Biological compounds

Type of physical science: Chemistry

Field of study: Chemistry of molecules: types of molecules

The chemical compounds that are made up and used by living cells are known as biological compounds. Without these compounds, life would not be possible; their study enables biologists to understand life processes and to intervene when these processes become defective--that is, when disease occurs.

Overview

Chemical compounds are classified according to the presence or absence of the element carbon in their molecules. Carbon is an element best known as coal. Chemical compounds in which carbon is absent are called inorganic compounds, whereas those containing carbon are known as organic compounds. Organic compounds found in living cells are called biological compounds. Biochemistry is the field of science that studies biological compounds and their reactions that result in the phenomenon of life.

Living organisms are composed of a large variety of molecules, and it is difficult to single out one group of molecules as the most important one for life. By definition, however, life is possible only in the presence of proteins and nucleic acids. Nevertheless, other groups of organic molecules, such as carbohydrates and lipids, also play a very significant role in life processes.

More than 50 percent of the dry weight of cells is made up of proteins, which constitute the building material for the framework of tissues in living organisms. Besides this function, proteins produce enzymes. Because essentially all chemical processes in living systems are controlled by enzymes, proteins have a crucial role in all biochemical reactions. As genes act through the agency of enzymes, inherited traits are expressed primarily through proteins. A human organism contains tens of thousands of different proteins, each with a specific structure and function. Nevertheless, proteins are all composed of similar units known as amino acids.

Each amino acid contains the same backbone composed of an organic acid group (carboxyl) connected to an amino group by way of a single carbon atom COOH-C-NH₂ which carries a side chain that may be as simple as a hydrogen atom or as complex as a ring system. Therefore, amino acids differ only by their side chains. Although there are about eighty amino acids known in nature, only twenty of these are used by organisms to manufacture proteins. Thus, proteins are long strands of amino acids linked by peptide bonds, which are bonds that are formed between the amino group of one amino acid and the carboxyl group of the next.

Because proteins differ from one another by the number of amino acids, the kinds of amino acids, and the sequence of amino acids making up the chain, as well as the three-dimensional conformation of the chain, it is not surprising that an almost infinite number of proteins is created from only twenty amino acids.

The types of proteins existing in a cell or, for that matter, in an organism, are determined by heredity; that is, an offspring will inherit from its parents the proteins that its cells contain. This is achieved by the fact that the amino acid sequence in a protein is determined by a unit of inheritance known as a "gene," which is located in a chromosome of a cell. The genes contain the "blueprint" that determines the characteristic traits of an individual. A fertilized egg receives one set of chromosomes from the father and one from the mother. Thus, the new individual developing from the egg has an equal number of genes from each parent.

The presence of both deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) is an obligatory condition for a cell to be considered alive. DNA is the carrier of the genetic code--that is, the hereditary message. It is the building block of the genes located in the chromosomes. Each time a cell reproduces by dividing, its DNA is copied and passed along from one generation of cells to the next. The instructions that program all the cell's activities are written in the structure of DNA. RNA, on the other hand, serves to translate this blueprint into the particular proteins that will provide the necessary enzymes or structural components of the cells.

Nucleic acids are long-chain strands of molecules composed of units called nucleotides.

Each nucleotide in turn is made up of three parts: a five-carbon atom sugar, a phosphate group, and a nitrogen-containing base. The two nucleic acids--DNA and RNA--differ from each other by several characteristics. RNA has only one strand, while DNA is double-stranded. The sugar in the RNA nucleotides is ribose, whereas in DNA it is deoxyribose (one less oxygen atom). Three of the nitrogenous bases in the nucleotides of both nucleic acids are either adenine (A), guanine (G), or cytosine (C); the fourth base is thymine (T) in DNA, but uracil (U) in RNA. Whereas the sugar and phosphate molecules alternate to form the backbone of the strands, the nitrogenous bases stick out and may link to other nitrogenous bases:

In the case of DNA, two of these strands are twined together. This "double helix" of DNA consists of two complementary strands wound around each other like a twisted ladder. The nitrogenous bases from one strand face the bases from the other strand to which they are connected by hydrogen bonds.

In 1953, James D. Watson and Francis Crick elucidated the structure of DNA and were able to explain how nucleic acids function. They based their theory on "Chargaff's rule," which states that a particular base on one strand can bond only to a specific base on the other strand.

Thus, guanine bonds only to cytosine, whereas adenine pairs with thymine in DNA and with uracil in RNA. If one strand of DNA carries the sequence A, T, C, G, T, A, then the matching bases on the second strand will be T, A, G, C, A, T. This rule explains how DNA molecules replicate to allow cells to reproduce by cell division (mitosis), but it also explains how DNA can manufacture RNA.

When the cell prepares to divide, the hydrogen bonds between the two strands of DNA break and the strands separate and unwind to serve as templates for the synthesis of new DNA.

Each base on a strand will attract a free-floating nucleotide with the matching nitrogenous base.

The free-floating nucleotide will attach itself by a new hydrogen bond to the complementary nucleotide on the unwound strand. By linking together, the nucleotides form new complementary strands, each paired with one of the original ones, resulting in two new double helices. During cell division, each of the two new DNA double helices becomes part of one of the two daughter cells, which will contain exactly the same hereditary blueprint as the mother cell did.

How can only four nitrogenous bases make up the blueprint for the thousands of protein molecules used to build a whole individual? The answer was provided by Watson and Crick. They discovered that a sequence of three nitrogenous bases serves as a code for one amino acid. Thus, ATC codes for methionine, AGC for alanine, and so on. A sequential series of triplet "words" is a code for a whole protein molecule, which is composed of a long strand of amino acids.

There are at least three types of RNA: messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA). Each of these has a specific function in the expression of genetic information. As proteins can be manufactured only by ribosomes found in the cytoplasm outside the nucleus--whereas DNA is permanently located in the chromosomes, inside the nucleus--there must be an intermediary that takes the genetic message from the DNA to the ribosomes, allowing them to manufacture proteins. Messenger RNA acts as the intermediary.

The double strands of DNA uncoil, but this time the DNA nitrogenous bases attract RNA nucleotides. T attracts A, C attracts G, and A attracts U. After the mRNA strand is formed, it detaches itself from its DNA template and floats out into the cytoplasm. This process is called transcription, and the triplet nitrogenous bases on the mRNA strand are known as "codons." The mRNA molds itself on the ribosomes in the cytoplasm and becomes activated, serving as a template for the synthesis of a protein molecule.

Ribosomal RNA is also produced in the nucleus. It becomes part of the large macromolecular ribosomes that catalyze the formation of the individual peptide bonds of the growing protein chains.

Transfer RNA is unusual because, although single stranded, it is doubled back on itself, assuming a cloverleaf configuration by hydrogen bonding between the bases of its own strand. It functions in recognizing, capturing, and transferring specific amino acids to the ribosomes. Each of the twenty amino acids found in proteins has at least one tRNA that is specific for it. The tRNA attaches its specific amino acid to one end of its molecule and carries it to the ribosome, where it binds by a base triplet (anticodon)--located on another part of its molecule--to the complementary codon of the mRNA. When enough tRNAs are lined up, the amino acids that they carry will link to one another by peptide bonds and will detach themselves from the tRNA, becoming free protein molecules. This is the process by which the DNA hereditary blueprint is translated into the protein content of the cell.

Applications

The conquest of the gene is one of the great accomplishments of modern biology. The discovery of the structure and functions of nucleic acids gave rise to the discipline called molecular biology, which is the study of the process of heredity at the molecular rather than the organismal level. The central thesis of molecular biology--that the uniqueness of the individual is derived from the information (genetic blueprint) stored in the nucleic acids of the chromosomes--allowed scientists to understand the chemistry behind the laws of inheritance. It also led to the understanding of how growth and embryonic development is regulated. The main practical application of molecular biology has been the development of a branch of biology known as biotechnology, which uses genetic engineering to alter the characteristics of bacteria, plants, and animals, including humans.

Biotechnology revolutionizes many fields of human endeavor, such as medical diagnostics and therapy, agriculture, and ecology. In medicine, human gene therapy may become routine. Diagnostic DNA probes may be used to detect possible genetic defects in the developing embryo which, if found, may be corrected through genetic engineering. In agriculture, plants with advantageous traits may be produced, and farm animals may be made healthier and more productive. Environmental pollutants may be eliminated by using microorganisms to degrade them.

Many human birth defects can be attributed to a genetic error, that is, the faulty structure of a gene. Because of the knowledge of the composition and functions of DNA, as well as the location on chromosomes of different genes, it is possible to do genetic testing--that is, to find out before birth if a baby will show an inherited genetic disorder. Genetic testing leads to the possibility of the prevention and treatment of genetic diseases. A genetic disease caused by the lack of a particular gene in a developing human embryo may be corrected by inserting the missing gene into the fertilized egg; all the cells derived from that egg will contain the new gene.

This method can be used to treat inborn errors of metabolism. Thus, physicians may be able to prevent or treat genetic defects, such as thalassemia (an overproduction of the blood pigment hemoglobin), cystic fibrosis (a thickening of mucus in the lungs preventing normal breathing), Tay-Sachs disease (impaired physical and neurological development, including blindness), phenylketonuria (the absence of an enzyme resulting in the accumulation of an abnormal breakdown product, phenylalanine), achondroplasia (dwarfism), Huntington disease (a degeneration of the brain in middle age), muscular dystrophy, and many others.

Biotechnology can also be used for the production of DNA probes and monoclonal antibodies. By acting on DNA to separate the two strands of the double helix, one obtains single strands that will seek out and bind to any complementary strand present in the body. This type of DNA probe may be used in paternity suits to identify a child's father or in sexual assault cases to detect the attacker. Monoclonal antibodies are chemicals which are manufactured by white blood cells to fight foreign proteins entering the body. By fusing white blood cells to other, rapidly dividing cells in a test tube, the production of large amounts of specific antibodies can be achieved.

Recombinant (genetically engineered) DNA technology can produce safe vaccines. A vaccine was developed by genetic engineering against hepatitis B. Researchers are working to produce vaccines by the same method against AIDS (acquired immune deficiency syndrome) and malaria. Another application of genetic engineering is the manufacture of synthetic organic compounds. It was possible to isolate, alter, and insert into bacteria a gene coding for phenylalanine, which is used to manufacture aspartame, the synthetic sweetener known by the brand name Nutra-Sweet.

Plants lend themselves even more to genetic manipulation. Thus, it may be possible to engineer varieties that are resistant to diseases and pests, that possess the ability to fix nitrogen from the air, that can grow in soil with a high salt content, and that contain all the essential amino acids in the protein of their seeds. This process allows one to grow these plants without pesticides, with less fertilizer, and in arid regions where irrigation is a problem. Similarly, genetic engineering may be used in farm animals to produce varieties with advantageous traits.

Context

In the past, chemists and biologists alike thought that there was an unbridgeable chasm between organic (present in living organisms) and inorganic compounds and that, therefore, the chemistry of living things was different from that of inanimate ones. This belief was shaken in 1828 by the laboratory synthesis by Friedrich Wohler of a breakdown product of a protein metabolism, urea, from an inorganic compound. Following this discovery, which became the landmark in the demarcation of organic chemistry, scientists started to accept the idea that the properties of life could be explained in chemical terms. In the 1840's another step brought organic chemistry into even closer relationship with biology: the discovery by Matthias Jakob Schleiden and Theodor Ambrose Hubert Schwann that the cell is the basic structural unit of all living organisms. Although Johann Friedrich Miescher discovered nucleic acids in 1872, he did not realize their role or their importance.

Biochemistry lies in the border area between the biological and the physical sciences, between biology and chemistry. It became a separate science only around the beginning of the twentieth century, but since that time, it has advanced at a phenomenal rate. Modern biology and medicine are firmly rooted in biochemistry. Emil Fischer, considered the father of biochemistry, demonstrated the specificity of enzymes and discovered the amino acid structure of proteins. By the middle 1920's, it was recognized that DNA and RNA are present in all cells. Their role as carriers of genetic information, however, was not clear even in 1940, when George Beadle and Edward Lawrie Tatum published the one gene-one enzyme hypothesis, which stated that each enzyme is determined by one gene only. This statement represented the key issue that explained the function of the units of heredity in chemical terms; it created biochemical genetics. Molecular biology developed from biochemical genetics when scientists realized that the sequence of molecules making up the genes corresponded to the sequence of amino acids found in a protein.

The discoveries that led to this realization were the fact that genes were made up of DNA, the elucidation of the structure of DNA, and the fact that proteins differ from one another by the sequence of their constituting amino acids.

The discovery by Oswald Avery, Colin MacLeod, and Maclyn McCarty in 1944 that the genetic material was DNA prepared the ground for the breakthrough to molecular biology, which had its beginning in 1953 when Watson and Crick published their discovery of the structure and function of DNA. A consequence of molecular biology was the advent of recombinant DNA techniques in the 1970's which ushered in the era of biotechnology.

Principal terms

AMINO ACID: the organic subunit of a protein, composed of an organic acid (carboxyl) group and an amino (-NH2) group, that may bind to another amino acid by a peptide bond

BIOCHEMISTRY: the branch of chemistry that deals with chemical compounds found in living organisms and their reactions to these compounds

CHROMOSOMES: the stainable bodies in the cell nucleus that contain the genes

DEOXYRIBONUCLEIC ACID (DNA): the building blocks of genes, which are composed of a double helix of nucleotides

ENZYME: an organic catalyst which speeds up biochemical reactions

GENE: the unit of inheritance made up of DNA occupying a specific site on a chromosome that is passed on to the offspring by reproduction

NUCLEIC ACIDS: DNA and RNA (ribonucleic acid)

PROTEIN: the basic chemical matter that composes living cells; long chains of amino acids linked together by peptide bonds

RIBONUCLEIC ACID (RNA): composed of one strand of nucleotides; involved in protein synthesis

RIBOSOMES: cell organelles found in the cytoplasm, which is the site of protein synthesis

Bibliography

Armstrong, Frank B. BIOCHEMISTRY. 3d ed. New York: Oxford University Press, 1989. Covers the entire field of biochemistry. Chapters 5 and 6 discuss amino acids, chapters 7 and 8 discuss the structure and functions of proteins, and chapter 12 discusses nucleic acids. The text is complemented by numerous illustrations, diagrams, and tables, which make the material easily comprehensible.

Darnell, James. "RNA." SCIENTIFIC AMERICAN 253 (October, 1985): 68-78. Describes the similarities and differences between nucleic acids. Goes into detail about the three types of RNA and their functions. Covers protein synthesis and how genes determine amino acid sequences. Clear diagrams illustrate the text. Written in nontechnical language.

Drlica, Karl. UNDERSTANDING DNA AND GENE CLONING. New York: John Wiley & Sons, 1984. Written for the general reader, this book covers the known aspects of nucleic acid functions, including DNA replication and protein synthesis. Well illustrated and includes a helpful glossary.

Kleinsmith, Lewis, J., and Valerie M. Kish. PRINCIPLES OF CELL BIOLOGY. New York: Harper & Row, 1988. This text is written for college students, but it is not too technical for informed readers. Chapter 1 covers the molecular composition of cells, including proteins and nucleic acids. Chapter 2 deals with enzymes and catalysis, whereas chapters 10 and 11 discuss information flow in the cell from DNA to RNA to protein synthesis. Includes bibliographies after each chapter and contains a useful index. Prefixes, symbols, and abbreviations of technical terms are listed in the appendix. Well illustrated.

Mader, Sylvia S. BIOLOGY. 3d ed. Dubuque, Iowa: Wm. C. Brown, 1990. An excellent textbook geared for first-year college students. Chapter 3 covers compounds, molecules, and chemical bonds. Chapter 4 discusses proteins and nucleic acids. Chapters 13-18 cover chromosomes, genes, the regulation of gene activity, recombinant DNA, and biotechnology. The book is superbly illustrated, and includes a glossary and a well-organized index.

Merrell, David J. AN INTRODUCTION TO GENETICS. New York: W. W. Norton, 1975. A well-written account of the entire field of genetics. Part 1 covers classical genetics (Mendel's laws, the physical basis of heredity, gene interactions, and chromosomal variations); part 2 deals with the nature of the gene (structure, replication, function, recombination); part 3 treats the genetics of populations, and part 4 covers human genetics. Well illustrated. Includes a glossary, an index, and excellent references after each chapter.

Watson, James D. THE DOUBLE HELIX: A PERSONAL ACCOUNT OF THE DISCOVERY OF THE STRUCTURE OF DNA. Edited by Gunther S. Stent. New York: W. W. Norton, 1980. An interesting critical edition of Watson's book. Contains commentaries and reviews by well-known scientists, representing different views. Easy to understand and includes good illustrations and a handy index of names.

Nitrogenous bases in an RNA strand stick out

Carbon and Carbon Group Compounds