Rna Synthesis

Front 1

what is the coding strand in transcription?

Back 1

non-template strand

Front 2

Describe the subunits of E. coli RNA polymerase

Back 2

-a: DNA binding domain that binds to UP elements in promoter
-BB': active site in junction
sigma: binds to specific promoters (70kD most common)
w: unknown function

Front 3

Describe the prokaryotic promoter elements

Back 3

1) UP element: enhances binding of RNA pol to DNA; only in genes expressed really well/high levels
2) -35 region (recognized by sigma subunit)
3) -10 region (recognized by sigma subunit)

Front 4

what is significant about sigma subunit 70 kD binding to various promoter sequences?

Back 4

-affiniity of sigma to the promoters vary depending on how closely they match the consensus sequences
-genes that are closer to the consensus sequence will be transcribed more efficiently
-fundamental for bacterial gene regulation

Front 5

Generally describe transcription in E. coli

Back 5

-sigma subunit of RNA pol binds to promoter
-helicase in RNA pol makes bubble and separates DNA strands
-sigma falls off once committed

Front 6

What are 2 ways that transcription can be terminated in prokaryotes?

Back 6

Rho-dependent and Rho-independent

Front 7

Describe Rho-dependent termination

Back 7

-Rho (trans acting factor) is an ATP-dependent RNA helicase
-Binds to RUT site on RNA
-When RNA pol pauses at termination site, Rho catches up to RNA pol and unwinds DNA:RNA hybrid in transcription bubble and everything falls off

Front 8

Describe Rho-independent termination

Back 8

-termination site is U rich (weak interaction with A in DNA)
-when RNA pol transcribes a GC rich region, the RNA will hybridize with itself, causing tension and causing the streak of U on the RNA to separate from A streak in DNA
-can bypass and go to next termination site

Front 9

What are the 3 different eukaryotic RNA Pol and what do they make?

Back 9

-RNA Pol I: rRNA
-RNA Pol II: mRNA
-RNA Pol III: tRNA and 5S RNA

Front 10

Describe initiation at RNA Pol promoters

Back 10

-eukaryotic
-Upstream binding factors bind to Upstream Core element and Core Promoter Element (brings 2 sequences close together)
-recruits SL1
-recruits other factors and RNA Pol I

Front 11

Describe initiation at RNA Pol III promoters

Back 11

-TFIIIC binds to A box and B box
-recruits TFIIIB binding upstream to initiation site
-recruits RNA Pol III and transcription begins
-For 5S RNA, TFIIIA binds to C box first

Front 12

Describe initiation at RNA Pol II promoters

Back 12

-TBP recognizes TATA box
-TFIIB can help bind TBP to DNA
-TFIIF binds RNA Pol II to prevent it from binding at wrong location

Front 13

List the conserved elements of a eukaryotic promoter

Back 13

-Downstream Promoter Element
-initiation site
-TATA box (not always there, cn also have INR element) (upstream)
-BRE (upstream)
-Proximal Promoter Region (upstream)
-Distal Promoter Region (upstream)

Front 14

what do actinomycin D and acridine do?

Back 14

Transcriptional inhibitors by intercalating between successive GC basepairs in duplex DNA
-work in both prokaryotes and eukaryotes

Front 15

How does rifampicin function?

Back 15

-transcriptional inhibitor in prokaryotes by binding B subunit of RNA Pol; blocks promoter clearance

Front 16

What does a-amanitin do?

Back 16

-transcriptional inhibitor of RNA pol II and RNA pol III