Amino Acids- Proteins exist in diverse, complex structures that specify their particular function. Despite the variety of structures, however, all proteins comprise about 20 amino acids. Each amino acid is composed of an amino group and a carboxyl group as well as a carbon side chain, which specifies the characteristics of the particular amino acid. A primary protein is simply a long chain of amino acids linked together by a peptide bond between the amino group of one and the carboxyl group of another. In addition, the sequence of the amino acids in the chain varies with each type of protein. The amino acids constituting a protein are arranged in such a way as to give rise to periodic, secondary structures. The way in which a protein folds into its final conformation, or shape, is vital to its function.

Special Chemical Groups- Most proteins are polymers of amino acids, but some have other chemical groups attached to them. Lipoproteins contain lipid sub-units in addition to the amino acid, glycoproteins contain carbohydrate sub-units, phosphoproteins contain phosphoric acid, and nucleoproteins contain nucleic acids. Some proteins have important smaller molecules, known as prosthetic groups, attached to their surfaces; heme, a porphyrin ring containing an iron atom, is an example. It gives hemoglobin and myoglobin the ability to transport and store oxygen.

The information dictating the structures of the enormous variety of protein molecules found in living organisms is encoded in and translated by molecules known as nucleic acids. Just as proteins consist of long chains of amino acids, nucleic acids consist of long chains of nucleotides. A nucleotide, however is a more complex molecule than an amino acid. It consists of three sub-units: a phosphate group, a five-carbon sugar, and a nitrogenous base- a molecule that has the properties of a base and contains nitrogen. The sugar sub-unit of a nucleotide may be either ribose deoxyribose, which contains one less oxygen than ribose. Ribose is the sugar sub-unit in nucleotides that form deoxyribonucleic acid(DNA). Five different nitrogenous bases are found in the nucleotides that are the building blocks of nucleic acids. Two of these, adenine and guanine, have a two-ring structure and are known as purines. The other three, cytosine, thymine, and uracil, have a single-ring structure and are known as pyrimidines. Adenine, guanine, and cytosine are found in both DNA and RNA while thymine is found only in DNA and uracil only in RNA. Adenine and ribose sugar are also found in the nucleotides that are essential participants in the chemical reactions occurring within living systems. Although their chemical components are very similar, DNA and RNA play very different biological roles. DNA is the primary constituent of the chromosomes of the cell and is the carrier of the genetic message. The function of RNA is to transcribe the genetic message in DNA and translate it into proteins. The discovery of the structure and function of these molecules is undoubtedly the greatest triumph thus far of the molecular approach to the study of biology.

Lipids are found in all organisms as structural components of the CELL membrane. In most animals the major membrane lipids are lecithin, phosphatidyl ethanolamine (PE), and phosphatidyl serine (PS), and a sterol, CHOLESTEROL. Cell membranes of the central nervous system contain, in addition to the above, sphingomyelin, cerebrosides, and gangliosides. In higher plant membranes, lecithin and PE predominate, although phosphatidyl glycerol (PG) and phosphatidyl inositol (PI) are also present. Cholesterol is absent, but other sterols, known as phytosterols, are commonly present. Bacterial membranes are unique in that lecithin is rarely present and sterols are completely absent; PE and PG are usually the major lipids. Although triglycerides are not important membrane lipids, they are stored in most animals and plants as a metabolic energy reserve . In vertebrates, TG is located in adipose (FAT) tissue, which is widely distributed in the body. In insects, TG is concentrated in a specific fat body that functions both as a depot and as a center for triglyceride metabolism. In higher plants, TG is found in the seeds of most plants and is the source of most vegetable oils. In a few plants, such as the avocado, the palm, and the olive, the fruit also contains large amounts of triglycerides. Lipids have a number of specialized functions. In mammals living in cold climates, subcutaneous fat retards loss of body heat. Hydrocarbons and waxes on insect cuticle, as well as on plant leaves and fruit, aid in water retention. Certain cyclic FA, the prostaglandin’s, are involved in blood clotting and hormonal responses in mammals, and a variety of other FA derivatives serve as sex attractants and growth regulators in insects. sex hormones and the adrenal corticoids of higher animals are lipids derived from cholesterol. Essential dietary lipids include certain polyunsaturated fatty acids as well as the vitamins A, D, E, and K.

There are two common groups of proteins: fibrous and globular. In fibrous proteins, polypeptide chains are arranged into long strands or sheets. They play a major role in the defense and protective structures of many animals fur, quills, scales, nails, feathers, horns, antlers, hooves, and parts of the skin. The fibrous proteins collagen and elastin are essential to connective tissues, including tendons, cartilage, bone, and the deeper skin layers. Leather is almost pure collagen. Other fibrous proteins, such as tubulin, are the building blocks of microtubules, tiny hollow tubes inside cells. Microtubules play a role in cell movement, in material transport within nerve cells, and in the maintenance of cell shape. Fibrin, derived from fibrinogen, is a fibrous protein that binds platelets together to form blood clots. Actin and myosin are fibrous proteins that play a major part in skeletal muscle contraction. Globular proteins consist of amino acid chains that are tightly folded into a spherical or globular shape. Unlike most fibrous proteins, they have many electrically charged groups of atoms exposed to cytoplasm and bodily fluids. This feature makes many globular proteins highly soluble.

Immunoglobulins, or antibodies, make up perhaps the largest category of globular proteins. They help animals disarm potentially harmful foreign materials that enter their bodies. Most enzymes are globular proteins. They catalyze the hundreds of reactions that together constitute cellular metabolism. Through these enzymatic reactions, cells are able to generate, conserve, and transform chemical energy for other processes, such as nutrient metabolism and the production of large molecules from smaller ones. Some globular proteins are hormones, or chemical messengers made in endocrine glands. Hormones are circulated to target tissues, where they stimulate biochemical or physiological responses. The hormones insulin and glucagon, for example, maintain safe glucose levels in the blood.

DNA- DNA occurs as the genetic material in most viruses and in all cellular organisms. Some viruses, however, have no DNA; instead, their genetic material is in the form of RNA. Depending on the particular DNA-containing organism, most DNA is found either in a single chromosome, as in bacteria, blue-green algae, and DNA viruses, or in several chromosomes, as in all other living things. In addition to its presence in chromosomes, DNA is also found in many cell organelles such as plasmids in bacteria, chloroplasts in plants, and mitochondria in both plants and animals.

All DNA molecules consist of a linked series of units called nucleotides. Each DNA nucleotide is composed of three sub-units: a 5-carbon sugar called deoxyribose, a phosphate group that is joined to one end of the sugar molecule, and one of several different nitrogenous bases linked to the opposite end of the deoxyribose. The four nitrogenous bases that predominate in DNA are adenine and guanine, which are double-ringed purine compounds, and thymine and cytosine, which are single-ringed pyrimidine compounds. Four types of DNA nucleotides can be formed, depending on which nitrogenous base is involved.

The phosphate group of each nucleotide bonds to one of the carbon atoms of the adjacent nucleotide's deoxyribose sub-unit, forming a polynucleotide chain. In 1953, James D. Watson and Francis Crick hypothesized, and later confirmed, that the DNA of most organisms consists of two polynucleotide chains that are twisted into a coil, forming a double helix. The backbone or outside margin of each polynucleotide chain consists of a sugar-phosphate sequence, and the nitrogenous bases project inward. The nitrogenous bases of one chain are attracted to bases on the other chain by means of hydrogen bonds; this holds the double helix together. Exceptions to this type of structural organization of DNA are found in some viruses whose genetic material consists of a single DNA polynucleotide chain.

In a DNA double helix the pairing between bases of the two chains is highly specific. Adenine is always linked to thymine by two hydrogen bonds, and guanine to cytosine by three hydrogen bonds. This arrangement--a purine linked to a pyrimidine--results in a molecule of uniform diameter. The particular specificity of bases by which DNA nucleotides are paired indicates that the base sequence of the two strands is complementary. In other words, the base sequence of either strand may be converted to that of its partner by replacing adenine by thymine, and vice versa, and guanine by cytosine, and vice versa.

The genetic material of an organism, in this case DNA, has two specific functions: to provide for protein synthesis, and hence the growth and development of the organism; and to furnish all descendants with protein-synthesizing information by replicating itself and passing a copy to each offspring. The information, known as the GENETIC CODE, lies in the sequence of bases of DNA, which specifies the sequence of amino acids in a protein. DNA does not act directly in the process of protein synthesis but indirectly through the formation of a particular type of ribonucleic acid, messenger RNA (mRNA), during the process of transcription.

DNA replication depends on complementarily. During the process of replication, the two strands of the DNA double helix separate from one another. As separation occurs, each nitrogenous base on each strand attracts its complementary base-containing nucleotide, to which it becomes attached by hydrogen bonds. For instance, the base adenine attracts and bonds to thymine; guanine bonds to cytosine. As the complementary nucleotides are fitted into place, an enzyme called DNA polymerase binds the phosphate of one nucleotide to the deoxyribose of the adjacent nucleotide, forming a new polynucleotide chain. The new strand of DNA remains hydrogen-bonded to the old strand, and together they form a new DNA double helix molecule. This type of replication, in which each newly formed double-stranded DNA molecule consists of one previously existing and one recently produced strand, is called semiconservative replication. Single-stranded DNA viruses replicate by a slightly more complicated process. When it enters a cell, the virus makes a complementary copy of itself, to which it remains attached. In this condition, the virus is in its replicative form (RF) and temporarily becomes a double-stranded DNA virus. During replication, the two chains separate; however, only the recently formed strand attracts complementary nucleotides. These newly attracted nucleotides are joined together by the enzyme DNA polymerase, their base sequence being exactly the same as the original DNA virus. The newly formed polynucleotide chain is released from the RF of the original virus and functions independently.

Many environmental factors--some physical, others chemical--can alter the structure of a DNA molecule. A MUTATION occurs when such alterations lead to a permanent change in the base sequence of a DNA molecule. Mutations result in an inherited change in protein synthesis. A number of mechanisms can repair the damage done to DNA by environmental factors, reducing the occurrence of mutation, which generally tends to be deleterious. This self-repair process has been studied in the case of damage caused to DNA by exposure to ultraviolet (UV) light. The energy absorbed by DNA during UV exposure results in the formation of chemical bonds between adjacent bases of the same polynucleotide strand. This condition interferes with base pairing during replication and leads to the production of mutations.

RNA- RNA is the genetic material of some viruses (referred to as RNA viruses) and is necessary in all organisms for protein synthesis to occur. Like DNA, all RNA molecules have a similar chemical organization, consisting of nucleotides. Each RNA nucleotide is also composed of three sub-units: a 5-carbon sugar called ribose, a phosphate group that is attached to one end of the sugar molecule, and one of several different nitrogenous bases linked to the opposite end of the ribose. Four nitrogenous bases predominate in RNA: adenine and guanine, which are double-ringed purine compounds, and uracil and cytosine, which are single-ringed pyrimidine compounds.

RNA differs from DNA in two aspects of its chemical organization. First, the sugar in RNA is of the ribose type, indicating that the second carbon molecule in the ring has a hydroxyl (OH) group attached to it; in DNA the second carbon in the ring has only a hydrogen (H) atom, resulting in the prefix deoxy, which means lacking oxygen, in the term deoxyribose. Second, the nitrogenous base uracil is present only in RNA; thymine, the base comparable to uracil, is present only in DNA. Both uracil and thymine are single-ringed pyrimidines, and their nucleotides substitute for one another, depending on whether the polynucleotide strand is RNA or DNA.

The nucleotides of RNA are joined in a polynucleotide chain by means of bonding the phosphate of each nucleotide to a carbon atom of the adjacent nucleotide's ribose sub-unit. In RNA viruses the RNA is in the form of either a double or a single polynucleotide chain. In double-stranded RNA viruses, the geometric arrangement of the two polynucleotide chains is similar to that of double-stranded DNA and, as in DNA, the pairing between bases of the two RNA chains is highly specific. Adenine is always linked to uracil by two hydrogen bonds, and guanine to cytosine by three hydrogen bonds. Again as in DNA, the particular specificity of bases by which the RNA nucleotides are paired indicates that the base sequence of the two RNA strands is complementary--if the base sequence of one strand is known, then the base sequence of the other strand can be determined.

Replication of double-stranded RNA follows the pattern outlined for DNA. The RNA chains separate, and each base attracts an RNA nucleotide carrying the complementary base, to which it is attached by hydrogen bonds. As the complementary nucleotides are fitted into place, the enzyme RNA replicase binds the nucleotides together, forming a new polynucleotide chain. The new strand of RNA remains hydrogen-bonded to the old strand, another example of semiconservative replication. Single-stranded RNA viruses fall into two classes. The first group includes the polio virus that attacks the nerve cells of humans and other primates. When this type of virus enters a cell, the virus makes a complementary copy of itself, to which it remains attached. In this stage the virus is said to be in its replicative form (RF) and temporarily becomes a double-stranded RNA virus. During replication, although the two chains separate, only the recently formed strand attracts nucleotides with complementary bases. The newly attracted nucleotides are joined together by the enzyme RNA replicase and in their base sequence are exactly the same as the original RNA virus. The newly formed polynucleotide chain is released from the RF of the original virus and functions independently. The second group of single-stranded RNA viruses contains some that cause tumors in animals, such as mouse leukemia virus and mouse mammary tumor virus. Upon entering a cell, this type of virus makes a complementary strand of itself. This newly formed chain, however, is composed of DNA nucleotides. This single strand of DNA in turn makes a complementary DNA strand of itself, forming a DNA double helix. The newly formed DNA double helix becomes incorporated into one of the chromosomes of the host cell, where it is replicated along with the host DNA. While in the host cell, the RNA-derived viral DNA produces single-stranded RNA viruses that leave the host cell and enter other cells. The enzyme involved in making a DNA complement of RNA is called RNA-directed DNA polymerase, or reverse transcriptase, a name based on the virus's action of reversing the transcription process.

RNA that is involved in protein synthesis is single-stranded and belongs to one of three distinct types: ribosomal (rRNA), transfer (tRNA), and messenger (mRNA). A cell's ribosomal RNA is associated with protein, forming bodies called ribosome’s. Ribosome’s are the sites of protein synthesis. Ribosomal RNA varies in size and constitutes 85% to 90% of total cellular RNA. Transfer RNA, also called soluble RNA or adapter RNA, is a group of small molecules, each of which has a specific attraction for one of the amino acids. The function of each type of tRNA is to bring its specific amino acid to a ribosome for possible inclusion in the particular protein that is being synthesized. The tRNA molecules consist of about 80 nucleotides and are structured in a cloverleaf pattern. They constitute about 5% of the cell's total RNA. The third type of cellular RNA involved in protein synthesis is messenger RNA, which constitutes 5% to 10% of the cell's RNA and acts as an intermediary between the genes located in the chromosomes and the ribosome’s located in the cytoplasm. As its name implies, mRNA carries the genetic code contained in the sequence of bases in the cell's DNA. Since the DNA’s from various organisms differ only in the sequence of their bases, mRNA from different organisms must reflect this difference in base sequence. The synthesis of mRNA, called transcription, involves the formation of an RNA polynucleotide chain that is complementary to one of the two strands of a DNA double helix. In the transcription process, only nucleotides that contain ribose are used. In this process, uracil acts as the complement of adenine. The enzyme involved in transcription is known as RNA polymerase.