Biological macromolecules nucleotides

Understand the application of FRET to the dynamic processes in living cells, the measurement of distances in biological macromolecules and the recognition of specific nucleotide sequences in DNA samples. 

The spontaneous self-assembly or template-directed assembly of component monomeric units into polymeric biological macromolecules. 2. The enzyme-catalyzed joining of monomeric units (such as amino acids, sugars, nucleotides) into covalently linked oligomeric or polymeric forms. 

Electrospray (ESI) is an atmospheric pressure ionization source in which the sample is ionized at an ambient pressure and then transferred into the MS. It was first developed by John Fenn in the late 1980s [1] and rapidly became one of the most widely used ionization techniques in mass spectrometry due to its high sensitivity and versatility. It is a soft ionization technique for analytes present in solution therefore, it can easily be coupled with separation methods such as LC and capillary electrophoresis (CE). The development of ESI has a wide field of applications, from small polar molecules to high molecular weight compounds such as protein and nucleotides. In 2002, the Nobel Prize was awarded to John Fenn following his studies on electrospray, for the development of soft desorption ionization methods for mass spectrometric analyses of biological macromolecules. ... 

If the terminal pyrophosphate is removed from a molecule of ATP, the remainder is AMP, adenosine monophosphate, one of the four building blocks of the important biological macromolecules, the nucleic acids. There are two types of nucleic acids (26) ribonucleic acid (RNA), and deoxyribonucleic acid (DNA). RNA is a polymer of four different nucleotides, one of which is AMP, the ribose phosphate of adenine. The other three nucleotides are also ribose phosphates of heterocyclic bases, guanine, cytosine, and uracil. The structure of the four bases is shown in Figure 6. 

Aptamers, as biosensors, find many applications. Possible aptamer ligands are proteins, other biological macromolecules, as well as the biological context in which these occur (i.e., viruses, bacteria, and eukaryotic cells). Aptamers can interact with small molecules such as metal ions and drugs, as well as primary and secondary metabolites (amino acids, nucleotides, sugars, peptides). 

As noted above, the nucleophilicity of water allows it to enter into reactions that cause the degradation of biological macromolecules, including DNA and proteins. Analogous problems are associated with the assembly of biopolymers. In water, the assembly of nucleosides from component sugars and nucleobases, the assembly of nucleotides from nucleosides and phosphate, and the assembly of oligonucleotides from nucleotides are all thermodynamically uphill in water. 

DNA is a polydeoxynucleotide and among the largest of the biological macromolecules some DNA molecules comprise more than 108 nucleotides. They contain adenine, thymine, guanine, and cytosine as the bases, and the genetic information is encoded within the nucleotide sequence, which is precisely defined over the entire length of the molecule. One of the simplest methods for determining the nucleotide sequence of DNA makes use of an enzyme, DNA polymerase, which catalyzes the synthesis of DNA. The properties of this enzyme are discussed in Chap. 16. 

The Protein Data Bank (PDB http //www.pdb.org) is the worldwide repository of three-dimensional structural data of biological macromolecules, such as proteins and nucleic acids (Berman et al. 2003). The Protein Data Bank uses several text file-based formats for data deposition, processing, and archiving. The oldest of these is the Protein Data Bank format (Bernstein 1977), which is used both for deposition and for retrieval of results. It is a plain-text format whose main part, a so-called primary structure section, contains the atomic coordinates within the sequence of residues (e.g., nucleotides or amino acids) in each chain of the macromolecule. Embedded in these records are chain identifiers and sequence numbers that allow other records to reference parts of the sequence. Apart from structural data, the PDB format also allows for storing of various metadata such as bibliographic data, experimental conditions, additional stereochemistry information, and so on. However, the amount of metadata types available is rather limited owing to the age of the PDB format and to its relatively strict syntax rules. 

X-ray crystallographers have now determined the structures of approximately one hundred biological macromolecules — proteins, nucleic acids, and viruses — to atomic resolution. These investigations have demonstrated that, unlike synthetic polymers, the biological molecules have specific three-dimensional conformations. Indeed, all information required to specify the structure of a protein is contained in the sequence of amino acids, and therefore the structure is also implicit in the sequence of nucleotides in the DNA or RNA genome. Analysis of the structures has provided explanations of their biological functions, and has revealed that there are recurrent architectural themes in their de-sign (J, 2). 

There was a time when proteins were considered the only biological macromolecules capable of catalysis. The discovery of the catalytic activity of RNA has thus had a profound impact on the way biochemists think. A few enzymes with RNA components had been discovered, such as telomerase (Chapter 10) and RNase P, an enzyme that cleaves extra nucleotides off the 5 ends of tRNA precursors. It was later shown that the RNA portion of RNase P has the catalytic activity. The field of catalytic RNA (ribozymes) was launched in earnest by the discovery of RNA that catalyzes its own selfsplicing. It is easy to see a connection between this process and the splicing... 

Biological macromolecules present special problems for substructure searching. In many cases the feature of interest is the one-dimensional sequence of amino-acid or nucleotide residues, and a number of databases of such sequences are now available for searching. Searching of the three-dimensional structure of such macromolecules is also of interest. ... 

Biological Macromolecules Sugars and Polysaccharides Amino Acids and Proteins Nucleotides and Nucleic Acids... 

This chapter is organized around the four major classes of biological macromolecules. Recognize what most macromolecules have in common They are assembled from simple monomer units. Proteins are assembled from amino acids, carbohydrates are assembled from monosaccharides, and nucleic acids are assembled from nucleotides. Lipid is a catchall classification that includes fats, oils, phospholipids, waxes, steroids, and some other molecules. Organize your study into these four categories. 

The unique properties of oligonucleotides create crosslinking options that are far different from any other biological molecule. Nucleic acids are the only major class of macromolecule that can be specifically duplicated in vitro by enzymatic means. The addition of modified nucleoside triphosphates to an existing DNA strand by the action of polymerases or transferases allows addition of spacer arms or detection components at random or discrete sites along the chain. Alternatively, chemical methods that modify nucleotides at selected functional groups can be used to produce spacer arm derivatives or activated intermediates for subsequent coupling to other molecules. 

The binding of small molecules to larger ones is basic to most biological phenomena. Substrates bind to enzymes and hormones bind to receptors. Metal ions bind to ATP, to other small molecules, and to metalloproteins. Hydrogen ions bind to amino acids, peptides, nucleotides, and most macromolecules. In this section we will consider ways of describing mathematically the equilibria involved. 

Structural elucidation of natural macromolecules is an important step in understanding the relationships between the chemical properties of a biomolecule and its biological function. The techniques used in organic structure determination (NMR, IR, UV, and MS) are quite useful when applied to biomolecules, but the unique nature of natural molecules also requires the application of specialized chemical techniques. Proteins, polysaccharides, and nucleic acids are polymeric materials, each composed of hundreds or sometimes thousands of monomeric units (amino acids, monosaccharides, and nucleotides, respectively). But there is only a limited number of these types of units from which the biomolecules are synthesized. For example, only 20 different amino acids are found in proteins but these different amino acids may appear several times in the same protein molecule. Therefore, the structure of... 

Proteins are the most abundant of cellular components. They include enzymes, antibodies, hormones, transport molecules, and even components for the cytoskeleton of the cell itself. Proteins are also informational macromolecules, the ultimate heirs of the genetic information encoded in the sequence of nucleotide bases within the chromosomes. Structurally and functionally, they are the most diverse and dynamic of molecules and play key roles in nearly every biological process. Proteins are complex macromolecules with exquisite specificity each is a specialized player in the orchestrated activity of the cell. Together they tear down... 

Sequence analysis is a core area of bioinformatics research. There are four basic levels of biological structure (Table 1), termed primary, secondary, tertiary, and quaternary structure. Primary structure refers to the representation of a linear, hetero-polymeric macromolecule as a string of monomeric units. For example, the primary structure of DNA is represented as a string of nucleotides (G, C, A, T). Secondary structure refers to the local three-dimensional shape in subsections of macromolecules. For example, the alpha- and beta-sheets in protein structures are examples of secondary structure. Tertiary structure refers to the overall three-dimensional shape of a macromolecule, as in the crystal structure of an entire protein. Finally, quaternary structure represents macromolecule interactions, such as the way different peptide chains dimerize into a single functional protein. 

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