ORGANIC COMPOUNDS OF LIFE

      In this life, to be able to continue to live and thrive, organisms must be able to do everything that will be able to maintain their lives. Organisms in demand to be able to exchange matter and energy with the environment, transform matter and energy into a different form, responding to any changes in their environment, grow and reproduce. In this case there are organic compounds that play a major role in it. These compounds are called macromolecules.

     Macromolecules is a combination of many similar smaller molecules polymerized into a chain structure. In living organisms, there are three main types of macromolecules that controls all the activities and determine what an organism will do and be. Macromolecules that are proteins, carbohydrates, and lipids.

     In this article I specialize discussion on proteins. 

     Proteins are polymers of amino acids. With 20 different fundamental amino acids as building blocks, an extraordinarily large variety of proteins can be biosynthesized under the direction of the genetic code.

     Structure of Amino Acids
A. Fundamental Structure - An Amine and An Acid
As the term amino acid describes, each monomer has an amine group and a carboxylic acid group attached to a prochiral carbon. In addition side chains can also be present. These range from a simple
hydrogen to long carbon chains with functional groups.

B. Ionization of Amino Acids
The amine and carboxyl groups exhibit typical acid-base behavior which is pH-dependent. At low pH both groups are protonated: the amine group has a plus (+) charge and the carboxyl is neutral (0). As the pH rises the carboxyl loses its proton becoming negatively charged (-). At higher pH values the amine (+) deprotonates to produce a neutral amine (0). The result of this sequential deprotonation is a series of charged forms ranging from + to 0 to -. If the side chains are capable of acid-base reactions, the number of possible charged forms depends upon the number and types of amino acids present,
the pH, and the pKa of each ionizable group. This is true of proteins as well as amino acids. The pH at which the molecule has a net charge of zero, the zwitterion form, is called the pI or isoelectric
(isoelectronic) state. The pI can be calculated by taking the average of the two pKa values on either side of the zwitterion form. At a pH lower than the pI the molecule will be in a net + charged form while at a pH greater than the pI it will be in a net - charged form. Charged forms can be separated in an electric field, a process known as electrophoresis.
 
C. The Common Amino Acids
There are 20 common amino acids which can be grouped by the nature of the R side chain. Our groups are acidic, basic, alkyl, polar, aromatic, sulfur-containing, and cyclic.

      The Peptide Bond: Formation of Polypeptides and Proteins
Polypeptides and proteins are the products of amide, or peptide, bond formation between the amine group of one amino acid and the carboxyl of another.

      The Hierarchy of Protein Structure
A. Primary Protein Structure - The Sequence of Amino Acids
The sequence of amino acids in the polymer, from the free amino- or Nterminus to the free carboxyl- or C-terminus, is called the primary (10) structure of a protein. This sequence is dictated by the genetic code.
 
B. Secondary Protein Structure - Helices and Pleated Sheets
A peptide bond has partial double bond character that makes it planar; the geometry is usually trans. As the polypeptide chain grows, the peptide bond can participate in hydrogen bonding - amide hydrogen to carbonyl oxygen. Because of the geometry of the peptide bond, this hydrogen bonding goes on between amino acids which are distant from each other. Organized, folded secondary (20) structures are formed. The alpha helix and beta pleated sheet are the two most common secondary structures. In the alpha helix hydrogen bonding usually occurs between the peptide bonds of four amino acids distant from each other. Beta structure involves the polypeptide chain in its fully extended form coming back on itself to hydrogen bond side-to-side. The two polypeptide strands in beta structures may be parallel or antiparallel to each other.

Secondary structures are, in turn, organized into domains, or supersecondary structures. Collagen, which is the most abundant protein of the body, has unique primary and secondary structures. A high glycine and proline content leads to fairly rigid, kinked strands which can intertwine in a triple helical structure held together by hydrogen bonding between strands. The collagen helices aggregate to form skin, bone and connective tissue.

C. Protein Tertiary Structure
Side chains of the amino acids participate in tertiary (30) structure, that is, they stabilize the overall conformation of the protein molecule. The forces which hold tertiary structure together include covalent (disulfide bridges) and noncovalent (hydrogen bonding, salt bridge, hydrophobic) interactions. Shapes of tertiary structure subunits can be globular or fibrous.
 
D. Quaternary Protein Structure - Association of Subunits
Many proteins have more than one folded subunit, linked by the same types of noncovalent forces which hold 30 structure together. All of the subunits are needed for the protein to function properly. This is known as quaternary (40) structure.
 
E. Complex Proteins - Proteins Plus
All of the interactions mentioned above are integral parts of the simple structure of a protein. In addition proteins may have cofactors such as metal ions, carbohydrates or lipids, and/or organic molecules associated with them. This makes the proteins complex. Myoglobin and hemoglobin are examples of related complex proteins. Myoglobin has a single globular protein subunit complexed with an organic heterocyclic system known as heme. The heme in turn holds an iron (II) ion which
can bind molecular oxygen, O2. All of these components contribute to the function of myoglobin: the storage of oxygen in muscle tissue. Hemoglobin is related to myoglobin both structurally and functionally. It contains four myoglobin-type subunits each of which has an iron(II)- heme complex that can bind O2. However, the four subunits interact cooperatively in order to transport oxygen in the blood from the lungs to the cells.

F. Denaturation
The forces which hold a protein molecule together can be disrupted by changes in temperature and pH as well as by organic solvents and mechanical manipulation. This is known as denaturation.

     The protein itself has many functions in our bodies. Basically support the presence of protein each cell of the body, the immune process. Every adult should consume at least 1 gram of protein per kg of body weight. The need for protein increases in women who are pregnant and athletes.  
      Protein deficiency can be fatal. Hair loss (Hair consists of 97-100% of the protein-Keratin). The worst was called kwashiorkor, a protein deficiency disease. Usually in small children who are suffering, can be seen from the name of malnutrition, caused by the filtration of water in the blood vessels resulting in Odem. Other symptoms that can be recognized are: hipotonus, growth disorders, fatty liver. Ongoing shortage caused berkibat marasmus and death.  
      Protein obtained from our food. Protein in the digestive system will be broken down into peptide-peptide structurally simpler composed of amino acids. This is done with the help of enzymes. The human body requires a 9 amino acids. That is nine amino acids can not be synthesized by the body essential, while some amino acids can be synthesized alone or essential by the body. Total of 21 amino acids. After absorption in the intestine it will be given to the blood. Blood carries amino acids to every cell of the body. Code for essential amino acids can not be synthesized by the DNA. This is called DNAtranskripsi. Then, because the transcription process further ribosomes or endoplasmic reticulum, known as translation.  
      Advantage Protein is a source of energy, play a role in the formation and repair of cells and tissues, the synthesis of hormones, enzymes, and antibodies as well as regulating the levels of acid-base balance in the cell.