Friday, 24 April 2020

Basic Structure and Function of DNA

Basic Structure and Function of DNA

DNA, Chromosomes, and genomes

The ability of organisms necessary to sustain life depends on the ability of cells to store and translate by translating and retrieving genetic instructions. This hereditary information is passed on from a cell to its daughter cells at cell division, and from one generation of an organism to the next through the organism’s reproductive cells. The instructions are stored within every living cell as its genes, the information-containing elements that determine the characteristics of a species as a whole and of the individuals within it.

As soon as genetics emerged as a science at the beginning of the twentieth century, scientists became intrigued by the chemical structure of genes. The information in genes is copied and transmitted from cell to daughter cell millions of times during the life of a multicellular organism, and it survives the process essentially unchanged. What form of a molecule could be capable of such accurate and almost unlimited replication and also be able to exert precise control, directing multicellular development as well as the daily life of every cell? And how can the enormous amount of information required for the development and maintenance of an organism fit within the tiny space of a cell?.

The answers to several of these questions began to emerge in the 1940s. At this time researchers discovered, from studies in simple fungi, that genetic information consists largely of instructions for making proteins. Proteins are phenomenally versatile macromolecules that perform most cell functions. They serve as building blocks for cell structures and form the enzymes that catalyze most of the cell’s chemical reactions. They also regulate gene expression and they enable cells to communicate with each other and to move The properties and functions of cells and organisms are determined to a great extent by the proteins that they are able to make.

Painstaking observations of cells and embryos in the late nineteenth century had led to the recognition that the hereditary information is carried on chromosomes—threadlike structures in the nucleus of Light microscopy that makes a cell visible by eukaryotic as soon as the cell begins to divide. Later, when the biochemical analysis was possible, the chromosomes were found to contain deoxyribonucleic acid DNA and protein, both of which were present in approximately equal amounts. For many decades, DNA was considered only a structural one. However, the other crucial advance made in the 1940s was the identification of DNA as the likely carrier of genetic information. This breakthrough in our understanding of cells came from studies of inheritance in bacteria.

But still, as the 1950s began, both how proteins could be specified by instructions in the DNA and how this information might be copied for transmission from cell to cell seemed completely mysterious. The puzzle was suddenly solved in 1953 when James Watson and Francis Crick derived the mechanism from their model of DNA structure. The determination of the double-helical structure of DNA immediately solved the problem of how the information in this molecule might be copied, or replicated. It also gave the first clue as to how DNA uses a sequence of its subunits to form a molecule protein and encode a directive. Today, the fact that DNA is the genetic material is so fundamental to biological thought that it is difficult to appreciate the enormous intellectual gap that was filled by this breakthrough discovery.

The DNA structure of the chemical properties of DNA makes it ideally suited as the raw material of genes. This DNA arranges how many proteins and packages in chromosomes. The packing has to be done in an orderly fashion so that the chromosomes can be replicated and apportioned correctly between the two daughter cells at each cell division. And it must also allow access to chromosomal DNA, both for the enzymes that repair DNA damage and for the specialized proteins that direct the expression of its many genes.

In the past two decades, there has been a revolution in our ability to determine the exact order of subunits in DNA molecules. As a result, we now know the sequence of the 3.2 billion nucleotide pairs that provide the information for producing a human adult from a fertilized egg, as well as having the DNA sequences for thousands of other organisms. Detailed analyses of these sequences are providing exciting insights into the process of evolution.

This is the first of four chapters that deal with basic genetic mechanisms—the ways in which the cell maintains, replicates, and expresses the genetic information carried in its DNA. We shall discuss the mechanisms by which the cell accurately replicates and repairs DNA; we also describe how DNA sequences can be rearranged through the process of genetic recombination. Gene expression—the process through which the information encoded in DNA is interpreted by the cell to guide the synthesis of proteins—is we describe how this gene expression is controlled by the cell to ensure that each of the many thousands of proteins and RNA molecules encrypted in its DNA is manufactured only at the proper time and place in the life of a cell.

The Structure and Function of DNA

The molecule seemed too simple: a long polymer composed of only four types of nucleotide subunits, which resemble one another chemically. In the early 1950s, by X-ray analysis of DNA, a technique for determining the three-dimensional atomic structure of a molecule. Initially X-ray diffraction results in two strands of DNA polymer lesion formed in the helix. The observation that DNA was double-stranded provided one of the major clues that led to the Watson–Crick model for DNA structure that, as soon as it was proposed in 1953, made DNA’s potential for replication and information storage apparent.

The nucleotide DNA molecule has two complementary chains

Deoxyribonucleic acid (DNA) the molecule consists of two long polynucleotide chains composed of four types of nucleotide subunits. The chains run antiparallel to each other, and hydrogen bonds between the base portions of the nucleotides hold the two chains together nucleotides are composed of a five-carbon sugar to which are attached one or more a nitrogen-containing based and phosphate groups. Among nucleotides, a single phosphate group is deoxyribose attached to sugar, and its base may be either adenine (A), cytosine (C), guanine (G), or thymine (T). Nucleotides are covalently linked together in a series of phosphates and sugars, which thus "sugar" the sugar-phosphate-sugar-phosphate alternatively. Because only the base differs in each of the four types of nucleotide subunit, each polynucleotide chain in DNA is analogous to a sugar-phosphate necklace (the backbone), from which hang the four types of beads the bases A, C, G, and T. These same symbols A, C, G, and T) are commonly used to denote either the four bases or the four entire nucleotides—that is, the bases with their attached sugar and phosphate groups.
Building blocks of DNA diagram
Fig. DNA and its building blocks

The way in which the nucleotides are linked together gives a DNA strand a chemical polarity. If we think of each sugar as a block with a protruding knob (the 5 ʹ phosphates) on one side and a hole (the 3 ʹ hydroxyls) each completed Interlocking series with holes made by knobs, all of its subunits will be lined up in the same orientation.  Moreover, the two ends of the chain will be easily distinguishable, as one has a hole (the 3 ʹ hydroxyls) and the other a knob (the 5 ʹ phosphates) at its terminus. This polarity in a DNA chain is indicated by referring to one end as the 3 ʹ ends and the other as the 5 ʹ ends, names derived from the orientation of the deoxyribose sugar. With respect to DNA’s information-carrying capacity, the chain of nucleotides in a DNA strand, being both directional and linear, can be read in much the same way as the letters on this page.
DNA Complementary base pairs diagram

Fig.  Complementary base pairs in the DNA double helix.

The three-dimensional structure — the double helix of DNA — arises from the structural and chemical characteristics of its two polynucleotide chains. Because the two chains are held together by hydrogen bonding based on different strands, all the bases are inside the double helix, and the sugar-phosphate backbones are paired with a single-ring base (a pyrimidine): A always pairs with T, and G with C.This complementary base-pairing enables the base pairs to be packed in the interior of the double helix has the most energetically friendly arrangement. In this arrangement, each base pair is of similar width, thus holding the sugar-phosphate backbones a constant distance apart along the DNA molecule. To maximize the efficiency of base-pair packing, the two sugar-phosphate backbones wind around each other to form a right-handed double helix, with one complete turn every ten base pairs.

The members of each base pair can fit together within the double helix only if the two strands of the helix are antiparallel—that is, only if the polarity of one Is oriented opposite to the other strand. A consequence of DNA’s structure and base-pairing requirements is that each strand of a DNA molecule contains a sequence of nucleotides that is exactly complementary to the nucleotide sequence of its partner strand.

DNA structure for the mechanism of heredity

The discovery of the structure of DNA immediately suggested answers to the two most fundamental questions about heredity. First, how could the information specify an organism be carried in a chemical form? And second, how could this information be duplicated and copied from generation to generation?
The answer to the first question came from the realization that DNA is a linear polymer of four different kinds of monomer, strung out in a defined sequence like the letters of a document written in an alphabetic script.

The answer to the second question came from the double-stranded nature of the structure: because each strand of DNA contains a sequence of nucleotides that is exactly complementary to each strand can serve as a template for the synthesis of a strand complementary to the nucleotide sequence of its new partner strand. In other words, if we designate the two DNA strands as S and S ʹ, strand  S can serve as a template for making a new strand S ʹ, while strand S ʹ can serve as a template for making a new strand S.Thus, the genetic information in DNA can be accurately copied by the beautifully simple process in which strand S separates from strand S ʹ, and each separated strand then serves as a template for the production of a new complementary partner strand that is identical to its former partner.
DNA double helix diagram

Fig. The DNA double helix

The ability of each strand of a DNA molecule to act as a template for producing a complementary strand enables a cell to copy or replicate, its genome before passing it on to its descendants. We shall describe the elegant machinery that the cell uses to perform this DNA. Before determining the structure of DNA, genes contain instructions for the production of proteins. If genes are made of DNA, the DNA must therefore somehow encode proteins. A protein that is responsible for a biological function is characterized by its three-dimensional structure. This structure is determined in turn by the linear sequence of the amino acids of which it is composed. The exact correspondence between the four-letter nucleotide alphabet of DNA and the twenty-letter amino acid alphabet of proteins—the genetic code—is not at all obvious from the DNA structure. We will describe this code in detail in the course of elaborating the process of gene expression, through which a cell converts the nucleotide sequence of an RNA molecule first consists of genes, then an amino acid sequence of the protein.
 Duplication of DNA diagram

Fig. DNA as a template for its own duplication

The complete store of information in an organism’s DNA is called its genome, and it specifies all the RNA molecules and proteins that the organism will ever synthesize. The amount of information contained in genomes is staggering. The nucleotide sequence of a very small human gene, written out in the four-letter nucleotide alphabet, while the complete sequence of nucleotides in the human genome would fill more In addition to other critical information, it includes roughly 21,000 protein-coding genes, which give rise to a much greater number of distinct proteins.

In Eukaryotes, DNA Is Enclosed in a Cell Nucleus

Nearly all the DNA in a eukaryotic cell is sequestered in a nucleus, which in many cells occupies about 10% of the total cell volume. This compartment is delimited by a nuclear envelope formed by two concentric lipid bilayer membranes. These membranes are punctured at intervals by large nuclear pores, through which molecules move between the nucleus and the cytosol. The nuclear envelope is directly connected to the extensive system of intracellular membranes called the endoplasmic reticulum, which extends out from it into the cytoplasm. And it is mechanically supported by a network of intermediate filaments called the nuclear lamina—a thin feltlike mesh just beneath the inner nuclear membrane.
The nuclear envelope allows the many proteins that act on DNA to be concentrated where they are needed in the cell, and it also keeps nuclear and cytosolic enzymes separate, a feature that is crucial for the proper functioning of eukaryotic cells.

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