Chapter 3 – DNA Structure & Transcription (Production of RNA)DNA structure, Transcription, Processing of eukaryotic transcriptsPart 1: DNA StructureI. DNA A. General1. “Information molecule”: musta. contain necessary informationb. be passed to offspringc. be variable, but still accurate (ex. binary)2. Reminder: DNA is a polymer of nucleotidesB. Terminology1. Nucleotide vs. Nucleoside a. Nucleoside = sugar + baseb. Nucleotide = sugar + base + at least 1 phosphatei. Can be identified as “nucleoside mono, di, tri, phosphate”II. Structure 2 nucleotides are linked by series of covalent bonds called a phosphodiester bond (C-O-P-O-C)A. The Backbone1. Linear strand of alternating phosphate & sugar groups2. Nonvariable3. Negatively charged 4. Tail-end phosphate (not connected to a sugar) will beHPO4 (H attached to top O), instead of PO4 (see diagram)5. All sugars in strand are oriented in same direction (5’ 3’ or 3’ 5’)6. Strand has polarity or directionB. Base Sequence1. Variable part of DNA – holds info2. Absolutely no constraints on what bases are in what orderC. Double-helix (for BDNA – only DNA we talk about)1. 2 antiparallel strands in a double helix2. 2 strands stay together by H-bonds that form between complimentary bases (1 purine—1 pyrimidine)a. A-T, G-Ci. This specificity is what keep width of DNA constantb. Bases also interact noncovalently with the ones above & below and “stack” (tightly group), which stabilizes helixi. **clicker question (unrelated): Make sure the Oxygen on the 3’ carbon isn’t there if you’re working in DNA.D. IN the cell, DNA is coiled & packaged with proteins. The 2 together are called chromatin1. *Don’t worry about H2A, H2B, etc. in the bookPart 2: Transcription – Making an RNA Product From a GeneI. General A. “Gene” – sequence of DNA that codes for a product, and its associated control regions II. 1 scenario of gene structure (eukaryote): III. Process of Transcription A. Specific proteins associate with the controlregions of a gene (ex. start/stop) (fig. 3.17) B. RNA polymerase complex separates theDNA strands to form the “transcriptionbubble” (fig. 3.18)C. 1 DNA strand (half-strand) used to buildRNA1. RNA built from its 5’ to 3’ end (so, from 3’to 5’ on the half-strand of the DNA)D. RNA polymerase checks for correct basepairing & catalyzes pyrophosphate release &phosphodiester bond formation (3.19)E. If the transcript contains information tobuild a protein, it’s mRNA (messenger RNA)1. Prokaryotes can immediately use mRNAto build proteins 2. Eukaryotes first process mRNA because some of the transcript isn’t useful (introns/exons splicing)Can be a gap between enhancer & rest:-DNA sequence that gets transcribed-Terminator: ends transcription Promoter: general transcription factors bind hereEnhancer Sequence: transcriptional activator proteins bind hereIV. Splicing (Introns/Exons) A. The –DNA sequence that gets transcribed- above contains introns (useless) and exons (useful)B. mRNA processing1. Adds special nucleotide to the 5’ end (5’ cap)2. Adds poly-A (adenine) tail to 3’ end3. Removes introns & covalently bond exons togethera. One eukaryotic transcript can be processed different ways (fig. 3.25)b. Splicepsomes (snRNP’s) – RNA & protein machines used to remove introns4. Remember, not all transcripts are mRNA.a. rRNA (ribosomal)b. tRNA (transfer)c. small nuclear (snRNA)d. micro RNA
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