Peptide bonds are formed by a biochemical reaction that extracts a water molecule as it joins the amino group of one amino acid to the carboxyl group of a neighboring amino acid.
The linear sequence of amino acids within a protein is considered the primary structure of the protein. Proteins are built from a set of only twenty amino acids, each of which has a unique side chain. The side chains of amino acids have different chemistries.
The largest group of amino acids have nonpolar side chains. Several other amino acids have side chains with positive or negative charges, while others have polar but uncharged side chains. The chemistry of amino acid side chains is critical to protein structure because these side chains can bond with one another to hold a length of protein in a certain shape or conformation.
Charged amino acid side chains can form ionic bonds, and polar amino acids are capable of forming hydrogen bonds. Hydrophobic side chains interact with each other via weak van der Waals interactions. The vast majority of bonds formed by these side chains are noncovalent. In fact, cysteines are the only amino acids capable of forming covalent bonds, which they do with their particular side chains.
Because of side chain interactions, the sequence and location of amino acids in a particular protein guides where the bends and folds occur in that protein Figure 1.
Figure 1: The relationship between amino acid side chains and protein conformation The defining feature of an amino acid is its side chain at top, blue circle; below, all colored circles. When connected together by a series of peptide bonds, amino acids form a polypeptide, another word for protein. The polypeptide will then fold into a specific conformation depending on the interactions dashed lines between its amino acid side chains.
Figure Detail. Figure 2: The structure of the protein bacteriorhodopsin Bacteriorhodopsin is a membrane protein in bacteria that acts as a proton pump.
Its conformation is essential to its function. The overall structure of the protein includes both alpha helices green and beta sheets red. The primary structure of a protein — its amino acid sequence — drives the folding and intramolecular bonding of the linear amino acid chain, which ultimately determines the protein's unique three-dimensional shape. Hydrogen bonding between amino groups and carboxyl groups in neighboring regions of the protein chain sometimes causes certain patterns of folding to occur.
Known as alpha helices and beta sheets , these stable folding patterns make up the secondary structure of a protein. Most proteins contain multiple helices and sheets, in addition to other less common patterns Figure 2. The ensemble of formations and folds in a single linear chain of amino acids — sometimes called a polypeptide — constitutes the tertiary structure of a protein.
Finally, the quaternary structure of a protein refers to those macromolecules with multiple polypeptide chains or subunits. The final shape adopted by a newly synthesized protein is typically the most energetically favorable one. As proteins fold, they test a variety of conformations before reaching their final form, which is unique and compact. Folded proteins are stabilized by thousands of noncovalent bonds between amino acids. In addition, chemical forces between a protein and its immediate environment contribute to protein shape and stability.
For example, the proteins that are dissolved in the cell cytoplasm have hydrophilic water-loving chemical groups on their surfaces, whereas their hydrophobic water-averse elements tend to be tucked inside.
In contrast, the proteins that are inserted into the cell membranes display some hydrophobic chemical groups on their surface, specifically in those regions where the protein surface is exposed to membrane lipids. It is important to note, however, that fully folded proteins are not frozen into shape. Rather, the atoms within these proteins remain capable of making small movements. Even though proteins are considered macromolecules, they are too small to visualize, even with a microscope.
So, scientists must use indirect methods to figure out what they look like and how they are folded. The most common method used to study protein structures is X-ray crystallography.
Learning Objectives Define or describe the following: amino acid "R" group peptide bond peptide polypeptide primary protein structure secondary protein structure tertiary protein structure quaternary protein structure gene Describe how the primary structure of a protein or polypeptide ultimately detemines its final three-dimensional shape.
Describe how the order of nucleotide bases in DNA ultimately determines the final three-dimensional shape of a protein or polypeptide. Summary Amino acids are the building blocks for proteins.
To form polypeptides and proteins, amino acids are joined together by peptide bonds, in which the amino or NH 2 of one amino acid bonds to the carboxyl acid or COOH group of another amino acid. A peptide is two or more amino acids joined together by peptide bonds; a polypeptide is a chain of many amino acids; and a protein contains one or more polypeptides.
The actual order of the amino acids in the protein is called its primary structure and is determined by DNA. The order of deoxyribonucleotide bases in a gene determines the amino acid sequence of a particular protein.
The secondary structure of the protein is due to hydrogen bonds that form between the oxygen atom of one amino acid and the nitrogen atom of another and gives the protein or polypeptide the two-dimensional form of an alpha-helix or a beta-pleated sheet. Other interactions between R groups of amino acids such as hydrogen bonds, ionic bonds, covalent bonds, and hydrophobic interactions also contribute to the tertiary structure. Start this free course now.
Just create an account and sign in. Enrol and complete the course for a free statement of participation or digital badge if available. The primary structure of a protein is defined as the sequence of amino acids of which it is composed. This sequence ultimately determines the shape that the protein adopts, according to the spatial limitations on the arrangement of the atoms in the protein, the chemical properties of the component amino acid residues, and the protein's environment.
The peptide bonds that link amino acid residues in a polypeptide are formed in a condensation reaction between the acidic carboxyl group of one amino acid and the basic amino group of another amino acid.
In the context of a peptide, the amide group CO—NH is referred to as the peptide group. Crucial to an understanding of protein structure is a knowledge of the structure of the peptide bond. Linus Pauling, in the s, used X-ray diffraction to examine the nature of the peptide bond formed between two amino acids. He reported that the peptide group CO—NH has a rigid planar structure.
This effect is an example of resonance which can be thought of as a sharing of electrons between bonds. The bond lengths in the peptide group are indicated in Figure 3. Considering the spatial arrangement and the proximity of the atoms in the cis and trans conformations of the peptide bond, which conformation do you think would be favoured? The trans conformation would be energetically more favourable than the cis conformation, since it minimises steric hindrance. Generally speaking, peptide bonds are in the trans conformation.
However, cis forms can occur in peptide bonds that precede a proline residue. In such cases, the cis form is more stable than usual since the proline side-chain offers less of a hindrance. Figure 4 shows part of a polypeptide with two planar peptide groups in the trans conformation. The angles of rotation, termed torsion angles , about these bonds specify the conformation of a polypeptide backbone. It is possible to calculate these permitted values for a given residue in the context of a polypeptide.
It is most readily done for a polypeptide containing just one kind of amino acid. Such a plot allows us to identify those conformations i. These conformations lie in the blue areas in Figure 5. They lie in the green areas in Figure 5. These lie in the white areas in Figure 5. Thus the green strip at the bottom left corner of the plot in Figure 5 is contiguous with the field at the top left corner. Ramachandran plots can be constructed for polymers of each of the 20 amino acids.
It is significant to note that the Ramachandran plots for many amino acid residues are generally very similar, having only three regions with favourable or tolerated conformations labelled 1—3 in the plot for poly- l -alanine in Figure 5. Differences do occur, however.
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