Nucleic acids terms Links

In today s discussion of the origin of life, the RNA World (Chapter 6) is seen as much more important, and is much better publicized, than the protein world . However, nucleic acids and proteins are of equal importance for the vital metabolic functions in today s life forms. Peptides and proteins are constructed from the same building blocks (monomers), the aminocarboxylic acids (generally known simply as amino acids). The way in which the monomers are linked, the peptide bond, is the same in peptides and proteins. While peptides consist of only a few amino acids (or to be more exact, amino acid residues), proteins can contain many hundreds. The term protein (after the Greek proteuein, to be the first) was coined by Berzelius in 1838. 

The bases are either monocyclic pyrimidines or bicyclic purines (see Section 14.1). Three pyrimidine bases are encountered in DNA and RNA, cytosine (C), thymine (T) and uracil (U). Cytosine is common to both DNA and RNA, but uracil is found only in RNA and thymine is found only in DNA. In the nucleic acid, the bases are linked through an A-glycoside bond to a sugar, either ribose or deoxyribose the combination base plus sugar is termed a nucleoside. The nitrogen bonded to the sugar is that shown. 

In this chapter, the term oligomeric compound refers to products prepared by repeatedly linking one or several types of monomer to a growing chain of monomers. Included are biopolymers, such as peptides or oligonucleotides, and non-natural products, such as peptide nucleic acids, peptoids, or other synthetic polyamides. 

Direct labeling of a biomolecule involves the introduction of a covalently linked fluorophore in the nucleic acid sequence or in the amino acid sequence of a protein or antibody. Fluorescein, rhodamine derivatives, the Alexa, and BODIPY dyes (Molecular Probes [92]) as well as the cyanine dyes (Amersham Biosciences [134]) are widely used labels. These probe families show different absorption and emission wavelengths and span the whole visible spectrum (e.g., Alexa Fluor dyes show UV excitation at 350 nm to far red excitation at 633 nm). Furthermore, for differential expression analysis, probe families with similar chemical structures but different spectroscopic properties are desirable, for example the cyanine dyes Cy3 and Cy5 (excitation at 548 and 646 nm, respectively). The design of fluorescent labels is still an active area of research, and various new dyes have been reported that differ in terms of decay times, wavelength, conjugatibility, and quantum yields before and after conjugation [135]. New ruthenium markers have been reported as well [136]. 

A large number of variants of gel electrophoresis are used in bioanalytical analysis to allow separation and characterization of biomolecules, in particular nucleic acids (DNA, RNA) and proteins. The term gel refers to the matrix used to separate biomolecules, and in most cases is a cross-linked polymer. 

The term "nucleoside refers to the A -glycosylpurines and jV-glycosylpyrimidines derived from nucleic acids. The common chemical feature of purine nucleosides is a -D-ribofuranosyl or a 2 -deoxy- 8-D-ribofuranosyl moiety linked to N9 of the purine base. Adenosine (1) and guanosine (2) are the most common purine nucleosides of RNA, whereas DNA contains 2 -de-oxyadenosine (3) and 2 -deoxyguanosine (4). 

The life of a cell depends on thousands of chemical interactions and reactions exquisitely coordinated with one another in time and space and under the influence of the cell s genetic instructions and its environment. How does a cell extract critical nutrients and information from its environment How does a cell convert the energy stored in nutrients into work (movement, synthesis of critical components) How does a cell transform nutrients into the fundamental structures required for its survival (cell wall, nucleus, nucleic acids, proteins, c3Aoskeleton) How does a cell link Itself to other cells to form a tissue How do cells communicate with one another so that the organism as a whole can function One of the goals of molecular cell biology Is to answer such questions about the structure and function of cells and organisms In terms of the properties of Individual molecules and Ions. 

Oligonucleotide analogues have commonly been considered as nucleic acids even in the absence of an acidic group, e.g., methyl phosphon-ates. In a formal sense, peptide nucleic acids are neither peptides nor composed of nucleic acids, nor should they be confused with peptide/protein oligonucleotide conjugates as described in the previous section. The PNA monomeric unit contains features of both amino acids and nucleosides. The four common base portions of nucleosides—adenyl, cytosyl, guanidyl, and thymidyl—are tethered to the PNA backbone, which carries the functionality of common amino acids. Amide bonds then consecutively link these monomer units. The term polyamide is more chemically appropriate thus an alternative name is polyamide nucleoside analogue, which is still abbreviated PNA. 

QM calculations (on nucieobase dimers) reveal the binding energy between two bases in the gas phase, i.e., in complete isolation. They thus describe the intrinsic interactions of the systems with no perturbation by external effects such as solvent. The intrinsic intermolecular stabilities are directly linked to moiecuiar structures and can be derived in any selected geometry. However, the gas phase interaction energies do not correspond to the stability of the interactions in nucleic acids, as measured by thermodynamics experiments. It is not possible to easily correlate the QM calculations with measured base pairing and stacking stabilities in nucleic acids. The apparent (measured) strength of the base-base interactions in nucleic acids in various experiments is determined by a complex interplay of many factors and the intrinsic base-base term is only one of them. Many researchers incorrectly believe that the experiments reflect the true stabilities of base-base interactions and vice versa. 

We propose that there was a template upon which the nucleic acid base pairs were preorganized prior to their incorporation into oligonucleotides to form proto-RNAs. These templates would have been heterocyclic molecules available in the prebiotic chemical inventory, produced by reactiorrs arrd starting materials similar to those that made the nucleic bases in the srrtall molecule world. We have used the term molecttlar midwife to describe arty such molecttle that facilitated the formation of proto-RNA, but was not covalently linked to the polymer (61). These midwife molecules wottld have aided in the birth of a proto-RNA, but wortld have no longer been necessary for RNA... 

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