Current LectureMCB 250 1st Edition Lecture 13Outline of Current Lecture 1. RNA vs DNA2. Denaturation3. 3 Major types of RNA (largest concentrations)4. TranscriptionCurrent Lecture1. RNA vs DNA- Contains ribose instead of 2’-deoxyribose- Uracil instead of thymine- DNA is frequently intermolecular (two strands of the DNA are separate molecules that come together to form b form DNA- RNA is usually intramolecular. There is usually one piece of RNA that folds up on itself- Looks like DNA with 3’ and 5’ end, it just has the 2’ OH group in the structure- Substrates are the NTP (not DNTP)- ATP, UTP, GTP, CTP- RNA has secondary and tertiary structure as wello All forces in DNA that drive the b form helix, it still drives the structure of RNAo Base pairs: all H bonds group want to hydrogen bond. They may be forced to hydrogen bond with water, but if it can it can H bond to other things. All bases of RNA want to hydrogen bond with somethingo Base stackingo Hydrophobic interactionso Repulsion of negative phosphate groups drive the structure of RNA as well. Thereare cations associated with any nucleic acids ( not drawn because it isn’t in a fixed position)- In DNA: there is a perfect b form and one strand sequence defines the sequence of the other strand. RNA isn’t like that, it wants to fold up however it can, it is not constrained by the one strand defines another strand (like DNA). There is more variation in RNA. o Stem loops, bulges, and base-pairingThese notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.- RNA-RNA duplexes (hydroproteins) where basepair matches up perfectly and run antiparallel. Makes a structure more like A-form DNA. The ‘OH group at ribose does affect the structure. - RNA duplexes structure are different than B-form DNA- Non Watson-Crick bp can form!o G U can come together with 2 H bondso It is not constrained like DNA2. Denaturation- Temperature, hydrogen bond reagents, increase hydrophobicity, and decreased- PH can actually degrade RNA (not like DNA)- Fundamental difference between DNA and RNA3. 3 Major types of RNA (largest concentrations)- mRNA: template for protein synthesis. Relatively unstable. Average half life is 3 minutes. This is because you want to transcribe the gene -> protein. Want it to be unstable because make when need it and go away. When you want more just make another mRNA. - Transfer RNA: Adapter between mRNA and amino acids. Relatively stable because you the same ones over and over again. It will exist more than the lifetime of the cell. - Ribosomal RNA: heart of ribosome that you synthesize protein. S= spenberg units: size. Relatively stable: major machines in the cell you use over and over.- Other RNA’s in cell: Regulatory RNA’s. Small RNA’s can be critical for regulation of many things. They are Unstable, come and go giving it a regulatory role- Catalytic RNA’s: ribozymes and are almost exclusively acting on other RNA’s. 4. Transcription- Use DNA as a template to make an mRNA- Prokaryotes takes place in one environment so when mRNA begins to be made, it will berecognized by a ribosome and translated into protein. The RNA world hypothesis comes from the fact that this is the fundamental machinery in the cell, and it’s all RNA (mRNA, tRNA, rRNA). Fundamental machines of the cell. Because of the instability of RNA, evolved DNA (technically)- In bacteria, all RNA are synthesized by RNA polymerase. - RNA polymerase:- Core RNA polymerase is made up of 4 subunits: enzymatic unit. Capable of performing DNA dependent, RNA synthesis.- Lots of regulatory proteins that interacts the polymerase to control the activity: auxillary protein- Holoenzyme: core polymerase + sigma factor. Sigma subunit is part of the holoenzyme that is required for recognition of the promoter. Promoter: the sequence in the DNA that dictates where the start site of transcription is.- There are 7 different sigma factors in E. coli that recognize different promoter sequences for different genes- Sigma 70 is the house keeping sigma: mostly sigma 70 is mainly the one that recognizes promoter. - As an RNA pol is elongating an DNA, its primer is already set up. The DNA enters through a DNA entry channel and is separated by a wedge. The wedge separates 2 strands of DNA as it passes through the enzyme and creates a transcription bubble. The transcription bubble is 17bp of dna that is separated WITHIN the RNA polymerase. Then one strand is the template strand which ribonucleotides come in achannel and the new RNA passes off back and exits channel. The duplex of RNA-DNA hybrid is around 8bps long. If it is the correct ribonucleotide and can bp appropriately with the template, it takes place in the active site and metal protons will deprotonate the OH group and attack the phosphate, which makes the phosphodiester bond.- rNTP vs dNTP: there is an important hydrogen bond that occurs to the 2’ OH group tocheck if the sugar has that group and will allow it to take place.- RNA Polymerase is not as accurate but it does not matter because there are lots of copies of mRNA and it is not permanent or passed down to