genetics chapter 13

is rna or dna easily degraded

rna

what makes rna more reactive than dna

the OH group on the 2’ carbon

primary structure of rna

single stranded

secondary structure of rna

intramolecular base pairing causes rna to fold upon itself

which structure of rna provides function

secondary

ribosomal rna (rRNA) cell type, location of function in eukaryotic cells, function

prokaryotic and eukaryotic

cytoplasm

structural and functional components of the ribosome

messenger rna (mRNA) cell type, location of function in eukaryotic cells, function

prokaryotic and eukaryotic

nucleus and cytoplasm

carries genetic code for proteins

transfer rna (tRNA) cell type, location of function in eukaryotic cells, function

prokaryotic and eukaryotic

cytoplasm

helps incorporate amino acids into polypeptide chain

all rna is transcribed from a ____ template

DNA

RNA is translated into ____

protein

dna replication versus transcription

requirements for transcription

1. dna template strand - single stranded

2. rNTPs = ribonucleoside triphosphates (A, U, G, C)

3. the transcription apparatus, consisting of the proteins necessary for catalyzing the synthesis of RNA (e.g. rna polymerase and other proteins)

nontemplate dna strand

not transcribed; sequence same as rna (except T versus U)

template dna strand

used for transcription; complementary and antiparallel to RNA

where and how is transcription initiated? (does not use a primer)

gene structure, especially the promoter

promoter

dna sequence immediately upstream of transcription start site; where transcription apparatus binds

rna-coding region

serves as template for rna synthesis

terminator

DNA sequence that causes transcription to stop; usually part of the RNA

in transcription, nucleotides are always added to the __’ end of the RNA molecule

3

which dna strand (top or bottom) can be the template strand

both

bacterial rna polymerase components

core enzyme: composed of 5 subunits (2x alpha, beta, beta’, omega) form of the enzyme that synthesizes RNA

sigma factor: guides the core enzyme to specific gene promoters to start transcription

holoenzyme: form of the enzyme that initially binds to promoter. core enzyme + sigma

bacterial transcription initiation

sigma factor associates with the core enzyme to form the holoenzyme

holoenzyme then binds to the promoter

consensus sequence

set of most commonly encountered nucleotides found at a specific location of dna or rna

what does Y mean in a consensus sequence

pyrimidine - C, T, U

what does R mean in a consensus sequence

purine - A, G

bacterial promoters often have ___ consensus sequences

2 (-10 and -35)

holoenzyme recognizes _____ ____ in bacterial promoters

consensus sequences

third step of bacterial transcription initiation

holoenzyme changes conformation, unwinds the dna, forms “transcription bubble”

fourth step of bacterial transcription initiation

addition of 1st RNA nucleotide; complementary to DNA template

last steps of bacterial transcription initiation

RNA nucleotide added to the 3’ end of growing RNA molecule

sigma factor is released as RNA polymerase moves beyond promoter

transcription elongation

core enzyme continues to move downstream along gene synthesizing RNA in a 5’ to 3’ direction, adding 1 nucleotide at a time to 3’ end of RNA

transcription bubble

DNA strands transiently separated to expose template strand

includes the short DNA sequence base paired with 3’ end of RNA

transcription pausing

certain DNA sequences or RNA secondary structures cause RNA polymerase to pause

incorporation of incorrect nucleotide can also cause RNA polymerase to ____

pause

2 ways bacteria can terminate transcription

rho-dependent

• requires Rho protein to terminate transcription

rho-independent

• intrinsic process that does not require additional protein factors

rho-dependent transcription termination

RNA polymerase pauses at a downstream sequence

rho factor binds to rut site and moves 5’ to 3’

when rho catches up with rna polymerase, its helicase activity unwinds rna-dna hybrid and releases rna

rho-independent transcription termination

terminator region: inverted repeats followed by > or equal to 6 A-Ts

rna transcribed from inverted repeats forms hairpin

hairpin causes rna polymerase to pause

weakness of U-A bp’s causes rna to separate from dna template

RNA polymerase I, II, & 3

I: all eukaryotes; transcribes large rRNAs

II: all eukaryotes; transcribes pre-mRNA, some snRNAs, snoRNAs, some miRNAs

III: all eukaryotes; transcribes tRNAs, small rRNAs, some snRNAs, some miRNAs

basal transcription apparatus in eukaryotes

rna polymerase + general transcription factors (TFs)

transcription factors

proteins that bind DNA sequences and affect levels of transcription

RNA polymerase II promoters

core promoters

conserved sequences are binding sites for general transcription factors

eukaryotic transcription initiation

assembly of transcription preinitiation complex

TFIID binds to the TATA box of the core promoter

transcription factors and RNA polymerase II bind to the core promoter

TBP

TATA binding protein; bends and partly unwinds DNA

TBP subunit of TFIID binds to ___ groove of DNA

minor

eukaryotic transcription elongation

entering DNA is gripped

DNA is unwound to form transcription bubble

RNA added to 3’ end at active site

different mechanisms used for eukaryotic transcription termination by each rna polymerase

1: requires termination factor (similar to rho in bacteria)

3: transcribes terminator sequence (similar to rho-independent)
2: does not occur at specific sequences; rat 1 exonuclease mechanism

rat 1 transcription termination

rna pol 2 continues past the sequences that will be in mRNA

RNA cleaved to generate 3’ end of RNA
rat 1 is a 5’ to 3’ exonuclease

binds to 5’ end of RNA on cleavage site and degrades RNA

when rat 1 reaches RNA pol 2, transcription terminates