[DOWNLOAD] Chemistry Chapter 7 Test Answer Key
The primary sequence of a protein is linked together using dehydration synthesis that combine the carboxylic acid of the upstream amino acid with the amine functional group of the downstream amino acid to form an amide linkage. Within protein structures, this amide linkage is known as the peptide bond. Subsequent amino acids will be added onto the carboxylic acid terminal of the growing protein. Thus, proteins are always synthesized in a directional manner starting with the amine and ending with the carboxylic acid tail. New amino acids are always added onto the carboxylic acid tail, never onto the amine of the first amino acid in the chain. In addition, because the R-groups can be quite bulky, they usually alternate on either side of the growing protein chain in the trans conformation.
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For example, think about a tripeptide made from this amino acid pool. At each position there are 20 different options that can be incorporated. Thus, the total number of resulting tripeptides possible would be 20 X 20 X 20 or , which equals 8, different tripeptide options! Now think about how many options there would be for a small peptide containing 40 amino acids. There would be options, or a mind boggling 1. Each of these options would vary in the overall protein shape, as the nature of the amino acid side chains helps to determine the interaction of the protein with the other residues in the protein itself and with its surrounding environment. Thus, it is useful to learn a little bit about the general characteristics of the amino acid side chains. The different amino acid side chains can be grouped into different classes based on their chemical properties Figure For example, some amino acid side chains only contain carbon and hydrogen and are thus, very nonpolar and hydrophobic.
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Others contain electronegative functional groups with oxygen or nitrogen and can form hydrogen bonds forming more polar interactions. Still others contain carboxylic acid functional groups and can act as acids or they contain amines and can act as bases, forming fully charged molecules. The character of the amino acids throughout the protein help the protein to fold and form its 3-dimentional structure.
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It is this 3-D shape that is required for the functional activity of the protein ie. For proteins found inside the watery environments of the cell, hydrophobic amino acids will often be found on the inside of the protein structure, whereas water-loving hydrophilic amino acids will be on the surface where they can hydrogen bond and interact with the water molecules. Proline is unique because it has the only R-group that forms a cyclic structure with the amine functional group in the main chain. This cyclization is what causes proline to adopt the cis conformation rather than the trans conformation within the backbone.
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This shift is structure will often mean that prolines are positions where bends or directional changes occur within the protein. Methionine is unique, in that it serves as the starting amino acid for almost all of the many thousands of proteins known in nature. Cysteines contain thiol functional groups and thus, can be oxidized with other cysteine residues to form disulfide bonds within the protein structure Figure Disulfide bridges add additional stability to the 3-D structure and are often required for correct protein folding and function Figure Disulfide bonds are formed between two cysteine residues within a peptide or protein sequence or between different peptide or protein chains.
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In the example above the two peptide chains that form the hormone insulin are depicted. Disulfide bridges between the two chains are required for the proper function of this hormone to regulate blood glucose levels. Protein Shape and Function The primary structure of each protein leads to the unique folding pattern that is characteristic for that specific protein. Recall that this is the linear order of the amino acids as they are linked together in the protein chain Figure These specific motifs or patterns are called secondary structure.
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Common secondary structural features include alpha helix and beta-pleated sheet Figure Within these structures, intramolecular interactions, especially hydrogen bonding between the backbone amine and carbonyl functional groups are critical to maintain 3-dimensional shape. Every helical turn in an alpha helix has 3. The R groups are attached to the carbons and extend above and below the folds of the pleat. The pleated segments align parallel or antiparallel to each other, and hydrogen bonds form between the partially positive nitrogen atom in the amino group and the partially negative oxygen atom in the carbonyl group of the peptide backbone. The alpha helix and beta-pleated sheet are common structural motifs found in most proteins. They are held together by hydrogen bonding between the amine and the carbonyl oxygen within the amino acid backbone. The most highly traveled and culturally significant of these was called the Silk Road.
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The reason that the Silk road was so culturally significant was because of the great distance that it covered. Essentially the entire ancient world was connected by one trade route. The silk road had an astounding effect on the creation of many societies. It was able to bring economic wealth into areas along the route, and new ideas traveled the distance and influence many things including art. An example of this is Buddhist art that was found in India. The painting has many western influences that can be identified in it, such as realistic musculature of the people being painted. Also, the trade of gun powder to the West helped influence warfare, and in turn shaped the modern world. The real reason the Silk Road was started though was for the product that it takes its name from: Silk. The Silk showed that the rulers had power and wealth because the silk was not easy to come by, and therefore was definitely not cheap.
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Silk was first developed in China, and is made by harvesting the silk from the cocoons of the mulberry silkworm. The silk itself is called a natural protein fiber because it is composed of a pattern of amino acids in a secondary protein structure. The secondary structure of silk is the beta pleated sheet. The primary structure of silk contains the amino acids of glycine, alanine, serine, in specific repeating pattern. These amino acids are used as side chains and affect things such as elasticity and strength. The beta pleated sheet of silk is connected by hydrogen bonds. The hydrogen bonds in the silk form beta pleated sheets rather than alpha helixes because of where the bonds occur. The hydrogen bonds go from the amide hydrogens on one protein chain to the corresponding carbonyl oxygen across the way on the other protein chain.
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This is in contrast to the alpha helix because in that structure the bonds go from the amide to the carbonyl oxygen, but they are not adjacent. The carbonyl oxygen is on the amino acid that is four residues before. The formation of this secondary structure in the silk protein allows it to have very strong tensile strength. Silk also helped to form one of the greatest trading routes in history, allowing for the exchange of ideas, products and cultures while advancing the societies that were involved. Silk contains both anti-parallel and parallel arrangements of beta sheets. In consequence very bulky side chains make the structure unstable. This explains why silk is composed almost entirely of glycine, alanine, and serine, the three amino acids with the smallest side chains. The complete 3-dimensional shape of the entire protein or sum of all the secondary structures is known as the tertiary structure of the protein and is a unique and defining feature for that protein Figure Primarily, the interactions among R groups creates the complex three-dimensional tertiary structure of a protein.
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The nature of the R groups found in the amino acids involved can counteract the formation of the hydrogen bonds described for standard secondary structures. For example, R groups with like charges are repelled by each other and those with unlike charges are attracted to each other ionic bonds. When protein folding takes place, the hydrophobic R groups of nonpolar amino acids lay in the interior of the protein, whereas the hydrophilic R groups lay on the outside.
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The former types of interactions are also known as hydrophobic interactions. Interaction between cysteine side chains forms disulfide linkages in the presence of oxygen, the only covalent bond forming during protein folding. The tertiary structure of proteins is determined by a variety of chemical interactions. These include hydrophobic interactions, ionic bonding, hydrogen bonding and disulfide linkages. All of these interactions, weak and strong, determine the final three-dimensional shape of the protein. When a protein loses its three-dimensional shape, it is usually no longer be functional. In nature, some proteins are formed from several polypeptides, also known as subunits, and the interaction of these subunits forms the quaternary structure. Weak interactions between the subunits help to stabilize the overall structure. For example, insulin a globular protein has a combination of hydrogen bonds and disulfide bonds that cause it to be mostly clumped into a ball shape.
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Insulin starts out as a single polypeptide and loses some internal sequences during cellular processing that form two chains held together by disulfide linkages as shown in figure Three of these structures are then grouped further forming an inactive hexamer Figure The hexamer form of insulin is a way for the body to store insulin in a stable and inactive conformation so that it is available for release and reactivation in the monomer form. Insulin is produced and stored in the body as a hexamer a unit of six insulin molecules , while the active form is the monomer.
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