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Chemistry Review


Proteins

Proteins are the third major group of macromolecules that make up the bodies of organisms. Proteins play diverse roles in living things. Perhaps the most important proteins are enzymes, proteins capable of speeding up specific chemical reactions. Other short proteins called peptides are used as chemical messengers within your brain and throughout your body. Collagen, a structural protein, is an important part of bones, cartilage, and tendons. Despite their varied functions, all proteins have the same basic structure: a long chain of amino acids linked end to end.
     
Amino acids are small molecules containing an amino group (-NH2), a carboxyl group (-COOH), a hydrogen atom, a carbon atom, and a side chain that differs among amino acids. In a generalized formula for an

R
|
H2N--C--COOH
|
H

amino acid, the side chain is shown as R. The identity and unique chemical properties of each amino acid are determined by the nature of the R group.


     
Only 20 different amino acids make up the diverse array of proteins found in living things. Each protein differs according to the amount, type, and arrangement of amino acids that make up its structure. Notice that each has the same chemical backbone (shown by the box) as in the generalized formula. The R groups are outside these boxes. Those amino acids with R groups that form ring structures are termed aromatic compounds and those without ring structures are nonaromatic. (This term was coined as chemists discovered that many fragrant compounds had this distinctive ring structure.) Those amino acids that are ionizable have R groups that become charged when in solution.


Figure 15 How a polypeptide chain is formed and broken. (a) During dehydration synthesis, peptide bonds are formed between adjacent amino acids, forming a polypeptide. (b) During hydrolysis, a molecule of water is added to each peptide bond that links adjacent amino acids, breaking the bond between them. This separates the molecules into individual amino acids.


     
Those with special chemical (structural) properties play important roles in forming links between protein chains or forming kinks in their shapes.
      Each amino acid has a free amino group (-NH2) at one end and a free carboxyl group (-COOH) at the other end. During dehydration synthesis, each of these groups on separate amino acids loses a molecule of water between them, forming a covalent bond that links the two amino acids (Figure 15a). This bond is called a peptide bond. A long chain of amino acids linked by peptide bonds is a polypeptide. Proteins are long, complex polypeptides. The great variability possible in the sequence of amino acids in polypeptides is perhaps the most important property of proteins, permitting tremendous diversity in their structures and functions.
      The sequence of amino acids that makes up a particular polypeptide chain is termed the primary structure of a protein (Figure 16 ).
This sequence determines the further levels of structure of the protein molecule resulting from bonds that form between these groups. Having the proper sequence of amino acids, then, is crucial to the functioning of a protein. If the protein does not assume its correct shape, it will not work properly or at all. Because different amino acid functional groups have different chemical properties, the shape of a protein may be altered by a single amino acid change.


Figure 16 Primary structure determines a protein's shape due to bonding along the chain.


      The functional groups of the amino acids in a polypeptide chain interact with their neighbors, forming hydrogen bonds. In addition, portions of a protein chain with many nonpolar side chains tend to be shoved into the interior of the protein because of their hydrophobic properties. Because of these interactions, polypeptide chains tend to fold spontaneously into sheets or wrap into coils. This folded or coiled shape is called its secondary structure 2. Proteins made up largely of sheets often form fibers such as keratin fibers in hair, fibrin in blood clots, and silk in spiders' webs. Proteins that have regions forming coils frequently fold into globular shapes such as the globin subunits of hemoglobin in blood.
      Hydrogen bonding can also result in proteins with more complex shapes than the secondary structure. The next level of structure is called tertiary structure 3. For proteins that consist of subunits (separate polypeptide chains), the way these subunits are assembled into a whole is called the quaternary structure 4.