Double-stranded DNA consists of two polynucleotides that are arranged so that the nitrogenous bases within one polynucleotide are linked to the nitrogenous bases within another polynucleotide by means of special chemical bonds called hydrogen bonds. A single double-stranded DNA molecule is composed of two helically shaped polynucleotides and they are connected to each other by hydrogen bonds. Polynucleotides are made up of a long, unbranched chain with a backbone of sugar (ribose or deoxyribose) and phosphate units with heterocyclic bases that protrude from the chain at regular intervals. You might find these chapters and articles related to this topic. Nucleic acids are distributed unevenly within the cell.
DNA, which is the genetic material (page 28), is found in the nuclear chromatin of the resting cell and in the chromosomes of the dividing eukaryotic cell. Small amounts are also found in mitochondria (page 200) and in plasmids in bacterial cells. Unlike DNA, RNA is found primarily in the cytoplasm, where it is present in three different shapes. The nucleus contains approximately 5% of the total RNA.
Most of it is found in the nucleolus, although small amounts are found associated with chromatin. The molecular weights of DNA molecules are difficult to accurately determine using chemical methods because they are so high. Physico-chemical methods are more reliable, but even with them, the results can be questionable due to the difficulty of preparing intact molecules. This is because very large molecules are susceptible to hydrodynamic shear and also to the action of nucleases that are commonly present in tissues.
Their molecular weights are thought to range from approximately one million (10) to one billion (10) or even more. Just as the composition and sequence of amino acids vary from one protein molecule to another, the composition and sequence of nucleotides vary from one nucleic acid molecule to another and, since the sugar and phosphate groups are the same for each nucleotide component, the variation only refers to the composition and sequence of bases. The first studies carried out by Chargaff (1950) on the basic composition of DNA from various sources yielded very striking results, whose importance was not fully appreciated in at that time. He observed that (the sum of the purines (adenine + guanine) present was equal to the sum of the pyrimidines (cytosine + thymine); (the sum of the amino bases (adenine + cytosine) was equal to the sum of the oxo bases (guanine + thymine); (adenine and thymine were present in equal quantities as were guanine and cytosine).
The rigor with which base pairing occurs means that there is a complementary relationship between the two chains of each DNA molecule. Consequently, if the base sequence of a chain is known, the base sequence of the complementary chain can be predicted. The method makes it possible to determine the sequence of up to 1000 base pairs in one day and, since it is so fast and efficient, it is now also used to determine the amino acid sequence of proteins. This is achieved by isolating and cloning the protein gene (page 30) and determining its base sequence. The base sequence is then translated into terms of amino acid sequence using the genetic code (page 300).
Ribonucleic acid molecules are single-stranded and vary in size depending on their type (page 29), but are usually much smaller than those in DNA. They differ from DNA in that they replace thymine with uracil and that they contain ribose in place of deoxyribose. Although C-2′, C-3′ and C-5′ all carry hydroxyl groups that are available for esterification, the nucleotides are linked through sugar, as in DNA, through 3′—5′ phosphodiester bonds. Although single-stranded, RNA molecules can be folded so that they have a secondary structure.
This is due to the pairing of residues A and U, and of residues G and C located at different points on the same polynucleotide chain, which folds back on itself to form loops formed by short regions of imperfect double helices (Figure 20.1). Hydrogen bonds between base pairs are broken by heat, causing the molecule to unfold. For the pentose sugar ring, in Fig. The difference between DNA and RNA lies in the C-2' position of the ribose sugar ring.
In RNA, the carbon in the C-2 position is attached to a hydroxyl (OH) group. In DNA, the C-2 carbon does not contain this hydroxyl group, but is replaced by a hydrogen atom (H). Therefore, the pentose ring in DNA is considered a deoxyribose (it is a deoxygenated sugar ring of five carbons). In the absence of the C-2' hydroxyl group in DNA, the sugar is more specifically referred to as 2-deoxyribose.
If a molecule is composed of a purine or pyrimidine base and a ribose or deoxyribose sugar, this chemical unit is called a nucleoside (fig. The nitrogenous base and the pentose sugar are linked by a glucosidic bond between the C-1' position of the sugar and the nitrogenous base. If the base is a purine, the N-9 atom is covalently attached to the sugar. If the base is a pyrimidine, the N-1 atom attaches to the sugar.
When a phosphate group is attached to a nucleoside through a phosphoester bond, the entire complex is converted to a nucleotide. This phosphoester bond is linked between the 5′-hydroxyl group of the sugar and a phosphate group. Because it involves a phosphate group and only one sugar, it is a bond phosphomonoester. The individual units within nucleotides are also called nucleoside monophosphates.
The addition of one or two phosphate groups results in nucleoside diphosphates and triphosphates, respectively. The triphosphate form is important because it serves as a precursor molecule during the synthesis of nucleic acids within the cell. The formation of ADP from AMP requires the addition of an inorganic phosphate molecule and is accompanied by the release of a water molecule. Likewise, the formation of ATP from ADP requires the addition of an inorganic phosphate molecule and is accompanied by the release of a water molecule.
On the other hand, the hydrolysis of ATP to ADP, which releases an inorganic phosphate (Pi) molecule, is accompanied by the release of a large amount of energy in the cell. When these chemical conversions are combined with other reactions, the energy produced is used to drive the reactions and sustain life. During DNA synthesis, the two phosphate groups, which are the beta and gamma phosphates, are removed from dATP, dGTP, dCTP and dTTP. Therefore, all four nucleotides contain only monophosphates in a polynucleotide chain.
This chapter discusses nucleotides and nucleic acids. Nucleotides, which consist of three parts, namely, a nitrogenous base, a pentose sugar and a phosphate radical, are a very important group of compounds, since one or more of them participate in practically all biochemical processes. Adenosine diphosphates and triphosphates play an essential role in cellular energy exchanges, as they have a nucleotide-like structure, as do many of the coenzymes. Nucleotides constitute the monomeric units of which nucleic acids are composed; this means that nucleic acids are polynucleotides. Nucleic acids are of two types: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) and are responsible for directing protein synthesis.
They specify the unique sequence of amino acids in any particular protein and, consequently, must be considered as primary molecules on whose existence the existence of proteins depends. However, since the synthesis of nucleic acids depends on enzymes that are themselves proteins, the fundamental evolutionary question arises as to which the biochemical version of the chicken and the egg problem came first. In addition to their role in protein synthesis, nucleic acids transmit genetic information from parents to children and it is believed that the full range of inherited characteristics of any organism is defined in terms of the deoxyribonucleic acid contained in its cells. The single-cell human genome is estimated to have approximately 6.4 billion nucleotides. With so much genetic information stored in a single cell, it needs to be packaged and stored efficiently.
In humans, DNA is packaged in two steps. First, two chains of polynucleotides are linked together by hydrogen bonds, forming a structure that we call a double helix of DNA. The two strings are complementary to each other and one string is designated as a direct chain and the other as the reverse chain. A chain is complementary to another chain when the sequence of one chain is joined to a specific sequence of another chain. Specifically, an adenine in one chain will only be attached to a thymine in the other chain through two hydrogen bonds and the cytosine in one chain will only be linked to a guanine in the other chain through three hydrogen bonds.
During the second step of DNA packaging, double-helical DNA is wrapped around histone proteins and these proteins are packed close together until they form a chromosome. Each normal human cell contains a total of 46 chromosomes that are made up of two sets of 22 chromosomes and a pair of sex chromosomes. Since a normal human cell has two sets of chromosomes, this is called a diploid. An abnormal human cell can have different multiples of chromosomes, called aneuploidy (e.g.
For DNA to be inherited, replication has to occur. Replication occurs when DNA strings are copied, resulting in identical copies of the original (template) DNA. An important concept to understand is that DNA has a directionality, where one end of the DNA chains is the 5′ end (five primes) and the other end is the 3′ end (three primes). By convention, DNA reads from 5′ to 3′, making the oriented strand from 5′ to 3′ the front strand and its complementary strand the reverse strand.
This is important because DNA polymerase adds additional nucleotides during replication at the 3' end and not at the 5' end. By convention, the continuously replicated strand is the main strand and the opposite strand is the lagging strand. The central dogma of molecular genetics is that DNA is transcribed into RNA that is translated into proteins. In transcription, a focus or region of a DNA molecule is copied to form a complementary RNA sequence.
The RNA can be a coding messenger RNA (mRNA), which will serve as a template for protein translation, or it can be a non-coding RNA, such as a microRNA, a ribosomal RNA, a transfer RNA, or ribozymes. During transcription, an RNA polymerase binds to a promoter region located higher than the region of interest on the DNA molecule and RNA polymerase separates the two complementary DNA chains and creates a transcription bubble. RNA polymerase then adds one RNA nucleotide at a time to one strand of the DNA molecule. An RNA nucleotide differs from a DNA nucleotide in that RNA nucleotides have a ribose backbone instead of a deoxyribose skeleton.
In addition, although they have the same nitrogenous bases of guanine, adenine and cytosine, instead of thymine, the nucleotides in RNA have uracil. Once the RNA chain of the gene of interest is synthesized, the hydrogen bonds in the twisted helix of RNA and DNA are broken, freeing the RNA chain from the DNA. The RNA strand is then further processed with the addition of a 5-foot layer, a polyA tail and the splice. A 5-foot layer is a single G that is added to make the 5-foot end look like a 3-foot end, which serves to protect it against exonuclease (an enzyme that attacks and degrades the 5-foot end).).
In addition, the 5' cap can be recognized by a nuclear core complex that allows mRNA to leave the nucleus. Polyadenylation occurs when several adenines are added to the 3' end of an RNA transcript, which is important for mRNA stability, nuclear export and translation. Within the RNA chain there are coding (exons) and non-coding (introns) regions. During splicing, introns are removed from the RNA chain and the remaining exons are rejoined to form the final mRNA product that is translates into a protein.
Nucleoside 5'-monophosphates are sometimes referred to as adenylate, deoxyadenylate, uridylate, guanylate, cytidylate, and thymidylate because of the presence of the phosphate group. The sugar (ribose or deoxyribose) and the base (purine or pyrimidine) together form a nucleoside (ribonucleoside or deoxyribonucleoside) (fig. A water molecule is removed between the hydroxyl of C1′ and the base (N1 of pyrimidine or N9 of purine) and a glucosidic bond (also called an N-glucosidic bond) is formed (fig. In the same way, phosphate binds to sugar by removing a water molecule between the phosphate and the phosphate C5′ hydroxyl, resulting in the formation of a phosphomonoester 5′.
The addition of 1, 2, or 3 phosphates to a nucleoside creates a nucleotide. In other words, a nucleotide is the result of a glucosidic bond between the base and the sugar and a phosphomonoester bond between sugar and phosphoric acid (fig. Nucleotides, in turn, can be linked together by removing a water molecule between the C3′ hydroxyl (also called 3′ hydroxyl) of a nucleotide and the phosphate (5′ phosphate) attached to the 5′ hydroxyl of another nucleotide, thus forming a phosphodiester bond (fig. The intermediate phosphoryl group has the sugars on both sides esterified through a 3' hydroxyl and a 5' hydroxyl, respectively. Under certain conditions (discussed in the chapter), nucleotides assemble one after the other to synthesize a chain of polynucleotides.
The phosphodiester bonds create a repetitive pattern of the sugar and phosphate backbone of the chain. The asymmetry of the nucleotides and the manner in which they bind result in an inherent polarity of the polynucleotide chain with a free 5' phosphate or 5' hydroxyl at one end and a free 3' phosphate or 3' hydroxyl at the other. Both DNA and RNA are polynucleotides that are linked together by phosphodiester bonds between the ribose moiety of the nucleotides. This creates a “ribose-phosphate backbone” and a phosphorylated 5' end; the 3' end has a free 3′-hydroxyl (fig.
Like the primary structure of a polypeptide, polynucleotides have a sequence of side chains, in this case, bases. Polynucleotide chains make up DNA and RNA; in DNA, sugar is deoxyribose, while in RNA, sugar is ribose. In either case, the recurring sugar-phosphate backbone is a “regular feature” of the chain. However, the “irregularity of the chain, and with it the enormous capacity of DNA or RNA to store genetic information, arises from the order of the bases.
Each nucleotide in DNA or RNA has the same sugar, but each nucleotide has only one of the four bases attached to it. In DNA there are two purines, adenine (A) and guanine (G), and two pyrimidines, cytosine (C) and thymine (T). RNA contains uracil (U) instead of thymine (fig. DNA and RNA molecules can be single-stranded (ss; each contains a chain of polynucleotides) or double-stranded (ds; each contains two chains of polynucleotides with base pairs to each other).
Most RNA molecules in the living system are single-stranded; the genetic material of some viruses and small interfering RNA (siRNA) are double-stranded RNA molecules. DNA is mostly double-stranded, two chains of polynucleotides are intertwined together in the form of a double helix (fig. Each strand of the helix consists of alternate sugar and phosphate residues) with the bases that project inward. The two chains are held together, in an antiparallel way (i.e., with opposite polarity), through weak, non-covalent interactions (discussed in Chapter 1 between base pairs).
A can form base pairs with T, while C can form base pairs with G, this Watson-Crick (WC) base pairing is the result of the complementarity between form and hydrogen bonds (see fig. The transition from a state with two separate chains to a double helix state leads to a decrease in entropy. However, the formation of double-stranded DNA is thermodynamically favorable compared to single-stranded DNA. It may initially be thought that the formation of the double helix is primarily driven by hydrogen bonding between the paired bases.
However, before mating, the edges of the unpaired bases are already involved in hydrogen-bonding interactions with surrounding water molecules in the aqueous solution. While hydrogen bonds between unpaired bases in single-stranded DNA and water are enthalpically less favorable than those between paired bases in double-stranded DNA, hybridization between two chains basically replaces one set of hydrogen bonds with another; the overall contribution of hydrogen bonds to double-helix stability is modest. The main contribution to the stability of the double helix comes from the stacking of bases. Bases are flat molecules that are relatively insoluble in water.
In the double-stranded structure, they are stacked on top of each other almost perpendicularly to the direction of the helical axis. Polar bonds are found at the edges of the bases, while their upper and lower surfaces are relatively non-polar. Therefore, when DNA is single-stranded, water forms ordered structures around bases. The formation of duplex DNA releases ordered water molecules, resulting in increased entropy.
Base stacking also enthalpically contributes to the stability of double-stranded DNA by facilitating van der Waals interactions between dipoles that form instantaneously on the hydrophobic surface of bases. Although in the double helix structure of DNA the bases project inwards, they can be accessed through two grooves of unequal width, the largest and the smallest. To understand the basics of groove formation, let's look at the geometry of pairs of bases (fig. In each case, the glucosidic bonds that connect the bases with the sugars form an angle (~ 120° on the narrowest side or 240° on the widest side) between them.
As base pairs are stacked one on top of the other, they rotate ~ 36° on each step (fig. The double helix of DNA can take on more than one conformation (fig. Early X-ray diffraction studies discovered two types of DNA structures in solution, termed forms B and A.Form B is more like the average structure of DNA under physiological conditions. Experimentally, this form is observed at high humidity.
There are about 10 base pairs per turn of the helix. As expected, the main groove is wide and the minor groove is narrow. Form A, on the other hand, is observed at low humidity. It has about 11 base pairs per turn.
Compared to form B, its main groove is narrower but deeper, and its smaller groove is wider and shallower. The cell's DNA isn't always as regular as the idealized “B DNA”.”. There are variations from one base pair to another in the structure. For example, in some cases, two members of a base pair are not in the same plane, but are “twisted” (called “torsion of the propeller”) with respect to each other.
In addition, rotation per base pair is not a constant throughout DNA. However, form B is a good approximation to the structure of cellular DNA and helps explain several macromolecular interactions and functions. Structure A is found in certain protein-DNA complexes. The B-shaped and A-shaped DNA helices are right-handed.
Under certain conditions, DNA containing alternate purine and pyrimidine residues can adopt a left-handed structure. A prominent feature of the left-handed helix relates to the orientation of the purine base around the glucosidic bond. In nucleosides, rotation around the glucosidic bond allows the bases to occupy either of the two main positions syn and anti (fig. In right-handed DNA, the bases are always in the anticonformation.
In left-handed DNA, pyrimidines exist in anticonformation, but purine residues adopt the sinar conformation. The purine-pyrimidine dinucleotide is the fundamental repeating unit of left-handed DNA. The alternation of non-anticonformations gives your spine a “zigzag” appearance, which is why it is called Z-DNA. However, left-handed DNA helices are rarely found in the cell.
It goes without saying that, whatever its shape, B, A or Z, DNA has a flexible structure. The precise molecular parameters of the double helix, such as the number of times the two chains are intertwined with each other, depend on the ionic environment and the nature of the protein that binds to the DNA and forms a complex with it. A linear DNA molecule admits a change in this number, since it can rotate freely. Pallardy, in Physiology of Woody Plants (second edition), 1997 Purine and pyrimidine substituted bases are constituents of many extremely important compounds.
These include nucleic acids (RNA and DNA); nucleosides such as adenosine, guanosine, uridine and cytidine; nucleotides such as AMP, ADP and ATP; nicotinamide nucleotides (NAD+ and NADP+); thiamine; coenzyme A; and cytokinins (see Fig. Nucleotides are phosphated esters of nucleosides, and nucleic acids (DNA and RNA) are high molecular weight polymers made up of long chains of four types of nucleotide units, which in DNA are derived from adenine, guanine, thymine and cytosine. The genetic material of the nucleus is DNA; each molecule is made up of two chains of polynucleotides arranged in a double propeller. In mitochondria and chloroplasts, small amounts of DNA are found outside the nucleus.
These compaction structures guide interactions between DNA and other proteins, helping to control which parts of the DNA are transcribed. The ability to cause two chains of polynucleotides, either DNA or RNA, containing complementary base sequences, to hybridize to form a double helix, has proven to be of great value in various areas of nucleic acid research and technology. Genomic DNA is packaged in a compact and orderly way in a process called DNA condensation, to adapt to the small available volumes of cell. An important difference between DNA and RNA is sugar, since the 2-deoxyribose in DNA is replaced by the related pentose ribose sugar in RNA.
Cell division is essential for an organism to grow, but when a cell divides, it must replicate the DNA in its genome so that the two daughter cells have the same genetic information as their mother. These guanine-rich sequences can stabilize the ends of chromosomes by forming structures of stacked sets of four-base units, instead of the usual base pairs found in other DNA molecules. In this way, four DNA digests are prepared, each containing labeled fragments of various sizes that end at a point originally occupied by a specific base. But it would also seem absurd to argue that dsDNA is not a molecule but is converted into one after, for example, chemical cross-linking.
The most obvious defense against forensic DNA matches is to assert that there has been cross-contamination of evidence. For example, in transcription, when a cell uses information from a gene, the DNA sequence is copied into a complementary RNA sequence through the attraction between the DNA and the correct RNA nucleotides.
