Study Guide: Chapter 16(i) - TRANSCRIPTIONThe role of proteins • Proteins control most cell processes like chemical reactions and also give cells their structure and shape. Cell function is dependent on protein function. If one or more proteins do not work correctly, the cell may become abnormal and die. The central dogma Proteins are synthesized in a two-step process: transcription of genes into messenger RNAs and translation of messenger mRNAs into proteins. DNA  RNA  ProteinExceptions to central dogma?I. An Overview of Transcription A. RNA polymerase enzyme (DNA-dependent RNA Polymerase)1. This enzyme is responsible for synthesizing RNA from DNA. 2. The enzyme uses only one of the DNA strands as a template. a. This is called the template strand (non coding strand, anti sense or negative strand)b. The other strand is called the non-template or coding strand or sense strand. c. The coding strand matches the mRNA sequence, except that it has thymine where the mRNA has uracil. B. Characteristics of RNA polymerase 1. RNA polymerase reads the DNA template and synthesizes a complementary RNA strand. 2. It builds RNA in the 5' → 3' direction by reading the DNA template. 3. It does not require a primer to begin RNA synthesis. 4. Bacteria have one RNA polymerase; eukaryotes have three distinct types: pol I, pol II, and pol III. - RNA polymerase II (pol II) transcribes genes that code for proteins; thus, it synthesizes mRNAs. -RNA Pol I? RNA Pol III?C. Initiation: How does transcription begin? 1. In bacteria, a protein, called sigma factor, binds to RNApolymerase before transcription begins. a. RNA polymerase + sigma = holoenzyme. b. RNA polymerase is the core enzyme. 2. David Pribnow studied promoters in Bacteria: a. Sigma binds tightly to specific regions of DNA called promoters. b. Pribnow analyzed the base sequence of promoters 1(1) Promoters are 40−50 base pairs long. (2) Within the promoter, there is a region known as the –10 box (the –10 box is 10 base pairs upstream from where transcription will start (the +1 site). And another about 35 bases upstream of the start site; it is called the –35 box. [ In eukaryotic cells, most promoters include a unique sequence called the TATA box, centered about 30 base pairs upstream from the transcription initiation site]c. Researchers found that sigma is required to facilitate RNA polymerase binding to DNA. . Transcription begins when sigma binds to the –35 and the –10 boxes. d. The holoenzyme binds to DNA at specific locations called promoters. e. Promoters are sites on the DNA template where transcription begins. f. Sigma appeared to be responsible for guiding (and binding) RNA polymerase to promoters. 3. Events inside the holoenzyme a. After sigma binds to a promoter for a bacterial gene, the DNA double helix opens. b. The template strand is threaded through a channel in RNA polymerase that leads to the active site. c. Ribonucleoside triphosphates (NTPs) enter another channel in RNA polymerase, moveto the active site, and are incorporated into the mRNA when they are complementary to the template strand. d. Sigma is released once RNA synthesis is under way  Initiation is now complete. D. Elongation and termination1. Elongation - RNA polymerase moves in the 3' → 5' direction along the template DNA strand. New mRNA strand is synthesized 5’  3’- RNA polymerase catalyzes the addition of the nucleotide to the 3' end of the growing RNA - It inserts a uracil whenever it encounters adenine in the template DNA. - A group of amino acids called the enzyme’s zipper helps separate the new mRNA strand from the template strand. Rudder? The Enzyme’s structure is correlatedwith its function. (1) Double-stranded DNA goes into and out of one groove. (2) NTPs enter another channel. (3) The growing RNA structure exits through the rear. 2. Termination - Specific sequences in template DNA act as termination sites. (1) In bacteria, the bases in the transcriptional termination sequence form complementary base pairs. (2) This results in a hairpin structure, which causes the RNA strand to separate from the RNA polymerase, terminating transcription. (3) RNA polymerase and the mRNA strand are released from the DNA template. E. Polysome or Polyribosome? 2II. RNA Processing in Eukaryotes :The startling discovery of eukaryotic genes in pieces: 1. In prokaryotes, translation of mRNA can take place while the mRNA is still being transcribed. 2. In eukaryotes, pre-mRNA is produced by transcription, and this must be processed before translation can occur. Locations? 3. Eukaryotic genes have intervening sequences called introns  the expressed portions of genes (translated regions) exons and the intervening portions introns. a. The protein-coding region of eukaryotic genes is interrupted by stretches of noncoding DNA. b. Noncoding sequences must be disposed of to make a functional mRNA. c. Eukaryotic gene organization is very different from that in prokaryotes. (i) RNA splicing: 1. Eukaryotic genes are first transcribed into aprimary transcript that contains both introns andexons. 2. Intron splicing (removing the extra sequences) occurs inside the nucleus. 3. Intron splicing is catalyzed by a complex of proteins and small RNAs (snRNPs that is, small ⎯nuclear ribonucleoprotein particles. snRNPs assemble on the primary mRNA transcript, forming a spliceosome. (ii) Adding caps and tails to transcripts: Protect mRNAs from degradation by enzymes in the cytosol and increase the efficiency of translation. 1. A cap of 7-methylguanylate-P-P-P is attached to the 5' end of each mRNA. It serves as a recognition signal for the translational machinery (helps with mRNA binding to ribosomes) and protects the transcript from degradation. 2. A tail, consisting of 100−250 adenines (“poly(A) tail”), is added to the 3' end of mRNA increase