Fundamentals of Bioorganic Chemistry (Study Guide) - G. O. Syrova - 2018

Topic

Structure and Biochemical Functions of Nucleosides, Nucleotides, and Nucleic Acids

Relevance of the topic. One of the most fascinating and fundamental problems related to Protein Synthesis is to determine what directs the Amino Acids that make up a protein to link together in a specific sequence, strictly defined for each type of protein. Closely related to this is the question of how the information regarding Amino Acid Sequence is replicated in every new generation of Cells. Today, it is known that certain substances are located in the Chromosomes of Cell nuclei, are responsible for the transmission of hereditary traits (Genetic information), and participate in the Regulation of Protein Biosynthesis. Because these substances were first isolated from the Cell Nucleus (from the Latin nucleus) and exhibit acidic properties, they are called NUCLEIC ACIDS.

Knowledge of the Structure and properties of these vital Biopolymers is essential for future physicians to understand normal physiological and pathological processes, the origins of various hereditary disorders, and promising approaches to regulating certain metabolic processes.

General objective: to study the structure and BIOLOGICAL Functions OF nucleic acids—the fundamental Structural components of The Cell—at the level of their Primary and secondary structure.

Specific objectives:

1. Analyze The Significance of mononucleotides in the Structure of Nucleic Acids and the action of nucleotide Coenzymes.

2. Interpret the mechanisms by which Vitamins are incorporated into coenzymes that catalyze biochemical transformations in the body.

Theoretical questions

1. Selection/9.html">NUCLEIC ACIDS AS biopolymers that store and transmit hereditary information and participate in METABOLISM/35.html">Protein Biosynthesis.

2. Composition and Structure of nucleic acid components: nitrogenous bases and Monosaccharides.

3. Nucleosides and NUCLEOTIDES as products of partial nucleic acid Hydrolysis. Structure of Nucleotides.

4. Structure and significance of 3', 5'-cAMP.

5. Structure and Biochemical functions of DNA.

6. Types of RNA, their structural Organization, and biological role. Differences in structure, localization, and functions of DNA and RNA.

7. Phosphorylated nucleotide derivatives. Significance of ADP and ATP.

8. Participation of nucleotides in the composition of coenzymes. MECHANISM OF ACTION of NAD⁺.

1. Nucleic acids (derived from nucleus) were first discovered in 1868 by the Swiss chemist Friedrich Miescher in cell nuclei. Later, similar substances were also found in the cell protoplasm.

Nucleic acids ensure the storage and transmission of hereditary traits and take direct part in the synthesis of cellular Proteins. They are constituents of Conjugated Proteins known as Nucleoproteins, which are found in all cells of humans, animals, plants, Bacteria, and Viruses. The nucleic acid content in nucleoproteins (excluding viruses) ranges from 40 to 65 %.

Nucleic acids are biopolymers whose monomers are mononucleotides, which undergo hydrolysis to yield a pyrimidine or purine base,

the monosaccharides ribose or deoxyribose, and phosphoric acid. Nucleic acids are essentially polynucleotides.

2. Nucleic acids containing deoxyribose are called Deoxyribonucleic Acids (DNA). Ribonucleic Acids (RNA) contain the monosaccharide ribose. Both monosaccharides are incorporated into nucleic acids in the β-furanose form:

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The nitrogenous bases that form nucleic acids are derivatives of pyrimidine or purine.

The principal nucleic acid bases include 3 pyrimidine bases (uracil, thymine, cytosine) and 2 purine bases (adenine, guanine):

Thymine is found exclusively in DNA, uracil exclusively in RNA, while the other bases occur in both DNA and RNA. Because purine and pyrimidine derivatives exhibit NH acidity, these compounds undergo lactim-lactam Tautomerism:

Of the two forms, the lactam (oxo) form is more thermodynamically stable; consequently, nitrogenous bases are incorporated into nucleic acids in the lactam form.

3. The hydrolysis of nucleic acids can be represented by the following scheme:

Accordingly, the pathway for assembling the Introduction/19.html">Primary Structure of a nucleic acid (polynucleotide) proceeds in the reverse direction.

The linkage between the monosaccharide and the base involves the glycosidic hydroxyl group of ribose or deoxyribose and either the first nitrogen atom of a pyrimidine base or the ninth nitrogen atom of a purine base:

This bond is designated as an N-glycosidic bond, and the resulting compounds are called N-Glycosides or nucleosides. Nucleoside names are derived from the trivial names of the bases using the suffixes -idine for pyrimidine nucleosides and -osine for purine nucleosides: uridine (U), thymidine (T), cytidine (C), deoxycytidine (dC), adenosine (A), deoxyadenosine (dA), guanosine (G), and deoxyguanosine (dG). Nucleosides are stable to hydrolysis in weakly alkaline media but undergo Cleavage in acidic media to yield their constituent components.

Nucleotides are 5'-phosphate esters of nucleosides linked via the monosaccharide residue. Depending on the pentose structure, they are classified into ribonucleotides (RNA monomers) and deoxyribonucleotides (DNA monomers).

Nucleotides can be viewed both as esters (phosphates) and as acids, owing to the presence of the phosphoric acid residue. Therefore, two nomenclature systems are used for nucleotides.

Major nucleotides found in nucleic acids

* - "monophosphate" is frequently replaced simply by "phosphate".

4. Certain nucleotides are known in which phosphoric acid forms an ester bond with two alcoholic hydroxyl groups of the monosaccharide—specifically at positions 3' and 5'. Virtually all cells contain two cyclic phosphates: cyclic 3',5'-adenylic (cAMP) and cyclic 3',5'-guanylic (cGMP) acids.

These nucleotides play a regulatory role in crucial intracellular processes. For instance, cAMP converts inactive proteins into Enzymes known as cAMP-dependent protein Kinases. These enzymes catalyze biochemical reactions that underlie Nerve Impulse Conduction and other physiological functions.

5. The formation of the primary structure of a nucleic acid (polynucleotide) occurs through the Esterification of the alcoholic hydroxyl group at C-3' of the monosaccharide unit in the preceding mononucleotide by the phosphoric acid residue at C-5' of the next mononucleotide. Ribonucleotides polymerize to form RNA, whereas deoxyribonucleotides form DNA.

For example, the primary structure of a DNA chain fragment dA-dC-dG-T can be represented as shown (see Fig. 7).

The structural principle of an RNA chain is identical, with two exceptions: the pentose residue in RNA is β-D-ribofuranose, and uracil replaces thymine in the set of heterocyclic bases.

The Nucleotide Composition of nucleic acids serves as a vital characteristic. Genetic information—that is, the instructions for synthesizing specific proteins—is encoded within The nucleotide sequence of DNA. A single amino acid is encoded by a triplet of nucleotides termed a codon.

Figure 7 - Primary structure of a DNA chain segment dA-dC-dG-T

The Secondary structure of DNA refers to the Spatial Organization of the polynucleotide chains within its molecule. The secondary structure of DNA is a right-handed double helix (J. Watson and F. Crick, 1953), maintained by Van der Waals forces acting along the helix and stabilized by Hydrogen Bonds between the complementary nitrogenous bases of the two strands. The diameter of the helix is 1.8–2.0 nm, and each turn of the helix contains 10 Base Pairs. The pitch of the helix is 3.4 nm, and the distance between adjacent base planes is 0.34 nm. The polynucleotide chains in the helix are antiparallel, meaning that in one strand the phosphodiester bonds are formed in the 3'→5' direction, while in the other they run 5'→3'.

Complementarity of strands in the DNA double helix

Consequently, the nucleotide composition of DNA from various sources obeys specific regularities known as Chargaff's rules:

1) The amount of purine bases equals the amount of pyrimidine bases: A + G = C + T;

2) the amount of adenine equals that of thymine (A = T), and the amount of guanine equals that of cytosine (G = C);

3) the number of bases containing an amino group at position 4 of the pyrimidine ring and position 6 of the purine ring equals the number of bases containing an oxo group at the same positions, i.e., A + C = G + T.

Chargaff's rules do not apply to RNA.

Chain complementarity serves as the chemical foundation for the most critical function of DNA—the storage and transmission of hereditary traits.

During Cell Division, The Double Helix unwinds and separates into two strands. Using each of these strands as a template, new DNA is biosynthesized according to THE PRINCIPLE OF complementarity. As a result, two identical new double-stranded DNA molecules are formed, one of which remains in the parent cell while the other passes into the daughter cell. This process is called Replication. Similarly, on the uncoiled DNA strand within The Nucleus, a messenger (mRNA) molecule is synthesized, which serves as a template for protein biosynthesis in the Cytoplasm. The synthesis of mRNA represents the Transcription of genetic information from DNA to mRNA.

DNA is located primarily in the cell nuclei, whereas RNA is predominantly found in Ribosomes and the cell protoplasm. The general role of RNA is its direct participation in protein biosynthesis.

6. Depending on their functions, three MAIN TYPES OF RNA are distinguished: Transfer RNA (tRNA), Messenger RNA (mRNA), and ribosomal RNA (rRNA). They differ in cellular localization, composition, size, and functions.

tRNA accounts for 10–20% of all cellular RNA. The primary role of tRNA is to transport amino acids to the site of protein synthesis, namely the ribosomes. The tRNA macromolecule is a single-stranded structure that folds in space to form a secondary structure known as the "cloverleaf." This structure is characterized by the presence of four base-paired stems and three unpaired loops.

1. The 5'-terminal region in virtually all RNAs terminates with a guanylic acid residue.

2. The dihydrouridine arm contains several dihydrouridylic acid residues.

3. The anticodon arm contains a triplet of bases called the anticodon, which corresponds to a specific amino acid.

4. The extra loop is located between the anticodon arm and the TΨC arm; this loop varies in length across different tRNAs.

5. The universal arm is identical in all tRNAs and contains the TΨC oligonucleotide sequence.

6. The 3'-terminal region ends with the CCA triplet, which serves as the attachment site for The amino acid.

The chemical essence of Amino Acid Transport by tRNA is that the amino acid acylates the 3'-OH group of the adenylic acid located at the 3'-end of the tRNA in the presence of ATP (acting as an activator). Subsequently, the tRNA transports the attached amino acid to the ribosome, where, through hydrogen bonding of complementary bases, it recognizes the codon in the mRNA corresponding to its own anticodon. mRNA serves as the template for protein synthesis. It consists of a single strand whose length is determined by the size of the protein molecule being synthesized. In the polynucleotide chain of mRNA, ribonucleotides form a sequence determined by complementary interactions with DNA nucleic bases, meaning that a DNA codon corresponds to an anticodon in the mRNA (often referred to simply as the codon). tRNAs carrying amino acids attach via their anticodon regions to the mRNA positioned on the ribosome. A peptide bond is then formed between adjacent amino acids. Ribosomal RNA (rRNA) directly participates in protein synthesis within ribosomes, accounting for up to 80% of total cellular RNA.

Ribosomes are complex structures composed of four rRNAs and several dozen proteins. They function as protein-producing "factories." The topic of protein biosynthesis will be explored in greater detail in the course of biological chemistry.

7. Certain mononucleotides are involved not only in The structure of nucleic acids but also serve as precursors for the Synthesis of Other vital biological substances in the Organism. For instance, the sequential phosphorylation of AMP yields ADP (adenosine-5'-diphosphate) and ATP (adenosine-5'-triphosphate), respectively.

These three nucleotides are capable of reversible interconversion. The formation of ADP and ATP is accompanied by the storage of energy within the P-O anhydride (high-energy) bonds. During the hydrolysis of ATP and ADP, this energy (32 kJ/mol) is released, which is why ATP acts as an energy "source" in biochemical transformations (coupled reactions). Furthermore, in many biochemical processes, ATP serves as an activator for Fatty acids, amino acids, Bile acids, and Other Compounds through the formation of Acyl phosphates.

Other triphosphates that perform similar functions are also known: CTP is required for Lipid Biosynthesis, and GTP for protein biosynthesis. AMP is additionally involved in the structure of certain nucleotide coenzymes. For instance, AMP is a structural component of coenzyme A (CoA-SH).

Coenzyme A activates carboxylic acids by converting them into reactive thiol esters:

8. Another important group of AMP-containing nucleotide coenzymes consists of nicotinamide adenine dinucleotide (NAD⁺) and nicotinamide adenine dinucleotide phosphate (NADP⁺). These substances function as coenzymes for oxidation-reduction enzymes known as dehydrogenases.

During biological dehydrogenation (one of the possible oxidation pathways), the substrate loses two hydrogen entities—a proton (H+) and a hydride ion (H^-). In the course of the reaction, the NAD⁺ coenzyme attaches the hydride ion to the C-4 position of the pyridine ring, as this carbon carries the highest positive charge. This results in the Formation of the reduced form of NAD⁺, designated as NADH. This process is marked by the loss of aromaticity in the pyridine ring and its conversion into a quinoid form, which is accompanied by an increase in the system's energy. Oxidation occurs in the reverse reaction, and The energy released in the process is utilized to drive biochemical pathways. For example, The oxidation of lactic acid proceeds with the participation of the enzyme Lactate dehydrogenase, which utilizes NAD+ as its coenzyme:

Complete the tasks and check your solutions against the answer keys

Task No. 1

1. Identify the structure of uracil:

2. Purine nitrogenous bases form an N-glycosidic bond with the monosaccharide via the nitrogen atom at position:

A. 3. B. 1. C. 7. D. 9.

3. NAD+ is a coenzyme for:

A. Decarboxylases. B. Dehydrogenases. C. Transferases. D. Catalases.

Answer keys: 1-A; 2-D; 3-B.

Task No. 2

1. Identify the formula of adenine:

2. A mononucleotide is the product of nucleoside phosphorylation at the -OH group of the monosaccharide at position:

A. 2'. B. 3'. C. 5'. D. 3' and 5'.

3. Coenzyme A is required in the body:

A. For the activation of carboxylic acid residues.

B. To participate in decarboxylation processes.

C. To participate in carboxylation processes.

D. To participate in protein synthesis.

Correct Answers: 1-B; 2-C; 3-A.

Task No. 3

1. What products are formed as a result of the complete hydrolysis of thymidylic acid?

A. Thymidine and phosphoric acid.

B. Thymine, ribose, and phosphoric acid.

C. Thymine, deoxyribose, and phosphoric acid.

D. Thymine and deoxyribose.

2. What is the relationship between the amounts of purine and pyrimidine bases in DNA?

A. They are equal.

B. The number of pyrimidine bases is greater than that of purine bases.

C. The number of pyrimidine bases is smaller than that of purine bases.

D. Their ratio does not matter.

3. Which of the following is a high-energy compound in the body?

А. НАД⁺. В. НАДФ+. С. Кофермент А. D. АТФ.

Correct answers: 1-C; 2-A; 3-D.