Deoxyribonucleic Acid (DNA)
DNA is the hereditary material found in the nucleus of eukaryotic cells (animal and plant) and the cytoplasm of prokaryotic cells (bacteria) that determines the composition of the organism. DNA is found in the nucleus of cell (where it is called nuclear DNA), but a small amount of DNA can also be found in the mitochondria (where it is called mitochondrial DNA or mtDNA) and cytoplasm (where it is called cytoplasmic DNA or ctDNA), and it is exactly the same in each cell.
The information in DNA is stored as a code made up of four chemical bases: adenine (A), guanine (G), cytosine (C), and thymine (T). Human DNA consists of about 3 billion bases, and more than 99 percent of those bases are the same in all people. The order, or sequence, of these bases determines the information available for building and maintaining an organism.
DNA bases pair up with each other, A with T and C with G, to form units called base pairs. Each base is also attached to a sugar molecule and a phosphate molecule. Together, a base, sugar, and phosphate are called a nucleotide. Nucleotides are arranged in two long strands that form a spiral called a double helix. The structure of the double helix is somewhat like a ladder, with the base pairs forming the ladder’s rungs and the sugar and phosphate molecules forming the vertical sidepieces of the ladder.
An important property of DNA is that it can replicate, or make copies of itself. Each strand of DNA in the double helix can serve as a pattern for duplicating the sequence of bases. This is critical when cells divide because each new cell needs to have an exact copy of the DNA present in the old cell.
DNA is a double helix formed by base pairs attached to a sugar-phosphate backbone.
Ribonucleic Acid (RNA)
There is another type of genetic material found in cells and viruses known as ribonucleic acid (RNA). RNA is a polymeric molecule essential in various biological roles in coding, decoding, regulation, and expression of genes. Unlike DNA it is more often found in nature as a single-strand folded onto itself, rather than a paired double-strand. Double-stranded RNA (dsRNA) is RNA with two complementary strands, similar to the DNA found in all cells. dsRNA forms the genetic material of some viruses (double-stranded RNA viruses)
RNA was the first genetic molecule
Experiments in the 1960s showed that the first genetic material was RNA not DNA. Thomas Cech and Altman found that RNA can carry out a number of enzyme like catalytic functions. Cech called these RNA catalysts ribozymes.
Messenger RNA has the ability to store genetic information, while transfer and ribosomal RNA have the ability to translate genetic information into proteins. Experiments performed two decades later showed that some RNAs can even act as an enzyme to self-edit their own genetic code.
RNA has great capability as a genetic molecule; it once had to carry on hereditary processes on its own. It now seems certain that RNA was the first molecule of heredity, so it evolved all the essential methods for storing and expressing genetic information before DNA came onto the scene. However, single-stranded RNA is rather unstable and is easily damaged by enzymes. By essentially doubling the existing RNA molecule, and using deoxyribose sugar instead of ribose, DNA evolved as a much more stable form to pass genetic information with accuracy.
DNA as the Genetic Material
As the DNA is located in nucleus and it is subsequently identified as a component of chromosomes it was implicated as a carrier of genetic information.
Bacterial transformation implicates DNA as the substance of genes
The first unambiguous evidence that DNA was the hereditary material came from Frederick Griffith’s studies in 1928. Griffith used chemical mutagens to isolate a nonvirulent form of the bacterium that causes pneumonia, Diplococcus pneumoniae. Virulence required the presence of a polysaccharide capsule around the bacterium. The nonvirulent mutants lacked this capsule. Colonies of nonvirulent capsuleless bacteria appeared rough and were designated R. In contrast, the virulent form produced colonies that appeared smooth, so it was designated S. Several virulent forms were known, each with a characteristic polysaccharide capsule (called IS, IIS, IIIS, etc.), which is genetically inherited and is immunologically distinct from other forms. A smooth bacterium of a particular capsule type (say IIS) can mutate to a non-encapsulated, nonvirulent form (IIR, because it derives from a type II cell).
This happens at a very low frequency (in less than one in a million cells), but it is inherited when it does occur. Similarly, the IIR cell can mutate back to the IIS virulent form at low frequency. However, the IIR cell line cannot mutate to an IIIS virulent form. This property provides the key to the experiment.
Griffith mixed Pneumococcus type IIR with IIS cells that had been killed and rendered nonvirulent by heating them to 65°C, and he injected them into a host rabbit or, in other experiments, into a mouse. Neither strain injected alone produced disease, nor was a disease expected from the mixed injections, as neither strain was virulent. However, many of the rabbits given mixed injections did come down with pneumonia and died. When analyzed, they all contained living virulent type IIIS cells! These cells could not have arisen from the type IIR cells by mutations (they would have produced type IIS cells), and the type IIIS cells were demonstrably dead (injected alone they caused no disease). Some factor must have passed from the dead IIIS cells to the live IIR ones, endowing them with the ability to make a capsule of the III type. Griffith called the factor “transforming principle” and the process genetic transformation.
The chemical make-up of protein and of DNA is quite different. Hershey and Chase used these differences to distinguish between them. DNA contains phosphorus and proteins do not; proteins, on the other hand, usually contain sulfur, and DNA does not. By specifically labeling the phosphorus and sulfur atoms with radioisotopes, Hershey and Chase could distinguish.
Avery, MacLeod, McCarty Experiment: Identity of the Transforming Principle
The Avery–MacLeod–McCarty experiment was an experimental demonstration, reported in 1944 by Oswald Avery, Colin MacLeod, and Maclyn McCarty, that DNA, the key component of Griffith’s experiment ,is the substance that causes bacterial transformation. Oswald Avery, C. M. MacLeod, and M. J. McCarty succeeded in isolating a highly purified preparation of DNA from the type IIIS bacteria. The preparation of this type IIIS DNA was fully active as a transforming agent and could transform type IIR cells into type IIIS cells in a test tube. If the DNA was destroyed by deoxyribonuclease (an enzyme that specifically attacks DNA), all transforming activity was lost. It therefore seemed clear that DNA was “functionally active in determining the biochemical activities and specific characteristics of pneumococcal cells.” These experiments by themselves, however, do not establish that DNA is itself the genetic material.
HERSHEY AND CHASE’S EXPERIMENT
These experiments that clearly linked DNA and heredity were those performed by Alfred Hershey and Martha Chase in 1952. They chose to explore the genetic properties of DNA using bacterial viruses. Viruses are small, very simple aggregates of nucleic acid and protein. Several types of viruses attack bacteria and are known as bacteriophages (literally: “bacteria-eaters”). One of the viruses that attacks the bacterium Escherichia coli is the bacteriophage T2. It contains only protein and DNA; the DNA forms the central core of the virus, while the protein surrounds the core like a coat.
Phages infect bacteria by adsorbing to the cell walls and injecting the genetic material into the bacteria. This material causes the production of many new viruses within the cell. Eventually the cell is ruptured (lysed), and the new viruses are released.
Unambiguously between the protein and the DNA of the phage and determine whether either or both were injected into the bacterial cell during the course of infection. When bacteriophage labeled with 32P DNA were allowed to infect a cell, almost all the label entered the cell. If such infected cells were allowed to lyse, the label was found among the progeny viruses.
The opposite occurred when 35S-labeled phage infected a bacterial culture. Almost all label remains on the outside of the bacterium, bound to fragments of the cell wall. A small amount of protein did enter the bacterial cell in the course of infection. That this was not involved in the production of new bacteriophage could be demonstrated by repeating the experiment with bacteria stripped of their cell walls (protoplasts). If protoplasts were infected with 32P phage DNA free of protein, virulent phage were produced. If the purified 32P was first treated with DNAase, no progeny phage were produced. Clearly the labeled DNA contained all the information necessary to produce new virus particles.
DNA replication is a fundamental aspect of cell biology. The process is essential for chromo‐ some doubling and segregation during cell division. The formation of DNA from DNA is called DNA replication. At each cell division, a cell must copy its genome with extraordinary accuracy. In this section, we explore how the cell achieves this feat, while duplicating its DNA
The Watson-Crick Model: DNA is a double helix
Double helical structure.
• The two strands are antiparallel
• It is a right handed helix, this structure is called the B DNA.
• Complementary base pairing:
– Three hydrogen bonds between C and G;
– Two hydrogen bonds between A and T.
• The arrangement of the nitrogen bases determines the genetic message.
• At each position, there are 4 possibilities, therefore for a 100 base pair long molecule of DNA, there are 4100 variations possible.
Chargaff’s rules states that DNA from any cell of all organisms should have a 1:1 ratio of pyrimidine and purine bases and, more specifically, that the amount of guanine is equal to cytosine and the amount of adenine is equal to thymine.
· A=T and G=C
A+T does not have to equal G+C
At rates as high as 1000 nucleotides per second. Base-Pairing
|Enables DNA Replication. Each strand of a DNA double helix contains a sequence of nucleotides that is exactly complementary to the nucleotide sequence of its partner strand. Each strand can therefore serve as a template, or mold, for the synthesis of a new complementary strand. In other words, if we designate the two DNA strands as S and Sʹ, strand S can serve as a template for making a new strand Sʹ, while strand Sʹ 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 Sʹ, 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. 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 genes before passing them on to its descendants. But the task is awe-inspiring, as it can involve copying billions of nucleotide pairs every time a cell divides. The copying must be carried out with incredible speed and accuracy: in about 8 hours, a dividing animal cell will copy the equivalent of 1000 books like this one and, on average,
get no more than a letter or two wrong. This impressive feat is performed by a cluster of proteins that together form a replication machine.
DNA replication produces two complete double helices from the original DNA molecule, with each new DNA helix being identical (except for rare copying errors) in nucleotide sequence to the original DNA double helix. Because each parental strand serves as the template for one new strand, each of the daughter DNA double helices ends up with one of the original (old) strands plus one strand that is completely new; this style of replication is said to be semiconservative. In How We Know, pp. 200–202, we discuss the experiments that first demonstrated that DNA is replicated in this way
The gene is the basic physical and functional unit of heredity. It consists of a specific sequence of nucleotides at a given position on a given chromosome that codes for a specific protein (or, in some cases, an RNA molecule). Genes consist of three types of nucleotide sequence: coding regions, called exons, which specify a sequence of amino acids non-coding regions, called introns, which do not specify amino acids regulatory sequences, which play a role in determining when and where the protein is made (and how much is made) A human being has 20,000 to 25,000 genes located on 46 chromosomes (23 pairs). These genes are known, collectively, as the human genome.
Eukaryotic chromosomes The label eukaryote is taken from the Greek for ‘true nucleus’, and eukaryotes (all organisms except viruses, Eubacteria and Archaea) are defined by the possession of a nucleus and other membrane-bound cell organelles. The nucleus of each cell in our bodies contains approximately 1.8 metres of DNA in total, although each strand is less than one millionth of a centimetre thick. This DNA is tightly packed into structures called chromosomes, which consist of long chains of DNA and associated proteins. In eukaryotes, DNA molecules are tightly wound around proteins – called histone proteins – which provide structural support and play a role in controlling the activities of the genes. A strand 150 to 200 nucleotides long is wrapped twice around a core of eight histone proteins to form a structure called a nucleosome. The histone octamer at the centre of the nucleosome is formed from two units each of histones H2A, H2B, H3, and H4. The chains of histones are coiled in turn to form a solenoid, which is stabilised by the histone H1. Further coiling of the solenoids forms the structure of the chromosome proper. Each chromosome has a p arm and a q arm. The p arm (from the French word ‘petit’, meaning small) is the short arm, and the q arm (the next letter in the alphabet) is the long arm. In their replicated form, each chromosome consists of two chromatids. The chromosomes – and the DNA they contain – are copied as part of the cell cycle, and passed to daughter cells through the processes of mitosis and meiosis. Human beings have 46 chromosomes, consisting of 22 pairs of autosomes and a pair of sex chromosomes: two X sex chromosomes for females (XX) and an X and Y sex chromosome for males (XY). One member of each pair of chromosomes comes from the mother (through the egg cell); one member of each pair comes from the father (through the sperm cell). A photograph of the chromosomes in a cell is known as a karyotype. The autosomes are numbered 1-22 in decreasing size order.
The prokaryotes (Greek for ‘before nucleus’ – including Eubacteria and Archaea) lack a discrete nucleus, and the chromosomes of prokaryotic cells are not enclosed by a separate membrane. Most bacteria contain a single, circular chromosome. (There are exceptions: some bacteria – for example, the genus Streptomyces – possess linear chromosomes, and Vibrio cholerae, the causative agent of cholera, has two circular chromosomes.) The chromosome – together with ribosomes and proteins associated with
Gene expression – is located in a region of the cell cytoplasm known as the nucleoid. The genomes of prokaryotes are compact compared with those of eukaryotes, as they lack introns, and the genes tend to be expressed in groups known as operons. The circular chromosome of the bacterium Escherichia coli consists of a DNA molecule approximately 4.6 million nucleotides long. In addition to the main chromosome, bacteria are also characterised by the presence of extrachromosomal genetic elements called plasmids. These relatively small circular DNA molecules usually contain genes that are not essential to growth or reproduction.
Genetic code contains the information of the protein manufactured from RNA. It is the sequence of base pairs for amino acids that code for protein to be synthesised. Thus a change in this sequence can alter the amino acids to be formed. Decoding of the genetic code was a real challenge for scientists.
A physicist named George Gamow suggested a solution to break this challenge. He applied the concepts of permutation and combination to decipher this genetic code. He suggested that genetic code should be made of three nucleotides which code for 20 amino acids with four bases.
Mutation is defined as a change in the genetic code resulting in a loss or gain of a codon. Mutations are triggered by chemical, physical and environmental factors that lead to the addition or deletion or replacement of one or more base pairs of a codon, which, in turn, causes frame-shift mutations and point mutations. In point mutation, only one base is substituted by another base in mRNA template, resulting in a change in the genetic code. Such a change in a single base pair in the gene for the beta globin chain results in a change in amino acid residue glutam
|Four nitrogenous bases and three nucleotides together form a triplet codon which codes for one amino acid. Thus, the number of possible amino acids would be 4 x 4 x 4 = 64. But we have 20 naturally existing amino acids.|
THE TOBACCO MOSAIC VIRUS (TMV)
Some viruses do not contain DNA, being made up instead of protein and RNA (ribonucleic acid). The tobacco mosaic virus (TMV) is such an RNA virus. H. Fraenkel-Conrat and others were able to dissociate the TMV into its constituent protein and RNA parts. When the parts were mixed, they reformed TMV particles that were normal in every respect. That the RNA contained the genetic information was demonstrated by isolating protein and RNA from several different types of TMV, with subsequent combinations of protein and RNA mixed together. These reconstituted viruses, containing protein from one type and RNA from another, were then allowed to infect
Tobacco cells. In every case the progeny TMVs proved to have the protein coats of the type that had contributed the RNA, and not of the type that had contributed the protein. Thus, in the tobacco mosaic virus, the RNA, rather than the protein, must be acting as the genetic material.
ate to valine, which ultimately leads to sickle cell anemia.
In frame-shift mutation, two or more bases are either inserted or deleted from the mRNA template, resulting in the deletion or insertion of a codon. This changes the reading frame only from the point of deletion or insertion.
Frame-shift mutation is common among textile workers, often exposed to acridine dyes, which enters their bodies through inhalation or physical contact. These dyes get intercalated or wedged between two adjacent purines, thus increasing the distance between them from 3.4 angstroms to 6.8 angstroms, leading to frame-shift mutation.