11/29/2023 0 Comments Peptide backbone nitrogen atom![]() The α-helix and β-pleated sheet are secondary structures of proteins that form because of hydrogen bonding between carbonyl and amino groups in the peptide backbone. Beta pleated sheets can be formed both through either the antiparallel or the parallel alignment of the peptide chains, though the former structures are more stable. Practice: Note that in the structure of the beta pleated sheet drawn below one chain is drawn in the N to C direction while the other is drawn C to N (stop to try to figure out what I mean by this, and which strand is drawn which way- this is great practice). In a beta pleated sheet (shown below) the hydrogen bonded partners might be very far away from each other in the primary structure of the protein (i.e., the 15th and 100th amino acids in the chain) but the secondary structure holds these amino acids in close proximity to one another. The hydrogen bonding in alpha helices stabilizes the formation of a rigid cylinder of amino acids. In the alpha helix, this partnering amino acid is always four amino acids farther along the chain. More specifically, the oxygen atom in the carboxyl group from one amino acid can form a hydrogen bond with a hydrogen atom bound to the nitrogen in the amino group of another amino acid. These secondary structures are held together by hydrogen bonds forming between the backbones of amino acids in close proximity to one another. The most common shapes created by secondary folding are the α-helix and β-pleated sheet structures. The local folding of the polypeptide in some regions gives rise to the secondary structure of the protein. The order in which you would read this peptide chain would begin with the N-terminus as Glycine, Isoleucine, etc and end with methionine. The primary structure of a protein is depicted here as "beads on a string" with the N terminus and C terminus labeled. However, each amino acid can twist relative to the next amino acid between the C alpha and C carbons. By "planar" we mean that the 2 alpha carbons, the nitrogen, and carbon and oxygen associated with the peptide bond all lie in a single plane (the peptide bond is resistant to twisting). The shaded quadrilateral represents planar nature of this bond. The peptide bond between two amino acids is depicted. The primary structure is coded for in the DNA, a process you will learn about in the Transcription and Translation modules. The linear sequence of amino acids in the polypeptide chain are held together by peptide bonds and result in the N-C-C-N-C-C patterned backbone. The unique sequence of amino acids in a polypeptide chain is its primary structure. The carboxyl group of one amino acid and the amino group of the incoming amino acid combine, releasing a molecule of water and creating the peptide bond. Each amino acid is attached to another amino acid by a covalent bond, known as a peptide bond, which is formed by a dehydration synthesis (= condensation) reaction. The sequence and the number of amino acids ultimately determine the protein's shape, size, and function. The pattern you are looking for is: N-C-C-N-C-C Try finding the backbone in the dipeptide formed from this reaction. In the process, a molecule of water is released and a peptide bond is formed. The carboxyl group of the first amino acid is linked to the amino group of the second incoming amino acid. Peptide bond formation is a condensation reaction. When we write the sequence of a protein, we will always write it from the from "N to C". When looking at a chain of amino acids it is always helpful to first orient yourself by finding this backbone pattern starting from the N terminus to the C terminus. The amino acids are arranged in a single line- there are no branches. ![]() Where the first ("alpha") C will always carry the R group and the second will have a double (ketone) bond to oxygen. There are 20 genetically encoded amino acids available to the cell to build in proteins and all of these contain the same core sequence: These will be used to make the peptide bonds between amino acids in a protein (only the amino groups at very beginning (the "N terminus") and the carboxyl group at the very end (the C terminus) will remain in a polypeptide (= protein). The name "amino acid" is derived from the fact that all free amino acids contain both an amino group and carboxylic acid group. ![]()
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