Cellular Nanomachines and the Building Blocks of Life

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Nanotechnology is of great importance to molecular biology and medicine because life processes are maintained by the action of a series of biological molecular nanomachines in the cell machinery. By evolutionary modification over trillions of generations, living organisms have perfected an armory of molecular machines, structures, and processes. The living cell, with its myriad of biological components, may be considered the ultimate "nano factory." Figure 1.1 shows a schematic diagram of a cell with its

Vesicle

Actin filament

Intermediate filament

Mitochondrion

Cell membrane

Rough endoplasmic reticulum

Ribosome

Centriole

Golgi

Golgi vesicle

Smooth endoplasmic reticulum

Nuclear membrane

Nucleus

Nuclear pore

Lysosome

Peroxisome

Cytosol

Actin filament

Golgi

Intermediate filament

Golgi vesicle

Mitochondrion

Smooth endoplasmic reticulum

Cell membrane

Rough endoplasmic reticulum

Nuclear membrane

Nucleus

Ribosome

Nuclear pore

Centriole

Lysosome

Microtubule

FIGURE 1.1 Schematic diagram of a cell and its components.

Peroxisome

TABLE 1.1 Typical Nanosizes of Cellular Species

Biological Species

Example

Typical Size

Typical Molecular Weight

Nucleic acids Small proteins Large proteins

Small assemblies Large assemblies

Ribosome

Viruses tRNA

Chymotrypsin

Aspartate transcarbamoylase

10 nm rod 4 nm sphere 7 nm sphere

20 nm sphere 100 nm sphere l05-l07

lO7-lOl2

l04-l05

l04-l05

l05-l07

various components. Some typical sizes of nucleic acids, proteins, and biological species are shown in Table 1.1. Nucleic acids and proteins are important cellular components that play a critical role in maintaining the operation of the cell. DNA is a polymeric chain made up of subunits called nucleotides. The polymer is referred to as a "polynucleotide." Each nucleotide is made up of a sugar, a phosphate, and a base. There are four different types of nucleotides found in DNA, differing only in the nitrogenous base: adenine (A), guanine (G), cytosine (C), and thymine (T). The basic structure of the DNA molecule is helical, with the bases being stacked on top of each other. DNA normally has a double-stranded conformation, with two polynucleotide chains held together by weak thermodynamic forces. Two DNA strands form a helical spiral, winding around a helical axis in a right-handed spiral. The two polynucleotide chains run in opposite directions. The sugar-phosphate backbones of the two DNA strands wind around the helical axis like the railing of a spiral staircase. The bases of the individual nucleotides are inside the helix, stacked on top of each other like the steps of a spiral staircase.

Genes and proteins are intimately connected. The genetic code encrypted in the DNA is decoded into a corresponding sequence of RNA, which is then read by the ribosome to construct a sequence of amino acids, which is the backbone of a specific protein. The amino-acid chain folds up into a three-dimensional shape and becomes a specific protein, which is designed to perform a particular function. Ribosomes are important molecular nanomachines that build proteins essential to the functioning of the cell. Although the size of a typical ribosome is only 8000 cubic nanometers (nm3), this nanomachine is capable of manufacturing almost any protein by stringing together amino acids in a precise linear sequence following instructions from a messenger RNA (mRNA) copied from the host DNA. To perform its molecular manufacturing task, the ribosome takes hold of a specific transfer RNA (tRNA), which in turn is chemically bonded by a specific enzyme to a specific amino acid. It has the means to grasp the growing polypeptide and to cause the specific amino acid to react with, and be added to, the end of the polypeptide. In other words, DNA can be considered to be the biological software of the cellular machinery, whereas ribosomes are large-scale molecular constructors, and enzymes are functional molecular-sized assemblers.

Proteins are nanoscale components that are essential in biology and medicine [1]. They consist of long chains of polymeric molecules assembled from a large number of amino acids like beads on a necklace. There are 20 basic amino acids. The sequence of the amino acids in the polymer backbone, determined by the genetic code, is the primary structure of any given protein. Typical polypeptide chains contain about 100-600 amino-acid molecules and have a molecular weight of about 15,000-70,000 Da. Because amino acids have hydrophilic, hydrophobic, and amphiphilic groups, they tend to fold to form a locally ordered, three-dimensional structure, called the secondary structure, in the aqueous environment of the cell; this secondary structure is characterized by a low-energy configuration with the hydrophilic groups outside and the hydrophobic groups inside. In general, simple proteins have a natural configuration referred to as the a-helix configuration. Another natural secondary configuration is a b-sheet. These two secondary configurations (a-helix and b-sheet) are the building blocks that assemble to form the final tertiary structure, which is held together by extensive secondary interactions such as van der Waals bonding. The tertiary structure is the complete three-dimensional structure of one indivisible protein unit, i.e., one single covalent species. Sometimes, several proteins are bound together to form supramolecular aggregates, which make up a quaternary structure. The quaternary structure, which is

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