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    The eukaryotic cytoplasmic ribosome, which has a molecular mass of about 4 x 106 Da and a sedimentation coefficient of 80S, consists of one small and one large subunit. Small or 40S subunits, which are fairy constant in size (approximately 1.5 X 106 Da) in ribosomes from all eukaryotes, contain an 18S rRNA (approximately 1900 nucleotides) and about 33 different polypeptides. Large or 60S subunits vary in size from one species to another. For instance, large subunits in plants and mammals have molecular masses of 2.5 x 106 Da and 3.0 X 106 Da, respectively. Part of this size variation is due to variations in the size of the largest of the three rRNA molecules in the large subunit. This rRNA is about 5000 nucleotides long (sedimentation coefficient 28S) in mammals but only 3400 nucleotides long (sedimentation coefficient 25S) in yeast. The two other rRNA components in the large subunit are the 5.8S rRNA (approximately 160 nucieotides) and the 5S rRNA (approximately 120 nucleotides). Large subunits from mammals also have about 50 polypeptide subunits, whereas those from lower eukaryotes have somewhat fewer polypeptides. The 5.8S, 18S, and 25S/28S rRNAs are synthesized by RNA polymerase I, whereas the 5s rRNA is synthesized by RNA polymerase I, whereas the 5S rRNA is synthesized by RNA polymerase III.

    Transcriptional processing and RNA editing have important consequences for the eukaryotic proteome (the complete set of proteins expressed during an organism's lifetime). The best current estimate is that the human genome contains approximately 35, 000 transcription units that code for proteins. Alternative splicing, which affects at least 42% of the pre-mRNAs, probably results in the production of a few hundred thousand different kinds of proteins in the human proteome. RNA editing, alternative transcription initiation sites and alternative transcription termination sites also contribute to protein diversity. Furthermore, many proteins are modified after they are formed to produce additional variants. The most common types of posttranslational modifications are cleavage, phosphorylation, acetylation, glycosylation, and methylation. Thus, knowing a transcription unit's DNA sequence is a starting point for understanding how information is transferred from DNA to protein but it is not sufficient by itself to tell us the exact nature of the proteins that are present in a given cell at some specific time. As we see in the final section of this chapter, the situation is even more complex because even synthesis of mRNA does not guarantee that it will be translated.

    Alternative processing raises many fundamental issues, perhaps none more important than the very concept of the gene itself. Prior to the discovery of alternative promoters, splicing, and poly (A) sites, a eukaryotic gene could be defined as a hereditary unit that codes for a specific polypeptide. However, this one gene-one polypeptide hypothesis does not work for alternatively processed transcription units that can code for two or more protein isoforms. We must therefore find some other way to define a gene. Although an exon has the minimal amount of information that is expressed as a discrete unit, we cannot define a gene as an exon because exons do not contain all of the information that we normally associate with genes. Perhaps the best definition that we can devise at this time is that a gene is a linear collection of exons that are incorporated into a specific mRNA. However, the term gene continues to be used in a more general sense when referring to a transcription unit or protein coding region. Alternative processing also presents challenges for genetic engineering. Some alternatively processed transcription units are known to produce isoforms that have antagonistic effects. Therefore, transforming a cell with an alternatively spliced gene may result in the production of a harmful rather than a beneficial protein.

    Although it might seem that only a few specific endonucleases and a ligase might suffice to catalyze splicing reactions, eukaryotic cells use a very sophisticated piece of machinery to carry out the steps involved in splicing. As often happens in science, the first clue to the nature of this machinery came from studies in a seemingly unrelated field. People suffering from autoimmune diseases known as mixed connective tissue disease and systemic lupus erythematosus make aberrant antibodies that attack components of their own cells. One such antibody, called the anti-Smith or anti-Sm antibody, binds to small ribonucleoprotein particles in the cell nucleus. Joan Steitz and coworkers suspected that these small ribonucleoproteins might help to process pre-mRNA and set about isolating them so that they could study their function(s). The isolation method they devised was to first tag the ribonucleoprotein particles in a human cell extract with antibodies from the serum of a lupus patient and then pull the tagged ribonucleoproteins out of the extract with an insoluble Stapbylococcus aureus cell wall preparation that binds to antibodies. When Steitz and coworkers analyzed RNA molecules that had been extracted from the ribonucleoprotein particles by polyacrylamide gel electrophoresis, they observed discrete bands corresponding to RNA molecules with chain lengths between 100 and 200 nucleotides long. Because each of the small nuclear RNA molecules is uridine-rich, they are called U1 snRNA, U2 snRNA, U4 snRNA, U5 snRNA, and U6 snRNA. The reason that there is no U3 snRNA is that the lupus antibodies do not bind to the ribonucleoprotein that contains this RNA. U3 snRNA is involved with rRNA rather than mRNA formation. The U1, U2, U4, and U5 snRNAs each has a 2, 2, 7 trimethyl guanosine cap at its 5'-end while U6 has a ?-methyl phosphate cap.
    Each snRNA is present in its own small nuclear ribonucleoprotein particle (snRNP; or 'snurp' f......

    Splicing may occur so that (1) each and every exon in a pre-mRNA is in-corporated into one mature mRNA through the joining of all successive exons, or (2) one combination of exons in a pre-mRNA is incorporated in one pre-mRNA while other combinations are incorporated in other mRNAs. At present it appears that about 42% of total human transcription units use the latter form of splicing, to produce mRNA. However, this estimate is probably low because the ESTs used to detect alternative splicing come from a limited number of tissues or developmental states, and cover only part of each mRNA. More thorough studies of chromosome 22 show that 59% of its genes are alternatively spliced and even this number may be low.
    Exons are either constitutive or regulated. A constitutive exon is included in all mRNAs formed. A regulated exon, also called a cassette exon, is an exon that is included in some mRNAs and excluded from other mRNAs. Many alternate spiicing patterns are possible for a typical multi-exon pre-mRNA. A cassette exon located between two constitutive exons may either be included or skipped when a pre-mRNA is spliced to form mRNA. Inclusion of one cassette exon may prevent the inclusion of other cassette exons. Mutually exclusive splicing occurs when an array of cassette exons is located between two constitutive exons and only one of the cassette exons can be incorporated into mature mRNA. An intron between two constitutive exons may be included in some mRNAs but not in others. Thus, a single DNA sequence may act as either an intron (when it is excised) or an exon (when it is incorporated). Some exons have alternative splice sites at their 3'-end or their 5'-end. When mRNAs formed by alternative splicing of a given pre-mRNA are translated, the proteins formed usually share common functions but differ within one or more domains. Sometimes, alternative splicing introduces a termination codon in mRNA, causing a premature end......

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