Introduction to Molecular Biology: From Cells to Atoms - Anthony Rees, Michael Sternberg 2002

Cells and Viruses
Scale of Objects in Molecular Biology

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Fig. 1.1.

According to one of the standard Structure/97.html">Definitions, molecular biology is the branch of science that investigates the functioning of living organisms through the prism of the Chemical Structure of their constituent molecules and atoms. The largest living Organism (such as a tree) reaches up to 30 m in its largest dimension, whereas the diameter of a carbon atom is approximately 0.3 nm (i.e., 0.3 ∙ 10~⁹ m). Thus, The ratio of the sizes of living organisms to those of atoms can be on the order of 10¹¹. To span this entire range, various Levels of Organization are required: the organism as a whole, Tissues, individual Cells, intracellular (subcellular) Organelles, macromolecules, small molecules, and, ultimately, their constituent atoms.

Based on the type of cells they comprise, living organisms can be divided into eukaryotes (ch. 3) and prokaryotes (ch. 2). In eukaryotes, the genomic DNA is surrounded by a nuclear envelope, meaning that Eukaryotic cells possess a nucleus, whereas prokaryotes lack a distinct, well-defined nucleus (derived from Greek, *eu* roughly corresponds to the preposition "with", *pro* to "before, in front of", and *karyon* means nucleus).

Multicellular Organisms represent an organized assembly of cells. The main groups of such organisms are plants, animals, Fungi, and certain colonial forms of Bacteria and blue-green Algae. In multicellular prokaryotic colonies, all cells are identical, whereas in eukaryotic organisms, cells vary in shape and function, i.e., they are differentiated. Although the size of the organism itself can range from 50 µm (a typical representative of the fungal kingdom) to 30 meters or more (a tall tree), the sizes of their constituent cells are strikingly similar, with their average diameter falling within the range of 10 to 50 µm. Rare exceptions to this rule are found in certain highly specialized cells: the giant squid axon (ch. 36) has a thickness of about 1 mm. Unicellular organisms can be either eukaryotes or prokaryotes. The unicellular amoeba, which belongs to eukaryotes (diameter 100 µm), is several times larger than most eukaryotic cells (10–15 µm) of multicellular plants and animals. Evidently, unicellular prokaryotes are generally smaller than eukaryotic cells, with the diameter of most being 1–5 µm. However, both exceptionally large and very small Prokaryotic Cells are known. [In unicellular giant algae, for example, Cell dimensions can reach up to 5 mm, while the bacterium *Pneumococcus* has a diameter of only about 100 nm (= 0.1 µm).]

A cell can be defined as the minimal unit of life capable of self-reproduction. All cells contain numerous smaller structural units called organelles, which perform specific Functions, such as generating energy or enabling cell motility. These organelles are surrounded on all sides by liquid Cytoplasm, and The Cell itself is delimited from the external environment by a lipid-protein envelope known as The cell membrane.

Organelles are substructures located within the cell that perform various specific functions. They serve to partition the cell into regions (or compartments) characterized by distinct conditions and containing different sets of biological molecules. The sizes of organelles vary from 20 nm to 10 µm. The largest organelles, such as nuclei, Mitochondria, and METABOLISM/14.html">Chloroplasts, have so far been found only in eukaryotic cells; their diameter is approximately the same as that of a typical Prokaryotic Cell (i.e., 1–10 µm). The diameter of smaller organelles, such as Ribosomes (which are found in both eukaryotic and prokaryotic cells), is approximately 20 nm.

Genes contain the information that uniquely determines the Structure and function of the cell. All genes are composed of DNA (deoxyribonucleic acid), and a single cell may contain many thousands of such genes. However, these genes do not exist there as separate DNA fragments, but are incorporated into larger structural units called Chromosomes. These chromosomes are copied (or replicated, as it is commonly called; ch. 20, 21) during Cell Division (ch. 29), and the new, daughter cells receive an exact copy of the parent Gene set. In this way, all CHARACTERISTICS OF THE cell are transmitted, or inherited, from generation to generation.

Viruses (ch. 4, 5) can be considered simply as a collection (ensemble) of macromolecules. The diameter of a viral particle ranges from 20 to 300 nm. Thus, viruses are significantly smaller than the smallest cells and are incapable of self-reproduction without the assistance of the host cell's synthetic machinery. Viruses can also be conditionally classified into one of two types based on whether their host cell is a prokaryote or a eukaryote. The sizes of the largest viruses infecting eukaryotes (such as the poxvirus) are of the same order of magnitude (300 nm in diameter) as the largest prokaryotic viruses (such as T4-type Bacteriophages). This is because not all large macromolecular assemblies are stable, which imposes restrictions on the maximum size of Viral Particles.

Macromolecules—Proteins (ch. 6–16), Nucleic Acids (ch. 17–19), and Polysaccharides (ch. 31)—are giant molecules whose sizes range from 3 to 300 nm. One of the largest macromolecules is the protein Collagen (ch. 11), a component of Connective Tissue: its length is about 300 nm¹, whereas the length of most macromolecules lies within the 4–20 nm range. However, macromolecular aggregates (such as the DNA-Protein Complexes that make up a mammalian chromosome; ch. 26) can form much larger structures, approaching the size of viral particles.

¹The length of DNA molecules in eukaryotic cells can reach several centimeters. — Ed. note.

Small molecules typically have a diameter of 0.5 to 1 nm. Three classes of small molecules play a particularly vital role in biology: Amino Acids (ch. 6), NUCLEOTIDES (ch. 17), and Monosaccharides (ch. 31). They serve as the "building blocks" from which polymeric biological macromolecules are constructed (proteins, nucleic acids, and polysaccharides, respectively). Since the diameter of a typical globular protein molecule consisting of 150 amino acids is only about 4 nm, it is evident that amino acid residues must be packed very compactly, meaning the polymer molecule must be folded. A similar, though less dense, packing is characteristic of DNA-protein complexes; conversely, in polysaccharides (ch. 31), the arrangement of monomers is such that they form much more extended structures.

Carbon, oxygen, nitrogen, and hydrogen atoms, which primarily comprise biological molecules, have diameters of less than 0.4 nm. Every atom contains a nucleus consisting of protons (the sole exception here being hydrogen) and neutrons; electrons Orbit The Nucleus at various distances from it, with the distance to the nucleus being uniquely determined by the electron's energy. The behavior of small molecules is governed by The properties of the atoms they are made of. Therefore, it is reasonable to assume that the behavior of large macromolecules can also be explained on The basis of atomic characteristics. And since organelles, whole cells, and Living organisms are essentially just collections of macromolecules, it is possible that someday in the distant future we will succeed in formulating an atomic theory of life.

Structural Methods applied in biological research include light Microscopy, Electron microscopy, and X-Ray Diffraction (on fibers and crystals). The Light Microscope makes it possible to resolve lines or objects separated by a distance of 0.3 µm or more (in other words, it has a resolving power of 0.3 µm); thus, it can be used to acquire information at a level ranging from large organelles down to cells. Electron microscopy employs electrons instead of light quanta, allowing objects or lines separated by a distance of 1 nm to be resolved; this method is used for a more detailed Study of Cells and cellular organelles. X-ray fiber diffraction makes it possible to identify periodic structural features within biological fibers, and is typically used to obtain information on the periodic architecture of fibers down to interatomic distances of 0.3 nm (an example being The structure of the DNA double helix; ch. 18). X-ray crystallography exploits The phenomenon of X-ray diffraction by regularly arranged atoms in a crystal, yielding an ordered diffraction pattern; it can be used to obtain information on the relative positions of atoms within a molecule with a resolution reaching 0.1 nm. Useful information regarding the shape and mass of macromolecules and organelles (such as ribosomes) can often be obtained using ultracentrifugation, the results of which are expressed in terms of the sedimentation coefficient (in Svedberg units, S). The latter is calculated According to the Procedure outlined in ch. 44. Thus, the methods available to the molecular biologist make it possible to acquire detailed structural information across the entire spectrum of biological objects, from cells down to atoms.