RNA Synthesis

Question 1

DNA vs. RNA

Answer 1

DNA: template for protein synthesis; double-stranded; 5’ deoxyribose sugar; bases A, C, G, and T
RNA: messenger for protein synthesis: single-stranded; ribose sugar; bases A, C, G, and U

Question 2

mRNAs

Answer 2

messenger RNAs; code for proteins

Question 3

rRNAs

Answer 3

ribosomal RNAs; form the basic structure of the ribosome and catalyze protein synthesis

Question 4

tRNAs

Answer 4

transfer RNAs; central to protein synthesis as adaptors between mRNA and amino acids

Question 5

transcription overview

Answer 5

transfer of genetic data from DNA to mRNA

Question 6

where does transcription occur

Answer 6

nucleus

Question 7

which DNA serves as the template for transcription

Answer 7

anti-sense strand; the anti-sense strand will vary based on what gene is being coded for

Question 8

what is the sense strand

Answer 8

the strand of DNA that has the SAME sequence as the synthesized mRNA, which is coded for by the anti-sense strand

Question 9

high processivity

Answer 9

the enzyme stays attached to the DNA sequence for a long period of time, allowing it to completely synthesize in one go; DNA Pol and RNA Pol have high processivity

Question 10

prokaryotes - transcription initiation

Answer 10

1) sigma factor associates with RNA polymerase, forming the holoenzyme
2) the holoenzyme seeks out a promoter region (often TATA box or -35 box) and binds it
3) transcription occurs for ~10 nt before sigma factor releases and elongation starts

Question 11

prokaryotes - transcription elongation

Answer 11

-once sigma factor releases from the holoenzyme, RNA Pol continues synthesizing mRNA until it finishes the transcript

Question 12

prokaryotes - Rho-dependent termination (of transcription)

Answer 12

*factor rho binds to the growing mRNA strand and moves toward RNA Pol
*Rho-termination sequence in DNA causes RNA Pol to pause and rho catches up to it
*factor rho causes dissociation of RNA Pol and releases mRNA

Question 13

prokaryotes - Rho-independent termination

Answer 13

*terminator sequence is a G:C-rich palindrome, followed by 6-7 Us
*the U-rich sequence at 3’ end allows for easier dissociation of RNA Pol
*forms a stem-loop structure often

Question 14

RNA Pol I - eukaryotes

Answer 14

eukaryotic polymerase responsible for transcribing rRNA genes (5.8S, 18S, and 28S rRNA genes)
**genes are located in the NUCLEOLAR ORGANIZING REGIONS (NOR), which are located on acrocentric chromosomes (13, 14, 15, 21, 22)
*rRNAs transcribed as a single unit and then separate into their subunits

Question 15

acrocentric chromosomes

Answer 15

ch 13, 14, 15, 21, and 22
*contain nucleolar organizing regions (NOR) on the ends; highly repetitive

Question 16

RNA Pol II - eukaryotes

Answer 16

eukaryotic polymerase responsible for transcribing all protein-coding (mRNA) genes

Question 17

RNA Pol III - eukaryotes

Answer 17

eukaryotic polymerase responsible for transcribing tRNA genes (and 5S rRNA)

Question 18

eukaryotes - transcription initiation

Answer 18

*general transcription factors (TFIIB, TFIID, etc) bind to generic promoter sequences
*specific transcription factors bind to enhancer/silencer sequences to regulate transcription
**these TFs must bind BEFORE RNA Pol (recruit it)
*complex forms and transcription begins

Question 19

modification of tRNA

Answer 19

1) introns removed
2) 5’ portion is removed by RNAse P (an endonuclease)
3) 3’ portion trimmed by an exonuclease
4) CCA is added to 3’ end by tRNA nucleotidyltransferase
5) correct amino acid added to CCA site

Question 20

5’ capping - modification of mRNA

Answer 20

3 enzymes modify the 5’ by:
1) removing a phosphate group
2) adding a GMP molecule (5’ to 5’)
3) methylating the GMP
*results in 7-methylguanosine

Question 21

mRNA splicing - modification of mRNA

Answer 21

-removes the introns (non-coding portions) of the gene
1) a specific A nucleotide attacks the 3’ end of upstream exon
2) the 5’ end of the intron becomes covalently linked to the A; the 3’ OH of the exon reacts with the 5’ end of the next exon
3) the lariat structure (intron) is released and degraded

Question 22

examples of splice-site mutations

Answer 22

beta-thalassemias can be caused by splice-site mutations (changing the consensus sequence can result in missing exons, inclusion of introns in final product, etc)

Question 23

C-terminal domain (CTD) in transcription

Answer 23

*phosphorylation of CTD of RNA Pol III tail initiates elongation
*the CTD recruits molecules for RNA processing (5’ capping, splicing, and poly-A tail)