Lecture 10

Question 1

Outline the general process of Transcription

Answer 1

1. RNA polymerase, together with one or more transcription factors, binds to promoter DNA
2. RNA polymerase creates a transcription bubble, which separates the two strands of DNA helix by breaking the hydrogen bonds between complementary DNA nucleotides
3. RNA polymerase adds RNA nucleotides complementary to DNA
   strand
4. RNA sugar-phosphate backbone forms with assistance from RNA polymerase to form a new RNA strand
5. Hydrogen bonds of the RNA-DNA helix break, freeing the new RNA strand
6. In eukaryotes post transcriptional processing includes polyadenylation, 5’ capping, and splicing
7. The RNA may remain in the nucleus or exit to the cytoplasm through the nuclear pore matrix via

Question 2

What is responsible for all of the catalytic action of transcription? what else is involved in transcription?

Answer 2

RNA Polymerase II ; activator proteins

Question 3

Does Transcription create superhelical tension?

Answer 3

yes, topoisomerase relieves the tension

Question 4

When are new mRNA capped?

Answer 4

They are capped as soon as they emerge from the RNA polymerase

Question 5

What must occur once the RNA polymerase is finished with one mRNA strand, before it can begin another round of transcription?

Answer 5

It must be dephosphorylated

Question 6

“what are the steps involved in eukaryote mRNA processing prior to leaving the nucleus?”

Answer 6

5’ capping
RNA splicing (removes intron sequences ; lariats are formed here)
3’ polyadenylation (poly A tail)

Question 7

What are the steps in capping mRNA? When does mRNA capping begin?

Answer 7

The 1st nucleotide is dephosphorylated

GMP is added in reverse linkage (5’ to 5’ instead of 5’ to 3’)

A methyl group is added to the guanosine

Capping begins when the mRNA is 25 nucleotides long

Question 8

Explain how Introns are ID’ed and removed during splicing

Answer 8

Introns are flanked by sequences that are recognized by spliceosome RNA’s to ID where the cut needs to happen, and then RNA brings in other proteins to actually cut the intron out.

Question 9

what performs splicing?

Answer 9

spliceosomes

Question 10

explain the process of splicing

Answer 10

the 5’ end of the intron is ID’ed

the “A” near the 3’ splice site of the intron in ID’ed

the Lariat structure is formed

the 3’ end of the intron is cut

the 2 exons are then joined

Question 11

Spliceosomes do not need to use ATP because they use energy already stored in the intron to exon bonds. True or False

Answer 11

False ; spliceosomes use ATP

Question 12

List the 5 types of snRNP’s and what they are involved in

Answer 12

U1: ID’s 5’ end of intron

U2: binds to A

U4 and U5: work together to recruit proteins to make the conformational and enzymatic changes in splicing

U6: recognizes the 3’ end and works with U4 and U5

(there is no U3)

Question 13

Why are mRNA sequences given a poly A tail?

Answer 13

it increases the stability of the sequence and makes it easier to be transported without being damaged.

Question 14

define Consensus sequences in the process of transcription

Answer 14

signal that the mRNA needs to be clipped (this sequence is complete)

Question 15

What is an exosome in the nucleus?

Answer 15

a protein complex that uses RNAses to digest damaged RNA sequences so that their nucleotides can be recycled

Question 16

describe the exosome type found in blood, urine, and cultured medium of cell cultures.

Answer 16

cell-derived vesicles that contain various molecular constituents of their cells of origin.

contain enzymes, heat shock proteins, and cytoskeletal proteins

Question 17

What mediates the “handoff” of mRNA through the nuclear pores into the cytoplasm?

Answer 17

nuclear export receptor proteins

Question 18

What is the final quality control point for mRNA prior to Translation? how does it work?

Answer 18

nonsense mediated decay ; it eliminates mRNA’s that have premature stop codons

Question 19

what are miRNA’s? what do they do?

Answer 19

small, noncoding RNA molecules that function in RNA silencing and post-transcriptional regulation of gene expression

basically “guide” molecules in RNA silencing

Question 20

Dysregulation of miRNA’s is associated with what?

Answer 20

many human diseases, especially cancer and neurodevelopment disorders

Question 21

where are noncoding RNA’s synthesized and processed?

Answer 21

in the nucleus, just like all other RNA’s

Question 22

What is rRNA for? where does this occur?

Answer 22

rRNA’s (ribosomal RNA’s) code for ribosome subunits ; the rRNA is processed and assembled into ribosome subunits in the nucleolus

Question 23

what is the nucleolus?

Answer 23

a structure in the nucleus visible during interphase when it is producing more ribosomes

“ribosome factory”

Question 24

what is the size of a cell’s nucleolus associated with?

Answer 24

that particular cell’s need to produce proteins (it will need many ribosomes for this)

Question 25

explain the full process of ribosomal subunit processing/ maturation

Answer 25

rRNA's are created and processed in the nucleolus rRNA is made into ribosomal subunits in the nucleolus final processing of the subunits does not occur until it is shipped through the nuclear pore into the cytoplasm

Question 26

where are most snoRNA's assembled into snRNP's?

Answer 26

cajal bodies (a type of aggregate in the nucleus)

Question 27

what is a scaffold protein?

Answer 27

attaches to the tail of RNA polymerase and keeps transcription accessor proteins in close proximity to the polymerase.