Stamm RNA intro 3-27

Question 1

define the term RNA World

Answer 1

RNA World describes the biological origins on earth, recreated in the Urey/Miller Experiment. Materials: N2, H2O, NH3, CH4. Generate spark to observe all 4 nucleotides and many amino acids- RNAs present after time passes. Ability to attach aa’s to tRNA made protein structure basis for life

Question 2

Describe the reactivity of the 2’OH or ribose in RNA

Answer 2

basic conditions: proton is extracted, breaks phosphodiester bond; acidic conditions: gets protonated and leaves as water. Must be stored as precipitate, because water reacts with it

Question 3

describe the mRNA caps

Answer 3

Only in eukaryotes. gamma phosphate removed from the beginning of the mRNA, GTP is added to make triphosphate bridge att the beginning of the mRNA, guanine methylated at the N7. Can create more methyl substitutions for signaling purposes.

Question 4

How is mRNA polyadenylated

Answer 4

carboxy-terminal domain is phosphorylated to recruit polyadenylation and cleavage factors when polyA is transcribed. Two factors bind COOPERATIVELY to the recognition site for cleavage of the mRNA while the RNAP continues. PAP is recruited by one of these proteins

Question 5

How are full length cDNAs cloned

Answer 5

Reverse transcriptase reverse transcribes using an oligo polyT

Question 6

2 main functions of the mRNA tail and cap

Answer 6

transportation from the nucleus, stability of binding with mRNA assoc. proteins

Question 7

CBP

Answer 7

cap-binding protein

Question 8

How are caps captured to analyze the mRNA

Answer 8

Oxidizing the diol at the 5’ end with NaIO4, allows attachment of biotin, which can be pulled down by avidin (creates CAGE tags)