Final Review1. TranscriptionChapter 17 pp. 331-336Transcription is the DNA-directed synthesis of RNAMolecular Components of Transcription- Messenger RNA (the carrier of information from DNA to the cell’s pro-tein-synthesizing machinery) is transcribed from the template strand of a geneo RNA polymerase pries the strands apart and joins RNA nucleotidesalong the template in a 5’ > 3’ direction RNA polymerase has the ability to start chain without a primero DNA sequence where RNA polymerase attaches and initiates tran-scription is called the promoter Bacteria have single type of polymerase that synthesizes all types of RNA Eukaryotes have at least 3 types of polymerases· RNA polymerase II is used for mRNA synthesis· Other polymerases transcribe RNA molecules that are not translated into a protein- Stretch of DNA that is transcribed into an RNA molecule is the transcrip-tion unitSynthesis of an RNA Transcript (Initiation, Elongation, Termina-tion)1. Initiationo After RNA polymerase binds to the promoter, the DNA strands unwind, and the polymerase initiates RNA syn-thesis at the start point on the template strand Promoter includes a start point and extends several nucleotide pairs upstream (promoter also includes a TATA box)o Promoter determines which of the 2 strands of the double helix is used as a template· In bacteria polymerase recognizes and binds to the pro-moter· In eukaryotes, transcription factors (collection of proteins that must recognize the TATA box) mediate the binding of RNA polymerase and initiation of tran-scription The complex of transcription factors and RNA polymerase II bound to the promoter is called a transcription initiation complex· A crucial promoter DNA sequence called a TATA box, forms the initiation complex at a eukaryotic pro-motero It controls eukaryotic transcription2. Elongationo The polymerase moves downstream, unwinding the DNA and elongating the RNA transcript 5’ > 3’. In the wake of transcription, the DNA strands reform a double helix RNA polymerase continues to untwist the double helix expos-ing 10-20 DNA bases at a time to pair with RNA nucleotides· Polymerase adds nucleotides to the 3’ end· The new RNA molecule peels away from its DNA tem-plate and the helix reformso This progresses at a 40 nucleotides per second rate The act of many polymerase molecules simultaneously tran-scribing a single gene increases the amount of mRNA tran-scribed · This helps the cell make the encoded proteins in big quantities3. Terminationo Eventually, the RNA transcript is released, and the poly-merase detaches from the DNA In bacteria, transcription has a terminator sequence that sig-nals the end of transcription· Terminator causes polymerase to detach from DNA andrelease the transcript for the mRNA to use In eukaryotes, RNA polymerase II transcribes a sequence on the DNA called the polyadenylation signal sequence which codes for a polyadenylation signal (AAUAAA) in the pre-mRNA· About 10-35 nucleotides down from this signal, pro-teins associated with the RNA transcript cut it free fromthe polymerase, releasing the pre-mRNAo Polymerase continues to transcribe DNA past the release of the pre-mRNAEukaryotic cells modify RNA after transcription- Next, RNA Processing is involved to modify pre-mRNA before the geneticmessages are dispatched by altering both ends of the primary transcripto 5’ end is synthesized first and receives a 5’ cap (a modified form of guanine added on the 5’ end after transcription of the first 20-40 nu-cleotides)o 3’ end is modified before the mRNA exits the nucleus An enzyme adds 50-250 more adenine nucleotides to form a poly-A tail to the 3’ endo The 5’ cap and the poly-A tail share the following: 1. They facilitate the export of the mature mRNA from the nu-cleus 2. They help protect the mRNA from degradation by hydrolyticenzymes 3. They help ribosomes attach to the 5’ end of the mRNA once the mRNA reaches the cytoplasmo Untranslated regions (UTRs) are parts of the mRNA at the 3’ and 5’ ends that will not be translated into protein Poly-A tail and 5’ cap are not translated either- Removal of the large portions of the RNA molecule that is initially synthe-sized is called RNA splicingo The sequence of DNA nucleotides that codes for a eukaryotic polypep-tide is usually not continuous, but is in segments The noncoding segments between the coding regions are calledintervening sequences, or introns The expressed segments are called exons (sequences of RNA that exit the nucleus)- RNA polymerase II transcribes both introns and exons from the DNAo The introns are cut outo The exons are joined together, forming an mRNA molecule with a continuous coding sequence This is the process of RNA splicingo The signal for RNA splicing is a short nucleotide sequence at each endof an intron Small nuclear ribonucleoproteins (snRNPs) recog-nize these splice sites on the ends of the introns· RNA in a snRNP is called a small nuclear RNA (snRNA) Several snRNPs join with additional proteins to form a larger spliceosome· The spiceosome interacts with sites along an intron, re-leasing the intron and joining together 2 exons- The catalytic role for snRNA arose from ribozymes (RNA molecules that function as enzymes)o The intron RNA functions as a ribozyme and catalyzes its own exci-sion by removing its own intronso 3 properties enable this: 1. Because RNA is single-stranded, a region of an RNA mole-cule may base pair with a complementary region elsewhere on the same molecule 2. Some of the bases in RNA contain functional groups that may participate in catalysis 3. The ability of RNA to hydrogen-bond with other nucleic acids adds specificity to its catalytic activity- Splicing is necessary for the passage of mRNA from the nucleus to the cyto-plasm- Alternative RNA splicing is a type of gene regulation in which different mRNA molecules are produced from the primary transcript depending on which segments are considered to be exons and which are intronso For example: sex differences in fruitflies are due to the differences in how males and females splice the RNA Result: The number of protein products an organism produces can be much greater than its number of genes- Proteins have a modular architecture consisting of discrete structural and func-tional regions called domainso Different exons code for the different domains of a proteino Presence of introns may
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