The polypeptide backbone is the repeating chain of atoms, nitrogen, alpha carbon and carbonyl carbon, that runs through every peptide and protein. Side chains hang off it. The peptide bond in each unit is flat and rigid, so the chain can only bend at the two single bonds beside each alpha carbon, measured as the angles phi and psi.
- The backbone repeats three atoms per residue: amide nitrogen, alpha carbon, carbonyl carbon.
- Resonance gives the peptide bond partial double-bond character, locking six atoms in one plane.
- Trans peptide bonds are favored about 1000 to 1 over cis, except before proline, where the ratio is about 4 to 1.
- Phi is rotation about N to C-alpha; psi is rotation about C-alpha to the carbonyl carbon.
- A right-handed alpha helix sits near phi -57 and psi -47 degrees.
- Glycine, with only a hydrogen side chain, can take angle pairs other residues cannot.
The spine of every peptide
Pick up a paper chain made of identical links. Whatever is glued onto each link, the chain underneath is the same all the way down. A peptide works that way. The side chains differ from residue to residue, but the chain they hang from repeats one pattern from end to end.
That repeating chain is the backbone. Each amino acid contributes three atoms to it in a fixed order: the amide nitrogen, the alpha carbon, and the carbonyl carbon. Written out, the backbone reads N, C-alpha, C, then N, C-alpha, C again, for as many residues as the chain has.
The side chain, or R group, attaches at the alpha carbon and points away from the backbone. So does a single hydrogen. The backbone itself carries the carbonyl oxygen on each carbonyl carbon and a hydrogen on each amide nitrogen, except at proline, where the nitrogen is tied into the side-chain ring.
Where does this repeating chain come from? Each free amino acid has an amino group and a carboxyl group on its alpha carbon. When the amino group of one attacks the carboxyl carbon of the next, the two join through an amide bond and a molecule of water leaves. Once joined, each amino acid is called a residue. Repeat the reaction and the N, C-alpha, C pattern grows one unit at a time, always in the same direction.
Nearly every protein made by living things uses L-amino acids, so the alpha carbons along a natural backbone share the same handedness. Glycine is the exception with no handedness at all, because its side chain is only a hydrogen. In a free amino acid at neutral pH, the amino and carboxyl groups both carry a charge, with pKa values near 9 and near 2. Once those groups are used up in peptide bonds, only the two ends of the chain keep them. Everything in between is neutral backbone amide, which is part of why a long chain behaves so differently from the amino acids it was built from.
- Amide nitrogen starts each unit
- Alpha carbon carries the side chain
- Carbonyl carbon ends the unit
- Peptide bond locks six atoms flat
- Phi and psi set the bend at each alpha carbon
Why is the peptide bond flat?
The peptide bond is flat because resonance gives it partial double-bond character. The link between one residue and the next is the peptide bond, the C-N bond between a carbonyl carbon and the following amide nitrogen. On paper it is drawn as a single bond. In the molecule it behaves partly like a double bond.
The reason is resonance. The nitrogen's lone pair of electrons is shared toward the carbonyl carbon, so the C-N bond takes on some double-bond character. The atoms involved are sp2 hybridized, with bond angles near 120 degrees.
The result is a flat unit of six atoms: the alpha carbon of one residue, the carbonyl carbon and its oxygen, the amide nitrogen and its hydrogen, and the alpha carbon of the next residue. All six sit in one plane. Rotation about the peptide bond itself is effectively locked, which is why chemists describe the backbone as a series of rigid planar units joined at the alpha carbons.
Which bonds hold a peptide together in the first place, and how they form, is covered in our guide to the bonds that link amino acids.
Trans and cis
A flat peptide unit can still be arranged two ways. The two alpha carbons can sit on opposite sides of the C-N bond, called trans, or on the same side, called cis.
Trans wins almost every time. For most peptide bonds, the trans arrangement is favored over cis by roughly a thousand to one, because in the cis form the two side-chain-bearing alpha carbons crowd each other.
Proline is the exception. When the residue after the bond is proline, its ring changes the crowding on both sides, and the preference drops sharply. In proteins, bonds to proline are found at a trans to cis ratio of about four to one. That is why a cis peptide bond, when a structure shows one, is most often found just before a proline.
Where can the backbone turn? Phi and psi
The backbone turns only at the alpha carbon, where two single bonds can rotate. It bends at the alpha carbon, where two single bonds meet the rigid planes on either side.
Rotation about the N to C-alpha bond is the angle phi. Rotation about the C-alpha to carbonyl carbon bond is the angle psi. Formally, each is a torsion angle defined by four atoms: phi by the previous carbonyl carbon, the nitrogen, the alpha carbon and the carbonyl carbon; psi by the nitrogen, the alpha carbon, the carbonyl carbon and the next nitrogen.
Both angles can in principle take any value from minus 180 to plus 180 degrees. In practice, many combinations bring atoms too close together and are ruled out. A plot of phi against psi, the Ramachandran plot, shows the combinations that remain.
The residues at the two ends of a chain lack a full set of neighbors, so the terminal residues do not have both angles defined.
Angles that make familiar shapes
Set every residue in a stretch of chain to the same pair of angles and a regular shape appears. The common secondary structures are exactly that.
| Structure | Phi | Psi |
|---|---|---|
| Right-handed alpha helix | about -57 degrees | about -47 degrees |
| Antiparallel beta sheet | about -139 degrees | about +135 degrees |
The helix and the sheet sit in different allowed regions of the Ramachandran plot. A chain that changes its angles partway along changes its shape there too, which is how a helix ends and a turn begins.
Glycine is the odd residue out. With only a hydrogen for a side chain, it is far less crowded than the others and can take angle pairs that other residues cannot. That freedom is why glycine turns up where a chain has to make a sharp turn.
How does the backbone differ from the side chains?
The backbone sets the chain's shape, while the side chains set its chemistry. Separating the two makes a peptide easier to read. The backbone is the same for every residue, so it decides the chain's geometry: direction, flat units, allowed angles. The side chains differ, so they decide the chemistry: charge, polarity, size and which residue is which.
Our guide to polypeptide chains covers how a chain is named and written from the N-terminus to the C-terminus. This page stays with the geometry of the repeating unit.
The backbone also has a direction built in. Every unit runs nitrogen first, carbonyl carbon last, so a chain has a free amine at one end and a free carboxyl at the other, unless one or both ends are capped. Short research peptides are often capped: an acetyl group on the N-terminus or an amide on the C-terminus changes the end groups without touching the backbone repeat in between.
What a short peptide does with its backbone
A long protein folds its backbone into helices and sheets held in place by the rest of the structure. A short peptide of a few residues usually has no such support. In solution its phi and psi angles move between allowed regions, and the molecule spends time in many shapes.
That has a practical side in the laboratory. The analytical methods used to confirm a research peptide, such as mass spectrometry and reversed-phase HPLC, read the sequence and the mass. They do not assume a fixed three-dimensional shape. Identity for a short peptide is a question of which residues are present and in what order, which is written into the backbone and side chains together.
A few features do leave their mark. Proline's ring restricts phi at that residue, and a cis bond before proline can give a small peptide two slowly interconverting forms. In a chromatogram those can occasionally appear as a broadened or split peak for one compound.
FOR LABORATORY AND IN-VITRO RESEARCH USE ONLY. NOT FOR HUMAN OR ANIMAL CONSUMPTION.
Common questions
What atoms make up the polypeptide backbone?
Why can't the peptide bond rotate?
What are phi and psi angles?
Why is proline special in the backbone?
More science guides
Sources
- LibreTexts Chemistry, Main Chain Conformations (CSU Chico, CHEM 451 Biochemistry I). Partial double-bond character, the six-atom plane, trans to cis ratios including proline, the phi and psi range, and angle values for helices and sheets.
- Proteopedia, Phi and Psi Angles. Four-atom definitions of the phi and psi torsion angles and the absence of both angles at terminal residues.
- LibreTexts Biology, Fundamentals of Biochemistry (Jakubowski and Flatt), 3.1 Amino Acids and Peptides. Proline's ring bonded to its own amine, and the partial double-bond character of the amide linkage.
