3. Нуклеинови киселини.pdf

# Nucleotides and polynucleotide chains Nucleotides are the fundamental building blocks of nucleic acids, forming chains through specific linkages [1](#page=1). ### 1.1 Nucleotides: the monomers of nucleic acids Nucleotides are organic compounds with low molecular mass, serving as the monomers for nucleic acids. Each nucleotide is composed of three smaller molecular components [1](#page=1): * A monosaccharide, specifically a pentose sugar [1](#page=1). * A nitrogenous base [1](#page=1). * Phosphoric acid [1](#page=1). #### 1.1.1 Pentoses in nucleotides The pentose sugar present in nucleotides can be either ribose or deoxyribose. This difference in the pentose sugar leads to two types of nucleotides [1](#page=1): * **Ribonucleotides:** Contain ribose [1](#page=1). * **Deoxyribonucleotides:** Contain deoxyribose [1](#page=1). #### 1.1.2 Nitrogenous bases Nitrogenous bases are ring structures containing both carbon and nitrogen atoms. They are categorized into two main groups based on their structure [2](#page=2): * **Purines (large bases):** Possess a double-ring structure. The purine bases are adenine (A) and guanine (G) [2](#page=2). * **Pyrimidines (small bases):** Possess a single-ring structure. The pyrimidine bases are thymine (T), uracil (U), and cytosine (C) [2](#page=2). In a single polynucleotide chain, four specific bases are utilized: adenine, guanine, cytosine, and either thymine or uracil. These nitrogenous bases are responsible for the individual identity of each nucleotide. Consequently, any nucleic acid chain incorporates four distinct monomers [2](#page=2). > **Tip:** Remember that the presence of uracil (U) indicates a ribonucleotide chain (RNA), while thymine (T) indicates a deoxyribonucleotide chain (DNA) [2](#page=2) [3](#page=3). #### 1.1.3 The rule of complementarity Nitrogenous bases can form hydrogen bonds with each other in a highly specific manner. This specific pairing is known as the **rule of complementarity** [2](#page=2): * Adenine (A) always pairs with thymine (T) via two hydrogen bonds, or with uracil (U) in RNA, also via two hydrogen bonds [2](#page=2). * Guanine (G) always pairs with cytosine (C) via three hydrogen bonds [2](#page=2). > **Example:** In a DNA molecule, if one strand has the sequence ATGC, the complementary strand would have the sequence TACG, with A pairing with T and G pairing with C through hydrogen bonds [2](#page=2). This specific base pairing mechanism is crucial for the accurate replication of genetic information stored within nucleic acid molecules [2](#page=2). ### 1.2 Polynucleotide chains Nucleotides can link together covalently through **phosphodiester bonds** to form long chains called polynucleotide chains. These bonds form between the pentose sugar of one nucleotide and the phosphate group of another nucleotide [3](#page=3). #### 1.2.1 The sugar-phosphate backbone The fundamental structure of a polynucleotide chain, or its "skeleton," is composed of alternating monosaccharide residues (pentoses) and phosphate groups. This repeating unit is termed the **sugar-phosphate backbone**. The numerous phosphate groups present in the chain contribute to the acidic nature of nucleic acids. The nitrogenous bases protrude from the pentose sugars along this backbone [3](#page=3). A single polynucleotide chain contains only one type of pentose sugar: either ribose or deoxyribose [3](#page=3). * If ribose is present, the nitrogenous bases are adenine (A), guanine (G), cytosine (C), and uracil (U), forming a **ribonucleotide chain** [3](#page=3). * If deoxyribose is present, the nitrogenous bases are adenine (A), guanine (G), cytosine (C), and thymine (T), forming a **deoxyribonucleotide chain** [3](#page=3). #### 1.2.2 Directionality of the polynucleotide chain Each end of a polynucleotide chain is distinct: * One end possesses a free phosphate group (designated as the **phosphate end** or **5' end**) [3](#page=3). * The other end has a pentose sugar with a free hydroxyl (-OH) group (designated as the **hydroxyl end** or **3' end**) [3](#page=3). The addition of new nucleotides to the growing chain always occurs in the direction from the phosphate end to the hydroxyl end (5' to 3') [3](#page=3). #### 1.2.3 Structural levels of polynucleotide chains The sequence of nitrogenous bases along a polynucleotide chain defines its **primary structure**. The complementary pairing of bases, either within the same chain or with another strand, determines the **secondary structure**. Some ribonucleotide chains can further fold and twist in three-dimensional space to form a **tertiary structure** [3](#page=3). > **Tip:** The concept of primary structure being the sequence of bases is fundamental to understanding how genetic information is encoded [3](#page=3). The arrangement of the four types of nucleotides in varying sequences and quantities results in an immense diversity of polynucleotide chains, especially considering their often great length [3](#page=3). --- # Types of nucleic acids: DNA and RNA Nucleic acids are classified into two primary types, Deoxyribonucleic Acid (DNA) and Ribonucleic Acid (RNA), distinguished by their structural components and functions [4](#page=4). ### 2.1 Nucleic acid structure and monomer Nucleic acids are heterobiopolymers composed of polynucleotide chains. Their monomers are nucleotides, with four distinct types present in each chain [4](#page=4). ### 2.2 Deoxyribonucleic acid (DNA) #### 2.2.1 DNA structure DNA molecules are characterized by a double helix structure. They consist of two long, complementary deoxynucleotide chains linked by hydrogen bonds along their length. These chains are antiparallel, with a 5' end of one chain facing the 3' hydroxyl (-OH) end of the other [4](#page=4). > **Tip:** The antiparallel nature of DNA strands is crucial for DNA replication and transcription processes. #### 2.2.2 DNA forms in different cell types In eukaryotic cells, DNA molecules are linear. Conversely, DNA in prokaryotic cells, as well as in mitochondria and chloroplasts, forms a circular structure where the two ends of the molecule are joined [4](#page=4). #### 2.2.3 DNA function The specific nucleotide sequence within DNA molecules encodes for the genetic information, acting as the hereditary program unique to each biological species and individual. DNA's primary roles are to store and transmit hereditary information across generations [4](#page=4). ### 2.3 Ribonucleic acid (RNA) #### 2.3.1 RNA structure RNA molecules are single-stranded and linear, forming a ribonucleotide chain. They are generally shorter and have a lower molecular mass compared to DNA strands. While predominantly single-stranded, transfer RNA (tRNA) and ribosomal RNA (rRNA) can contain complementary sequences. These sequences fold and bind to themselves, creating double-stranded regions often described as "loops". RNA can also undergo additional three-dimensional folding [4](#page=4). #### 2.3.2 Types of RNA and their functions There are three main types of RNA, each with distinct roles within the cell [4](#page=4): ##### 2.3.2.1 Messenger RNA (mRNA) * **Abundance:** Constitutes approximately 2% of cellular RNA [5](#page=5). * **Synthesis:** Synthesized from a DNA template, inheriting the genetic information from DNA. It is also known as informational RNA (iRNA) [5](#page=5). * **Function:** Serves as a template for protein synthesis in ribosomes [5](#page=5). ##### 2.3.2.2 Ribosomal RNA (rRNA) * **Abundance:** Can make up to 83% of cellular RNA [5](#page=5). * **Function:** Binds with proteins to form ribosomes, which are non-membranous organelles responsible for protein synthesis [5](#page=5). ##### 2.3.2.3 Transfer RNA (tRNA) * **Abundance:** Constitutes around 15% of cellular RNA [5](#page=5). * **Secondary Structure:** Possesses a secondary structure resembling a cloverleaf [5](#page=5). * **Function:** Transports amino acids to the ribosomes, ensuring they are placed correctly in the growing polypeptide chain [5](#page=5). > **Example:** During protein synthesis, mRNA carries the genetic code from DNA to the ribosome. rRNA forms the structural and catalytic core of the ribosome, while tRNA molecules pick up specific amino acids and deliver them to the ribosome according to the mRNA sequence. --- # Structure and properties of DNA This topic explores the fundamental structure of DNA, including its double helix, base pairing rules, and variations in prokaryotes and eukaryotes, alongside key properties like supercoiling, denaturation, renaturation, and hybridization. ### 3.1 The dna double helix The DNA molecule is composed of two long polynucleotide chains that wind around an imaginary central axis. These two chains are antiparallel, meaning the hydroxyl group (-OH) at the 5' end of one chain is near the 3' end of the other chain. The polynucleotide chains are held together by hydrogen bonds formed between the nitrogenous bases. This bonding always occurs between a purine and a pyrimidine base, following the rule of complementarity [8](#page=8). #### 3.1.1 Complementarity and base pairing The rule of complementarity dictates the specific pairing of nitrogenous bases: 1. Guanine (G) always pairs with cytosine (C) via three hydrogen bonds (G ≡ C) [7](#page=7) [8](#page=8). 2. Adenine (A) pairs with either uracil (U) or thymine (T), depending on the type of nucleotide. In ribonucleotides, adenine pairs with uracil via two hydrogen bonds (A=U). In deoxyribonucleotides within DNA, adenine pairs with thymine via two hydrogen bonds (A=T) [7](#page=7) [8](#page=8). The complementary base pairs (A-T and G-C) always lie in the same plane [8](#page=8). #### 3.1.2 Chargaff's rules The quantities of the four nitrogenous bases in a DNA molecule are not random but follow specific quantitative regularities known as Chargaff's rules. These rules state [8](#page=8): * The number of adenine bases in a DNA molecule equals the number of thymine bases (A=T) [8](#page=8). * The number of guanine bases in a DNA molecule equals the number of cytosine bases (G≡C) [8](#page=8). * The sum of purine bases (A+G) in a DNA molecule equals the sum of pyrimidine bases (T+C) [8](#page=8). > **Tip:** Chargaff's rules are crucial for understanding DNA replication and the base composition of DNA. #### 3.1.3 Structural dimensions of the double helix When viewed from the side, the DNA molecule forms two grooves: a minor groove and a major groove. The major groove is formed because the sugar-phosphate backbone is further from the spiral's axis than the nitrogenous bases are. The major groove serves as a site for the macromolecule to interact with regulatory proteins. The distance between adjacent base pairs is 0.34 nanometers (nm). Each full turn of the helix contains ten base pairs, meaning a distance of 3.4 nm. The diameter of the DNA molecule is 2 nm [8](#page=8). ### 3.2 DNA structure in prokaryotes In prokaryotic cells, DNA is a circular molecule and does not form stable complexes with proteins, often referred to as "naked" DNA. It is typically negatively supercoiled, meaning the axis is twisted counter-clockwise. This supercoiling is generally looser, making the molecule more prone to denaturation, with the exception of thermophilic bacteria which possess positively supercoiled DNA that is resistant to denaturation. Prokaryotic DNA consists of unique sequences with very few non-informative regions. Plasmids, which are small circular DNA molecules carrying one or two genes, are characteristic of prokaryotic cells [9](#page=9). ### 3.3 DNA structure in eukaryotes In eukaryotic cells, DNA found in mitochondria and plastids shares characteristics with prokaryotic DNA. The main quantity of DNA is located in the nucleus, and nuclear DNA exhibits several distinguishing features compared to prokaryotic DNA. These features include [9](#page=9): * Large, linear, supercoiled molecules organized into complexes with proteins, forming chromatin [9](#page=9). * The presence of numerous repeated nucleotide sequences, the number of which varies among DNA from different species. Repeated DNA is thought to have primarily regulatory functions [9](#page=9). * Repeated inverted sequences called palindromes, which read the same forwards and backwards. Large palindromes can reach thousands of nucleotide pairs and can form cross-like structures in DNA due to the pairing of complementary bases within a double-stranded loop. Shorter palindromes are also common and are believed to act as "signal" regions [9](#page=9). * Non-informative sequences known as introns, which do not encode amino acid sequences in a polypeptide product. A single gene can contain multiple introns interspersed between informative sequences called exons. Nearly all eukaryotic genes studied today contain introns; for example, the collagen gene has over 50 introns [9](#page=9). ### 3.4 Properties of dna #### 3.4.1 Supercoiling The DNA double helix possesses the property of supercoiling; the terms supercoiling, superhelix, and supertwisting are synonymous. Supercoiling is a natural tendency of the molecule, leading to a more compact form when maximally coiled. In eukaryotic cells, DNA coils at multiple levels, with maximal coiling observed in metaphase chromosomes. During the interphase nucleus, DNA exists at different levels of coiling: loosely coiled (euchromatin) and highly coiled (heterochromatin). The process of DNA replication and transcription requires the unwinding of the DNA, which consumes energy and involves numerous enzymes [10](#page=10). > **Tip:** Supercoiling is essential for packaging the vast amount of DNA into the nucleus and for regulating gene expression. #### 3.4.2 Denaturation and renaturation The two strands of DNA can be separated by breaking the hydrogen bonds between them. This can be easily achieved by adding an acid or a base. The separation, or denaturation, of the double helix occurs at a specific temperature known as the melting temperature ($T_m$). The melting temperature is defined as the temperature at which half of the helical structure of the molecule is disrupted [10](#page=10). The melting temperature is influenced by the nucleotide composition of the DNA. DNA molecules rich in G-C bonds have a higher melting temperature compared to molecules with a prevalence of A-T pairs. The melting temperature of DNA is generally high, ranging from 85 to 100 degrees Celsius (°C), unlike proteins which denature at significantly lower temperatures [10](#page=10). Following the separation of the two strands, they can re-anneal to form an intact molecule upon slow cooling of the solution, a process known as renaturation. The spontaneous re-association of strands and formation of a double-helical structure provides strong evidence for the "recognition" between nitrogenous bases in the double helix [10](#page=10). > **Example:** Scientists can use the melting temperature of DNA to estimate its G-C content. A higher melting temperature indicates a higher proportion of G-C base pairs. #### 3.4.3 Hybridization The property of separated DNA strands to spontaneously re-associate and form a double helix is utilized in the creation of hybrid DNA molecules. This process, known as hybridization, involves isolating DNA molecules from two different organisms, denaturing them by heating, and then mixing them. The mixture is incubated at approximately 65 degrees Celsius (°C) for a specified period. As a result of renaturation, the solution will contain double-stranded molecules of each individual species, as well as hybrid DNA molecules where specific segments of the strands from the two different species form double-stranded regions [10](#page=10). > **Tip:** DNA hybridization is a powerful technique used in molecular biology for detecting specific DNA sequences, determining evolutionary relationships, and in diagnostic tests. --- # Functions of nucleic acids and nucleotides Nucleotides serve crucial roles beyond their function as monomers for nucleic acids, including energy transfer and the storage and transmission of genetic information [11](#page=11) [6](#page=6). ### 4.1 Roles of nucleotides beyond nucleic acid monomers Nucleotides are not only the building blocks of nucleic acids but also participate in other vital cellular processes. They can be found as mono-, di-, or triphosphates [6](#page=6). #### 4.1.1 Nucleotides in energy transfer Nucleotide triphosphates, particularly adenosine triphosphate (ATP), are key energy carriers within the cell. The covalent bonds between their phosphate groups are considered high-energy or macroergic bonds, denoted by the tilde symbol `~`. Hydrolysis of these bonds releases significant energy that fuels various cellular activities [6](#page=6). **Example:** Adenosine triphosphate (ATP) is the universal molecule responsible for storing and transferring energy in cells. It is composed of adenine, ribose, and three phosphate groups [6](#page=6). ATP is synthesized through a process called phosphorylation, which involves the addition of a phosphate group. This reaction is fundamental to cellular energetics [6](#page=6). > **Tip:** Understand that the energy stored in macroergic bonds is significantly higher than in other covalent bonds, which is why their hydrolysis is an effective source of cellular energy. ### 4.2 Functions of DNA DNA is a remarkably stable and chemically inert molecule that acts as the repository for the cell's hereditary information. This genetic blueprint is encoded in the specific sequence of its four types of deoxyribonucleotides. A segment of DNA that carries the instructions for synthesizing a specific RNA molecule or polypeptide chain is defined as a gene, and a single DNA molecule can contain thousands of genes [11](#page=11). #### 4.2.1 Transmission of genetic information DNA's primary role is to transmit the hereditary program to daughter cells. Prior to cell division, DNA undergoes replication, a process where it is duplicated. During division, these two identical copies are distributed equally to the newly formed daughter cells, ensuring that each receives the complete set of genetic instructions necessary for its existence [11](#page=11). #### 4.2.2 Role in evolution DNA replication occurs at a high speed, which can occasionally lead to alterations in the nucleotide sequence. These changes in the encoded information are the fundamental reason for the vast diversity observed in the evolution of the living world [11](#page=11). ### 4.3 Functions of RNA RNA molecules play diverse roles within the cell, primarily related to protein synthesis and genetic information transfer [5](#page=5). #### 4.3.1 Messenger RNA (mRNA) Messenger RNA, also known as informational RNA (iRNA), constitutes approximately 2% of cellular RNA. It is synthesized using a DNA strand as a template, thereby copying the genetic information from DNA. mRNA then serves as the template for protein synthesis within the ribosomes [5](#page=5). #### 4.3.2 Ribosomal RNA (rRNA) Ribosomal RNA makes up the largest proportion of cellular RNA, accounting for up to 83%. rRNA associates with proteins to form ribosomes, which are non-membranous organelles where protein synthesis takes place [5](#page=5). #### 4.3.3 Transfer RNA (tRNA) Transfer RNA constitutes about 15% of cellular RNA. Its secondary structure is often depicted as a cloverleaf shape. The key function of tRNA is to transport specific amino acids to the ribosomes, ensuring they are incorporated into the correct position within the growing polypeptide chain [5](#page=5). > **Tip:** Remember the relative abundance of each RNA type (rRNA > tRNA > mRNA) as this often reflects their functional importance in protein synthesis. --- ## Common mistakes to avoid - Review all topics thoroughly before exams - Pay attention to formulas and key definitions - Practice with examples provided in each section - Don't memorize without understanding the underlying concepts

| Term | Definition | |---|---| | Nucleotide | The monomer unit of nucleic acids, composed of a monosaccharide (pentose), a nitrogenous base, and a phosphate group. | | Monosaccharide (Pentose) | A simple sugar with five carbon atoms. In nucleic acids, this can be ribose or deoxyribose. | | Nitrogenous Base | A heterocyclic compound containing nitrogen, forming a key part of nucleotides. They are classified as purines (adenine, guanine) or pyrimidines (thymine, uracil, cytosine). | | Purine | A type of nitrogenous base with a double-ring structure, including adenine (A) and guanine (G). | | Pyrimidine | A type of nitrogenous base with a single-ring structure, including thymine (T), uracil (U), and cytosine (C). | | Complementarity Rule | The specific base pairing rule in nucleic acids where adenine pairs with thymine (in DNA) or uracil (in RNA), and guanine pairs with cytosine, mediated by hydrogen bonds. | | Hydrogen Bond | A weak attraction between a hydrogen atom bonded to a more electronegative atom and another electronegative atom. These bonds hold the two strands of DNA together. | | Phosphodiester Bond | A covalent bond that links the 5' carbon of one nucleotide's sugar to the 3' carbon of another nucleotide's sugar via a phosphate group, forming the sugar-phosphate backbone of a polynucleotide chain. | | Polynucleotide Chain | A linear polymer formed by the sequential linking of nucleotides through phosphodiester bonds. | | Sugar-Phosphate Backbone | The structural framework of a polynucleotide chain, consisting of alternating sugar and phosphate groups. | | DNA (Deoxyribonucleic Acid) | A nucleic acid composed of two complementary deoxyribonucleotide chains that form a double helix, carrying the genetic information of most organisms. | | RNA (Ribonucleic Acid) | A nucleic acid composed of a single ribonucleotide chain, involved in protein synthesis and gene regulation. | | mRNA (Messenger RNA) | A type of RNA that carries genetic information transcribed from DNA to the ribosomes, serving as a template for protein synthesis. | | rRNA (Ribosomal RNA) | A type of RNA that is a structural component of ribosomes, the cellular machinery responsible for protein synthesis. | | tRNA (Transfer RNA) | A type of RNA that carries specific amino acids to the ribosomes during protein synthesis, matching them to the codons on mRNA. | | ATP (Adenosine Triphosphate) | A high-energy molecule that serves as the primary energy currency of the cell, composed of adenine, ribose, and three phosphate groups. | | Phosphorylation | The addition of a phosphate group to a molecule, often a key process in energy metabolism, such as the formation of ATP. | | Macroergic Bond | A high-energy covalent bond, typically found in phosphate compounds like ATP, that releases a significant amount of energy upon hydrolysis. | | Supercoiling | A process where a DNA molecule twists upon itself, leading to a more compact structure. This can be positive (overwound) or negative (underwound). | | Denaturation | The process by which the double-stranded structure of DNA is disrupted, typically by heat or chemical agents, separating the two strands. | | Renaturation | The process by which the separated strands of DNA can re-anneal to form a double helix under appropriate conditions, demonstrating the specificity of base pairing. | | Hybridization | The process of combining single-stranded nucleic acid molecules from two different sources to form a hybrid double helix, used to study genetic relationships. | | Chargaff's Rules | A set of rules stating that in double-stranded DNA, the amount of adenine (A) equals the amount of thymine (T), and the amount of guanine (G) equals the amount of cytosine (C). | | Prokaryote | A single-celled organism that lacks a membrane-bound nucleus and other membrane-bound organelles. Their DNA is typically circular. | | Eukaryote | An organism whose cells contain a nucleus and other membrane-bound organelles. Their DNA is typically linear and organized into chromosomes. | | Gene | A specific segment of DNA that contains instructions for building a protein or functional RNA molecule. | | Replication | The biological process of duplicating a DNA molecule, ensuring that each daughter cell receives a complete set of genetic information. | | Transcription | The process of synthesizing an RNA molecule from a DNA template, a crucial step in gene expression. | | Intron | A non-coding sequence within a eukaryotic gene that is removed during RNA processing (splicing). | | Exon | A coding sequence within a eukaryotic gene that is retained in the mature mRNA and translated into protein. |