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- Herausgeber: Bentham Science Publishers
- Kategorie: Wissenschaft und neue Technologien
- Sprache: Englisch
Fundamentals of Cellular and Molecular Biology is a comprehensive textbook designed to explain the molecular mechanisms that underpin the functions and structures within living organisms. This resource focuses on improving the reader’s understanding and exploration of the cellular and molecular basis of life, emphasizing the latest research findings and technological advancements. The book is structured into 18 chapters that systematically cover topics ranging from the basic structural components of cells to the complex processes of gene expression, protein synthesis, and cell signaling. It offers a detailed examination of DNA replication, repair mechanisms, and the molecular basis of genetic diseases. Additionally, the book explains the application of molecular biology in biotechnology, medicine, and environmental science, as well as advanced topics like cloning, gene therapy, and molecular diagnostics.
Key features
- Clear explanations of complex concepts, bridging basic biology concepts with applied scientific fields
- Uses real-world examples to illustrate scientific principles
- Includes information on the latest research and technological breakthroughs.
- Glossaries and references for each chapter
- Facilitates learning with diagrams, flowcharts, and tables that summarize critical information, making complex subjects accessible.
Fundamentals of Cellular and Molecular Biology is an essential resource for students in life science courses such as biology, biochemistry, biotechnology, and medicine.
Readership
Students in life science courses such as biology, biochemistry, biotechnology, and medicine.
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Veröffentlichungsjahr: 2024
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PREFACE
Cellular and molecular biology is a fascinating and rapidly evolving field that has revolutionized our understanding of the living world. From the intricacies of the genetic code to the complex interactions between cells, this field provides insights into the fundamental processes that make life possible.
The aim of this book is to provide a comprehensive introduction to the fundamentals of cellular and molecular biology, covering topics such as cell structure and function, DNA replication and repair, gene expression and regulation, protein synthesis and folding, and cell signaling. Through clear explanations, detailed diagrams, and engaging examples, readers will gain a deep understanding of the underlying principles and mechanisms that govern the behavior of cells and molecules.
Whether you are a student just starting in the field, or a researcher looking to review the basics, this book is an indispensable resource. With its focus on fundamental concepts and its emphasis on clarity and accessibility, it is the perfect guide to the exciting world of cellular and molecular biology.
We hope that this book will inspire readers to delve deeper into the mysteries of life and to pursue their investigations into the intricate workings of the cellular and molecular world.
List of Contributors
The Cell and its Molecular Constituents
Samiullah Sajid1,*,Imran Abdullah2Abstract
The cell is the basic unit of life and the fundamental building block of all living organisms. It is a complex and dynamic structure composed of various molecular constituents. These constituents include the plasma membrane, cytoplasm, organelles, and genetic material. The plasma membrane is a thin, flexible layer that separates the cell from its surroundings and regulates the movement of substances into and out of the cell. The cytoplasm is a gel-like substance that contains various organelles, such as mitochondria, ribosomes, and the endoplasmic reticulum, which are involved in multiple cellular functions. The genetic material, composed of DNA and RNA, contains instructions for synthesizing proteins, the building blocks of life. The cell and its molecular constituents play vital roles in maintaining the organism’s integrity, responding to environmental cues, and carrying out essential physiological functions. Understanding the organization and function of these molecular constituents is crucial for advancing our knowledge of biology and developing new therapies for various diseases.
INTRODUCTION
All living organisms are made up of small structures called cells. These structures, representing the smallest unit of life, are quite complex and diverse and contain the morphological and physiological characteristics of living organisms. The properties of a given organism depend on its cells, whose continuity occurs through their genetic material. Simple life occurs in isolated cells, which propagate by cell division. Higher organisms, on the other hand, like man himself, are made up of aggregates of cells that perform specialized functions. The cells of different organisms are very similar in structure and molecular constituents, despite fundamental organizational differences. When analyzing the molecular constituents, it is important to consider not only the individual properties of the
molecules but also the interactions between them and their location within the cell. That analysis is even more necessary when considering a multicellular organism and the events that occur inside to produce the differentiation and development of that organism. This chapter briefly reviews the cellular structure, its molecular constituents, and the interactions carried out by these compounds [1].
CELLULAR STRUCTURES
The first observations and the very name of cells for structural units, in which all functions necessary for the maintenance and preservation of life are performed, were made by Robert Hooke in 1665. Regardless of the organism's complexity, all cells have the same structure formed by the plasma membrane, which surrounds the cell contents and separates it from the extracellular environment by the cytosol and the nucleus (or nucleoid). The cytosol in the whole cell is composed of a complex aqueous solution with various dispersed particles and molecules. Cell size and shape vary greatly and have no relation to the organism's size. Some cells live in isolation, like unicellular organisms, but those of multicellular organisms generally relate to each other. The plasma membrane, which surrounds all cells, is formed by a double layer of lipids from the phospholipid class and, in variable amounts, if associated with protein molecules [2].
The plasma membrane defines the boundary between the intracellular and extracellular environment. To enter or leave a cell, a substance must cross the cell membrane, which will depend on the membrane's permeability. This lipid bilayer is permeable to certain gases, such as O2 and CO2, and impermeable to many substances, such as sugar, amino acids, and inorganic ions (K+ and Cl-); water can freely diffuse through the cell. Many proteins are bound to the plasma membrane (permeases or carriers), forming channels in the lipid bilayer and facilitating the passage of certain substances. Thus, all cells of organisms have the characteristic structural architecture of their membranes and many metabolic processes, even DNA replication, synthesis of protein, and chemical energy production.
PROKARYOTIC AND EUKARYOTIC CELLS
Despite the similarity between the cells that make living beings, organisms maintain fundamental differences at the cellular level and can be classified into two large groups: prokaryotes and eukaryotes [3]. Prokaryotic organisms are single-celled and simpler in an organization, although they occur in associated groups, forming colonies with some differentiation of functions. The prokaryotes include bacteria and archaea (bacteria that survive in unusual environments, such as saline lakes, swimming pools, thermals, and swamps). Eukaryotic organisms
are more complex and include not only multicellular plants, animals, fungi, protozoa, and some single-celled organisms such as yeast and green algae (Fig. 1).
Fig. (1)) Schematic representation of an animal cell (eukaryotic cell) with its main structures and cellular organelles. The main features are the presence of a well-defined nucleus containing the genome and the cell organelles, which compartmentalize certain functions.The main difference between prokaryotes and eukaryotes is that, in eukaryotes, organelles are found, mainly the nucleus, which contains the genome. Organelles are regions bounded by internal membranes, forming specialized functions compartments. In prokaryotes, the absence of an envelope nucleus puts the genome in direct contact with the rest of the cytoplasm in a space within the cell called the nucleoid, staying next to ribosomes, other particles, and a wide variety of dissolved molecules. Prokaryotic cells usually have a cell wall, whose function is to provide greater rigidity and mechanical protection. This membrane is also present in eukaryotic plant cells. The chemical composition of the cell wall of prokaryotes is quite complex, containing molecules of polysaccharides, lipids, and proteins.
In eukaryotic cells, the Nuclear DNA is split into two or more chromosomes. Each of these chromosomes comprises a linear DNA molecule that, except during cell division, is confined within the nucleus. These DNA molecules are associated with proteins, called histones, forming nucleosomes and components of chromatin. The number and size of individuals' chromosomes vary greatly among different eukaryotic organisms. Fungi, for example, has 12 to 18 chromosomes; human cells contain two sets of 23 chromosomes, each about thirty times the amount of DNA in a cell of the Escherichia coli bacterium.
Organelles are common to all eukaryotic cells, the nucleus being perhaps the most important of these organelles. The nucleus is surrounded by a double nuclear membrane, which has a characteristic, in addition to the chromatin, a region rich in RNA, called the nucleolus. In the nucleolus, RNAs are synthesized from a DNA template and exported to the cytoplasm across the nuclear membrane. Mitochondria, another important organelle, has enzymes specialized in oxidative processes that produce energy for the cell. In addition, DNA and ribosomes are found inside the mitochondria. The endoplasmic reticulum comprises membranes distributed throughout the cytoplasm and bound to the cell and nuclear membranes. The granular ER has ribosomes attached to its membranes, constituting the molecular machinery for protein synthesis. The Golgi complex is formed by membranes and vesicles, involved in the modification and secretion of proteins from cells. There are specific organelles for plant and animal cells. Animal cells, for example, contain lysosomes with digestion function, and plant cells have chloroplasts, where photosynthesis occurs. Another feature common to most cells of plants and some microorganisms is the presence of a vacuole, whose function is to store nutrients and metabolites. Each organelle has its collection of enzymes that catalyze specific reactions, developing a unique role in cell growth and metabolism. Cell organelles are linked to a network of microtubules of filamentous proteins called the cytoskeleton. This structure is responsible for maintaining cell shape and assisting in cellular movements.
Molecular Constituents
Molecular constituents are responsible for the biochemical interactions between thousands of molecules that enable cellular life. These chemical reactions occur in an aqueous medium, so water, with few exceptions (bone cell), is the component found in greater amounts in the cell, indispensable for metabolic activity. Due to its polar nature, water serves as a natural solvent for ions, minerals, and other substances and as a dispersion medium for the colloidal structure of the cytoplasm. The presence of ions, such as Cl-, Na+, and K+, is important for maintaining the cell's osmotic pressure and acid-base balance. Some inorganic ions, such as magnesium, are required as enzymatic cofactors, while others, such as inorganic phosphate, form adenosine triphosphate (ATP), the primary chemical energy source of vital processes, and calcium ions play a regulatory role.
In addition to water and the chemical elements mentioned above, the cell comprises small molecules and macromolecules. Small molecules such as amino acids, nucleosides, lipids, and sugars constitute the substrates and the products of metabolic pathways, providing energy for the cell and may also be the forming units of macromolecules. In this biological polymer structure, these molecules are called monomers. Cells comprise three polymers: nucleic acids formed by nucleotides (monomers); proteins, made up of amino acids; and carbohydrates or polysaccharides, whose monomers are sugars or monosaccharides. Cells have many lipids, not polymers, preferably small molecules, unlike the others. The simplest and most abundant lipid is the fatty acid, which participates in the composition of other more complex lipid molecules, such as triacylglycerols. Larger structures, such as the bilayer of biological membranes and the cytoskeleton fibers, are formed by the association of these macromolecules.
Amino Acids and Proteins
Proteins result from the expression of the information contained in the gene. Therefore, the gene will determine the amino acid sequence of a specific protein. Like this, every protein has a definite order of residues. Amino acids establish their active three-dimensional structure and are called native conformation. The three-dimensional structure of the molecule, established according to the amino acid sequence itself, can be observed in denaturation experiments of a given protein. The amino acid activity depends on the changes in conditions of the environment (changes in pH, temperature, addition of solvents) where the protein is found, with a consequent loss of their biological function, can sometimes be recovered.
Restoration of the native conformation (protein renaturation) can occur when the conditions of the environment in which the molecule is found are reestablished, allowing the amino acids to return to interact. The folding of a globular protein is an energetically favourable process under physiological conditions that enable interactions between chemical groups. Proteins are classified into two main classes: fibrous and globular. Fibrous proteins play a structural role in cells and animal tissues. This class includes collagen, a component of bones and connective tissue, and keratin in nails and hair. Globular proteins have a spiral and compacted structure with a globular shape; abundant and essential, they can be found in any organism. One example is enzymes, efficient biological catalysts that speed up chemical reactions. Except for some RNAs (ribozymes), which have catalytic activity, all enzymes are proteins. All globular proteins have a unique, coiled structure in a specific way and according to the particular function to be executed. Since the structure of a protein determines its function, it is important to know the structural characteristics of this molecule.
Proteins are long chains of amino acids and constitute more than half of the dry weight of a cell. They are also polymers that perform numerous biological functions in addition to determining the shape and structure of the cell. Proteins are also known as molecules that do cellular work. They catalyze an unexpected number of chemical reactions, control the permeability of membranes, regulate the concentration of metabolites, recognize and non-covalently bind other biomolecules, provide movement, and control gene function. Proteins consisting of only 20 amino acids joined by peptide bonds perform this diverse number of functions.
Like the native conformation, which allows the protein to perform its functions, is a consequence of the individual properties of the amino acids present in the protein molecule, it is important to review these properties. Amino acids are named after organic acids, with a carbon atom (C) attached to four chemical groups. An amino group (NH2), a carboxylic group (COOH), a hydrogen atom (H), and a variable group are called side chains or radicals (R). Except for glycine, which also has a hydrogen atom in the radical, all other amino acids have four different groups attached to C, giving rise to an asymmetric carbon. The presence of this asymmetric carbon generates two molecules (stereoisomers) called D (dextro) and L (levo) isomers. At physiological pH, the amino and carboxylic groups of amino acids are ionized (NH3+ and COO-), causing the amino acid to have positive and negative charges in the same molecule (dipolar molecule).
The simultaneous presence of these groups determines the acid-base behavior of amino acids (amphoteric molecules). The acid-base character and the amino acid's electrical charge are determined by the pH of the medium where it is found. The side chains of amino acids vary in size, shape, electrical charge, hydrophobicity, and reactivity. Amino acids with polar side chains are hydrophilic and tend to be located on the protein's surface due to their interactions with water. Furthermore, the more polar amino acids are present in the protein, the more soluble it will be in aqueous solutions. However, because they are hydrophobic, amino acids with non-polar R groups tend to be inside the proteins and cause their insolubility in water. Arginine and lysine (basic polar) are positively charged in the polar group, and glutamate and aspartate (acidic polar) are negatively charged. Four amino acids are primarily responsible for protein loads; histidine, which also has a positive charge, helps maintain the pH (physiological buffer) due to its ability to capture or release protons through the imidazole group in the radical. Belonging to the class of neutral polar amino acids, cysteine can react with other cysteine residues using the thiol group (SH), present in the para radical disulfide form (S–S) bridges in an oxidation reaction, and this link plays an important role in the conformation of proteins. Amino acids with hydrophobic side chains are almost insoluble in water due to the presence of hydrocarbons in these groups. Phenylalanine, tryptophan, and tyrosine are aromatic groups responsible for the ultraviolet light absorption of proteins at 280 nm. Proline is a unique amino acid since its side chain is covalently bonded to the nitrogen of the amino group, forming a rigid ring. The presence of proline in a protein chain can restrict the way the molecule will fold.
During the synthesis of the protein molecule, the amino acids are united by a covalent bond between an amino acid's carboxylic group and another amino acid's amino group, connected by a dehydration reaction with the loss of a water molecule. The molecule formed generates a peptide and maintains its amphoteric character since there will always be a free carboxylic group at one end (C-terminus) and a free amino group at the other (N-terminal) end. The combination of just two amino acids forms a dipeptide; the union of a few amino acids gives rise to oligopeptides, while a polypeptide comprises many amino acids (sometimes greater than 1,000). The sequence of a protein chain is written with the N-terminus on the left and the C-terminus on the right. The size of a protein is, overall, expressed by its mass in Daltons (Da). Enzymes form an important class of protein that catalyzes all chemical reactions. When involved in redox reactions, some are only active when covalently linked to a coenzyme (prosthetic group), such as nicotinamide adenine dinucleotide (NAD+), whose structure is formed by a nicotinamide ring, an adenine ring, and two linked phosphate sugar groups.
Three-dimensional Protein Structure
The formation of a polypeptide chain, considering the correct polymerization of amino acids, is carried out in the translation process and determined by the information in messenger RNA (mRNA). The protein chain synthesized assumes a precise spatial organization and is necessary for the protein to perform its function (native conformation). The three-dimensional structure of a protein is the combination of several factors, mainly interactions between chemical groups present in this protein and stereochemical limitations imposed by the peptide bond itself due to the water resonance character. This resonance prevents the rotation of the carbon attached to the nitrogen, leaving all the atoms involved in the peptide bond in the same position. Proteins are analyzed considering the four levels of structural organization. The primary structure is the first step in specifying the structural analysis of a protein and refers to the sequence of amino acids, that is, the order in which the amino acids are linked to form a peptide chain. Each protein has its specific primary structure, which, in turn, determines the three-dimensional structure. The biological importance of the amino acid sequence is well exemplified in the hereditary human disease called sickle cells. In this disease, profound biological changes occur, caused by replacing a single amino acid in the hemoglobin molecule.
Secondary structure refers to the various spatial arrangements of amino acids close in the central peptide chain, which causes folding; such folds are called secondary structures. These arrangements may feature an organization that repeats at regular intervals. The most common secondary structure organizations are the a-helix in which the peptide chain winds around an axis, are stabilized by hydrogen bonds formed between the amino group of the peptide bond of an amino acid and the carboxyl group located four residues ahead in the same polypeptide chain.
Tertiary structure refers to how the polypeptide chain is coiled, including the three-dimensional arrangement representation of all atoms in the molecule, including those in the side chain and the prosthetic group. This level of structure is established when different secondary structures are arranged among themselves. The structure's stability is maintained by hydrogen bridges between R groups, hydrophobic interactions, ionic bonds between positively and negatively charged groups, and disulfide (S–S) covalent bonds. In globular proteins, the side chains of the more hydrophobic amino acids aggregate inside the molecule, and the groups of hydrophilic proteins protrude from the surface of the protein. The final three-dimensional structure can comprise a specific combination of secondary structures and helices entwined, forming compactly folded globular units called domains. The tertiary structure of larger proteins is subdivided into domains; these domains have about 100 to 150 amino acids and are linked by the peptide chain. Proteins with more than one polypeptide, forming subunits (multimeric proteins), have a quaternary structure, and this structure refers to the arrangement of the protein subunits that make up the molecule. The number of subunits can vary, and the union between them occurs in a non-covalent way through electrostatic interactions with hydrogen and hydrophobic bonds. Some proteins, called allosteric, exhibit a cooperative effect between the subunits so that a change in one of these subunits can result in a change in another subunit. A good example is the tetrameric hemoglobin molecule composed of four polypeptide chains forming the subunits. Each subunit binds to an oxygen molecule cooperatively; that is, after a molecule of oxygen is bound to one subunit, the binding of the other molecules is facilitated.
Carbohydrates
Carbohydrates, or monosaccharides, are simple sugars and represent one of the large classes of biological molecules with various cellular functions. Polysaccharides are polymers with long chains of monosaccharide units and constitute the primary cellular energy source. They are also important structural features of the constituents of the cell wall, acting as specific recognition signals and playing an informational role. Carbohydrates are formed by carbon covalent bonds, in a 1:1 ratio, and water (CH2O). They are sorted according to the number of carbon atoms present in the molecule: trioses (3), pentoses (5), or hexoses (6). All monosaccharides can contain hydroxyl groups and an aldehyde or ketone group. Those two groups can react with a hydroxyl group in the same molecule through a reaction, converting a linear structure to a ring-shaped one (Fig. 2).
Fig. (2)) Schematic drawing of the formation of a peptide through the bond between the carboxylic group of one amino acid and the amino group of another (peptide bond).Glucose is a monosaccharide containing six carbon atoms and an aldehyde group. An example is D-glucose, the primary source of energy for most cells. The structure of D-glucose can be presented as a linear chain with two different structures. When the aldehyde group on carbon 1 reacts with the hydroxyl group on carbon 5, the resulting ring has six elements, generating a D-glucopyranose. If the hydroxyl group occurs with carbon 4, the structure is a D-glucofuranose, whose presence in nature is much rarer. All monosaccharides except dihydroxyacetone contain one or more asymmetric carbons, generating optically active stereoisomers (D and L). The cyclization of the linear structure generates new isomers, called anomers, because they are linked to anomeric carbon. Oligosaccharides are molecules formed mainly by linking a few monomeric units. An example is sucrose, a disaccharide formed by the union of a glucose molecule and a fructose that produces the common sugar used in food after being processed.
The most important polysaccharides in living organisms are starch and glycogen, as they represent reserved substances and energy storage in plants and animal cells. Glycogen is a polysaccharide formed by linking several glucose molecules. Cellulose is also an important polysaccharide and is the main structural element of the plant cell wall. Disaccharides, like polysaccharides, are made up of monosaccharides joined covalently by glycosidic bonds. These bonds are formed when a hydroxyl group on a carbohydrate's anomeric carbon reacts with another carbohydrate's hydroxyl group. Those free hydroxyl groups can also bind with other amino groups, sulfate, and phosphate of different molecules, forming more complex molecules, such as glycosaminoglycans, the main components of the extracellular matrix.
Lipids
Lipids form a distinct group of compounds with multiple cellular functions frequently occurring in nature. They are usually molecules with a strong tendency to associate with each other through non-covalent forces, forming lipid aggregates. Lipids are generally characterized by their fatty acid structure. One fatty acid molecule has two distinct regions: a polar, hydrophilic region connected to a non-polar hydrophobic region consisting of a hydrocarbon chain. This structure characterizes lipids as poorly water-soluble compounds but soluble in organic solvents. This molecular feature promotes an amphipathic-like association of lipid molecules with non-covalent interactions in an aqueous medium. These interactions have considerable consequences at the cellular level; the most important of these is the tendency of lipids to form micelles and bilayers, which make up biological membranes. The exact structure formed when the lipid is in contact with water depends on the specific molecular structure of the hydrophilic and hydrophobic regions of the molecule.
Fatty Acids
The simplest lipids are fatty acids, also constituents of more complex lipids. Its basic structure represents most lipid molecules in large amounts in human cells. The structure of the fatty acid is formed by a long hydrocarbon, hydrophobic, and little chemically reactive chain. In general, the fatty acids found in living organisms contain even more carbon atoms, and their hydrocarbon chain is unbranched. Fatty acids are classified as saturated, unsaturated, or polyunsaturated, depending on the bonds between the carbon atoms. In saturated fatty acids, the chain contains only single bonds; if there are double bonds, the fatty acids are unsaturated, while fatty acids with more than one double bond are called polyunsaturated. Two polyunsaturated fatty acids, classified as essential acid, linoleic acid, with 18 carbons and two double bonds, and linolenic acid, also with 18 carbons but with three double bonds. An extremely hydrophilic, ionizable carboxylic group forms the fatty acid molecule in solution (COO-), including triacylglycerols (triglycerides) fatty acid. Triacylglycerols are the storage form of lipids in the cytoplasm of many cells because they serve as an excellent power source due to the presence of the carbon chain. Thus, triacylglycerols are more efficient energy storage than carbohydrates and are widely used by various organizations, including higher animals.
Phosphoglycerates
Phosphoglycerates or phospholipids are small lipid molecules composed of long chains of fatty acid and glycerol linked to a highly polar group. They differ from triacylglycerols in having only two fatty acid molecules joined to a single glycerol molecule, in which a third hydroxyl is esterified to a phosphoric acid (phosphatidic acid). This phosphate can be linked to a hydrophilic molecule (choline, ethanolamine, inositol, or serine), depending on the type of phosphoryl. The amphipathic nature of Phosphoglycerates is responsible for the molecular associations that form the cell membrane and confer many of its properties [4].
Steroids
Steroids are a large group of molecules that aggregate several functions, including many hormones, like the sex hormones of higher animals. Cholesterol is the most important steroid, part of cell membranes, mainly from animals. The steroids derive from a general structure containing three rings of 6 carbons (A, B, and C) and a ring with five atoms. The cholesterol molecule is not very amphipathic, as a hydroxyl group is located at the end of the molecule. The fused cyclohexane rings of this molecule form a very rigid structure, and their presence in the membrane tends to break the regularity of the structure, giving it greater rigidity. This compact structure is also responsible for harmful health effects, such as atherosclerosis and cardiovascular disease, caused by cholesterol storage in the blood vessels.
Nucleic Acids
Nucleic acids are macromolecules of great biological importance in all living organisms. From nucleic acids, cells receive information about proteins to synthesize, the sequence of amino acids in their structure, and the function of these molecules. They are the molecules that store and transmit genetic information in the cell. All this information in genes located on the chromosomes of cells is deciphered through the genetic code, whose translation results in protein synthesis. There are two types of nucleic acids: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA); both are linear polymers of nucleotides joined by phosphodiester bonds.
In most cases, the number of monomers in a nucleic acid molecule is much larger than the number of amino acids in a protein molecule. RNAs vary in size and may have ten to thousands of nucleotides. DNA and RNA consist of only four different types of nucleotides. Each nucleotide comprises a group phosphate, a sugar (pentose), and a nitrogenous base (purine or pyrimidine) linked by covalent bonds. The differences between the two nucleic acids reside in the type of sugar and composition of the base of the molecule. In RNA, pentose is always ribose, and in DNA, it is deoxyribose. The fundamentals are adenine (A), guanine (G), and cytosine (C), found in both DNA and RNA; the base thymine (T) is present only in DNA, and uracil (U) in RNA. These letters (A, C, G, T, and U) indicate a sequence of nucleotides in a nucleic acid. In addition to these five bases, there are unusual bases with slightly different structures, which occur mainly in RNA, such as hypoxanthine and inosine, to link sugar and the phosphate group. A phosphate group replaces the hydroxyl group of C5 of the sugar, and without the phosphate group, a base and sugar combination constitute a nucleoside. When nucleosides polymerize to form a nucleic acid, the hydroxyl group attached to the C3 of the sugar of one nucleotide forms an ester bond with the phosphate of another (phosphodiester bond), thus eliminating a water molecule and forming a backbone of pentose phosphate repeating units with the bases attached to the side group. On a strand of DNA or RNA, at one end, there is a cluster bonded phosphate to the sugar's 5' carbon; at the other end, there is a hydroxyl group attached to the 3' carbon. The polynucleotide chain has individuality, determined by the sequence of its bases, known as the primary structure, that contain genetic information to a particular sequence of DNA (protein or RNA).
Deoxyribonucleic Acid
Deoxyribonucleic acid (DNA) [5] is found in living organisms as molecules of high molecular weight. For example, E. coli has a single circular DNA molecule of 4.2 x 106 bp and a total length of 1.4 mm. The amount of DNA in higher-level organisms can be hundreds of times larger (700 times in the case of a man); the DNA of a single fully extended diploid human body cell can be up to 1.7 m long.
All the genetic information of an organism is accumulated in the linear sequence of the four bases. The primary structure of all proteins (20 amino acids) must be encoded by a four-letter alphabet (A, T, G, and C). Between 1949 and 1953, Chargaff, studying the base composition of DNA, demonstrated that although the composition varied from one species to another, in all cases, the amount of adenine was equal to that of thymine (AT), and that of cytosine was equal to that of guanine (CG). Thus, the total number of purines was equal to that of pyrimidines (A+G, C+T). On the other hand, the AT/GC ratio varied considerably between the species. In 1953, based on X-ray diffraction data, Watson and Crick proposed a model for the structure of DNA. This model explained the regularities of base composition, mainly its duplication in the cell. DNA is composed of two associated polynucleotide chains, which coil to form a double helix around a central axis that rotates to the right most of the time. The bases are inside the helix, perpendicular to the helical axis, interacting through hydrogen bonds that unite the two chains. The only possible pairings are A/T and C/G, and it is important to note that two hydrogen bonds are present between A and T, and between C and G, three bonds; as a result, the G/C pair is more stable than the A/T. In addition to these hydrogen bonds, hydrophobic interactions stabilize the double helix. The orientation of the two types of DNA is antiparallel; that is, the 5' → 3' direction of each one is opposite to the other.
Ribonucleic Acid
Ribonucleic acid (RNA) [6] is a nucleic acid consisting, in general, of a single strand with a great diversity of conformations. The sequence of bases (primary structure) is similar to that of DNA, except for replacing deoxyribose with ribose and thymine with uracil. There are three main classes of ribonucleic acid: messenger RNA (mRNA), which contains the genetic information for the sequence of amino acids; transfer RNA (tRNA), which identifies and transports amino acid molecules to the ribosome; and ribosomal RNA (rRNA), which accounts for 50% of the mass of ribosomes. All types of RNAs are involved in protein synthesis. Although the RNA molecule comprises only one polynucleotide chain, its structure is complex. The molecule adapts in a helical structure similar to DNA in paired regions. Differences in the size and conformations of the various types of RNA allow them to perform specific functions. The tRNAs have a conformational structure that allows pairing the anticodon nucleotides in the molecule with the mRNA codon nucleotides.
GLOSSARY
Cell: The basic unit of life, consisting of a plasma membrane, cytoplasm, and a nucleus or nucleoid.
Plasma Membrane: The selectively permeable outer boundary of a cell, composed of a phospholipid bilayer with embedded proteins and carbohydrates.
Cytoplasm: The gel-like fluid that fills the cell, containing organelles, cytoskeleton, and other macromolecules.
Nucleus: The organelle in eukaryotic cells that contain genetic material in chromosomes.
Nucleolus: A sub-organelle within the nucleus that is responsible for the synthesis of ribosomal RNA.
Chromosome: A long, coiled-up structure of DNA and protein that carries genetic information.
Ribosome: An organelle synthesizes proteins by translating mRNA into amino acid sequences.
Endoplasmic reticulum (ER): An organelle composed of a network of membranous tubules and sacs that plays a role in protein synthesis, lipid metabolism, and calcium storage.
REVIEW QUESTIONS
1. What is the plasma membrane, and what is its function?
2. What is the role of the endoplasmic reticulum in a cell?
3. What is an enzyme, and how does it function in a cell?
REFERENCES
[1]Alberts B, Johnson A, Walter P, Lewis J, Raff M, Roberts K. Molecular cell biology. New York: Garland Science 2008.[2]Campbell MK, Farrell SO, Tasks A. Biochemistry. (5.), 5.They are Paul: Thomson 2007.[3]Devlin TM. Biochemistry manual with clinical correlations São Paulo: Edgard Blucher; 2007 Lewin B Genes IX 9. Porto Alegre: Artmed 2009.[4]Lodish H, Baltimore D, Berk A, Zipursky L, Matsudaira PT. Cellular and molecular biology 5. Porto Alegre: Artmed 2005.[5]Persing DH. Molecular microbiology: Diagnostic principles and practice. Washington: ASM Press 2004.[6]Alberts B. Molecular Biology of the Cell. New York: Imprint W.W. Norton & Company 2015. [http://dx.doi.org/10.1201/9781315735368]Nucleic Acid Structure
Atta Ur Rahman1,*Abstract
Nucleic acids are essential biomolecules that store and transmit genetic information in all living organisms. The structure of nucleic acids, specifically DNA (deoxyribonucleic acid) and RNA (ribonucleic acid), is crucial for their function. The backbone of nucleic acids is composed of alternating sugar and phosphate groups, while the nucleotide bases (adenine, guanine, cytosine, thymine and uracil) protrude from the sugar-phosphate backbone. The bases form specific hydrogen bonds with complementary bases on the opposite strand, resulting in the double-helical structure of DNA. RNA is usually single-stranded but can form secondary structures through base pairing. The three-dimensional structure of nucleic acids is also important for their function, as it determines the interactions between nucleic acids and other molecules, such as proteins. Understanding nucleic acid structure is fundamental for many areas of biology, including genetics, molecular biology and biotechnology.
INTRODUCTION
DNA and RNA are crucial nucleic acids that store and transfer genetic information in living organisms. DNA, a double-stranded molecule, acts as the blueprint for directing cellular functions. Cells transcribe the instructions encoded in DNA into the nucleotide sequence of single-stranded RNA molecules. RNA molecules have various tasks, including the creation of polypeptides, regulation of gene expression, and defense against invading nucleic acids, such as those encountered in viral infections. The study of nucleic acid structure and function, which began over 60 years ago, has provided an unprecedented understanding of biological processes and has transformed several professions, including illness detection, treatment, and forensic inquiry [1].
Throughout history, humans have observed patterns of heredity without grasping the underlying mechanisms responsible for conveying physical features and developmental processes from parents to offspring. However, these discoveries have been leveraged by diverse societies to strengthen their economic conditions through selective breeding and crop production. The scientific area of genetics began in the nineteenth century, dedicated to solving the secrets of heredity. At the start of the twentieth century, scientists largely recognized that physical attributes are inherited through discrete units known as genes, which sit on chromosomes within the nucleus of cells. After decades of tedious investigation, the chemical makeup of chromosomes was revealed, leading to the identification of DNA as the bearer of genetic information. The crucial discovery of the DNA structure by James Watson and Francis Crick in 1953 marked a turning point and gave rise to the science of molecular biology.
Molecular biology is a specialist field that focuses on researching the structure of genes and the complicated mechanisms involved in DNA manipulation. Researchers in life sciences, armed with cutting-edge technology developed by molecular biologists and biochemists, have been actively examining the manner in which living creatures organize and process genetic information. This huge corpus of efforts has uncovered numerous essential principles:
DNA serves as the central director of cellular operations and is inherited by offspring. It consists of two polynucleotide strands that interlock to form a double helix. The information stored in DNA is delivered by the unique sequence of purine and pyrimidine nucleotides. A gene is a particular sequence of DNA that comprises the required information, including both regulatory sequences that govern gene product synthesis and the instructions for encoding a gene product, such as a polypeptide or various types of protein molecules. DNA replication, known as the synthesis of new DNA strands, includes the precise matching of purine and pyrimidine bases between the original DNA strand and the newly produced strand. The functioning of DNA, both physiologically and genetically, relies on the synthesis of accurate copies of the original and pristine DNA strands. To maintain the fidelity of genetic information, various DNA repair mechanisms are employed by most organisms.The process by which genetic information is decoded and utilized to orchestrate cellular processes commences with the synthesis of another class of nucleic acid called ribonucleic acid (RNA). RNA synthesis, known as transcription, involves the complementary pairing of ribonucleotides' bases with the bases of a DNA molecule. Each newly synthesized RNA molecule is termed a transcript, and the entirety of RNA molecules transcribed from an organism's genome is referred to as the transcriptome.
