Proteins make up approximately 55% of the dry mass of a human cell. They perform an uncountable number of tasks that help keep an organism alive. Because of this, proteins are often called the cellular machinery or the muscle of the cell. Calling them the muscle of the cell is kind of funny, as they are required for muscle movement and function.
Proteins are what are known as polymers. Polymers are molecules that are made of a “chain” of smaller, nearly identical molecules called monomers. Proteins are made up of monomers called amino acids, which are hydrocarbons made up of an amino group (NH2 or NH3+), a carboxyl group (COO- or COOH), and a variable (unique to different amino acids) R side chain group, which we will talk about in a second.
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Whether or not the carboxyl group and amino group have a hydrogen attached depends on the relative pH of the solution. pH is the concentration of H+, which are positively charged hydrogen ions or, simply, protons because when hydrogens lose an electron to become a positively charged ion (cation), they are simply a proton. In basic solutions, the carboxyl group is negatively charged and does not have a hydrogen (deprotonated) and in acidic solutions, the carboxyl group has a neutral charge and does have a hydrogen attached (protonated). For the amino group, protonation occurs in acidic solutions for a positive charge and deprotonation occurs in basic solutions for a neutral charge.
Two amino acid monomers come together through a reaction known as dehydration synthesis. In this reaction, a water molecule is removed and the monomers come together. The resulting bond between the two amino acids is called a peptide bond. When multiple (>2) amino acids come together and form bonds, the result is a polypeptide. Multiple polypeptides can then come together to interact in various ways and form a protein.
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There are twenty different amino acids. All twenty contain the same backbone, which contains the amino group, the carboxyl group, and the hydrogen atom connected to the middle carbon. The differing factor that makes each amino acid unique is the R side chain. This R group allows for different chemical properties amongst the amino acids. These chemical properties allow proteins to perform their functions. Here is a list of the twenty amino acids grouped based on their general chemical properties:
Due to the uniqueness of each of the twenty amino acids and with this uniqueness, different chemical properties, proteins fold into different shapes and forms. Amino acids form four different levels of protein structure: primary (1*), secondary (2*), tertiary (3*), and quaternary (4*).
The 1* structure of a protein is simply the sequence of amino acids that come together in a linear polypeptide chain:
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The 2* structure is a little bit more complex, it is the structures that result from hydrogen bonding interactions between the backbone of the amino acid. Hydrogen bonding is the interaction between hydrogen atoms and more electronegative atoms (see: article on the weak interaction between atoms) and when the backbones of amino acids participate in hydrogen bonding, the polypeptide forms two shapes: the alpha helix, which twists around like a corkscrew, and the beta pleated sheet, which is a relatively flat structure with steep bends occurring at regular intervals.
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The 3* structure is the interaction between the R-groups of the amino acids in the polypeptide that results in a folded polypeptide. There are many different molecular interactions that occur that allow for the 3* shape to form, but the main force is hydrophobic interactions. Hydrophobic (water fearing and nonpolar) molecules are non-fearing and do not like to be in contact with the water. As a result, the amino acids with hydrophobic R-groups will move away from the water, folding inward while the amino acids with hydrophilic (water loving, polar) R-groups move outward, toward the water. This causes the protein to fold up into different shapes depending on the amino acid sequence.
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The 4* structure is the interaction between two or more polypeptide chains. Some proteins only need one polypeptide chain to be functional and thus only have 3* structure. However, many proteins require more than one polypeptide subunit in order to be functional and thus undergo many molecular interactions in order to form a large complex protein structure.
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