Quiz 3.1

Question 1

3 Types of RNA, and which do prok. and euk. organisms process

Answer 1

rRNA, Ribosomal RNA,BOTH PROKS + EUKS PROCESS
tRNA, transfer RNA, BOTH PROKS + EUKS PROCESS
mRNA, messenger RNA, ONLY EUKS PROCESS

Question 2

Where is rRNA processed, and what polymerase(s) make it during txn?

Answer 2

Ribosomal RNA is processed in the NUCLEOLUS, and is transcribed by RNA polymerases I (45s) and poly. III(5s). In prokaryotes, holoenzyme makes it.

Question 3

rRNA processing steps (for eukaryotes mainly, proks follow similar method but smaller size)

Answer 3

txn of pre-rRNA occurs in the nucleolus. Then, ribosomal proteins are imported into the nucleus and bind to the 45s rRNA. Some bases are methylated, some nucleotides have sugars attached, and uridines are modified. Finally, the pre-rRNA is cleaved into 3 pieces, 18s, 5.8s, and 28s.

Question 4

What do the 3 cleaved strands of rRNA become after the cleavage?

Answer 4

The 18s strand is folded into the small pre-ribosomal subunit, the 5.8s and 28s strands, along with previously made 5s rRNA and proteins, form the large subunit.

Question 5

How many proteins are there in each ribosomal subunit, and what are all the pieces called?

Answer 5

33 proteins with the small, 49 with the large in eukaryotes. 80s is the whole ribosome, 60s is the large subunit, and 40s is the small subunit.

Question 6

When do ribosomes move through the NPC?

Answer 6

While unfinished so they can be pushed through. They are fully formed once in the cytoplasm. So, pre-ribosomal particles are created in the nucleolus then exported through the NPC after.

Question 7

Where are ribosomes used in eukaryotes?

Answer 7

Rough ER, outer membrane of nucleus

Question 8

If studying RNA and proteins, what could be used?

Answer 8

RNA footprinting to study the RNA and protein interactions. Northern Blot could be used to probe for RNA that proteins interact with.

Question 9

Ribosomal sites for tRNAs

Answer 9

Ribosomes have an aminoacyl A site, Peptidyl site, and Exit site for tRNA, order E P A if reading mRNA 5’-3’. The Peptidyl site is where the first tRNA with amino acid enters. The Aminoacyl site is where every subsequent tRNA with amino acid binds. The Exit site is where the tRNA is released after its amino acid is removed.

Question 10

tRNA function, where is it transcribed and how

Answer 10

Transfer RNA is used in translation, carrying specific amino acids to where they are translated, ribosomes. Transcribed in the general nucleus in eukaryotes using RNA poly. III.

Question 11

tRNA processing

Answer 11

pre-tRNA forms a secondary structure, like a cloverleaf, by using hairpin inverted complimentary repeat sequences, like CGGUG and CACCG. 3 total hairpins are formed.
After the clover is formed, the pre-tRNA is cleaved at the 5’ and 3’ ends of the clover with RNase P ribozyme. Then, nucleotides CCA are added to the 3’ end. Certain bases are modified, and then the structure is ready for tRNA charging.

Question 12

tRNA charging summary

Answer 12

process of adding amino acid to 3’ end of tRNA, using aminoacyl tRNA synthetase.

Question 13

tRNA charging steps

Answer 13

Flip the tRNA so it is 3’-5’, antiparallel to mRNA 5’-3’. Look at the mRNA codon, 3 n.t. sequence, and determine its corresponding amino acid. The specific AA determined from the anticodon’s compliment is attached at its Carboxyl-terminal end, to the CCA added in processing. The tRNA’s anticodon should compliment the codon on mRNA

Question 14

mRNA and how is it made/processed?

Answer 14

Messenger RNA made by the RNA polymerase II in euks and Holoenzyme in proks, not processed in prokaryotes but translated in the cytoplasm. Eukaryotes process mRNA in the nucleus before it is used.

Question 15

Steps of mRNA processing, general

Answer 15

First the 5’ cap is added during transcription after initiation. Then, 3’ poly-A tail made of 200-250 Adenosine is signaled by the poly-A signal sequence AAUAAA . The pre-mRNA is then spliced using a spliceosome.

Question 16

5’ cap details

Answer 16

Made of 7-methyl-guanosine, which is G with a methyl group added to the 5’ end of RNA after txn initiation. The CTD on RNA poly II uses capping enzymes that move to the 5’ of the mRNA to add the cap. It stabilizes mRNA, prevents degradation, facilitates nuclear export of mRNA to cytoplasm, and helps to localize the small ribosomal subunit for TLN.

Question 17

3’ Poly-A tail details

Answer 17

Made of 200-250 Adenosines, signaled by the AAUAAA poly-adenylation signal sequence that cuts mRNA 10-30 nt. downstream. The signal uses poly-a polymerase enzymes on the CTD of RNA poly. II to add the 200-250 As to the 3’ end of the mRNA. The poly-A tail also stabilizes, prevents degradation, facilitates nuclear export, and helps localize the small ribosomal subunit.

Question 18

mRNA Splicing, general info

Answer 18

Process of cutting and putting mRNA sequences together. Exons(variably sized), coding and desired mRNA portions, are put together after Introns, non-coding and undesirable mRNA, are cut out at splice sites.

Question 19

Splice site ends and branch point

Answer 19

The 5’ splice site is a GU at the beginning of the intron. The 3’ splice site is AG at the end of intron. The Branch point is an Adenosine A more towards the 3’ end, where the 5’ end’s GU is bent towards after it is cut, forming a lariat.

Question 20

Spliceosome

Answer 20

made of U1, U2, U4 + U6, and U5, snRNPs, small nuclear RNA with proteins. All work together in mRNA splicing to cut out introns and stick together exons.

Question 21

Steps of snRNP binding and function during splicing

Answer 21

First, U1 binds at the 5’ Ss. U2 binds at the branch point A once recognized with a branch-point binding protein, coming from the 3’ Ss. U4-U6, and U5 all enter, bending the intron into a loop. Once all are bound, the 5’ Ss is cut by the spliceosome, with U5 holding the first exon as the lariat is formed. U2 and U6 hold the mRNA and U5 in place. U1 and U4(unbound from U6) then leave the complex. U2 and U6 finally cut the 3’ Ss with enzymatic function. All snRNPs are removed with the lariat, and exons are ligated/joined together using phosphodiester bonds. Process needs nucleases, RNases, and polymerases.

Question 22

Alternative splicing

Answer 22

Different exons on a gene can be spliced together by skipping over exons to combine with another. CANNOT splice out of order. E 1 can splice with E 5, but E 4 CANNOT go back to bind with E 2.