MIDTERM II TERMS AND FACTS

Question 1

RNASES

Question 2

RNA secondary structure

Question 3

RNA tertiary structure

Question 4

RNA modification

Question 5

isoacceptor tRNA

Question 6

aminoacyl-tRNA synthetases

Question 7

charging reaction/specificity

Question 8

hyperchromicity

Question 9

rRNA

Question 10

tRNA

Question 11

mRNA

Question 12

RNA/DNA differences

Answer 12

RNA has a 2’OH while DNA doesn’t, DNA is usually in the double helix stable structure while RNA, depending on the type, can make interesting secondary and tertiary structures, non-Watson Crick base pairing (such as wobble and Hoogsteen pairing) are more common in RNA than DNA, RNA has Uracil that pairs with A while DNA has Thymine, RNA can have triplexes, RNA has catalytic function and can act as enzymes

Question 13

alkaline hydrolysis

Answer 13

RNA can be cleaved if you raise the pH high enough because the 2’OH gets deprotonated by the base and the that O- is nucleophilic enough to attack the phosphate of the backbone, the ribose on the connecting nucleotide cleaves off and creates a 2’-3’ cycle phosphate linkage, then the molecule is reprotonated. This is how enzymes that cleave RNA works and this is also how RNA can get denatured. DNA lacks this 2’OH so it doesn’t undergo this mechanism. –> maybe an explanation for why DNA is more stable

Question 14

endonuclease

Question 15

E.coli RNA polymerase

Question 16

primary transcript

Question 17

asymmetric transcription

Question 18

core, holo enzyme

Answer 18

core enzyme is the RNAP with the B, B’ and the two a subunits while the holoenzyme includes the sigma factors

Question 19

promoter

Answer 19

Region upstream of the gene we are transcribing, this is where the RNA Polymerase and associated proteins assemble to get ready for transcription. RNAP often binds around the -10 and -35 regions. In prokaryotes, this is known as the Pribnow box while in eukaryotes some of the promoters are made of the conserved sequence of TATA box.

Question 20

close promoter complex

Answer 20

this is when the RNAP assembles onto the DNA but the DNA is still in its double helix form –> no separation of the strands yet (i.e., transcription doesn’t really start yet). This was really visualized by Darst of the Rockefeller foundation when he was able to get the structure of the closed and open complexes.

Question 21

open promoter complex

Answer 21

this is when the RNAP creates the transcription bubble and the catalytic part of the polymerase starts transcribing –> this was figured out by Sanger in his DMS foot printing experiments however was really only visualized by Darst