Proteins contain what type of atoms

Proteins may be defined as compounds of high molar mass consisting largely or entirely of chains of amino acids. Their masses range from several thousand to several million daltons Da. In addition to carbon, hydrogen, and oxygen atoms, all proteins contain nitrogen and sulfur atoms, and many also contain phosphorus atoms and traces of other elements. Proteins serve a variety of roles in living organisms and are often classified by these biological roles. Muscle tissue is largely protein, as are skin and hair.

Proteins are present in the blood, in the brain, and even in tooth enamel. Each type of cell in our bodies makes its own specialized proteins, as well as proteins common to all or most cells. We begin our study of proteins by looking at the properties and reactions of amino acids, which is followed by a discussion of how amino acids link covalently to form peptides and proteins. We end the chapter with a discussion of enzymes—the proteins that act as catalysts in the body. 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. 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. Silk protein, beta-keratin, spider webs, your nails, all contain proteins with high proportions of beta pleated sheet.

These proteins resist stretching since their chains are almost fully extended as it is. A series of weak hydrogen bonds form between the atoms of one peptide bond and the atoms of another peptide bond about 3 amino acids further down the chain. These tiny interactions, are, never the less, strong enough to coil the polypeptide into an alpha helix; a structure that looks some what as if the chain of amino acids had been wrapped around a cylinder. These spiral, helical molecules can be stretched.

Some proteins, with high helical content, extend easily. Hair and wool readily stretch, but, when the force is released, the helix snaps back into its original conformation, and the protein returns to its original shape.

Tertiary Structure; becoming a protein. Most proteins fold into complex, three dimensional, globular shapes. Hydrophilic R-groups interact positively with the surrounding water. The entire chain twists until the maximum number of these groups are in full contact with the surrounding water. The interplay between water and the hydrophilic R-groups support the huge protein molecule and help keep it in solution. Conversely, the hydrophobic R-groups become buried deep within the folding macromolecule, far away from the water molecules.

These forces, together with other cross-linking effects, hold the giant structure in a three dimensional shape which is distinctive and unique to that protein. It is at this level of structure that many proteins take on their cellular role or function. As a polypeptide chain, the molecule had no special properties, but as a three dimensional protein, the molecule is capable of performing an astonishing variety of feats.

Globular proteins catalyze chemical reactions, others act as defending antibodies within the immune system, and yet others trigger violent bodily reactions as they travel through the blood. Some globular proteins come together in complexes consisting of two or more subunits. Attached to these subunits can be other, non protein, molecules such as polysaccharides. These higher levels of structure can be seen in a protein molecule such as hemoglobin, a large, four subunit globular protein with four additional non protein additions.

This protein carries oxygen around in the blood. Most of the special properties of proteins stem from their unique three dimensional shapes.