Proteins are the most diverse and complicated macromolecules in organisms. They have numerous functions such as enzymes, hormones, contractile elements (e.g. used in the contraction of muscle), antibodies in the immune system, molecular receptors, structural components such as hair and fingernails, transport functions, and many others. Despite the wide diversity of proteins, all proteins are composed of long chains of smaller "building block" molecules known as amino acids.
The figure above shows a "typical" amino acid. One end of the molecule contains and amino group (-NH2) and the other end contains a carboxylic acid group (-COOH) thus the name amino acid. These two chemical groups are attached to one another through bonds with the middle carbon atom labeled the alpha carbon by biochemists. Notice that there are two other chemical moieties attached to the alpha carbon, a hydrogen atom and an R-group. The R does not represent a specific atom but is instead a variable (like x in algebra) and represents one of twenty different chemical groups found in amino acids in cells. Since there are twenty different R-groups, there are twenty different amino acids. R-groups can be simple as in the amino acid glycine where the R-group is just a hydrogen atom or it can be a complex ring structure as is tryptophan. Despite the variety of different amino acids, they all can be classified into one of four categories based upon the properties of the R-groups. These four groups are: positively charged amino acids, negatively charged amino acids, polar (uncharged) amino acids, and nonpolar (uncharged) amino acids.
Since all amino acids have NH2 and COOH groups, you should not be surprised to learn that it is these areas of the molecules that form the bonds connecting one amino acid to another. The bond that forms between two adjacent amino acids is known as a peptide bond and this is shown below (the red bond is the peptide bond). The covalent bond is formed between the N atom of one amino acid and the C of the next. While you generally do not have to know structures of most molecules, you will be responsible for the structure of the "typical" amino acid and of the peptide bond. Notice that the R- groups do not have a role in the formation of the peptide bonds, thus any amino acid can bind to any other amino acids irrespective of the identity of the R-groups. Also, since each amino acid is capable of forming two peptide bonds, long chains of amino acids can be formed by linking many amino acids together. Chains of amino acids are known as peptide chains.
The difference between peptide chains and proteins (at least for this class) is based on function. If a peptide chain has a function (i.e. "does" something), it is a protein. For any protein, the ability of the molecule to perform its specific function is dependent upon its structure. Although the general structure for a protein is a peptide chain, the actual structure of the protein is not a linear chain of amino acids. Proteins fold into a specific three-dimensional conformation which is required for its specific function. If this three-dimensional folding is altered in any way, the activity of the protein can be lost and the protein will not work properly. Therefore, there is a intimate relationship between the structure and function of a protein. Do not forget this!!
Since you have just learned that the function of a protein depends on the three-dimensional structure of the protein, it would be nice to have some understanding of the factors that influence the structure of proteins. In this manner, you would then have an understanding of what cellular and environmental factors would affect protein structure and thus the function. Biochemists describe the structure of proteins on 4 levels known as the primary, secondary, tertiary, and quaternary structures of proteins.
The primary structure is the most fundamental. It is defined as the amino acid sequence of a protein. The following figure depicts the primary structure of the protein human growth hormone, using the three letter abbreviations for amino acids (see your text). It is a listing (in order) of the amino acids that make up this protein. If you were to go home tonight, take out your home chemistry set and put these amino acids in the order shown, you would have made growth hormone - identical to that made by your pituitary gland. You can assume, therefore, that if two peptide chains have the same amino acid sequence (i.e. primary structure), the two chains are the same protein. The amino acids in the chain are held together by the peptide bonds. Since peptide bonds are a type of covalent bonds, these linkages are very strong. It is very difficult to break peptide bonds (and thus disrupt the primary structure). Either specific proteolytic ["protein breaking"] enzymes or concentrated hot acid are generally needed to break the peptide bonds.
|N-terminal PHE PRO THR ILE PRO
LEU SER ARG LEU PHE GLN ASN ALA
MET LEU ARG ALA HIS ARG LEU HIS GLN LEU ALA PHE ASP
THR TYR GLU GLU PHE GLU GLU ALA TYR ILE PRO LYS GLU
GLN LYS TYR SER PHE LEU GLN ALA PRO GLN ALA SER LEU
CYS PHE SER GLU SER ILE PRO THR PRO SER ASN ARG GLU
GLN ALA GLN GLN LYS SER ASN LEU GLN LEU LEU ARG ILE
SER LEU LEU LEU ILE GLN SER TRP LEU GLU PRO VAL GLY
PHE LEU ARG SER VAL PHE ALA ASN SER LEU VAL TYR GLY
ALA SER ASP SER ASP VAL TYR ASP LEU LEU LYS ASP LEU
GLU GLU GLY ILE GLN THR LEU MET GLY ARG LEU GLU ASP
GLY SER PRO ARG THR GLY GLN ALA PHE LYS GLN THR TYR
ALA LYS PHE ASP ALA ASN SER HIS ASN ASP ASP ALA LEU
LEU LYS ASN TYR GLY LEU LEU TYR CYS PHE ARG LYS ASP
MET ASP LYS VAL GLU THR PHE LEU ARG ILE VAL GLN CYS
ARG SER VAL GLU GLY SER CYS GLY PHE C-terminal
Primary Structure for Human Growth Hormone
To Secondary Structure
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