transcription

Spliceosome-

-the removal of introns is accomplished by a large complex made of priteins and small RNAs called a spliceosome. This complex binds to several short nucleotide sequences along the intron, including key sequences at each end. The intron is then released, and the spliceosome joins together two exons that flanked the intron. It turns out that the small RNAs in the spliceosome not only participate in the assembly of the spliceosome and recognition of the splice site but also catalyze the splicing process

RNA splicing-

A remarkable stage of RNA processing in the eukaryotic nucleus is the removal f large portions of te RA molecule and reconnection of the remaining portions. This cut-and-paste job, called RNA splicing, is similar to editing the video. This is beucase most eukarotic genes and their RNA transcripts have long noncoding stretches of nucleotides, regions that are nontranslated. Even more surpising is that most noncoding sequences are interspersed between coding segments of he gene and thus between coding segments of the pre-mRNA. In other words. The seuqnrce of DNA nucleotides that codes for a eukaryotic polypeptide is usually non continuous, it is split into segments. In maing primary transvript RNA polymerase II transcribs both introns and exons from the DNA, but the mRA molecule that enters the cytoplasm is the abridged version. The introns are cut out from the molecule and the exons joined together, forming a mRNA molecule with a continuous coding sequence. This process is called RNA splicing.

Elongation of the RNA strand-

As RNA polymerase moves along the DNA, it untiests the double helix, exposing about 10-20 DNA nucleotides at s time for pairing with RNA nuclotides. The enzyme adds nucleotides to the 3' end of the growing RNA molecule as it continues along the double heliz. Iun the wake of this advancing wave of RNA synthesis the new RNA molecule peels away from its DNA template, and the DNA double heliz reforms.

RNA polymerase-

Messenger RNA, the carrier of information from DNA to the cell's protein-synthesizing machinery is transcribed from the template of a gene. An enzyme called an RNA polymerase pries the two strands of DNA apart and joins together the RNA nucleotides complementary to the DNA template strand, thus elongating the RNA polynucleotide. Unlike DNA polymerases, however RNA polymerases are able to start a chain from scratch; they don't need a primer.

Upstream vs downstream

Molecular bioligists reger to the direction of transcription as "downstream" and the other direction as "upstream". These terms are also used to describe the ppsitions of nucleotide sequences within the DNA or RNA. This, the promoter sequence in DNA is said to be upstream from the terminator.

Promoter-

The DNA sequence where RNA polymerase attaches and initiates transcription is known as the promoter. In vast majority of cases, promotor will be upstream of the coding region. The RNA polymerase will come and start the process of RNA synthesis. RNA polymerase will not be able to find where the gene starts without the promotor. There is a core promotor and proximal sequence. Thereis a sequence such as enhancer and silencer for regulation of that gene. In eukaryotes it is one promotor per gene.

Transcription initiation complex-

The whole complex of transcription factors and RNA polymerase II bound to the promotor is called a transcription initiation complex.

Additional transcription factors after RNA polymerase II bind

additional transcription factors bind to the DNA along with RNA polymerase II, forming the transctiption initiation complex. RA polymerase II then unwinds the DNA double helix, and the RNA synthesis begins at the start point of the template strand

Initiation

after RNA polymerase binds to the promotor, the DNA strands unwind, and the polymerase initiates RNA synthesis at the start point on the template strand

A eukaryotic promotor/tata box

commonly includes a TATA box, a nucleotide sequence containing TATA, about 25 nucleotides upstream from the transcriptional start point. (by convention, nucleotide sequences are given as the occur on the nontemplate strand). transcription factors first bind to the tata box and recognize it before RNA polymerase II can bind to it.

Alternation of mRNA ends-

each end of a pre-mRNA molecule is modified in a particular way. The 5' end, which is synthesized first receives a 5' gap, a modified form of guanine nucleotide with three phosphate groups are added onto the 5' end after transcription fo the first 20-40 nucleotides. The 3' end of the pre-mRNA molecule is also modified beore the mRNA exits the nucleus. At the 3' end, an enzymes then adds 50-250 more adenine nucleotides, forming a poly-A tail. Tne 5' cap and poly-A tail share several important functions. First, they seem to facililtate the export of mature mRNA from the nucleus. Second, they help protect the mRNA from degradation by hydrolytic enzymes. And third they help ribosomes attatch to the 5' end of the mRNA onc the mRNA reaches the cytoplasm. 5' cap provides information about the mRNA to the rest of the cell.

RNA processing-

enzymes in the eukaryotic nucleus modify pre-mRNA in specific ways before the genetic message is dispatched in the cytoplast. During this RNA processing, both ends of the primary transcript are altered. Also in most cases, certain interior sections of RNA molecule are cut out and the remaining parts spliced together. These modifications produce an mRNA molecule ready for translation

Terminator-

in bacteriaThe sequence that signals the end of transcription is called the terminator.

Alternative RNA splicing-

one important consequence of the presence of introns in genes is that single gene can encode more than one kind of polypeptide. Many genes are known to give rise two or more different polypeptides, dpending on which segments are treated as econs during RNA processing; this is called alternative RNA splicing. Because alternative splicing, the number of different protein products an organsm produces can be much greater than its number of genes

Several transcription factors-

one recognizing the TATA box, bind to the DNA before RNA polymerase II can bind in the correct position and orientation

Ribozymes-3 proprties that can make RNA catalyze

the idea of a catalytic role for the RNAs in the splicosome arose from the discovery of ribozymes, RNA molecles that function as enzymes. It some organism, RNA splicing can occur without proteins or even additional RNA molecles: the intron RNA functions as a ribozyme and catalyzes its own excision. The pre-RNA actually removes its own introns. Here portions of RNA enable some RNA molecules to function as enzymes. Three properties of RNA enable some RNA molecules to function as enzymes. First, because RNA is a single-stranded, a region of an RNA molecule may base-pair, in an antiparallel arrangement, with a complemtnary region elsewhere in the same molecule; this give the molecule a particular three-demensional structure. A specific structure is essential to the catalytic function of ribosozymes, just as it is for enzymatic proteins. Second like certain amino acids in an enzymatic protein, some of the vases in RNA contain functional groups that can participate in catalysis. Third, the ability of RNA to hydrogen bond with other nucleic acd molecules adds specificity to its catalytic activity. For example, complementary base pairing between RNA of splicesome and the RNA of a primary RNA transcript precisely locates the region where ribozyme catalyzes splicing.

Termination of transcription-

the mechanism of termination diers between bacteria and eukaryotes. In bacteria. Transcritpipn proceeds through a terminator sequence in the DNA. The transcribed terminator(a RNA sequence) functions as the terminato signal, causing the polymerase to detatch from the DNA and release the transcript, which requires no further modification before translation. In eukaryotes. RNA polymerase II transcribes a sequence on the DNA called polyadenylation signal sequence which specifies a polyadenylation signal(AAUAAA) in the pre-mRNA. This is called a "signal" because when this stretch of six RNA nucleotides appears, it is immediate bound by certain proteins in the nucleus. Then at a point about 10-35 nucleotides downstream from the AAUAAA signal, these proteins cut from the RNA strajscript free from the polymerase, releasing the pre-mRNA. The pre-mRNA then undergoes processing

Introns-

the noncoding segments of nucleic acid that lie between coding regions are called intervening sequences or introns

Exons-

the other regions ate called exons, because they are eventually expressed, usually being translation into amino acid sequencesthe term exon and intron are used for both RNA sequences and the DNA sequence that specify them. (exceptions include the UTRs of the exo ns at the ends of the RNA, which make up part of the mRNA not translation into protein). Introns are intruders and you want to get rid of them. The UTR is an untralsnation region. It provides information of the stability of RNA and how much protein out of that specific RNA. Poly A adds a lot of codons to the mRNA. It becomes stable with poly-A-tail. The 5' cap and Poly-A- tail provides information on how stable MRNA molecule is and how much of it will be translated. At the 5' UTR is the ribosome binding site. The 3' UTR in a polysystronic operan, it is hard to define. Is the5' cap and poly-A tail part of the untranslated region of the RNA? They have the signals to incporate the UTR. They are part of untranslated region. By the time translation happens, they do not tralsated int protein.

Elongation-

the polymerase moves downstream, unwinding the DNA and elongating the RNA transcript 5'->3'. In the wake of transcription, the DNA strands re-form a double helix

Start point-

the promotor of a gene includes right after it the transcription starting point and typically extends several dozen or more nucleotide pairs upstream from the start point. RA polymerase binds in a precise location and orientation on the promoter, thereby determining where transcriptions stats and which of the two strands of the DNA helix is sued as the template. Certain sections of a promoter are especially important for bdinging RNA polymerase. In bacteria, part of RNA polymerase iself specifically recognizes and binds to the promoter.

Transcription unit

the stretch od DNA downstream from the promotor that is transcribed into an RNA molecule is called a transcriptional unit

Transcription factors-

transcription factors mediate the binding of the RNA polymerase and the initiation of transcription. only after transcription factors are attatched to the promoter does RNA polymerase II bind to it.