Ch 13 Transcription Flashcards
compare and contrast RNA and DNA
DNA:
- deoxyribose sugar
- no 2’-OH group
- A,G,C,T nucleotides
- usually double stranded
- stable
RNA:
- ribose sugar
- has 2’-OH group
- A,G,C,U nucleotides
- usually single stranded
- degraded easily
class of RNA: structural and functional components of ribosome, participating in protein assembly
ribosomal RNAs (rRNAs)
class of RNA: carries genetic code for proteins
messenger RNA (mRNAs)
class of RNA: precursor molecule that is modified to become mRNA
pre-messenger RNA (pre-mRNAs)
class of RNA: helps incorporate amino acids into polypeptide chain
transfer RNA (tRNAs)
class of RNA: processing of pre-mRNA into mRNA
small nuclear RNAs (snRNAs)
class of RNA: processing and assembly of rRNA
small nucleolar RNAs (snoRNAs)
class of RNA: inhibit RNA translation (RNAi)
micro RNAs (miRNAs)
class of RNA: degradation of RNA molecules (RNAi)
small interfering RNAs (siRNA)
class of RNA: suppress transcription of transposable elements in reproductive cells
Piwi-interacting RNAs (piRNA)
class of RNA: assist destruction of foreign DNA
CRISPR RNA (crRNA)
snRNAs that combine with small protein subunits
small nuclear ribonucleoproteins (snRNPs)
process of RNAs synthesized from a DNA template
transcription
three major components of transcription
DNA template –> single strand used
RNA strand transcribed complementary to template strand
transcription unit
DNA strand used for transcription
template strand (negative/noncoding strand)
two other names for template strand
noncoding strand
negative strand
other DNA not used for transcription
nontemplate strand (positive/coding strand)
two other names for nontemplate strand
coding strand
positive strand
why is the nontemplate strand called the coding strand?
it is identical to the RNA strand transcribed, except T=U
stretch of DNA that encodes RNA molecule and sequences needed for transcription
transcription unit
three components of transcription unit
promoter
RNA-coding region
terminator
DNA sequence (upstream) that transcription apparatus recognizes and binds to
promoter
first nucleotide to be transcribed
transcription start site
DNA sequence copied into RNA
RNA-coding region
sequence (downstream) that is copied into RNA and transcription stops
terminator
substrates required to build RNA
ribonucleoside triphosphates (rNTPs)
transcription apparatus
bacterial RNA polymerase
(only one RNA polymerase) - transcribes mRNA, tRNA, and rRNA
what subunits is core RNA polymerase composed of
five subunits: 2 alpha, 1 beta, 1 beta prime, and 1 omega
catalyzes elongation of RNA by addition of RNA nucleotides
core RNA polymerase enzyme
joins with core enzyme to form holoenzyme
sigma factor
controls binding of RNA polymerase to promoter
RNA polymerase holoenzyme
what happens if no sigma factor is present?
transcription starts at a random start point
difference between bacterial and eukaryotic RNA polymerases
bacteria only have one RNA polymerase that synthesizes all RNA classes
eukaryotes have multiple (three main types of RNA polymerases that synthesize different RNA classes)
polymerase that transcribes large rRNAs
RNA polymerase I
polymerase that transcribes pre-mRNAs
RNA polymerase II
polymerase that transcribes tRNAs
RNA polymerase III
set of most commonly encountered nucleotides among sequences
consensus sequence
describe bacterial promoter
consists of -35 consensus sequence and -10 consensus sequence
Pribnow box; most common consensus sequence that lies 10 nucleotides upstream of start site in promoter (TATAAT)
-10 consensus sequence
common consensus sequence that lies 35 nucleotides upstream of start site in promoter (TTGACA)
-35 consensus sequence
substitutions within -10 and -35 consensus sequences that slow down rate of transcription
down mutations
substitutions within -10 and -35 consensus sequences that increase rate of transcription
up mutations
describe bacterial initiation of transcription
- sigma factor joins with core RNA polymerase to form holoenzyme
- holoenzyme binds to -35 and -10 consensus sequences in promoter tightly and unwinds DNA
- complementary rNTP incorporated to transcription start site
- 2 phosphate groups cleaved for each rNTP added to 3’ end of growing RNA molecule
- sigma factor released and RNA polymerase moves beyond promoter
explain abortive initiation
while RNA polymerase complex is attached to the promoter, short transcripts are generated and released before it transitions to elongation
describe bacterial elongation of transcription
- RNA polymerase changes shape & leaves promoter
- RNA poly continues to add nucleotides and transcribe downstream
- RNA poly unwinds DNA at leading (downstream) edge and rewinds DNA at trailing (upstream) edge
- RNA poly proofreads by backtracking
area on DNA where transcription takes place
transcription bubble
RNA poly slides backward along template strand
backtracking
what kind of supercoiling is generated when RNA poly unwinds DNA at leading/downstream edge
positive supercoiling
what kind of supercoiling is generated when RNA poly unwinds DNA at trailing/upstream edge
negative supercoiling
describe bacterial termination of transcription
- RNA transcribes the terminator
- RNA stops synthesizing RNA
- new RNA released from RNA poly and dissociates from DNA template
- RNA poly detaches
describe rho-independent terminators
termination w/o rho factor
- inverted repeats in DNA cause transcribed RNA to form hairpin structure
- string of adenine nucleotides follow inverted repeats to produce string of uracil nucleotides in after hairpin
- causes RNA poly to pause
- hairpin structure destabilizes DNA-RNA pairing and RNA molecule separates
describe rho-dependent terminators
termination in presence of rho factor
- rho binds to unstructured region of RNA and moves towards 3’ end
- RNA poly encounters terminator sequence and pauses
- rho uses helicase activity to unwind DNA-RNA hybrid and ends transcription
accessory proteins that bind to DNA sequences and affect levels of transcription
transcription factors
transcription factors that combine with RNA poly and mediator to form basal transcription apparatus
general transcription factors (TFs)
complex of TFs + RNA poly + mediator that assembles on promoter and initiates transcription
basal transcription apparatus
transcription factors that stimulate assembly of basal transcription apparatus to increase levels of transcription
transcriptional activator proteins (TAPs)
which RNA polymerase transcribes genes in eukaryotes
RNA Poly II
parts of eukaryotic promoter
core promoter
regulatory promoter
describe the core promoter
immediately upstream from start site where basal apparatus binds
TATA box consensus sequence located -25 upstream
describe the regulatory promotor
immediately upstream of core promoter
TAPs bind and effect rate of transcription initiation
more distant sequences that regulate transcription if TAPS bind to them
enhancers
describe eukaryotic initiation of transcription
assembly of basal transcription apparatus
- TFIID contains TATA-binding protein that binds to TATA box within core promoter
- TAPs at regulatory promoter interact with basal transcription apparatus thru mediator
- TAPS at enhancers interact with basal transcription apparatus by forming loop in DNA
DNA unwinds to produce template strand
describe eukaryotic elongation of transcription
- DNA enters RNA Poly II through cleft and unwinds
- nucleotides added to growing 3’ end of RNA molecule
- hybrid DNA-RNA hits wall of amino acids and bends at right angle, positioning it at polymerase active site
- new RNA separates from DNA and exits
describe eukaryotic termination of transcription
- RNA poly II transcribes well past coding sequences
- pre-mRNA cleaves at specific sites
- Rat1 exonuclease attaches to 5’ end of RNA and moves toward RNA polymerase, degrading RNA
- Rat1 reaches polymerase and transcription terminates
is transcription in archaea more similar to transcription in eukaryotes or prokaryotes?
eukaryotes
