Proteins, Nucleic Acids.

Proteins

Amino acids

Proteins are among the most abundant and versatile macromolecules. They have different functions as enzymes, hormones, storage, transport, structural proteins, membrane proteins, and antibodies. Eventhough their strurctural and functional diversity is overwhelming, their properties depend as much on their final shape as on their constituent parts.

Proteins are polymers of amino acids. All amino acids have the same fundamental structure.

1.- An amino group (-NH2).- It is a weak base

2.- A carboxyl group (-COOH).- It is a weak acid

3.- A hydrogen (-H)

4.- A functional group that varies from one amino acid to the next and is generally called and -R group.

The only difference between the 20 life relevant aminoacids is that of ther lateral groups (-R). In 8 of the molecules, -R is formed by short chains or rings of C, H. These amino acids are non polar thus, hydrophobic. 7 of the amino acids have –R formed by weak acids or weak bases. Depending on the solution’s pH, they can be possitively or negatively charged.

Proteins

Amino acids link to each other in a condensation reaction. The “head” of an amino acid bonds to the “tail” of another one by the elimination of a molecule of water. This bond is called peptide bond and the molecule that forms by the union of several amino acids is called a polypeptide. The sequence of aminoacids in a polypeptide gives the molecule its particular biological function, even the slightest variation in the sequence can result in an alterated or nule protein function.

Because there are about 20 different amino acids commonly found in proteins and each protein can contain anywhere from 200 to 300 individual amino acids, the diversity of possible amino acid sequences for any given polypeptide is extremely large. For example, 400 different dipeptides are possible and 8,000 tripeptides. For peptides of 300 amino acids, the possible number of sequences is so large that there are not enough atoms in the entire universe to build one example of each possible sequence!

The final properties of a protein depend largely on its three dimensional shape. Before a polypetide can function within a cell, therefore, it must twist and fold into a unique and special properties and functions as a protein emerge.

The final shape of a protein molecule is determined by three set of conditions.

1.-The sequence of amino acids in the polypeptide.

2.-The interaction between the amino acids in the polypeptide.

3.-The interactions of the amino acids with the surrounding water.

The sequence of amino acids from one end of the molecule to the other is called primary structure. Under orders from the genetic and synthetic apparatus of the cell, aminoacids are joined together in a precise and predetermined fashion. The primary structure is only the start.

In water a polypeptide twists and turns until it takes up the most stable configuration, a shape that requires the least energy to maintain and the most to disrupt. It is termed the secondary structure of the molecule. For example, amino acids close to each other interact and form hydrogen bonds. This forces the polypeptide to into and alpha helix or a beta sheet.

Next comes the interaction with water. Many parts of the molecule are either polar and hydrophillic or nonpolar and hydrophobic. As the folded and coiled polypeptide chain interacts with the surrounding water molecules, hydrophobic –R groups are forced , as much as possible, into the interior of the emerging structure, away from the surrounding water. Hydrophilic –R in the other hand, are stabilized by the interaction with water; thus, they are found close to the surface of the protein and in contact with water. The shape taken on by the macromolecule as a result of these forces is called a tertiary structure.

For many proteins, this is the highest level of structure they achieve. At the tertiary level, the protein suddenly takes on its major property and begins to function as a vital macromolecular component of the cell. But for some, there is one more step., the highest order os structure called the quaternary structure. At this level, the functioning protein unit is a complex built by the combination of more than one polypeptide chain and /or by the addition of other substances such as metallic ions, carbohydrates, lipids, nucleic acids, or other carbon based structures.

Hemoglobin, the oxygen-carrying protein found in red blood cells is an example of a protein showing the all four levels of structure. This macromolecule, consists of four polypeptide chains. Each chain has its own amino acid sequence (primary structure), and parts of chain twists into regions of alpha helix (secondary structure). All the chains fold into unique shapes in water (tertiary structure) and the come together in a fourfold complex with four additional iron-containing structures called heme groups (quaternary structure).

Function of Proteins

Protein functions are as varied as their structures. Almost every vital chemical reaction in every living cell is mediated by its own highly specialized protein known as enzyme. These enzymes are critically important in the reactions that break down food molecules, build new cellular structures, or repair existing components. Very few, if any, chemical reactions within a living organism can take place at any appreciable rate without these proteins.

The hard shell of a turtle, the skin of a new born baby, the claws of a lion and the feathers of a hummingbird all contain a type of protein known as keratin. This protein helps build and maintain physical structures, as does collagen, an essencial component of ligaments and tendons that connect bones and muscles.

Other proteins are involved in movement. Actin and myosin are fibrous contractile proteins found in muscle cells and involved in changing the shape of individual cells.

When attacked by invading organisms, our bodies respond by producing antibodies, a type of protein designed to recognize and neutralize and invader. Messenger molecules called hormones help regulate complex processes such as immune responses, growth and metabolism. Some hormones are steroids but other are proteins.

Within the human body, there is a probable minimum of 10,000 different proteins, each with its own unique structure shape and function. Information needed to construct each of these proteins, with all amino acids in the correct sequence, is stored in the genetic and hereditary material of cells: The nucleic acids.

Nucleic Acids

The information that orders the myriad of proteins that are found in the organisms is coded by two macromolecules known as nucleic acids and is translated by them. Nucleic acids are polymers formed by long chains of monomers called nucleotides. A nucleotide is a molecule formed by three subunits: A phosphate group, a five-carbon sugar and a nitrogenous base.

The sugar subunit can be either a ribose or a deoxyribose, the latter having one oxygen atom less than the ribose. Ribose is the sugar that is present in ribonucleic acid (RNA) whereas, deoxyribose is present in deoxyribonucleic acid (DNA). There are five nitrogenous bases which are the primary skeleton of the nucleic acids. Two of them adenine (A) and guanine (G) have a two ring structure and are known as purines . The other three, cytosine (C), thymidine (T) and uracil (U) have only one ring and are known as pyrimidines.

Both nucleic acids present A,C,G but RNA presents U instead of T which is present in DNA.

Most RNA molecules found in cells consist of a single polynucleotide chain, whereas DNA molecules are almost invariably double stranded, consisting of two polynucleotide chains twisted around one another in a double helix, which resembles a spiral stair case. DNA is usually synthesized only at one specific time in the cell cycle whereas RNA is more or less produced constantly throught the cell cycle.

The sugar-phosphate backbones of both DNA strands are on the outside of the molecule, forming the handrails of the staircase, the nitrogenous bases face inward, forming the stairs. Each step in the staircase is a pair of bases, one from each strand. These bases are paired together in specific combinations. Adenine is always paired with thymine and guanine is always paired with cytosine. Using the letter abreviation A=T, G=C. These are the base pairing rules. Thus if the sequence of bases is known for one DNA strand, it is possible to deduce the sequence of the partner strand, known as the complementary strand. For example, if one of the strands has the sequence

ATGTTCAAT

The sequence for the complementary strand is

TACAAGTTA

The two strands would go together like this

ATGTTCAAT

TACAAGTTA

DNA stores information for the sequence of amino acids in polypeptides and also acts as the hereditary substance, passing along this stored information from one generation to the next. Cells utilize RNA in several ways: As a messenger molecule carrying information away from DNA molecules, as structural molecules, or as transfer molecules in protein synthesis.

For a nice review on macromolecules click here.