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How do cells determine RNA types?

How do cells determine RNA types?



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I was reading about the different types of RNA polymerases, and I am confused as to how a cell determines which type of RNA it is transcribing.

According to this nature article:

RNA pol I transcribes ribosomal RNAs (rRNAs), RNA pol II transcribes RNAs that will become messenger RNAs (mRNAs) and also small regulatory RNAs, and RNA pol III transcribes small RNAs such as transfer RNAs (tRNAs)

The system as to how the different types of RNA polymerase are selected makes sense to me, the core promoter's sequence determines the affinity of the polymerase to itself.

But, how does RNA polymerase II determine if the transcript is a regulatory RNA or a messenger RNA? Can someone explain that process to me or point me to where I would find it?

Another question: When RNA polymerases I and III transcribe their RNA, what prevents the cell from processing them the same way as mRNA and sending it off to a ribosome with a poly-a tail?


Well remember that an mRNA, the RNA that is destined for the ribosome, has already been processed by the time it gets there. This is done by the splicing machinery, among other things (capping enzymes, for example). But the splicing machinery isn't smart in itself. Rather, the gene has the elements, just like it does to select the RNA Pol it needs, to direct the sort of modification the RNA needs to obtain. The image below depicts two types of RNA transcribed by RNA Pol II and how the processing elements let the modification machinery know how to handle them:

Source


The structure of biological molecules

Cells are largely composed of compounds that contain carbon. The study of how carbon atoms interact with other atoms in molecular compounds forms the basis of the field of organic chemistry and plays a large role in understanding the basic functions of cells. Because carbon atoms can form stable bonds with four other atoms, they are uniquely suited for the construction of complex molecules. These complex molecules are typically made up of chains and rings that contain hydrogen, oxygen, and nitrogen atoms, as well as carbon atoms. These molecules may consist of anywhere from 10 to millions of atoms linked together in specific arrays. Most, but not all, of the carbon-containing molecules in cells are built up from members of one of four different families of small organic molecules: sugars, amino acids, nucleotides, and fatty acids. Each of these families contains a group of molecules that resemble one another in both structure and function. In addition to other important functions, these molecules are used to build large macromolecules. For example, the sugars can be linked to form polysaccharides such as starch and glycogen, the amino acids can be linked to form proteins, the nucleotides can be linked to form the DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) of chromosomes, and the fatty acids can be linked to form the lipids of all cell membranes.

Approximate chemical composition of a typical mammalian cell
component percent of total cell weight
water 70
inorganic ions (sodium, potassium, magnesium, calcium, chloride, etc.) 1
miscellaneous small metabolites 3
proteins 18
RNA 1.1
DNA 0.25
phospholipids and other lipids 5
polysaccharides 2

Aside from water, which forms 70 percent of a cell’s mass, a cell is composed mostly of macromolecules. By far the largest portion of macromolecules are the proteins. An average-sized protein macromolecule contains a string of about 400 amino acid molecules. Each amino acid has a different side chain of atoms that interact with the atoms of side chains of other amino acids. These interactions are very specific and cause the entire protein molecule to fold into a compact globular form. In theory, nearly an infinite variety of proteins can be formed, each with a different sequence of amino acids. However, nearly all these proteins would fail to fold in the unique ways required to form efficient functional surfaces and would therefore be useless to the cell. The proteins present in cells of modern animals and humans are products of a long evolutionary history, during which the ancestor proteins were naturally selected for their ability to fold into specific three-dimensional forms with unique functional surfaces useful for cell survival.

Most of the catalytic macromolecules in cells are enzymes. The majority of enzymes are proteins. Key to the catalytic property of an enzyme is its tendency to undergo a change in its shape when it binds to its substrate, thus bringing together reactive groups on substrate molecules. Some enzymes are macromolecules of RNA, called ribozymes. Ribozymes consist of linear chains of nucleotides that fold in specific ways to form unique surfaces, similar to the ways in which proteins fold. As with proteins, the specific sequence of nucleotide subunits in an RNA chain gives each macromolecule a unique character. RNA molecules are much less frequently used as catalysts in cells than are protein molecules, presumably because proteins, with the greater variety of amino acid side chains, are more diverse and capable of complex shape changes. However, RNA molecules are thought to have preceded protein molecules during evolution and to have catalyzed most of the chemical reactions required before cells could evolve (see below The evolution of cells).


Genes: The DNA Sentence

A gene is a set of nucleotides (DNA "words") which constitutes a unit of hereditary information. Each of the chromosomes within the nucleus of a human cell contains thousands of genes. All of the DNA contained on the 23 pairs of chromosomes within a single human cell contains all of the 80,000 genes (and therefore all of the genetic instructions) that make up the human genome.

But what do we mean by "a unit of hereditary information?" A more precise definition of a gene is a region of DNA that is transcribed. Transcription, a biological process that is carried out by enzymes, is the first step of the Protein Synthesis process. As its name implies, the protein synthesis process results in the production of a protein. Proteins are the biological molecules that give living cells their diverse forms and functions. So, a gene is a sequence of A's, T's, C's and G's - in a particular order - that codes for a defined biochemical function, usually through the production of a particular protein. It is the proteins produced using genes as atemplate, that are responsible for the characteristics of a particular cell or organism.

Genes have specific jobs, at specific times. Not all genes are "turned on" all the time. For example, many genes are turned on' (causing proteins to be produced) only during the development of the human fetus. Once the child is born, the proteins associated with these particular genes are no longer needed, and the genes are "turned off," perhaps never to be used again, except when passed on to future generations.

Other genes are turned on' only in times when they are needed by the body. As an example, a gene for producing insulin is regulated by the amount of glucose (sugar) in a person's bloodstream. Following the consumption of a meal, there is a higher concentration of glucose in the blood, which triggers higher levels of insulin being produced by pancreatic cells. Insulin stimulates the uptake of glucose by tissues like skeletal muscle and adipose (fatty) tissue, which brings the concentration of glucose in the bloodstream back to normal levels. Once the blood-glucose level has returned to normal, the amount of insulin secreted by pancreatic cells is also reduced.


How do cells determine RNA types? - Biology

The central dogma focuses on the production of the great nucleic acid and protein polymers of biology. However, the control and maintenance of the functions of the cell depends upon more than just synthesis of new molecules. Degradation is another key process in the lives of the macromolecules of the cell and is itself tightly controlled. Indeed, in the simplest model of mRNA production, the dynamics of the average level of mRNA is given by

where r is the rate of mRNA production and γ is the rate constant dictating mRNA decay. The steady-state value of the mRNA is given by

showing that to first approximation, it is the balance of the processes of production and decay that controls the steady-state levels of these molecules. If our equation is for the copy number of molecules per cell, there will be an abrupt change in the number each time the cells divide since the total mRNA and protein content is partitioned between the two daughter cells. If instead our equation is thought of in the language of concentrations, we do not have to face this problem because as the cell grows, so too does the number of molecules and hence the concentration varies smoothly. The growth effect on concentration can be absorbed into the rate constant for degradation to take account of the dilution. This is a common mathematically elegant solution but not immediately intuitive, and so we will try to clarify it below. But first, what are the characteristic values for mRNA and protein degradation times?

Figure 1: Measured half lives of mRNAs in E. coli, budding yeast and mouse NIH3T3 fibroblasts. (A, adapted from J. A. Bernstein et al., Proc. Natl Acad. Sci. USA 99:9697, 2002 B, adapted from Y. Wang et al., Proc. Natl Acad. Sci. USA 99:5860, 2002 C. adapted from B. Schwanhausser, Nature, 473:337, 2013).

The lifetime of mRNA molecules is usually short in comparison with the fundamental time scale of cell biology defined by the time between cell divisions. As shown in Figure 1A, for E. coli, the majority of mRNA molecules have lifetimes between 3 and 8 minutes. The experiments leading to these results were performed by inhibiting transcription through the use of the drug rifampicin that interacts with the RNA polymerase and then querying the cells for their mRNA levels in two minute intervals after drug treatment. In particular, the RNA levels were quantified by hybridizing with complementary DNAs on a microarray and measuring the relative levels of fluorescence at different time points. These degradation times are only several times longer than the minimal time required for transcriptional and translational elongation as discussed in the vignette on “What is faster, transcription or translation?”. This reflects the fleeting existence of some mRNA messages.

Given such genome-wide data, various hypotheses can be explored for the mechanistic underpinnings of the observed lifetimes. For example, is there a correlation between the abundance of certain messages and their decay rate? Are there secondary structure motifs or sequence motifs that confer differences in the decay rates? One of the big surprises of the measurements leading to Figure 1A is that none of the conventional wisdom on the origins of mRNA lifetime was found to be consistent with the data, which revealed no clear correlation with secondary structure, message abundance or growth rate.

Figure 2: L’éléphant et l’Escheria Coli, décembre 1972. “Tout ce qui est vrai pour le Colibacille est vrai pour l’éléphant”, or in English “What is true for the E. coli is true for the elephant”. From: http://www.pasteur.fr/infosci/ archives/mon/im_ele.html

How far does Monod’s statement that “what is true for E. coli is true for the elephant” (depicted by Monod in Figure 2) take us in our assessment of mRNA lifetimes in other organisms? The short answer is not very. Whereas the median mRNA degradation lifetime is roughly 5 minutes in E. coli, the mean lifetime is ≈20 minutes in the case of yeast (see Figure 1B) and 600 minutes (BNID 106869) in human cells. Interestingly, a clear scaling is observed with the cell cycle times for these three cell types of roughly 30 minutes (E. coli), 90 minutes (budding yeast) and 3000 minutes (human), under the fast exponential growth rates that the cells of interest were cultivated in for these experiments. As a rule of thumb, these results suggest that the mRNA degradation time scale in these cases is thus about a fifth of the fast exponential cell cycle time.

Messenger RNA is not the only target of degradation. Protein molecules are themselves also the target of specific destruction, though generally, their lifetimes tend to be longer than the mRNAs that lead to their synthesis, as discussed below. Because of these long lifetimes, under fast growth rates the number of copies of a particular protein per cell is reduced not because of an active degradation process, but simply because the cell doubles all its other constituents and divides into two daughters leaving each of the daughters with half as many copies of the protein of interest as were present in the mother cell. To understand the dilution effect, imagine that all protein synthesis for a given protein has been turned off while the cell keeps on doubling its volume and shortly thereafter divides. In terms of absolute values, if the number of copies of our protein of interest before division is N, afterwards it is N/2. In terms of concentrations, if it started with a concentration c, during the cell cycle it got diluted to c/2 by the doubling of the volume. This mechanism is especially relevant in the context of bacteria where the protein lifetimes are often dominated by the cell division time. As a result, the total protein loss rate α (the term carrying the same meaning as γ for mRNA) is the sum of a part due to active degradation and a part due to the dilution that occurs when cells divide and we can write the total removal rate in the form α=αactivedilution.

The statement that protein lifetimes in rapidly growing bacteria are longer than the cell cycle itself is supported by measurements already from the 1960s where radioactive labeling was used as a way to measure rates. In this case, degradation of labeled proteins was monitored by looking at the accumulation of radioactive amino acids in a rapidly exchanged perfusate. Only 2-7% of the proteome was estimated to be actively degraded, with a half-life of about 1 hour (BNID 108404). More recently, studies showed specific cases of rapid degradation including some sigma factors, transcription factors, and cold shock proteins, yet the general statement that dilution is the dominant protein loss mechanism in bacteria remains valid.

Figure 3: Measured half lives of proteins in budding yeast and a HeLa human cancer cell line. The yeast experiment used the translation inhibitor cycloheximide which disrupts normal cell physiology. The median half life of the 4100 proteins measured in the non-dividing HeLa cell is 36 hours. (A, adapted from A. Belle et al., Proc. Natl Acad. Sci. USA 103:13004, 2006 B, adapted from S. Cambridge et al, J. Proteome Res. 10:5275, 2011.)

Just like with the genome-wide studies of mRNA lifetimes described above, protein lifetimes have been subjected to similar scrutiny. Surprisingly, we could not find genome-wide information in the literature on the degradation times for proteins in E. coli but in budding yeast, a translation-inhibition drug (cycloheximide) was used to inhibit macromolecular synthesis and then protein content was quantified at later time points using Western blots. The Western blot technique is a scheme in which the proteins of interest are fished out by specific binding to some part of the protein (for example by antibodies) and the amount of protein is read off of the intensity of a reporter which has been calibrated against a standard. Inhibiting translation might cause artifacts, but with that caveat in mind, the measured lifetimes shown in Figure 3A using the method of translation-inhibition reveal the longer lifetimes of proteins in comparison with their mRNA counterparts, with a mean lifetime of roughly 40 minutes (BNID 104151). Issues with precision of these results still calls for the development of new methods for constructing such surveys.

Figure 4: Distribution of 100 proteins from a H1299 human cell line, comparing the rate of degradation to dilution to find which removal mechanism is dominant for each of the proteins. The overall removal rate alpha ranges between 0.03 and 0.82 hour-1 with an average of 0.1+/-0.09 hour-1. This is equivalent to half life of ≈7 hours via the relationship half-life, T1/2 = ln(2)/alpha. Adapted from E. Eden et al, Science, 331:764, 2011.

Using modern fluorescence techniques it has become possible to measure degradation rates of human proteins in vivo without the need to lyse the cells. The long removal times observed in human cells are shown in Figure 3B. The measurements were done by fusing the protein of interest to a fluorescent protein. Then, by splitting the population into two groups, one of which is photobleached and the other of which is not, and watching the reemergence of fluorescence in the photobleached population, it is possible to directly measure the degradation time. As shown in Figure 4, for human cells there is an interesting interplay between active degradation and protein removal by dilution. Active degradation half lives were seen to be broadly distributed with the fastest observed turnover of less than an hour and the slowest showing only negligible active degradation in the few days of time lapse microscopy. These results can be contrasted with a prediction based on the N-end rule that states that the amino acid at the N terminal of the protein has a strong effect on the active degradation performed through the ubiquitination system. For example, in mammalian systems it predicts that arginine, glutamate and glutamine will lead to degradation within about an hour while valine, methionine and glycine will be stable for tens of hours.

In trying to characterize the lifetimes of the most stable proteins, mice were given isotopically labeled food for a short period at an early age and then analyzed a year later. The results showed that most proteins turnover within a few days but a few show remarkable stability. Histone half lives were measured at ≈200 days even more tantalizing, the nuclear pore consists of a protein scaffold with half life >1 year while all the surrounding components are replenished much faster.


Nucleoproteins: Formation and Synthesis | Nuclei | Living Cell | Biology

In this article we will discuss about:- 1. Formation of Nucleoproteins 2. Types of Nucleoprotein 3. Synthesis.

Formation of Nucleoproteins:

Nucleoproteins contain phosphoric acid and also other prosthetic group. Hence, they should be placed in a special class. Nucleoproteins are formed by the union of nucleic acid with basic protein. The nucleic acids, viz., deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are found both in animal and plant cells.

In the animal cells DNA is the chief nucleic acid-specially found in chromosome, whereas RNA is found in smaller quantity in the nucleus. RNA is also found in ribosomes (claude’s particles) inside the cytoplasm where they help in the synthesis of proteins. The breakdown and synthesis of RNA are continuously going on within the cell with the help of intracellular enzymes.

DNA is a stable compound and controls the hereditary character­istics of the cell. The nucleic acid is made up of many nucleotides (mononucleotide) making a double helical structure of two polynucleotide chains. Each mononucleotide is again composed of nucleoside and phosphoric acid.

Each nucleoside is composed of a pentose and a base as follows:

The pentose, ribose, is present in ribonucleic acid (RNA), whereas deoxyribose is present in deoxy­ribonucleic acid (DNA).

The bases are of two types:

Adenine and guanine (Fig. 10.103) are present in both the nucleic acids.

Cytosine and uracil are present in RNA, whereas cytosine along with thymine is pres­ent in DNA. In addition to DNA and RNA, nucleosides are also component of a number of coenzymes, like NAD and NADP and metabolically important compounds, such as ATP, UDPG, etc.

Since nucleoprotein is a composite product, its complete metabolism will mean the life history of all the component parts in it. The protein parts of the nucleoprotein molecules contain a high proportion of di-amino acids and undergo the same fate as the other proteins in the body.

The phosphoric acid part and the pentose molecule are treated by the body in the same way as the phosphates and carbohydrates derived from other sources. The special importance of the metabolism of nucleo proteins lies in the life history of its characteristic ingredients- the purine and the pyrimidine bases.

Types of Nucleoprotein:

Nucleoprotein metabolism may be of two types:

1. Exogenous Nucleoprotein Metabolism:

Is undergone by the end products of nucleoprotein digestion, after they are absorbed. These end products are phosphoric acid, carbohydrate (pentose), the pyrimidine nucleosides (which are not further digested), the two purine bases (adenine and guanine) and probably some nucleotide.

2. Endogenous Nucleoprotein Metabolism:

Starts in a different way (Fig. 10.104). There are two kinds of tissue nucleotidases. The phosphonucleotidase splits off phosphoric acid and forms nucleosides. But the purine nucleotidase (more effective in slightly alkaline medium) takes away the purine bases, leaving phosphoric acid molecule combined with carbohydrate.

Taking everything together it will be seen that metabolism of purine may take place under two different conditions – first, when the purines remain combined as nucleosides and secondly, when they remain free as adenine and guanine.

The end product of purine metabolism is chiefly uric acid and slightly hypoxanthine and xanthine. But this is not all. All purine bases undergoing metabolic changes in the body, are not excreted in these forms. A good deal of it is lost in some unknown way. In dogs, excepting the Dalmatian variety, uric acid is further oxidised into allantoin and is excreted as such (Figs 10.103 & 10.105).

The intermediate metabolism of pyrimidine bases, e.g., cytosine, uracil and thymine is not clear. The catabolism of pyrimidines occurs mainly in the liver. Diets rich in thymine or DNA in rats produce increased ex­cretion of β-aminoisobutyric acid. Based on fragmentary evidences obtained so far, the catabolic pathway of pyrimidines is shown in Fig. 10.106.

Feeding with pyrimidine bases increases the output of urea in the urine of dogs indicating the breakdown of the pyrimidine ring. Little is known about the fate of pentose. Probably they are oxidised.

The way by which purine bases undergo metabolic changes is briefly summarised in Fig. 10.105.

Functions of DNA and RNA:

In recent years it has been definitely established that genetic information from one cell to the daughter one is carried by DNA and different forms of RNA that help in protein synthesis.

A chromosome of the cell nucleus is composed of DNA, which is responsible for the passage of genetic code from one cell to the other. Just before mitosis the double helix of DNA separate from each other and with the help of an enzyme, DNA polymerase, a second chain exactly similar to the parent one is formed, thus giving it the original double helical structure.

The two similar double helixes go to the two daughter cells formed as a result of cell division giving them the same amount of DNA as the parent cell. In the process of meiosis such duplication of DNA in the parent cell does not take place and so the daughter cell contains half the number of original chromosomes.

Two types of RNA are also formed in the nucleus. One of them is single stranded messenger RNA (mRNA) which has a smaller molecule than DNA. Its synthesis is catalysed by the enzyme RNA polymerase. On being synthesised the mRNA comes out of the nucleus and becomes incorporated into the ribosomes of the cyto­plasm.

The mRNA carries the genetic information to determine the sequence in which the amino acids are to be lined up in the polypeptide chain. In this process of synthesis, another type of RNA called soluble RNA (sRNA) or transfer RNA (tRNA) is also formed in the nucleus to participate in the process of synthesis. The tRNA attaches itself to the activated amino acids (amino acyl AMP) forming sRNA amino acid and carries them to the mRNA at the ribosomes.

The sRNA finds out the definite code word or codon on the mRNA, attaches to the specific amino acids and is set itself free to be used again. The long mRNA thread has a number of ribosomal structures known as polysomes (polyribosmoes, ergosomes) which are thus responsible for the syntheisis of many amino acids forming a polypeptide. Finally the mRNA is set free from the polypeptide chain of the completed protein and renews its help in protein synthesis.

RNA codes or codons for different amino acids are listed in Table 10.2.

Synthesis of Nucleoproteins:

Although in higher animals the power of protein synthesis is limited, yet nucleoproteins can certainly be synthesised in their bodies. A hen’s egg before incubation contains very little purine bases but after hatching the chick contains large amounts of nucleoproteins. Obviously, this must have been synthesised from other substances present in the egg.

In human infants the amount of nucleoprotein rapidly increases as growth advances, although, the chief food is milk which is almost free from nucleoproteins. From similar observations it has been definitely proved that the nucleoproteins can be synthesised in the body. Liver is the most probable site of nucleoprotein synthesis.

Nucleoproteins are compounds of simple basic proteins, protamines and histones with nucleic acid.

Nucleic acids are composed of:

(c) A nitrogenous base – purine and pyrimidine.

Both the nitrogenous bases are synthesised in the body not as such but as their corresponding nucleotides.

Purine nucleotides are adenylic acid and guanylic acid (guanosine-5′-phosphate). These nucleotides are not formed directly. At first the nucleotide inosinic acid (hypoxanthine-ribose-5′-phosphate) is synthesised from the metabolic products of carbohydrate and protein. Different compounds of the purine ring are derived from formic acid, CO2, glutamine, aspartic acid, and glycine and have been shown in Fig. 10.112. The inosinic acid nu­cleotide, after being formed, is then converted into adenylic acid and guanilic acid.

Pyrimidine is also synthesised as nucleotides. Pyrimidine nucleotides are cytidylic acid, thymidylic acid and uridylic acid. The first step in the synthesis of pyrimidine nucleotide is the formation of orotic acid. It has been found by both vitro and vivo experiments that orotic acid is utilised for the synthesis of pyrimidine nucleotides.

Carbamylphosphate and aspartic acid take the initial role in the synthesis of pyrimidine nucleotide. In the pyrimidine ring, nitrogen at position 1 and carbon at position 2 are donated by carbamyl phosphate. Carbons at positions, 4, 5, 6 and nitrogen at position 3 of the pyrimidine ring are donated by aspartic acid (Fig. 10.113).


Author information

Affiliations

Departments of Neurology and Radiology, Massachusetts General Hospital, and Neuroscience Program, Harvard Medical School, 149 13th Street, Charlestown, MA02129, USA

Johan Skog, Tom Würdinger, Sjoerd van Rijn, Dimphna H. Meijer, Laura Gainche & Xandra O. Breakefield

Department of Neurosurgery, Neuro-oncology Research Group, Cancer Center Amsterdam, VU Medical Center, Amsterdam, 1007, MB, The Netherlands

Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Yawkey 9 Fruit Street, Boston, MA02114, USA

William T. Curry Jr. & Bob S. Carter

Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, 4 Blackfan Circle, Boston, MA02115, USA


RNA: Definition, Types, Structure and Functions

Johannes Friedrich Miescher (a Swiss physician and biologist) first discovered the Nucleic acids as ‘nuclein’ from the nucleus in 1869. Severo Ochoa de Albornoz (a Spanish-American physician and biochemist) discovered the RNA synthesis mechanism in 1959. He won the Nobel Prize jointly with Arthur Kornberg in Physiology or Medicine for his discoveries. In 1965, Robert W. Holley sequences 77 nucleotides of yeast tRNA.

Ribonucleic acid or RNA is an essential biological macromolecule. Generally, it helps to exchange the hereditary information encoded by DNA into proteins. The nucleic acid of living cell having ribose sugar in its nucleotides and perform multiple vital roles in the coding, decoding, regulation and expression of genes is called Ribonucleic acid or RNA.

In prokaryotic cell these are found in cytoplasm, chromosome, ribosome, nucleolus, plastid and mitochondria. In eukaryotic cells, 90% RNA present in cytoplasm and 10% in other structures. In some virus, RNA exists as genetic material.

Physical Structure of RNA

Primarily RNA is single-stranded particle with an intra-strand pairing yet in their secondary structure there are a few U shaped loops. It can show a broad twofold helical structure and can also form different tertiary structures.

Chemical Structure of RNA

RNA molecule is a polymer of ribonucleotide. Each ribonucleotide consists of the following molecules:

Each nucleotide in a RNA molecule has one of four nitrogenous bases: adenine, guanine, cytosine and uracil. The first two are purine and the later two are pyrimidine bases.

Types of RNA

RNA is of two main types, such as:

1. Genetic RNA or gRNA: When RNA functions as genetic materials then it is known as genetic RNA, e.g. RNA of some viruses.

2. Non-genetic RNA: When RNA takes part in only protein synthesis, then it is called non-genetic RNA, e.g. RNA of eukaryotic and prokaryotic cells.

Non-genetic RNA is further divided into the following three types:

  1. Ribosomal RNA or rRNA
  2. Messenger RNA or mRNA
  3. Transfer RNA or tRNA

Ribosomal RNA or rRNA: It makes up about 80% of the total RNA in a cell. These are synthesized in nucleolus and occur in ribosome, the protein factories of the cells. Ribosomal RNA is composed of unbranhed, flexible polynucleotide chain. This chain remains coil in low ionic concentration but its nitrogen bases form helical part in high ionic concentration. In such case, adenine bound with uracil and guanine bound with cytosine.

Eukaryotic rRNA is of four types: 28S rRNA, 18S rRNA, 5.8S rRNA, and 5S rRNA.

Image showing Ribosomal RNA (rRNA)

Functions of rRNA

  • Ribosomal RNA gives a procedure for decoding mRNA into amino acids and interrelates with tRNAs during translation.
  • It comprises the predominant material within the ribosome. During protein synthesis.
  • It guarantees the proper alignment of tRNA, mRNA, and ribosome.
  • It catalyzes during peptide bond formation between amino acids.

Messenger RNA or mRNA

French scientists François Jacob and Jacques Monod coined the name mRNA in 1961. mRNA is a single-strand made of up to several thousand nucleotides. It is created as complementary strand of DNA hence it has base sequences as like as in DNA. In its linear structure, mRNA has two non-coding ends and middle coding zone. The two ends of mRNA recognized as 5´ leader and 3´ trailer end. mRNA makes up 3-5% of the total RNA in a cell.

mRNA is a copy of the hereditary information produced by transcription from the cell’s original blueprint, DNA. This hereditary information is brought to the protein factories of the cells, ribosome for using as instruction for the formation of proteins.

Functions of mRNA

  • mRNA is transcribed from the DNA template in the nucleus and carries coding information to the sites of protein synthesis in the ribosomes.

Transfer RNA or tRNA

Transfer RNA is also known as tRNA. It is a small and clover leaf shape RNA which helps transmission a specific amino acid to a new polypeptide chain. During translation, this transmission occurs at the ribosomal site of protein synthesis.

In this case, each of the 20 amino acids which have a specific tRNA that binds with it to form proteins. The tRNA is made up of 70 to 95 nucleotides. It is the essential component of translation and it performs to transfer of amino acids during protein synthesis as a main functions. Hence, it is called transfer RNA or tRNA. tRNA is also called adaptor molecules because it acts as adaptor in the transformation of the genetic sequence of mRNA into proteins. Sometimes tRNA ia also called soluble, or activator RNA.

Robert Willium Holley et al. (1965) proposed the clover leaf model structure of tRNA. He awarded the Nobel Prize in Physiology or Medicine in 1968 with Har Gobind Khorana and Marshall Warren Nirenberg for describing this model. According to this model the single polynucleotide chain of tRNA is folded upon itself to form five arms. The arms are:

  1. Acceptor arm
  2. Dihydrouridine (DHU) arm or D arm
  3. Anticodon arm
  4. Variable arm and
  5. Thiamine psedocytosine or TΨC arm.

tRNA also have DHU loop, variable loop, anticodon loop, T-loop or TΨC loop and amino acid acceptor end. It has four normal bases A, G, U, C and some unknown bases like isonine (I), dihydouridine, psedouradine, etc. Both end of single chain of tRNA (5´-3´) exist aside.

Image showing Clover Leaf Model Structure of tRNA

Functions of tRNA

  1. It identifies and transports the correct amino acid molecules to the site of protein synthesis in the ribosome.
  2. It primarily is familiar for carrying amino acids.
  3. It also takes part in the process of building proteins.

RNAa can also be broadly divided into the following types:

Non-coding RNAs (ncRNA) are of the following two types, such as:

Non-coding RNA (ncRNA) is further divided into the following two types based on their size such as:

1. IncRNA or Long ncRANS: As a minimum, 200 nucleotides are present in IncRNA.

2. Small ncRNAS: Less than 200 nucleotides are present in ncRNAS.

Small ncRNAs are subdivided into the following five types:

1. miRNA: It is also called micro RNA

2. snoRNA: It is also known as small nucleolar RNA

3. snRNA: It is also known as small nuclear RNA

4. siRNA: It is also called small-interfering RNA

5. piRNA: It is also called PIWI-interacting RNA

The size of t he miRNAs is about twenty two (22) nucleotides long and have particular importance. In most eukaryotic cells, they perform to function in gene regulation. Some miRNAs can regulate target genes which lead to tumour progression and tumorigenesis. The size of piRNA is about 26-31 nucleotide long. They are present in most animals. They can regulate the expression of jumping genes or transposon that move from one location to another on a chromosome. These genes were first identified by Barbara McClintock.

Concluding Remarks

Definitively, the RNA is as significant as DNA into molecular investigations as the evaluation of the gene expression is relies upon the complete mRNA present into the specific tissue. mRNA is fundamental to the procedure of transcription, while tRNA is essential to the procedure of translation, and rRNA makes up the ribosomes in which translation occurs. The amount of expression of gene can be estimated by utilizing the Reverse transcription polymerase chain reaction technique or RT-PCR technique through the evaluation of RNA.


What can a transcriptome tell us?

An RNA sequence mirrors the sequence of the DNA from which it was transcribed. Consequently, by analyzing the entire collection of RNA sequences in a cell (the transcriptome) researchers can determine when and where each gene is turned on or off in the cells and tissues of an organism.

Depending on the technique used, it is often possible to count the number of transcripts to determine the amount of gene activity - also called gene expression - in a certain cell or tissue type.

In humans and other organisms, nearly every cell contains the same genes, but different cells show different patterns of gene expression. These differences are responsible for the many different properties and behaviors of various cells and tissues, both in health and disease.

By collecting and comparing transcriptomes of different types of cells, researchers can gain a deeper understanding of what constitutes a specific cell type, how that type of cell normally functions, and how changes in the normal level of gene activity may reflect or contribute to disease. In addition, transcriptomes may enable researchers to generate a comprehensive, genome-wide picture of what genes are active in which cells.

An RNA sequence mirrors the sequence of the DNA from which it was transcribed. Consequently, by analyzing the entire collection of RNA sequences in a cell (the transcriptome) researchers can determine when and where each gene is turned on or off in the cells and tissues of an organism.

Depending on the technique used, it is often possible to count the number of transcripts to determine the amount of gene activity - also called gene expression - in a certain cell or tissue type.

In humans and other organisms, nearly every cell contains the same genes, but different cells show different patterns of gene expression. These differences are responsible for the many different properties and behaviors of various cells and tissues, both in health and disease.

By collecting and comparing transcriptomes of different types of cells, researchers can gain a deeper understanding of what constitutes a specific cell type, how that type of cell normally functions, and how changes in the normal level of gene activity may reflect or contribute to disease. In addition, transcriptomes may enable researchers to generate a comprehensive, genome-wide picture of what genes are active in which cells.


DNA stands for deoxyribonucleic acid.It is the information molecule and stores all the genetic material of a cell. It also contains instructions for the synthesis of other molecules, like proteins.

DNA is a polymerand is made of many smaller molecules (AKA monomers) called nucleotides.Each nucleotide contains a phosphate group, a 5-carbon sugar, and a nitrogenous base. The four types of nitrogenous bases in DNA molecules are:

The type of nitrogenous base determines the type of nucleotide. The four types of nucleotide are:

  • A nucleotide (containing adenine)
  • T nucleotide (containing thymine)
  • G nucleotide (containing guanine)
  • C nucleotide (containing cytosine)

The sequence of nucleotides in a DNA molecule determines the instructions contained in that stretch of DNA. Nucleotides are joined together by phosphodiester bonds,which form between the 3’ carbon atom of one nucleotide and the 5’ carbon atom of another.


Conclusion

DNA and RNA extraction has played important and crucial roles in helping researchers and scientists to manipulate molecular biology analysis to have a better understanding in the biology of the earth. Due to the rapid advancement of technology, DNA and RNA extraction has improved vastly however, weaknesses of the instruments should be bettered constantly by conducting quality control as it affects all subsequent results.

References:

Tan SC, Yiap BC. DNA, RNA, and protein extraction: the past and the present. J Biomed Biotechnol. 2009 2009: 574398.

Santella RM. Approaches to DNA/RNA extraction and whole genome amplification. Cancer Epidemiology, Biomarkers & Prevention. 2006 15(9): 1585-1587.


Watch the video: DNA vs RNA Updated (August 2022).