DNA (deoxyribonucleic acid) may be a polymer, a long, chainlike molecule made from subunits called monomers. Many important biological molecules, including not only DNA but also proteins, polysaccharides, and lipids, are polymers of 1 type or another. In DNA, the monomers are called nucleotides, and these are linked together to make a polynucleotide chain which will be hundreds, thousands, or maybe many nucleotides long. First, we'll study the structure of a nucleotide, then we'll examine how nucleotides are joined together to make a polynucleotide.
Nucleotides are the basic units of a DNA molecule
The basic unit of the DNA molecule is that the nucleotide. Nucleotides are found within the cell either as components of nucleic acids or as individual molecules. Nucleotides have several different roles and aren't just wont to make DNA. for instance, some nucleotides are important within the cell as carriers of energy won't power enzymatic reactions. The nucleotide is itself quite a complex molecule, is made from three distinct components. These are sugar, a nitrogenous base, and a phosphate group. We'll check out each of those successively.
The name 2’-deoxyribose indicates that the quality ribose structure has been altered by the replacement of the hydroxyl (–OH) attached to atom number 2’ with a hydrogen group (–H). The carbon atoms are always numbered within the same way, with the carbon of the group (–C=O), which occurs at one end of the chain structure, numbered 1’. it's important to recollect the numbering of the carbons because it's wont to indicate the positions at which other components of the nucleotide are attached to the sugar. It's also important to understand that the numbers aren't just 1, 2, 3, 4, and 5, but 1’, 2’, 3’, 4’, and 5’. The upper-right stroke is named a “prime,” and therefore the numbers are called “one-prime,” “two-prime,” then on. The prime is employed to differentiate the carbon atoms within the sugar from the carbon and nitrogen atoms within the nitrogenous base, which are numbered 1, 2, 3, and so on.
The nitrogenous bases are single- or double-ring structures that are attached to the 1’ carbon of the sugar. In DNA anybody of 4 different nitrogenous bases is often attached at this position. These are called adenine and guanine, which are double-ring purines, and cytosine and thymine, which are single-ring pyrimidines. the bottom is attached to the sugar by a b-N-glycosidic bond attached to nitrogen no 1 of the pyrimidine or number 9 of the purine.
A molecule comprising the sugar joined to a base is named a nucleoside. this is often converted into a nucleotide by attachment of a phosphate group to the 5’ carbon of the sugar. Up to 3 individual phosphates are often attached serial. The individual phosphate groups are designated a, b, and g, with the phosphate being the one attached to the sugar.
The full names of the four different nucleotides that polymerize to make DNA is:
2’-deoxyadenosine 5’-triphosphate
2’-deoxyguanosine 5’-triphosphate
2’-deoxycytidine 5’-triphosphate
2’-deoxythymidine 5’-triphosphate
Normally, however, we abbreviate these to dATP, dGTP, dCTP, and dTTP, or even just to A, G, C, and T, especially when writing out the sequence of nucleotides found during a particular DNA molecule.
Nucleotides join together to make a polynucleotide
The next stage in the build-up of the structure of a DNA molecule is to link the individual nucleotides together to make a polymer. This polymer is named a polynucleotide and is made by attaching one nucleotide to a different through the phosphate groups. The structure of a trinucleotide, a brief DNA molecule comprising three individual nucleotides. The nucleotide monomers are linked together by joining the phosphate group, attached to the 5’ carbon of 1 nucleotide, to the 3’ carbon of subsequent nucleotide within the chain. Normally a polynucleotide is made up of nucleoside triphosphate subunits, so during polymerization, the b and g phosphates are cleaved off.
The hydroxyl attached to the 3’ carbon of the second nucleotide is additionally lost. The linkage between the nucleotides during a polynucleotide is named a phosphodiester bond, “phospho-” indicating the presence of a phosphorus atom and “diester” pertaining to the 2 ester (C–O–P) bonds in each linkage. To be precise we should always call this a 3’-5’ phosphodiester bond in order that there's no confusion about which carbon atoms within the sugar participate within the bond.
An important feature of the polynucleotide is that the 2 ends of the molecule aren't equivalent. the highest of this polynucleotide ends with a nucleotide during which the triphosphate group attached to the 5’ carbon has not participated during a phosphodiester bond and therefore the b and g phosphates are still in situ. This end is named the 5’-P terminus or just the 5’ terminus. At the opposite end of the molecule, the unreacted group isn't the phosphate but the 3’ hydroxyl. This end is named the 3’-OH or 3’ terminus. The chemical distinction between the 2 ends means polynucleotides have a direction, which may be looked at like 5’ Æ 3’.An important consequence of the polarity of the phosphodiester bond is that the reaction needed to increase a DNA polymer within the 5’ Æ 3’ direction is different from that needed to form a 3’ Æ 5’ extension. All of the enzymes that make new DNA polynucleotides in living cells perform 5’ Æ 3’ synthesis. No enzymes that are capable of catalyzing the reaction needed to form DNA within the other way, 3’ Æ 5’, have ever been discovered.
There is apparently no limit to the number of nucleotides that will be joined together to make a private DNA polynucleotide. Molecules containing several thousand nucleotides are frequently handled within the laboratory, and therefore the DNA molecules in chromosomes are for much longer, sometimes several million nucleotides long. Additionally, there are no chemical restrictions on the order during which the nucleotides can join together. At any point within the chain, the nucleotide might be A, G, C, or T.
In living cells, DNA is a double helix
In living cells, DNA molecules nearly always contain two polynucleotides, wrapped around each other to make the famous double-helix structure discovered by Watson and Crick in 1953. The helix may be a complicated structure, but the key facts about it aren't too difficult to know.
First, we'll check out the essential features of the helix. the 2 polynucleotides within the helix are arranged in such how that their sugar-phosphate “backbones” are on the surface of the helix and their bases are on the within.
The bases are stacked on top of every other rather sort of a pile of plates. the 2 polynucleotides are antiparallel, meaning that they run in several directions, one oriented within the 5’ Æ 3’ direction and therefore the other within the 3’ Æ 5’ direction. The polynucleotides must be antiparallel so as to make a stable helix. Molecules during which the 2 polynucleotides run within the same direction are unknown in nature. The helix is right-handed, so if it were a spiral staircase then the bannister (that is, the sugar-phosphate backbone) would get on your right-hand side as you were climbing upward. the ultimate point is that the helix isn't absolutely regular. Instead, on the surface of the molecule, we will distinguish a serious and a minor groove.
Those are the key facts about the helix. There remains only one additional feature to think about, but this one is that the most vital of all. Within the helix, an adenine in one polynucleotide is usually adjacent to thymine within the other strand, and similarly, guanine is usually adjacent to cytosine. this is often called base pairing and involves the formation of hydrogen bonds between adenine and thymine, or between cytosine and guanine. A chemical bond may be a weak electrostatic attraction between an electronegative atom (such as oxygen or nitrogen) and an atom attached to a second electronegative atom. the bottom pairing between adenine and thymine involves two hydrogen bonds, which between guanine and cytosine involves three hydrogen bonds.
The two base-pair combinations—A base-paired with T, and G base-paired with C—are the sole ones that are permissible. this is often partly due to the geometries of the nucleotide bases and therefore the relative positions of the atoms that are ready to participate in hydrogen bonds, and partly because the pair must be between a purine and a pyrimidine. A purine–purine pair would be too big to suit within the helix, and a pyrimidine–pyrimidine pair would be too small. due to the bottom pairing, the sequences of the 2 polynucleotides within the helix are complementary—the sequence of 1 polynucleotide determines the sequence of the opposite.
The double helix exists in several different forms
The double helix is mentioned because of the B-form of DNA. This is often the structure that was studied by Watson and Crick, and it represents far and away from the foremost common sort of DNA in living cells, but it's not the sole version that's known. Other versions are possible because the three-dimensional structure of a nucleotide isn't entirely rigid. For instance, the orientation of the bottom relative to the sugar is often changed by rotation around the b-N-glycosidic bond. This features a significant effect on the helix because it alters the relative positioning of the 2 polynucleotides. The relative positions of the carbons within the sugar also can be changed slightly, affecting the conformation of the sugar-phosphate backbone.
The common, B-form of DNA has 10 base pairs (abbreviated as 10 bp) per turn of the helix, with 0.34 nm between adjacent base pairs and hence a pitch (the distance needed for one complete turn) of three .40 nm. The diameter of the helix is 2.37 nm. The second sort of DNA helix to be discovered, called the A-form, is more compact, with 11 bp per turn, 0.29 nm between each two base pairs, and a diameter of two .55 nm. But comparing these dimensions doesn't reveal what's probably the foremost significant difference between these two conformations of the helix.
This is the extent to which the interior regions of the DNA molecule are accessible from the surface of the structure. A-DNA, just like the B-form, has two grooves, but with A-DNA the main groove is even deeper, and therefore the minor groove shallower and broader. The expression of the biological information contained within a DNA molecule is mediated by DNA-binding proteins that attach to the helix and regulate the activity of the genes contained within it. to hold out their function, each DNA-binding protein must attach at a selected position, on the brink of the gene whose activity it must influence. The protein is able to do this, with a minimum of a point of accuracy, by reaching down into a groove, within which it can “read” the DNA sequence without opening up the helix by breaking the bottom pairs. this is often possible with B-DNA, but easier with A-DNA because the bases are more exposed within the minor groove. it's been suggested that some DNA-binding proteins induce the formation of a brief stretch of A-DNA once they attach to a DNA molecule.
A third type, Z-DNA, is more strikingly different. during this structure the helix is left-handed, not right-handed because it is with A- and B-DNA, and therefore the sugar-phosphate backbone adopts an irregular zigzag conformation. Z-DNA is more tightly wound, with 12 bp per turn and a diameter of just one .84 nm. It's thought to make around regions of B-DNA that became slightly unwound, as occurs when a gene is being transcribed into RNA. Unwinding leads to torsional stress, which could be relieved to some extent by forming the more compact Z version of the helix.
References :
An Introduction to genetics by Terry Brown.
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