Part 1: DNA dependent RNA synthesis

Cytoplasm

where is RNA made in a prokaryotic cell

Nucleus

where is RNA made in a eukaryotic cell

Cytoplasm

where are proteins made in all cells

Ribosomal RNA

makes up ribosomes and is noncoding

Messenger RNA

code for proteins

Transfer RNA

read the genetic code and helps the creation of polypeptide

DNA template

the process of transcription requires a

5 to 3

transcription occurs in this direction

Coding

the DNA nontemplate is the _ strand

Coding

the RNA transcript matches the _ strand of DNA

Transcription bubble

17 bp unwound area that occurs in RNA pol

Positive supercoils

occurs ahead of RNA pol

Negative supercoils

occurs behind RNA pol

40-80 nt/sec

transcription rate of RNA pol

250-1000 nt/sec

replication rate of DNA pol III

Core enzyme

RNA polymerase alone

Holoenzyme

RNA polymerase combined with sigma factor

2 Mg2+

ions present in the active site of RNA pol

2 Zn2+

the Beta subunit of RNA pol contains ____ for catalysis

Asp

residue that coordinates the Mg2+ and oxygen in the active site of RNA pol

Promoters

transcription initiation begins at…

Sigma factor

recognize promoter sequences and either allow or block the binding of RNA pol

+1

the start site of transcription is designated as ____ and anything behind that is -#

Spacer

conserved sequence between TATA -10 and -35 region of DNA that allos for the conformational fold of the DNA in the sigma factor and active site of RNA pol which promotes the initation of transcription

UP element

AT rich region that is -60-40 nt behind the promoter

Closed complex

when the sigma factor has bound the DNA to be transcribed but no separation of strands has occurred

Open complex

following the formation of the transcription bubble, transcription is initiated

NusA

elongation continues and sigma factor 70 dissociates and is replaced by …

Transcription Termination

occurs when NusA dissociates

Beta subunit

this part of RNA pol acts as the clamp and contributes to the stabilization and processivity of RNA polymerase

1x10^4

error rate of RNA polymerase

Factor independent

this type of transcription termination is triggered by hairpin formation when RNA pol randomly pauses, if a hairpin formed termination occurs

Isomerization

the conformational change that takes place in factor independent transcription termination when there is a hairpin formed

Factor dependent

this type of transcriptional termination involves rho helicase for RNAs that include a rut element

Rut element

recruits Rho helicase which will catch up to RNA polymerase and cause dissociation

RNA pol 1

synthesizes pre ribosomal RNA except 5S rRNA

RNA pol 2

eukaryotic that synthesizes mRNA and ncRNA

RNA pol 3

eukaryotic and synthesizes tRNA, 5S rRNA, and ncRNA

Mitochondrial rna pol

transcribes mitochondrial genes

Chloroplast RNA pol

transcribes chloroplast genes

Eukaryotic rna pol

have many non identical large subunits and require additional factors beyond sigma factors

TATA binding protein (TBP)

binds the TATA box and bends the promoter DNA, this is REQUIRED for initiation of eukaryotic transcription

Pol 2

recruited to the eukaryotic DNA by transcription factors, forms the closed and then open complex

Carboxyl terminal domain (CTD)

this is phosphorylated in a specific sequence during the initiation of eukaryotic transcription ,, allows for the polymerase to escape the promoter

Elongation factors

used in eukaryotic transcription and they aid in elongation steps once the transcription factors dissociate from the sequence

Termination factors

are used to de phosphorylated the CTD and promote the termination of eukaryotic transcription

Largest RNA pol II subunit

contains the CTD (which can identify the stage of transcription based on what residues are phosphorylated at a given time

Transcription inhibitors

have many uses in medicine and research to fight bacterial infection, cancer therapies, AIDs therapies, and to understand the mechanisms of transcription

DNA intercalating agents

can block RNA (and DNA) polymerases by binding tightly to the DNA

Actinomycin D

isolated from steptomyces antibioticus as is a DNA intercalating agent

Rifampin

semisynthetic derivative of rifamycin isolated from streptomyces Mediterranean and it binds the beta subunit of RNA polymerase and prevents extension of RNA beyond 2 to 3 nucleotides (main antibiotic against Mtb)

Alpha amanitin

isolated from poisonous mushroom and binds to and inhibits RNA polymerase 2