The wikipedia article "side chain" explains this use of "R" in detail. In chemical diagrams, the sidechain may be replaced by the letter R. The Amino Acid Gallery shows all sidechains seen in Foldit. The sidechain is what makes each amino acid different. The atom numbering is the same as for the N terminal. Both the amino and carboxyl groups are part of peptide bonds. Isoleucine in the middle of a protein chain. In it's non-ionized form, a carboxyl has the formula -COOH.
So it's formula is -COO, and it has a negative charge. Like the amino group, the carboxyl group is shown in ionized form. The C terminal still has two oxygen atoms in its carboxyl group, so its beta carbon is atom 6. For every atom in a protein chain except the last one (the C terminal), the sidechain starts with the beta carbon, atom 5. Oxygen is a heavy atom, and since it's part of the backbone, the atom numbering for the sidechain changes. This change is referred to as a condensation reaction, because the two hydrogens and an oxygen freed up as the peptide bond forms are also combined to form a water molecule (H 2O). As the peptide bond forms, the carboxyl loses an oxygen. The carboxyl group starts out as a carbon atom and two oxygen atoms. Like the amino group, the carboxyl group changes as segments are added to the protein. The carboxyl carbon has two oxygen atoms attached. Isoleucine as the C terminal of a protein chain. The amino group can also be shown in it's non-ionic form, with a nitrogen and only two hydrogens, formula NH 2. The ionic form is what would normally be found in the "aqueous" or water-based solution inside a cell. The amino group as seen in Foldit is in its "ionized" or charged form, with three hydrogens, formula NH 3-, and a positive charge. For subsequent segments, the amino group loses two of its hydrogen atoms. The amino group of the first segment in a chain, known as the N terminal, keeps all three hydrogen atoms. The nitrogen atom is always assigned atom number 1, both Foldit and in science tools like the PDB. The amino group starts out as a nitrogen atom bonded to three hydrogen atoms. The backbone of each amino acid starts with the same collection of atoms, but changes occur as peptide bonds are formed. The amino nitrogen at atom 1 has three hydrogens attached. Patterns of hydrogen bonds between these backbone points determine the secondary structure of the protein.Īn isoleucine residue as the N terminal of a protein chain. The oxygen(s) (atom 4, and sometimes atom 5) in the carboxyl group can accept hydrogen bonds. The backbone can form hydrogen bonds at two points: the nitrogen in the amino group (atom 1) can act as a hydrogen bond donor. Phi and psi can be viewed in the Rama map tool in Foldit. The critical backbone angles named phi and psi are determined relative to the alpha carbon. The alpha carbon connects the following parts of the amino acid: The alpha carbon (atom 2) is the central feature of the backbone. Except for the ends of a protein chain, the backbone of each segment contains the same atoms. Strong peptide bonds join the segments, forming the backbone. Switching to a view like "Stick + Polar H" and using EnzDes or CPK coloring reveals more about the backbone.Įach segment of a protein is the residue of an amino acid. The "cartoon" views in Foldit show the shape of the backbone, but hide most of the chemical structure. Protein sidechains receive most of the attention, but understanding the backbone is also important in Foldit. (Compare the backbone shown here to RNA backbone, which has over twice as many atoms.) Protein backbone is what holds a protein together and gives it an overall shape (or tertiary structure).Ĭompared to RNA and DNA backbone, protein backbone has a relatively simple chemical structure - a nitrogen atom, two carbon atoms, one or two oxygen atoms, and a few hydrogens. Here, a methionine sidechain is attached to the alpha carbon of the segment in the center. Peptide bonds join the carboxyl group of one segment to the amino group of the next.
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