Elements And Macromolecules In Organisms Pdf
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NCBI Bookshelf. Opportunities in Biology. All biological functions depend on events that occur at the molecular level.
Monomers and Polymers
NCBI Bookshelf. Opportunities in Biology. All biological functions depend on events that occur at the molecular level. These events are directed, modulated, or detected by complex biological machines, which are themselves large molecules or clusters of molecules.
Included are proteins, nucleic acids, carbohydrates, lipids, and complexes of them. Many areas of biological science focus on the signals detected by these machines or the output from these machines. The field of structural biology is concerned with the properties and behavior of the machines themselves.
The ultimate goals of this field are to be able to predict the structure, function, and behavior of the machines from their chemical formulas, through the use of basic principles of chemistry and physics and knowledge derived from studies of other machines. Although we are still a long way from these goals, enormous progress has been made during the past two decades.
Because of recent advances, primarily in recombinant DNA technology, computer science, and biological instrumentation, we should begin to realize the goals of structural biology during the next two decades.
Much of biological research still begins as descriptive science. A curious phenomenon in some living organism sparks our interest, perhaps because it is reminiscent of some previously known phenomenon, perhaps because it is inexplicable in any terms currently available to us. The richness and diversity of biological phenomena have led to the danger of a biology overwhelmed with descriptions of phenomena and devoid of any unifying principles.
Unlike the rest of biology, structural biology is in the unique position of having its unifying principles largely known. They derive from basic molecular physics and chemistry. Rigorous physical theory and powerful experimental techniques already provide a deep understanding of the properties of small molecules.
The same principles, largely intact, must suffice to explain and predict the properties of the larger molecules. For example, proteins are composed of linear chains of amino acids, only 20 different types of which regularly occur in proteins.
The properties of proteins must be determined by the amino acids they contain and the order in which they are linked. While these properties may become complex and far removed from any property inherent in single amino acids, the existence of a limited set of fundamental building blocks restricts the ultimate functional properties of proteins.
Nucleic acids are potentially simpler than proteins since they are composed of only four fundamental types of building blocks, called bases, linked to each other through a chain of sugars and phosphates.
The sequence of these bases in the DNA of an organism constitutes its genetic information. This sequence determines all of the proteins an organism can produce, all of the chemical reactions it can carry out, and, ultimately, all of the behavior the organism can reveal in response to its environment.
Carbohydrates and lipids are intermediate in complexity between nucleic acids and proteins. We currently know less about them, but this deficit is rapidly being eliminated. The central focus in structural biology at present is the three-dimensional arrangement of the atoms that constitute a large biological molecule. Two decades ago this information was available for only several proteins and one nucleic acid, and each three-dimensional structure determined was a landmark in biology.
Today such structures are determined routinely, and we have begun to see structures of not just individual large molecules, but whole arrays of such molecules.
The first three-dimensional structures were each consistent with our expectations based on fundamental physics and chemistry. Most of the structures determined subsequently, however, were completely unrelated, and a large body of descriptive structural data began to emerge as more and more structures were revealed by x-ray crystallography. From newer data, patterns of three-dimensional structures have begun to emerge; it is now clear that most if not all structures will eventually fit into rational categories.
Since biologists are ultimately interested in function, structural biology is often a means toward an end. The role played by structural biology differs somewhat depending on our prior knowledge of the function of particular molecules under investigation. Where considerable knowledge about function already exists, the determination of three-dimensional structure has almost inevitably led to major additional insights into function. For example, the three-dimensional structure of hemoglobin, the protein that carries oxygen in our blood stream, has helped us understand how we adapt to changes in altitude, how fish control their depth, and how a large number of human mutant hemoglobins relate to particular disease symptoms.
Often knowledge about structure can provide dramatic advances in our understanding about function even when prior knowledge is sketchy. For example, early biological experiments had shown that DNA contained genetic information, but these experiments offered no real clues to how a molecule could store information or how that information could be passed from cell to cell or from generation to generation. The structure of DNA, with bases paired between two different chains, led immediately to the correct conclusions about the mechanism of information storage and transfer.
The information resided in the sequence of the bases; the apparent redundancy of two strands with equivalent complementary information meant that each could serve to pass the information onto a daughter strand.
Furthermore, the redundancy offered a natural defense against loss of information. Even if one strand is damaged as by chemicals or radiation , in the vast majority of cases the information on the other strand can be used to recover the missing information. Indeed, cells have evolved truly elegant mechanisms to determine which strand contains the original undamaged information; such models could provide useful paradigms for the current human preoccupation with electronic information handling.
The ultimate challenge for structural biology occurs when we have a structure but no clues at all about its function. Because of dramatic advances in our ability to determine structures, this challenge is likely to occur with increasing frequency. There have been a few remarkable cases in which limited structural information, such as a knowledge of the sequence of amino acid residues in a protein, without any three-dimensional structural information, has led to significant insights into function.
In general, however, our current ability to predict function from structure in the absence of prior biological clues is limited, and one of our major needs is to improve our predictive abilities. The structures of large biological molecules such as proteins and nucleic acids are complex.
It is not practical or useful to describe these structures in words. In fact, highly specialized computer-driven graphics systems have been especially created to display molecular structures visually. An example of the output from one of these display systems is shown in Plates 1 and 2. Such devices are an invaluable aid to today's structural biologist, and future advances should make such devices cheaper, easier to use, and thus more readily available to all biologists.
This binding turns off expression of a bacteriophage gene. Anderson et al. Because of the complexity of biological structures, it is frequently convenient to deal only with certain aspects of these structures. It is common practice to describe structure at a series of hierarchical levels, called primary, secondary, tertiary, and quaternary structure. This hierarchy reflects some of the types of information provided by particular experimental techniques used to determine the structures of biological molecules.
The primary structure is the covalent chemical structure, that is, a specification of the identity of all the atoms and the bonds that connect them. The major molecules with which we work—proteins, nucleic acids, and carbohydrates— usually consist of linear arrays of units, each of which has a similar overall structure; they differ only in certain details.
The types of units are limited in numbers: 4 common ones in typical nucleic acids, roughly a dozen in typical carbohydrates, and 20 in proteins. Thus, the primary structure can be specified almost completely by naming the linear order, or sequence, of each type of unit of the chain.
The primary structure is given by the sequence plus a description of any additional covalent modifications or crosslinks. The sequence of proteins, nucleic acids, and carbohydrates is determined principally by chemical methods. This is understandable since it is, in fact, the chemical structure. These methods have advanced tremendously in the past decade, and the implications of these advances constitute the second section of this chapter.
The secondary structure refers to regular patterns of folding of adjacent residues. Most secondary structures are helices. Some of the most frequent and best-known helices are the alpha helices found in many proteins and double helices found in virtually all nucleic acids. Carbohydrates also form helices. Helices are convenient structural motifs: They are easy to recognize by inspection of a known three-dimensional structure, they are relatively easy to detect experimentally by physical techniques, and their appearance within many structures is relatively easy to predict just from a knowledge of the primary structure.
The tertiary structure is the complete three-dimensional structure of a single biological unit. Until recently the only available method for determining this structure was x-ray diffraction studies of a single crystal sample. Now electron and neutron diffraction have become available as tools for solid samples, and nuclear magnetic resonance spectroscopy has been developed to the point where it can be used to determine the tertiary structure of small proteins and nucleic acids in liquid solution, that is, close to the state in which they are usually found inside living cells.
The tertiary structure usually provides the starting point for studies that attempt to correlate structure and function. Quaternary structure describes the assembly of individual molecular units into more complex arrays. The simplest example of quaternary structure is a protein that consists of multiple subunits. The units may be identical or different. The arrangement of the subunits frequently has important functional implications. Some quaternary structures have been determined by experimental methods that reveal not only the arrangement of the subunits but also their individual tertiary structures.
However, Many quaternary structures are too complex to be addressed by existing techniques. Here a variety of methods ranging from electron microscopy to neutron scattering to chemical crosslinking can still provide information about the overall shape of the assembly and detailed arrangement of the components. In the sections that follow, we will first explore the levels of biological structures; our concerns will be improved methods for revealing these structures and the application of the resulting information to solving biological problems.
We will then consider the current and future prospects for predicting the higher order structure of biological macromolecules from more readily available information on lower order structure. Finally we will consider the power of our newfound abilities to alter macromolecular structure more or less at will. The amount of available information on the primary structure of biological polymers is increasing at an astounding rate. Two decades ago we knew the nucleotide sequence of only a single small nucleic acid, the yeast alanine transfer RNA.
We knew the amino acid sequence of fewer than different types of proteins. Today more than 18 million base pairs of DNA have been sequenced, and the data are accumulating at more than several million bases a year. The first completed sequences were research landmarks. Now sequences are appearing so rapidly that many research journals refuse to publish such information unless it has some particular novel or utilitarian aspects. Indeed, sequence data are currently accumulating faster than we can analyze them, and even faster than we can enter them into the data bases by existing methods.
The longest block of continuous DNA sequence known is the entire primary structure of Epstein-Barr virus. This ,base-pair genome is responsible for a number of human diseases including infectious mononucleosis, Burkitt's lymphoma, and nasopharyngeal carcinoma. Knowledge of the DNA sequence potentially unlocks for us all of the secrets of the virus.
The challenge now is to use this sequence information to learn how to prevent or control the diseases caused by the virus. Other landmarks of recent DNA sequencing include the complete DNA sequence of the maize corn chloroplast DNA about , base pairs and the complete sequence of the gene for human factor VIII, one of the proteins involved in blood clotting, which is defective in certain hemophilias.
We know the complete sequence of many other important proteins, RNAs, and viruses. Perhaps what is most important is that we have the technical ability to determine the sequence of virtually any piece of DNA, RNA, or protein.
Much valuable comparative sequence information awaits us as the data accumulate and as analytic methods become more reliable and informative. Already, one can do much using the data bases to help interpret any DNA sequence plucked more or less at random from a genome.
Monomers and Polymers
Students should be able to explain and apply core concepts of macromolecular structure and function, including the nature of biological macromolecules, their interaction with water, the relationship between structure and function, and frequently encountered mechanisms for regulating their function. The learning goals below are categorized as introductory A , intermediate B and upper C. Macromolecules are made up of basic molecular units. They include the proteins polymers of amino acids , nucleic acids polymers of nucleotides , carbohydrates polymers of sugars and lipids with a variety of modular constituents. These processes may involve multi-protein complexes e.
There are four classes of macromolecules (polysaccharides or carbohydrates, triglycerides or lipids, polypeptides or proteins, and nucleic acids such as DNA &.
Phytochemical Methods pp Cite as. The macromolecules of plants are distinguished from all other constituents by their high molecular weight. This may vary from 10, to over 1,,, whereas in other plant metabolites the molecular weight is rarely above 1, Chemical characterization in the first instance therefore depends on identifying these smaller units.
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Nucleotides polymerize to yield nucleic acids.
Food provides the body with the nutrients it needs to survive. Many of these critical nutrients are biological macromolecules, or large molecules, necessary for life. These macromolecules polymers are built from different combinations of smaller organic molecules monomers. What specific types of biological macromolecules do living things require? How are these molecules formed? What functions do they serve?
A macromolecule is a very large molecule , such as a protein. They are composed of thousands of covalently bonded atoms. Many macromolecules are the polymerization of smaller molecules called monomers. The most common macromolecules in biochemistry are biopolymers nucleic acids , proteins, and carbohydrates and large non-polymeric molecules such as lipids and macrocycles. A molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. In many cases, especially for synthetic polymers, a molecule can be regarded as having a high relative molecular mass if the addition or removal of one or a few of the units has a negligible effect on the molecular properties.