RNA Polymerases

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      • DNA/RNA/protein synthesis direction
        • DNA and RNA are both synthesized 5g 3.
        • The 5 end of the incoming nucleotide bears the triphosphate (energy source for bond).

1

            • The triphosphate bond is the target of the 3 hydroxyl attack.
              • Drugs blocking DNA replication often have modified 3 OH, preventing addition of the next nucleotide (“chain termination”).
            • Protein synthesis is N-terminus to C-terminus.

2

              • mRNA is read 5 to 3.
              •  
            • Start and stop codons
              • mRNA start codons
                • AUG (or rarely GUG).
                • Remember :AUG inAUGurates protein synthesis
                • Eukaryotes :Codes for methionine, which may be removed before translation is completed.
                • Prokaryotes :Codes for formylmethionine (f-met).
              • mRNA stop codons
                • UGA, UAA, UAG.
                  • UGA = U Go Away.
                  • UAA = U Are Away.
                  • UAG = U Are Gone.
              • Functional organization of a eukaryotic gene

3

              1. Promoter
                1. Site where RNA polymerase and multiple other transcription factors bind to DNA upstream from gene locus (AT-rich upstream sequence with TATA and CAAT boxes).
                2. Promoter mutation commonly results in dramatic decrease in level of gene transcription

4

                  • Enhancer
                    1. Stretch of DNA that alters gene expression by binding transcription factors.
                    2. Enhancers and silencers may be located close to, far from, or even within (in an intron) the gene
                  • Silencer
                    • Site where negative regulators (repressors) bind.whose expression it regulates.

5

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                    • RNA polymerases
                      • Eukaryotes
                        • RNA polymerase ImakesrRNA (most numerous RNA, rampant).
                        1. RNA polymerase II makes mRNA (largest RNA, massive).
                        2. RNA polymerase III makes tRNA (smallest RNA, tiny).
                        3. No proofreading function, but can initiate chains.
                        4. RNA polymerase II opens DNA at promoter site.
                        5. I, II, and III are numbered as their products are used in protein synthesis.
                        6. α-amanitin, found in Amanita phalloides (death cap mushrooms), inhibits RNA polymerase II.
                        7. Causes severe hepatotoxicity if ingested.
                      • Prokaryotes
                        • 1 RNA polymerase (multisubunit complex) makes all 3 kinds of RNA.


Transcription – promoter GTFs and RNA polymerase.
mRNA production and processing
RNA polymerase detail
RNA polymerase (RNAP or RNApol), also known as DNA-dependent RNA polymerase, is an enzyme that produces RNA. In cells, RNAP is necessary for constructing RNA chains using DNA genes as templates, a process called transcription. RNA polymerase enzymes are essential to life and are found in all organisms and many viruses. In chemical terms, RNAP is a nucleotidyl transferase that polymerizes ribonucleotides at the 3′ end of an RNA transcript.
RNA Polymerases
RNA polymerases are enzymes that initiate a new RNA chain on a DNA template. There are also such things as RNA-directed RNA polymerases. For the purposes of understanding synthetic biology, you are likely to encounter two of these enzymes. First is the one that produces the RNAs in the cell, and the other is T7 RNA polymerase. Though the native enzyme is important to understand in the context of gene expression, only the phage one is commonly used in vitro.
RNA Polymerase
DNA Replication, Transcription, Translation, DNA Polymerase III, Topoisomerase, RNA Polymerase
Transcription is when template DNA strand is converted to complementary coding RNA to begin gene expression. The RNA is very similar to DNA, except that it has Uracil (U) in place of Thymine (T) and it is single stranded. RNA is synthesized in a 3′ –) 5′ direction
• RNA Polymerase is the enzyme responsible for the conversion of DNA to RNA (transcription) in a 3′–)5′ direction. In Eukaryotes RNA Pol I makes Ribosomal RNA (rRNA), II makes Messenger RNA (mRNA) & III makes tRNA.
178-RNA Polymerase Structure
Review of the structure of RNA polymerase and comparison to DNA polymerase