A mutation which causes an amino acid substitution can have a great affect on protein structure and therefore protein function. For example the point mutation which substitutes valine for the polar amino acid glutamate causes haemoglobin to change its shape, due to the new hydrophilic region, leading to the condition known as sickle cell anaemia [5].
Jump to: navigation , search. Personal tools Log in. Namespaces Page Discussion. 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. With this method, solid crystals of purified protein are placed in an X-ray beam, and the pattern of deflected X rays is used to predict the positions of the thousands of atoms within the protein crystal.
In theory, once their constituent amino acids are strung together, proteins attain their final shapes without any energy input. In reality, however, the cytoplasm is a crowded place, filled with many other macromolecules capable of interacting with a partially folded protein. Inappropriate associations with nearby proteins can interfere with proper folding and cause large aggregates of proteins to form in cells.
Cells therefore rely on so-called chaperone proteins to prevent these inappropriate associations with unintended folding partners. Chaperone proteins surround a protein during the folding process, sequestering the protein until folding is complete. For example, in bacteria, multiple molecules of the chaperone GroEL form a hollow chamber around proteins that are in the process of folding. Molecules of a second chaperone, GroES, then form a lid over the chamber.
Eukaryotes use different families of chaperone proteins, although they function in similar ways. Chaperone proteins are abundant in cells. These chaperones use energy from ATP to bind and release polypeptides as they go through the folding process. Chaperones also assist in the refolding of proteins in cells. Folded proteins are actually fragile structures, which can easily denature, or unfold. Although many thousands of bonds hold proteins together, most of the bonds are noncovalent and fairly weak.
Even under normal circumstances, a portion of all cellular proteins are unfolded. Then the amino acid becomes more basic. The examples for this category include lysine , arginine and histidine. Polar amino acids with a negative charge have more carboxyl groups compared to amine groups. Then the amino acid becomes more acidic. Examples of this group include aspartic acid and glutamic acid. Nonpolar amino acids are amino acids that have no polarity.
That is because these amino acids have equal numbers of carboxylic acid groups and amine groups. This makes these nonpolar amino acids to have a neutral charge. Nonpolar amino acids are hydrophobic. Examples of nonpolar amino acids include alanine, valine, leucine, isoleucine, phenylalanine, glycine, tryptophan, methionine and proline. There are several different ways of grouping amino acids based on the structure and properties.
Polar amino acids and nonpolar amino acids are categorized based on the polarity of the amino acid. The difference between polar and nonpolar amino acids is that polar amino acids have polarity whereas polarity is absent in nonpolar amino acids.
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