]

The word names a relation between two stereoisomers. Merely finding two different spatial arrangements does not make them enantiomers: arrangements that are different but not mirror partners are diastereomers.

Gene expression uses a gene's information to produce functional RNA or a protein. Transcription makes RNA from a DNA template; for a protein-coding gene, biological translation then uses messenger RNA to specify an amino acid chain. Many genes instead produce functional RNA, including transfer RNA and ribosomal RNA, without a translated protein product. See Alberts et al., Molecular Biology of the Cell, 4th edition (2002): from DNA to RNA.

Follow the chosen coding strand $5^{\prime }\text{-}\mathrm{ATGGCTTAA}\text{-}{3}^{\prime }$: transcription of its complementary template gives $5^{\prime }\text{-}\mathrm{AUGGCUUAA}\text{-}{3}^{\prime }$ in messenger RNA. In the stated reading frame, its three codons are AUG, GCU and UAA: methionine, alanine and a stop codon. Thus nine nucleotides specify two amino acid residues followed by termination, not three residues. This is an illustrative coding segment embedded in suitable expression and initiation context, not a claim that an isolated nine-nucleotide RNA is sufficient to initiate biological translation.

The distinction between copying and use explains how biological cells can preserve the same DNA yet produce different products. DNA replication duplicates the record; gene expression selects and uses parts of it. Transcription does not use all DNA at once, and gene expression can be controlled at several steps, including transcription, RNA processing and biological translation. See Clark, Douglas and Choi, Biology 2e: regulation of gene expression. The arrows describe template-directed synthesis: the DNA does not physically turn into a protein, and the messenger RNA does not supply the amino acids from which that protein is assembled.

A polypeptide is a chain of amino acid residues linked by peptide bonds. The term describes chain chemistry; calling a chain a polypeptide alone does not establish that it is folded or functional. The gene expression example N–methionine–alanine–C contains two amino acid residues and one peptide bond; the twelve-residue example under protein contains eleven peptide bonds. See IUPAC-IUB: amino-acid symbols and representation of residues in chains.

A protein is a biological molecule made of one or more polypeptide chains: ordered amino acid residues joined by peptide bonds. Biological translation assembles a chain in the order specified by messenger RNA codons. Protein folding then brings parts of that chain into spatial relationships that support its function. See Cooper, The Cell: protein composition and structure. These processes can overlap in a biological cell; the sequence-to-shape explanation does not require waiting until biological translation finishes before any folding begins. See Cooper, The Cell: protein folding and processing.

The useful connection is from information to physical work. A protein's protein primary structure records an order; its protein tertiary structure can bring distant amino acid residues together at an active site. An enzyme uses such an arrangement to recognize a substrate and accelerate a chemical reaction. Other proteins serve as receptors, membrane transport proteins or structural material. For example, actin assembles into filaments whose mechanical properties can be described by biopolymer mechanics. See Alberts et al., Molecular Biology of the Cell: protein function and binding.

Order matters beyond composition. Let A stand for alanine and M for methionine, and read from the N-terminus to the C-terminus. The illustrative strings AMAMAMAMAMAM and AAAAAAMMMMMM each contain exactly six A and six M amino acid residues. Each has $12-1=11$ peptide bonds when made into one unbranched polypeptide chain. In the first string all eleven neighboring pairs have different letters; in the second only the pair at positions 6 and 7 does. A composition histogram therefore loses information about which amino acid residues are neighbors. Their arrangements can affect protein folding and function; these short invented strings neither specify a known functional protein nor establish what shape either would adopt.

Protein structure is a moving arrangement, not a permanently rigid outline. Substrate binding can change an enzyme's shape through induced fit, and a functional protein can include flexible regions. Sequence, surroundings and interacting molecules must therefore be considered together. See Alberts et al.: binding, conformational changes and protein function.

A proteinogenic amino acid is incorporated into proteins during translation. The conventional twenty include glycine, alanine, methionine and proline; they are a subset of amino acids, not a definition of the whole family. ^[ref]

The protein primary structure specifies the ordered amino acid residues of each polypeptide chain, joined through peptide bonds. A chain is conventionally written from its N-terminus to its C-terminus. In the broader chemical sense, a complete protein primary structure also specifies covalent bond crosslinks between chain positions, including protein disulfide bonds; a bare sequence string leaves that information unstated. This describes chemical connectivity rather than the spatial arrangement of protein tertiary structure or protein quaternary structure. See IUPAC Gold Book: primary structure, sequence and chain crosslinking and IUPAC-IUB, 3AA-16: writing residue sequences from the amino end. Some conventions reserve protein primary structure for sequence alone and call the complete chemical connectivity the covalent structure; the distinction should be stated when comparing descriptions. See IUPAC-IUB polypeptide-conformation recommendations, section 6.1: the narrower sequence-only convention.

In this toy example M denotes methionine, A alanine and G glycine. Both polypeptide chains have six amino acid residues, five peptide bonds, an M at the N-terminus and a G at the C-terminus. Their amino acid composition is identical, yet position 2 is A in MAGAMG and M in MMAAGG. There are $6!/(2!2!2!)=90$ distinct orders with these counts, a multinomial coefficient. Even fixing those two end residues leaves $4!/(1!2!1!)=12$ orders. The counts constrain the answer without determining it.

For multiple polypeptide chains, record each sequence separately and specify any protein disulfide bonds between cysteine positions. Mature insulin, for example, has an A chain of 21 amino acid residues and a B chain of 30 amino acid residues. Their combined 51 residues give $(21-1)+(30-1)=49$ peptide bonds, rather than the 50 of one unbroken 51-residue chain. See Cooper, The Cell: insulin's two chains and cysteine crosslinks, figure 2.16. A protein disulfide bond joins side groups; it does not concatenate the C-terminus of one chain with the N-terminus of another. The three insulin protein disulfide bonds connect A6 to A11 within the A chain, and A7 to B7 and A20 to B19 between chains. Positions are numbered from each chain's N-terminus. See Replacement of the interchain disulfide bridge-forming amino acids A7 and B7 by glutamate impairs the structure and activity of insulin: native disulfide positions.

Why keep this information? Protein primary structure lets us distinguish changes of chemical identity from changes of shape, and compare corresponding positions between proteins. Protein folding can bring distant amino acid residues together at a protein binding site while preserving their sequence. The attractive idea is that a readable linear record can constrain a complicated three-dimensional object; it is not, by itself, a guarantee of a unique fold in every environment. See protein folding and the ribonuclease A refolding experiment. Merely bending an intact chain preserves its protein primary structure; hydrolysis of a peptide bond, or changing which positions a protein disulfide bond connects, changes its chemical connectivity.

A ribosome is the molecular machinery for biological translation: it reads messenger RNA and joins amino acids into a polypeptide that can become a protein. Both prokaryotes and eukaryotes have ribosomes. A ribosome consists of ribosomal RNA and proteins organized into small and large subunits, with no enclosing membrane. Ribosomal RNA contributes to both structure and the active site that forms peptide bonds; a ribosome is therefore not merely a collection of proteins. See Clark, Douglas and Choi, Biology 2e, 4.3: ribosome composition and Nissen et al., The structural basis of ribosome activity in peptide bond synthesis, Science 289, 920–930 (2000).

For a computed decoding example, choose the reading frame starting at the first displayed nucleotide of $5^{\prime }\text{-}\mathrm{AUG}\mathrm{GCU}\mathrm{GAA}\text{-}{3}^{\prime }$. Under the standard genetic code, AUG specifies methionine (Met), GCU specifies alanine (Ala), and GAA specifies a glutamic acid residue (Glu) in the growing polypeptide. Nine nucleotides divide into three codons, giving the ordered three-amino acid residue segment Met–Ala–Glu. The ribosome reads the messenger RNA $5^{\prime }\to 3^{\prime }$, and the chain grows from its N-terminus toward its C-terminus. If synthesis begins at this AUG in an appropriate eukaryotic initiation context, these are the first three amino acid residues before any subsequent processing. See Clark, Douglas and Choi, Biology 2e, 15.1: standard codon assignments.

For this three-amino acid residue segment, joining the three delivered amino acids requires two peptide bonds, one between Met and Ala and another between Ala and Glu. There is no stop codon in the displayed nucleotide sequence, so this is a growing segment rather than a complete released protein. An isolated nine-nucleotide RNA is not claimed to supply all signals needed for initiation. This small calculation separates three jobs: the messenger RNA specifies order, transfer RNA delivers the amino acids, and the ribosome catalyzes their joining. Each new amino acid residue is added at the C-terminus. See Clark, Douglas and Choi, Biology 2e, 15.5: initiation and chain elongation.

The beauty of a ribosome is its reusable chemistry: the same machinery can assemble many different proteins by following different messenger RNA templates. The genetic code connects an alphabet of nucleotides to an alphabet of amino acids, while transfer RNA links recognition of the message to delivery of building material. Changing the message can therefore change the product without building a different ribosome for every protein.

In 1955 George E. Palade described small particles in the cytoplasm, both free and associated with membranes, in A small particulate component of the cytoplasm, Journal of Biophysical and Biochemical Cytology 1, 59–68. The paper documents the structural observations, rather than the full modern decoding mechanism. Complementary biochemical work by Hoagland, Stephenson, Scott, Hecht and Zamecnik described a soluble RNA intermediate in protein synthesis in 1958, helping establish the role now assigned to transfer RNA; see A soluble ribonucleic acid intermediate in protein synthesis, Journal of Biological Chemistry 231, 241–257. Together, structural observations and biochemical experiments connected visible cellular machinery with its working parts.

Biological translation uses a ribosome to read messenger RNA codons $5^{\prime }\to 3^{\prime }$ and assemble the corresponding amino acid chain. Transfer RNA adaptors match codons through base pairing and carry the amino acids; the genetic code supplies the correspondence. The chain grows from the N-terminus toward the C-terminus, by adding each new residue at the C-terminus. See Clark, Douglas and Choi, Biology 2e: ribosomes, transfer RNA and protein synthesis.

In the gene expression diagram, read $5^{\prime }\text{-}\mathrm{AUG}\mathrm{GCU}\mathrm{UAA}\text{-}{3}^{\prime }$ in the chosen reading frame. Under the standard genetic code, AUG specifies methionine and GCU specifies alanine; UAA is a stop codon. The result before any subsequent processing is the two-residue chain N–methionine–alanine–C, followed by termination. The stop codon contributes zero amino acids. See Clark, Douglas and Choi, Biology 2e: the standard genetic code. This example assumes appropriate initiation at the displayed AUG in a suitable context in a eukaryote; the diagram displays the coding segment, not a complete independently translatable messenger RNA.

Initiation establishes the starting position and reading frame, using a ribosome, an initiating transfer RNA and additional factors. At a standard stop codon, a release factor promotes release of the chain rather than delivery of another amino acid by transfer RNA. See Clark, Douglas and Choi: initiation and termination of translation. A short two-residue example illustrates decoding, not the size or folding of a typical functional protein.

The useful connection is between two different alphabets: nucleotides specify the order of amino acids through the genetic code. Base pairing helps select transfer RNA, while the ribosome catalyzes joining the delivered amino acids. The messenger RNA remains a template rather than being consumed as the chain's building material. Separating template, adaptor and product makes clear why transcription and biological translation are distinct mechanisms.