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    RNA
    Experiments, Studies and Background Information
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    RNA Experiments and Studies

    • Road to the RNA World: Intersections of Theory and Experiment [View Experiment]
    • Did Your RNAi Experiment Work? Reliably Validating RNA Interference with qRT-PCR [View Experiment]
    • RNA Isolation And RT-PCR Analysis [View Experiment]
    • Changes in RNA Content and Base Composition In Cortical Neurons of Rats in a Learning Experiment Involving Transfer of Handedness [View Experiment]
    • RNA: Transcription and Processing [View Experiment]
    • A simple and efficient method for isolating small RNAs from different plant species [View Experiment]
    • Choosing the right coverage depth and read length for an RNA-seq experiment [View Experiment]
    • Bachelor Thesis: RNA Secondary Structure Prediction [View Experiment]
    • Effect of Amino Acids on Liver RNA Synthesis in the Chick [View Experiment]
    • Dissertation: Formal Grammars for Describing RNA Pseudoknotted Structure and Their Application to Structure Analysis [View Experiment]
    RNA Background Information

    Definition

    RNA (Ribonucleic acid) serves as the template for translation of genes into proteins, transferring amino acids to the ribosome to form proteins, and also translating the transcript into proteins.

    Basics

    RNA is an acronym for ribonucleic acid, a nucleic acid. RNA is transcribed from DNA by an enzyme called RNA polymerase and further processed by other enzymes.

    RNA translates genes into proteins, transferring amino acids from the nucleus to the ribosome to form proteins, and also translating the transcript into proteins. This process is called translation.

    RNA is physically different from DNA: DNA contains two intercoiled strands whereas RNA only contains one single strand. RNA also contains different bases from DNA. It contains: (A) Adenine (G) Guanine (C) Cytosine (U) Uracil

    The first three bases are also found in DNA, but Uracil replaces Thymine as a complement to Adenine. RNA also contains ribose as opposed to deoxyribose found in DNA.

    RNA is the carrier of genetic material in different types of viruses such as AIDS virus i.e. HIV (HUMAN IMMUNO DEFICIENCY VIRUS) and in that case called a retrovirus.

    mRNA, or Messenger RNA is the complement strand of DNA. A single strand of DNA is a blueprint for mRNA which is transcribed from that DNA strand. DNA cannot leave the nucleus because of its size, but mRNA can. Once transcribed, the mRNA leaves the nucleus and is attached to tRNA which attached to the Ribosomes.

    tRNA, or Transfer RNA is the complement (opposite) strand to mRNA and attaches to Ribosomes to be translated into a polypeptide (protein) chain. Each tRNA codon, group of three nitrogenous bases, codes for a specific amino acid which all bind together to form a protein. For example, codons UUU or UUC code for the amino acid Phenylalanine.

    Topics of Interest

    Ribonucleic acid (RNA) is a biologically important type of molecule that consists of a long chain of nucleotide units. Each nucleotide consists of a nitrogenous base, a ribose sugar, and a phosphate. RNA is very similar to DNA, but differs in a few important structural details: in the cell, RNA is usually single-stranded, while DNA is usually double-stranded; RNA nucleotides contain ribose while DNA contains deoxyribose (a type of ribose that lacks one oxygen atom); and RNA has the base uracil rather than thymine that is present in DNA.

    RNA is transcribed from DNA by enzymes called RNA polymerases and is generally further processed by other enzymes. RNA is central to protein synthesis. Here, a type of RNA called messenger RNA carries information from DNA to structures called ribosomes. These ribosomes are made from proteins and ribosomal RNAs, which come together to form a molecular machine that can read messenger RNAs and translate the information they carry into proteins. There are many RNAs with other roles – in particular regulating which genes are expressed, but also as the genomes of most viruses.

    Structure: Each nucleotide in RNA contains a ribose sugar, with carbons numbered 1' through 5'. A base is attached to the 1' position, generally adenine (A), cytosine (C), guanine (G) or uracil (U). Adenine and guanine are purines, cytosine and uracil are pyrimidines. A phosphate group is attached to the 3' position of one ribose and the 5' position of the next. The phosphate groups have a negative charge each at physiological pH, making RNA a charged molecule (polyanion). The bases may form hydrogen bonds between cytosine and guanine, between adenine and uracil and between guanine and uracil. However other interactions are possible, such as a group of adenine bases binding to each other in a bulge, or the GNRA tetraloop that has a guanine–adenine base-pair.

    Comparison with DNA: RNA and DNA are both nucleic acids, but differ in three main ways. First, unlike DNA which is double-stranded, RNA is a single-stranded molecule in most of its biological roles and has a much shorter chain of nucleotides. Second, while DNA contains deoxyribose, RNA contains ribose (there is no hydroxyl group attached to the pentose ring in the 2' position in DNA). These hydroxyl groups make RNA less stable than DNA because it is more prone to hydrolysis. Third, the complementary base to adenine is not thymine, as it is in DNA, but rather uracil, which is an unmethylated form of thymine.

    Like DNA, most biologically active RNAs, including mRNA, tRNA, rRNA, snRNAs and other non-coding RNAs, contain self-complementary sequences that allow parts of the RNA to fold and pair with itself to form double helices. Structural analysis of these RNAs have revealed that they are highly structured. Unlike DNA, their structures do not consist of long double helices but rather collections of short helices packed together into structures akin to proteins. In this fashion, RNAs can achieve chemical catalysis, like enzymes. For instance, determination of the structure of the ribosome—an enzyme that catalyzes peptide bond formation—revealed that its active site is composed entirely of RNA.

    Synthesis: Synthesis of RNA is usually catalyzed by an enzyme—RNA polymerase—using DNA as a template, a process known as transcription. Initiation of transcription begins with the binding of the enzyme to a promoter sequence in the DNA (usually found "upstream" of a gene). The DNA double helix is unwound by the helicase activity of the enzyme. The enzyme then progresses along the template strand in the 3’ to 5’ direction, synthesizing a complementary RNA molecule with elongation occurring in the 5’ to 3’ direction. The DNA sequence also dictates where termination of RNA synthesis will occur.

    Generally speaking, different RNA types have different functions in translation, regulation and processing of proteins. Some of them are listed below.

    mRNA (Messenger ribonucleic acid) is a molecule of RNA encoding a chemical "blueprint" for a protein product. mRNA is transcribed from a DNA template, and carries coding information to the sites of protein synthesis: the ribosomes. Here, the nucleic acid polymer is translated into a polymer of amino acids: a protein. In mRNA as in DNA, genetic information is encoded in the sequence of nucleotides arranged into codons consisting of three bases each. Each codon encodes for a specific amino acid, except the stop codons that terminate protein synthesis. This process requires two other types of RNA: transfer RNA (tRNA) mediates recognition of the codon and provides the corresponding amino acid, while ribosomal RNA (rRNA) is the central component of the ribosome's protein manufacturing machinery.

    Transfer RNA (abbreviated tRNA) is a small RNA molecule (usually about 74-95 nucleotides) that transfers a specific active amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation. It has a 3' terminal site for amino acid attachment. This covalent linkage is catalyzed by an aminoacyl tRNA synthetase. It also contains a three base region called the anticodon that can base pair to the corresponding three base codon region on mRNA. Each type of tRNA molecule can be attached to only one type of amino acid, but because the genetic code contains multiple codons that specify the same amino acid, tRNA molecules bearing different anticodons may also carry the same amino acid.

    Ribosomal RNA (rRNA) is the central component of the ribosome, the protein manufacturing machinery of all living cells. The function of the rRNA is to provide a mechanism for decoding mRNA into amino acids and to interact with the tRNAs during translation by providing peptidyl transferase activity.The tRNA then brings the necessary amino acids corresponding to the appropriate mRNA codon.

    tmRNA (transfer-messenger RNA, also known as 10Sa RNA and by its genetic name SsrA) is a bacterial RNA molecule with dual tRNA-like and messenger RNA-like properties. The tmRNA forms a ribonucleoprotein complex (tmRNP) together with Small Protein B (SmpB), Elongation Factor Tu (EF-Tu), and ribosomal protein S1. In trans-translation, tmRNA and its associated proteins bind to bacterial ribosomes which have stalled in the middle of protein biosynthesis, for example when reaching the end of a messenger RNA which has lost its stop codon. The tmRNA is remarkably versatile: it recycles the stalled ribosome, adds a proteolysis-inducing tag to the unfinished polypeptide, and facilitates the degradation of the aberrant messenger RNA. In the majority of bacteria these functions are carried out by standard one-piece tmRNAs. In other bacterial species, a permuted ssrA gene produces a two-piece tmRNA in which two separate RNA chains are joined by base-pairing.

    Precursor mRNA (pre-mRNA) is an immature single strand of messenger ribonucleic acid (mRNA). pre-mRNA is synthesized from a DNA template in the cell nucleus by transcription. pre-mRNA comprises the bulk of heterogeneous nuclear RNA (hnRNA). The term hnRNA is often used as a synonym for pre-mRNA, although strictly speaking hnRNA may include nuclear RNA transcripts that do not end up as cytoplasmic mRNA. Once pre-mRNA has been completely processed, it is termed "mature messenger RNA", "mature mRNA", or simply "mRNA".

    A spliceosome is a complex of specialized RNA and protein subunits that removes introns from a transcribed pre-mRNA (hnRNA) segment. This process is generally referred to as splicing.

    RNA genomes Like DNA, RNA can carry genetic information. RNA viruses have genomes composed of RNA, and a variety of proteins encoded by that genome. The viral genome is replicated by some of those proteins, while other proteins protect the genome as the virus particle moves to a new host cell. Viroids are another group of pathogens, but they consist only of RNA, do not encode any protein and are replicated by a host plant cell's polymerase.

    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). Double-stranded RNA such as viral RNA or siRNA can trigger RNA interference in eukaryotes, as well as interferon response in vertebrates.

    RNA extraction is the purification of RNA from biological samples. This procedure is complicated by the ubiquitous presence of ribonuclease enzymes in cells and tissues, which can rapidly degrade RNA. Several methods are used in molecular biology to isolate RNA from samples, the most common of these is Guanidinium thiocyanate-phenol-chloroform extraction. This method often uses a proprietary formulation of this reagent called Trizol.

    An RNA virus is a virus that has RNA (ribonucleic acid) as its genetic material. This nucleic acid is usually single-stranded RNA (ssRNA) but may be double-stranded RNA (dsRNA). The ICTV classifies RNA viruses as those that belong to Group III, Group IV or Group V of the Baltimore classification system of classifying viruses, and does not consider viruses with DNA intermediates as RNA viruses. Notable human diseases caused by RNA viruses include SARS, influenza and hepatitis C.

    RNA polymerase (RNAP or RNApol) is an enzyme that produces RNA. In cells, RNAP is needed for constructing RNA chains from DNA genes as templates, a process called transcription. RNA polymerase enzymes are essential to life and are found in all organisms and many viruses. In chemical terms, RNAP is a nucleotidyl transferase that polymerizes ribonucleotides at the 3' end of an RNA transcript.

    Small interfering RNA (siRNA), sometimes known as short interfering RNA or silencing RNA, is a class of double-stranded RNA molecules, 20-25 nucleotides in length, that play a variety of roles in biology. Most notably, siRNA is involved in the RNA interference (RNAi) pathway, where it interferes with the expression of a specific gene. In addition to their role in the RNAi pathway, siRNAs also act in RNAi-related pathways, e.g., as an antiviral mechanism or in shaping the chromatin structure of a genome; the complexity of these pathways is only now being elucidated.

    A non-coding RNA (ncRNA) is a functional RNA molecule that is not translated into a protein. Less-frequently used synonyms are non-protein-coding RNA (npcRNA), non-messenger RNA (nmRNA), small non-messenger RNA (snmRNA), functional RNA (fRNA). The term small RNA (sRNA) is often used for bacterial ncRNAs. The DNA sequence from which a non-coding RNA is transcribed as the end product is often called an RNA gene or non-coding RNA gene.

    RNA splicing: In molecular biology, splicing is a modification of an RNA after transcription, in which introns are removed and exons are joined. This is needed for the typical eukaryotic messenger RNA before it can be used to produce a correct protein through translation. For many eukaryotic introns, splicing is done in a series of reactions which are catalyzed by the spliceosome, a complex of small nuclear ribonucleoproteins (snRNPs), but there are also self-splicing introns.

    Discovery: Nucleic acids were discovered in 1868 by Friedrich Miescher, who called the material 'nuclein' since it was found in the nucleus. It was later discovered that prokaryotic cells, which do not have a nucleus, also contain nucleic acids. The role of RNA in protein synthesis was suspected already in 1939. Severo Ochoa won the 1959 Nobel Prize in Medicine after he discovered how RNA is synthesized. The sequence of the 77 nucleotides of a yeast tRNA was found by Robert W. Holley in 1965, winning Holley the 1968 Nobel Prize in Medicine. In 1967, Carl Woese realized RNA can be catalytic and proposed that the earliest forms of life relied on RNA both to carry genetic information and to catalyze biochemical reactions—an RNA world. In 1976, Walter Fiers and his team determined the first complete nucleotide sequence of an RNA virus genome, that of bacteriophage MS2. In 1990 it was found in petunia that introduced genes can silence similar genes of the plant's own, now known to be a result of RNA interference. At about the same time, 22 nt long RNAs, now called microRNAs, were found to have a role in the development of C. elegans. The discovery of gene regulatory RNAs has led to attempts to develop drugs made of RNA, such as siRNA, to silence genes.

    Source: Wikipedia (All text is available under the terms of the GNU Free Documentation License and Creative Commons Attribution-ShareAlike License.)

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