Lecture 5 - Overview of transcription and mRNA formation

Question 1

During transcription, incoming ________________ base-pair with bases in the ________________. They are joined together by ______ from ___ to ______ on the RNA**

Answer 1

ribonucleoside triphosphates (rNTPs). template DNA strand. RNA polymerase. 5’ to 3’

Question 2

Why is polymerization energetically favoured during elongation.

Answer 2

High energy bond between alpha and beta phosphates on rNTPs is replaced by low energy phosphodiester bond between the rNTPs

Question 3

Transcription starts at the ____ position. The coding sequence is ________ from this position and the promoter is _________. The ______ strand is read from ___ to ____.

Answer 3

+1. downstream. upstream. template DNA. 3’ to 5’

Question 4

________ is the critical mechanism for gene expression regulation

Answer 4

initiation

Question 5

During initiation, 3 things that RNAP does

Answer 5

Binds to promoter sequence. Denatures DNA. Catalyzes first phosphodiester linkage

Question 6

During elongation, RNAP advances from ___ to ____ down the _______ strand and ________ DNA. It polymerizes _______.

Answer 6

3’ to 5’. template. denatures. polymerizes RNA

Question 7

During termination, 3 things RNAP does

Answer 7

polymerase recognizes stop site, releases completed RNA, dissociates from DNA.

Question 8

_______ (which type) RNAP requires associated proteins called _________ which help it _________ and ________

Answer 8

eukaryotic. GTFs. find promoter. initiate transcription

Question 9

When RNAP binds to promoter sequence on DNA ____, we call that ________ complex. when DNA melted and ___________ (__bp longs) is created, the ________ complex is formed

Answer 9

duplex, closed, transcription bubble - 14bp, open

Question 10

During elongation, there is a ____________ behind the nascent RNA. Multiple _________ can transcribe the ________ DNA strand at the ________ time. This is shown on the _________.

Answer 10

hybrid region (DNA:RNA). polymerases. same template. same. EM image

Question 11

Speed of elongation is around ___________. small genes are transcribed in __________ whereas big genes (with big ____) can take ________.

Answer 11

1000 nt/min. a few minutes. introns. hours.

Question 12

Completed RNA molecule is called the __________

Answer 12

primary transcript

Question 13

What signals the bound RNAP to terminate transcription

Answer 13

specific sequence in the TEMPLATE DNA strand

Question 14

the terminating sequence has to be on the ________ strand

Answer 14

template

Question 15

E.Coli RNAP has ___________ which are ___, ___, ___, ___, ___

Answer 15

five subunits. alpha, beta, alpha prime, beta prima, omega.

Question 16

RNAPs have structures that are ________ because _________

Answer 16

similar. all deal with DNA.

Question 17

What happens to DNA when it enters RNAP (an enzyme) (3)

Answer 17

1) Bends sharply 2) Template strand is open 3) Template strand can go in active site of enzyme

Question 18

Gene organization in prokaryotes. How it is called and amount of non coding genes

Answer 18

Genes with common function arranged linearly in operons and transcribed together on a SINGLE mRNA. Called coordinate expression. Few non coding gaps of DNA prokaryotic genomes.

Question 19

Gene organization in eukaryotes. In eukaryotes, gene _______________ is not achieved by simple _______________.

Answer 19

Analogous genes (related proteins) are scattered on several chromosomes. co-regulation. physical linkage.

Question 20

mRNA in prokaryotes vs mRNA in eukaryotes

Answer 20

in prokaryotes mRNAs directly transcribed from DNA. in eukaryotes, transcripts go through several PROCESSING steps before becoming mRNAs.

Question 21

The cap of the primary transcript will be __________ by other _________ when _________ does its function

Answer 21

recognizes. molecules. RNA

Question 22

Steps of RNA processing. RNA retains ____________ at its ____ and _____ ends.

Answer 22

Capping, cleavage at poly(A) site and polyadenylation. Intron excision. Exon ligation. RNA retains untranslated regions (UTRs) at its 3’ and 5’ ends.

Question 23

What process can increase protein diversity and how

Answer 23

Alternative splicing. Cell types produce different forms of the protein encoded by a gene.

Question 24

Exemple of alternative splicing

Answer 24

Fibronectin gene. in fibroblasts, the fibronecting mRNA transcript contains EIIIB and EIIIA regions of the gene but in liver cells, hepatocyte fibronectin mRNA doesn’T contain EIIIB and EIIIA regions of the gene

Question 25

Different forces and mechanisms that unwind DNA (2)

Answer 25

1) TFIIH helicase activity necessary for ATP hydrolysis which provides energy for a TFIIH subunit to unwind DNA at start site (it also pushes DNA into the polymerase)
2) As DNA is held in place in the PIC (preinitiation complex) by binding of TBP of TFIID to tatabox, this force and force of TFIIH unwinding subunit both ASSIST N-terminal region of TFIIB and pol II to melt the DNA at transcr. site