Protein and Polypeptide Structure

Protein and Polypeptide Structure There are four levels of structure found in polypeptides and proteins. The primary structure of a polypeptide protein determines its secondary, tertiary, and quaternary structures. Primary Structure The primary structure of polypeptides and proteins is the sequence of amino acids in the polypeptide chain with reference to the locations of any disulfide bonds. The primary structure may be thought of as a complete description of all of the covalent bonding in a polypeptide chain or protein. The most common way to denote a primary structure is to write the amino acid sequence using the standard three-letter abbreviations for the amino acids. For example  gly-gly-ser-ala  is the primary structure for a polypeptide composed of glycine, glycine, serine, and alanine, in that order, from the N-terminal amino acid (glycine) to the C-terminal amino acid (alanine). Secondary Structure Secondary structure is the ordered arrangement or conformation of amino acids in localized regions of a polypeptide or protein molecule. Hydrogen bonding plays an important role in stabilizing these folding patterns. The two main secondary structures are the alpha helix and the anti-parallel beta-pleated sheet. There are other periodic conformations  but the ÃŽ ±-helix and ÃŽ ²-pleated sheet are the most stable. A single polypeptide or protein may contain multiple secondary structures. An ÃŽ ±-helix is a right-handed or clockwise spiral in which each peptide bond is in the trans conformation and is planar. The amine group of each peptide bond runs generally upward and parallel to the axis of the helix; the carbonyl group points generally downward. The ÃŽ ²-pleated sheet consists of extended polypeptide chains with neighboring chains extending anti-parallel to each other. As with the ÃŽ ±-helix, each peptide bond is trans and planar. The amine and carbonyl groups of peptide bonds point toward each other and in the same plane, so hydrogen bonding can occur between adjacent polypeptide chains. The helix is stabilized by hydrogen bonding between amine and carbonyl groups of the same polypeptide chain. The pleated sheet is stabilized by hydrogen bonds between the amine groups of one chain and the carbonyl groups of an adjacent chain. Tertiary Structure The tertiary structure of a polypeptide or protein is the three-dimensional arrangement of the atoms within a single polypeptide chain. For a polypeptide consisting of a single conformational folding pattern (e.g., an alpha helix only), the secondary and tertiary structure may be one and the same. Also, for a protein composed of a single polypeptide molecule, tertiary structure is the highest level of structure that is attained. Tertiary structure is largely maintained by disulfide bonds. Disulfide bonds are formed between the side chains of cysteine by oxidation of two thiol groups (SH) to form a disulfide bond (S-S), also sometimes called a disulfide bridge. Quaternary Structure Quaternary structure is used to describe proteins composed of multiple subunits (multiple polypeptide molecules, each called a monomer). Most proteins with a molecular weight greater than 50,000 consists of two or more noncovalently-linked monomers. The arrangement of the monomers in the three-dimensional protein is the quaternary structure. The most common example used to illustrate quaternary structure is the hemoglobin protein. Hemoglobins quaternary structure is the package of its monomeric subunits. Hemoglobin is composed of four monomers. There are two ÃŽ ±-chains, each with 141 amino acids, and two ÃŽ ²-chains, each with 146 amino acids. Because there are two different subunits, hemoglobin exhibits heteroquaternary structure. If all of the monomers in a protein are identical, there is homoquaternary structure. Hydrophobic interaction is the main stabilizing force for subunits in quaternary structure. When a single monomer folds into a three-dimensional shape to expose its polar side chains to an aqueous environment and to shield its nonpolar side chains, there are still some hydrophobic sections on the exposed surface. Two or more monomers will assemble so that their exposed hydrophobic sections are in contact. More Information Do you want more information on amino acids and proteins? Here are some additional online resources on  amino acids  and  chirality of amino acids. In addition to general chemistry texts, information about protein structure can be found in texts for biochemistry, organic chemistry, general biology, genetics, and molecular biology. The biology texts usually include information about the processes of transcription and translation, through which the genetic code of an organism is used to produce proteins.

Learn About the Science of Marine Biology

Learn About the Science of Marine Biology The field of marine biology or becoming a marine biologist sounds fascinating, doesnt it? Whats involved in marine biology, or becoming a marine biologist? First, its important to understand what, exactly, makes up the marine biology branch of science. Marine biology is the scientific study of plants and animals that live in salt water. When many people think about a marine biologist, they picture a dolphin trainer. But marine biology is so much more than making a dolphin or sea lion follow commands. With the oceans covering over 70 percent of the Earth’s surface and providing habitat for thousands of species, marine biology is a very broad field. It involves a strong knowledge of all science along with principles of economics, legal matters, and conservation. Becoming a Marine Biologist A marine biologist, or someone who studies marine biology, can learn about a variety of organisms during their education from tiny plankton only visible under a microscope to the largest whales that are over 100 feet long. Marine biology can also include the study of different aspects of these organisms, including the behavior of animals in the ocean environment, adaptations to living in salt water and interactions between organisms. As a marine biologist, one would also look at how marine life interacts with different ecosystems such as salt marshes, bays, reefs, estuaries, and sand bars. Again, its not just learning about things that inhabit the ocean; its also about conserving resources and protecting a valuable food supply. Plus, there are many research initiatives to discover how organisms can benefit human health. Marine biologists have to have a thorough understanding of chemical, physical, and geological oceanography. Other people who study marine biology do not go on to conduct research or work for activist organizations; they can wind up teaching others about the vast scientific principles that make up the field. In other words, they can become teachers and professors at universities and colleges. Tools to Study Marine Biology The oceans are difficult to study, as they are vast and foreign to humans. They also vary depending on geographic locations and environmental factors. Different tools used to study the oceans include sampling mechanisms such as bottom trawls and plankton nets, tracking methods and devices such as photo-identification research, satellite tags, hydrophones, and â€Å"critter cams,† and underwater observation equipment such as remotely operated vehicles (ROVs).   Importance of Marine Biology Among other things, the oceans regulate climate and provide food, energy, and income. They support a variety of cultures. They are so important, yet there is so much we don’t know about this fascinating environment. Learning about the oceans and the marine life inhabiting them is becoming even more critical as we realize the importance of the oceans to the health of all life on the planet.