The synthesis of proteins is the result of the reading of the genetic code. When we say that one's genes, inherited from mother and father, determine our traits - everything from the shape of our facial features, to how efficiently our digestive system processes food - we mean that those genes code for the synthesis of proteins that construct our form (anatomy) and produce and regulate our functions (physiology).
When plant geneticists add a gene from a petunia to a soybean that makes the soybean resistant to herbicides (resulting in higher crop yeild), and when a gene from bacteria is added to a potato to make it resistant to a potato virus, what is happening is that the donor gene's product, a protein, confers the new "improved" properties on the recipient organism.
When geneticists working for branches of the armed forces create pathogens (disease-causing organisms) that are resistant to most antibiotics, and that possess greatly increased virulence (disease-causing power), they are unleashing genes whose protein products confer these traits to the bacteria (the bacteria now being considered weapons for warfare).
Proteins are clearly incredibly important macromolecules. Let's learn more about them.
A living cell is about 70% water (by weight) and about 15% protein (by weight). The remaining 15% of a cell's wet weight is divided among its carbohydrates, lipids, vitamins, minerals, and other organic molecules. So, after water, protein is the most abundant molecular type in cells. Another way to look at it is by harvesting and drying cells (to remove their water) and then analyzing their contents. Under such "dry weight" conditions about 1/3 of a cell's weight consists of the cellular machinery that produces protein. This is mostly the weight of the cellular organelles called ribosomes. Clearly, protein synthesis is the major activity of living cells and the proteins produced occupy a major position in the cell's day-to-day activities.
Proteins are long chains of smaller molecules called amino acids. Each amino acid is bonded to the next one in the chain by a covalent bond specifically called a peptide bond. Two amino acids linked together is referred to as a dipeptide. A three amino acid chain is called a tripeptide. In general, a long chain of amino acids is called a polypeptide. However, the word polypeptide has a more precise meaning: each gene is said to code for one polypeptide. Proteins are composed of one or more polypeptides. The majority of proteins are composed of just one polypeptide which may contain as few as the 51 amino acids making up the insulin molecule to as many as 1000 amino acids in proteins of silk. So in the majority of cases, a protein is a single polypepetide. However some proteins, like hemoglobin, are composed of several polypeptides that have bonded with each other. In such cases, the protein is composed of polypeptides coded for by more than one gene. In general, one gene codes for one polypeptide, and proteins can be made up of one or more polypeptides.
There are 20 different amino acids found commonly in proteins. These amino acids are coded for by the genetic code. Some proteins contain amino acids other than the common twenty; these are produced after a protein has already been synthesized by modification of a specific amino acid in the protein. Amino acids are grouped into 4 categories. Some readily interact with water; they are called hydrophilic. Some will not mix with water; these are called hydrophobic. Others are acidic, and the last category are basic amino acids. The sequence of specific amino acids in a protein is called the protein's primary structure.
With 20 different amino acids available for positioning in proteins, the diversity of proteins is incredible! A very short polypeptide just 5 amino acids long has 20 to the 5th power as the number of possible, different amino acid sequences in the polyepetide. That's 3,200,000 possible sequences. Another way to say this is that a 5-amino acid long polypeptide has 3,200,000 possible primary structures. For a polypetide with 500 amino acids (a typical number for amino acids in a protein), there are 20 to the 500 power possible amino acid sequences, or primary structures. This is a first look at the diversity of proteins and the corresponding diversity of organisms whose structure and function are based in great part on protein.
Proteins have four dimensional shapes. This means that each protein has a certain length, width and height, which constitute three dimensions, and the protein changes its shape in each second of time as it interacts with its substrates, with membranes, and with changing chemical (e.g., pH) the physical (e.g., temperature) conditions. In this discussion, we will address the first three dimensions of protein structure.
The exact and specific sequence of different amino acids that are occur sequentially in a protein (polypeptide) is called the protein's primary structure. One could envision a long, straight string as representing a long chain of amino acids. Based on the location of the specific types of amino acids (hydrophilic, hydrophobic, acidic, and basic) along the length of the protein, the string of amino acids spontaneously twists, pleats and folds into a unique three dimensional shape that is influenced by temperature and pH. This twisting, pleating and folding is caused by interactions (bonding) between the different amino acids along the chain.
When molecular biologists study protein shapes, they frequently observe regions of the polypeptide chain coiled into helices (singular is helix) referred to as an alpha helix. Another common arrangement of amino acids is into pleated sheets called beta sheets. The alpha helices look like cylinders in which amino acids are hydrogen bonded to each other as they snake their way up into the helical shape. The pleated sheets occur as the string of amino acids in the polypeptide chain fold back on themselves and form parallel, zig-zag patterns with hydrogen bonding between amino acids in the adjacent regions of the chain. Alpha helices and beta sheets are the most commonly recognized three diminsional shapes assumed by chains of amino acids in polypeptides. These two shapes are called secondary structural shapes in a protein. More frequently, they are just called the protein's secondary structure.
Besides forming cylinders of corkscrewing amino acids, and zing-zagging beta sheets, the polypeptide chain also folds into a unique shape called its conformation. This uniquely folded shape is called the protein's tertiary structure. This unique shape gives an enzyme its catalytic ability and its ability to recognize unique substrates. The protein's unique folded conformation allows it to fit precisely into a membrane of an organelle where it may seve both structural and functional roles.
Most proteins are complete with the formation of their final unique shape as they fold into their tertiary structure. However, some proteins are actually several polypeptides interacting to form a final structure called a quarternary structure. Hemoglobin is a very well known protein that has a quanternary structure. It consists of two alpha-globin chains interacting with two beta-globin chains. In addition, hemoglobin has additional non-protein groups attached to the protein chains. These are four iron-containing heme groups.
Frying an egg is a good example of protein denaturation. The clear, slimy egg protein, albumin, upon heating., is converted into an opaque, white, hard material that is still albumin, but now called denatured albumin.
What happens when the native albumin, fresh from theee egg, is heated is that the heat energy disrupts the bonding that exists naturally in the egg albumin at room or refrigerator temperatures. With the heat applied, the bonds bread and reform in new ways that give the protein a new physical identity that we consider more pleasing to eat than the slimy, native albumin.
There are other ways to denature proteins. If you squeeze a lemon into milk you will see the milk proteins denature. We commonly say they become coagulated or congealed. In essence they form lumps different in structure than what was present before the acid in the lemon juice brought about the denaturation. Strong base can also denature, as can high salt concentration.
Sometimes when the denaturing agent can be removed, the protein will reform its native shape. It essentially reverses its denaturation. When this happens, it is proof that a protein's primary structure is generally all that is required for the complex folding we call secondary, tertiary, and quarternary structures. Some forms of denaturation performed on some proteins is not reversible, such as heating albumin.