Genetics and Fundamentals of Selection - M.P. Myhun - 2008

CHAPTER II. Material Foundations and Molecular Mechanisms of Heredity

2.4. Nucleic Acids: Carriers and Guarantees of the Realization of Genetic Information

Genetic information concerning all properties and traits of an Organism—such as its Structure, physiological features, and developmental processes—is encoded in the molecules of genetic NUCLEIC ACIDS (gNAs).

The discrete unit of heredity—the Gene—is nothing other than a fragment of a gNA molecule.

Not all nucleic acids existing within a Cell are genetic. For instance, Messenger RNA (mRNA), Transfer RNA (tRNA), ribosomal RNA (rRNA), and even certain DNA molecules are not genetic because they do not form genes. However, they ensure the Selection/27.html">Realization of Genetic information within The Cell, namely the synthesis of Polypeptides encoded in the genes.

In nature, The Role of gNAs is performed by DNA in the majority of organism species, as well as by RNA (in Viruses).

In Eukaryotic Cells, genetic DNA is double-stranded and forms part of supramolecular complexes: Chromosomes, Mitochondria, and Plastids.

Molecules of genetic DNA and RNA can be linear or circular, single-stranded or double-stranded. Information from DNA is transcribed into various structurally diverse RNAs which, together with Ribosomes, ensure the synthesis of corresponding polypeptides.

Based on their structural Organization, nucleic acids are divided into several

levels.

Primary Structure. DNA and RNA are Biopolymers formed by repeating NUCLEOTIDES. Each nucleotide consists of three components:

1. A nitrogen-containing cyclic compound known as a nitrogenous base. There are 5 known nitrogenous bases: adenine (A), thymine (T), guanine (G), cytosine (C), and uracil (U). Uracil is found exclusively in RNA, whereas thymine is found in DNA. Bicyclic bases—adenine and guanine—belong to Purines, while monocyclic bases—cytosine, thymine, and uracil—belong to Pyrimidines.

2. A pentose sugar containing 5 carbon atoms. DNA contains deoxyribose, while RNA contains ribose.

3. Phosphoric acid.

One of the crucial characteristics of DNA is described by the rule of equivalence, The Essence of which is that the molar ratios of purines to pyrimidines in DNA and RNA molecules equal unity.

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These rules revealed a consistent correlation between the contents of A and T, and C and G. This regularity, discovered by E. Chargaff in 1950 (of Ukrainian descent, who worked in the USA), played a pivotal role in the creation of the double-stranded DNA model.

The carbohydrate component within the nucleotide is linked to the heterocyclic base via an N-glycosidic bond.

Nucleotide monomer residues in nucleic acids are interconnected by phosphodiester bonds formed between the 3'-carbon atom of one nucleotide residue and the 5'-carbon atom of another. Therefore, the bond between two adjacent nucleotides is referred to as a 3'-5' phosphodiester bond.

Polynucleotide chains of DNA and RNA are polar: one end always features a free or substituted 3'-OH group, while the opposite end features a 5'-OH group.

Thus, the Introduction/19.html">Primary structure of DNA and RNA encompasses The structure of their monomer residues, the Chemical Nature of the inter-nucleotide covalent bonds, and The sequence of monomer units within the polynucleotide chain.

The Spatial Organization of DNA and RNA is determined by their nucleotide sequences through two structural levels: secondary and tertiary.

Secondary structure—characterized by a specific degree of helicity—is established by the interaction of adjacent nucleotides within the polynucleotide chain, and in the case of double-stranded molecules, also by the interaction of opposing nucleotide residues within The Double Helix.

In 1953, J. Watson and F. Crick constructed the first model of the Molecular organization of DNA, according to which the molecule is a right-handed helix formed by two polynucleotide chains wound around each other and a common axis. The authors proved that this rule holds true if adenine (A) of one chain forms a hydrogen-bonded stabilized pair with thymine (T), and guanine (G) with cytosine (C). These interacting pairs were named complementary pairs.

Watson and Crick proposed their DNA model based on X-Ray Diffraction data obtained by M. Wilkins and R. Franklin, along with Chargaff's rules.

DNA is a double-stranded helical structure with paired nitrogenous bases (A - T) (G - C) on the inside and the nucleotide phosphate groups on the outside.

The helix is twisted in such a way that two grooves are formed on its surface: a major groove (about 2.20 nm wide) and a minor groove (1.2 nm wide). The polynucleotide chains in the DNA helix are antiparallel, meaning that at each end of a linear double-stranded DNA molecule, There is a 5'-end of one chain and a 3'-end of the other. The diameter of the helix is 1.8 nm, the turn length is approximately 3.4 nm, and one helical turn accommodates 10 nucleotide residues (Fig. 2.5).

Figure 2.5

Model of the double-stranded DNA helical molecule

Later it was discovered that the Watson and Crick model describes the STRUCTURE OF THE single most common double helix, which was named the B-form, or B-conformation. Other forms of DNA also exist and can reversibly transition into one another (A, C, Z).

Tertiary Structure of DNA. Linear and circular DNA molecules exist in nature. In eukaryotic nuclei, a linear molecule is packed into a compact structure and occupies only 1/5 of the cell's volume. The length of DNA in a human chromosome can reach 8 cm, yet it is compacted in such a way that it fits into a chromosome only 5 nm long. Consequently, the spiraled DNA molecule can undergo further compaction to form even denser structures, including circular configurations and supercoils.

DNA Supercoiling is characteristic of eukaryotic chromosomes, as well as those of viruses and Bacteria.

The DNA molecules of mitochondria, METABOLISM/14.html">Chloroplasts, bacterial chromosomes and Plasmids, as well as the DNA of many viruses, have a circular form that is nearly protein-free and supercoiled.

In Addition to double helices, single-stranded DNAs also occur, such as the DNA of phages phiX174, M13, and others.

Macromolecular structure of RNA. The vast majority of RNAs in Living organisms are single-stranded. However, in some viruses (such as reoviruses), double-stranded RNAs are found that act as carriers of genetic information. Furthermore, double-stranded RNAs are formed during the Replication of certain viruses whose genomic RNA is single-stranded. Genomic RNA is linear in almost all viruses (tobacco mosaic virus, poliovirus, Influenza virus).

Among non-genetic RNAs, Eukaryotic cells contain three MAIN TYPES OF single-stranded molecules:

- ribosomal RNA (rRNA),

- transfer RNA (tRNA),

- messenger or mRNA (mRNA).

Each of these types plays a specific role in the complex process of Protein Biosynthesis.

Ribosomal RNAs account for up to 90% of all cellular RNA and are quite stable. In prokaryotes, there are three distinct types of rRNA with sedimentation coefficients of 23S, 16S, and 5S; in eukaryotes, there are four: 28S, 18S, 5S, and 5.8S. The S (Svedberg unit) is a coefficient unit proportional to The rate of molecular sedimentation under a given centrifugal acceleration and, consequently, depends on the mass and shape of the molecule. All rRNAs, together with ribosomal Proteins, make up the structure of ribosomes. The primary structure of rRNA is characterized by the presence of modified bases. The secondary structure is represented by short double-helical regions formed by the pairing of folded single-stranded segments within the same molecule.

Transfer RNAs are single-stranded molecules consisting of 70–90 nucleotides, with a sedimentation coefficient of 4S. tRNAs account for 10-20% of the RNA in a cell. A tRNA molecule is capable of covalently binding its specific Amino Acid and attaching via a system of Hydrogen Bonds to one of the triplets (codons) of the mRNA molecule. Thus, tRNAs establish the code correspondence between mRNA codons and Amino Acids. Their tertiary structure is highly compact, giving the entire molecule the appearance of an L-shaped rod. Most eukaryotic cells contain about 60 tRNAs, meaning that there is more than one tRNA for each amino acid. Different tRNA molecules that accept the same amino acid are called isoacceptors.

Messenger RNA (mRNA) carries genetic information regarding the Amino Acid Sequence in polypeptides and serves as a template for their biosynthesis. The primary structure of mRNA contains codons corresponding to those of the DNA template upon which it is synthesized. mRNA mass in the cell accounts for no more than 5% of the total RNA. Individual mRNA molecules are heterogeneous; their sedimentation coefficient sizes range from a few Svedberg units to 20S or more, depending on the length of the polypeptide being encoded. mRNA is metabolically very active compared to Other types of RNA, representing a highly labile, short-lived form. In eukaryotes, mRNAs are more stable; their lifespan in the cell can range from tens of minutes, hours, or even days.