2.3. Transcription Flashcards
DNA-dependent synthesis of RNA wherein the information in a DNA strand is copied into a new molecule of RNA
transcription
transcription is important as it is the** initial step** in the process of information flow within the cell
transcription regulation
transcription is highly regulated
(1)** protein demand-dependent** : cells adjust transcription based on their immediate needs, e.g., response to stress
(2) allow conservation of cell resources : this regulation allows energy and resource conservation in cells
(3) allows enhanced cell fitness : also helps cells to quickly adapt to new conditions and thrive
evidences of RNA as an intermediate molecule in the genetic information flow
(1) DNA does not appear to participate directly in protein synthesis : DNA is associated with the chromosomes in the nucleus; however, protein synthesis occurs in ribosomes located outside the nucleus
(2) RNA is synthesized in the nucleus or nuclear region : RNA acts as a messenger, carrying the genetic code transcribed from DNA
(3) RNA migrates to the cytoplasm where protein synthesis occurs : shows RNA’s role as intermediary
(4) RNA is chemically similar to DNA : allows RNA to effectively copy and transport genetic instructions
these observations suggested that genetic information, stored in DNA, is transferred to an RNA intermediate, which directs the synthesis of proteins
what are the different transcription components?
(1) RNA polymerase core enzyme
(2) σ factor
(3) nucleoside triphosphates (NTPs)
(4) promoters
catalyzes polymerization of RNA molecule in a 5’ to 3’ direction; can inititate new RNA on its own (primer is not needed)
RNA polymerase
how many types of RNA polymerase do eukaryotes and prokaryotes have?
eukaryotes : three (RNA Pols I, II, and III)
prokaryotes : one
products and locations of RNA Pols I, II, III
RNA pol I : produces rRNA in nucleolus
RNA pol II : produces mRNA and snRNA (small nuclear) in the nucleoplasm
RNA pol III : produces 5SrRNA, tRNA (transfer) in the nucleoplasm
RNAP II also synthesizes a variety of other RNAs, such as snRNA, miRNAs (micro), and IncRNAS (long non-coding)
transcription component that provides catalytic basis and active site for transcription
RNA polymerase core enzyme
transcription component that (1) regulates initiation of transcription and (2) recognizes the appropriate site on the DNA to initiate transcription
sigma (σ) factor
true or false : similar to other subunits, sigma σ factor is tightly bound to the core enzyme.
false. sigma factor is not as tightly bound as the other subunits in order to easily dissociate to yield the RNA polymerase core enzyme
how is RNA polymerase core enzyme different from RNAP holoenzyme?
RNAP holoenzyme has sigma factor + core enzyme
transcription component recognized by the sigma factor; a cis-acting DNA element
promoter
where is the promoter located?
upstream of the gene
true or false : the promoter is not transcribed.
true
template strand vs coding strand
template strand : DNA strand that serves as the template for RNAP
coding strand : complementary DNA strand
the template strand runs in what direction? the direction of RNA synthesis follows what direction?
3’ to 5’: template strand
5’ to 3’ : direction of synthesis
segment of DNA that gets transcribed into RNA, along with the sequences necessary for its transcription
def not in the ppt
transcriptional unit : composed of (1) promoter, (2) initiation site also known as transcription start site or TSS (+1), (3) transcribed region, and (4) termination site
cluster of genes under a single promoter that are transcribed as a group
operons
not from ppt
actual genes transcribed into mRNA and subsequently translated into proteins
structural genes
when these genes are part of an operon in prokaryotes, they are transcribed together into a single polycistronic mRNA; not in ppt
describe the promoter consensus sequences in bacteria. what are some examples of this?
promoter consensus sequences are specific DNA sequences found in the promoter region of genes that are highly conserved across different genes within the same or related organisms
(1) sequences are similar (homologous) in different genes of the same organism
(2) sequences are similar (homologous) in one or more genes of related organisms
(3) degree of RNAP binding influences strength of promoters : RNAP attaches to specific promoter sequences; the efficiency of this binding affects how strongly the promoter initiates transcription. the better RNA polymerase binds to the promoter, the more likely it is that the gene will be transcribed regularly.
examples : -35 region and pribnow box
describe the (1) structure of promoter and (2) recognition sequences in the promoter in bacteria and in archaea
structure of promoter
🔸for bacteria, it does not resemble eukarya
🔸archaea resembles eukarya
recognition sequences in the promoter
🔸bacteria : TTGACA (-35) and TATAAT or pribnow box (-10)
🔸archaea : TATA (-18 to -27)
recognition sequences in the promoter region of eukaryotic genes
(1) TATA (-30) or Goldberg-Hogness box
(2) CAAT/CCAAT box (-50 to -200)
(3) GC
different types of cis-acting DNA elements in eukaryotes
cis-acting DNA elements are adjacent parts of the same DNA molecules
(1) core promoter
(2) proximal-promoter element
(3) enhancers and silencers
a cis-acting DNA element in eukaryotes that determines the binding site of RNAP II; includes the TSS (transcription start site)
core promoter
a cis-acting DNA element in eukaryotes that helps modulate the level of transcription; located upstream of the start site
proximal-promoter element
a cis-acting DNA element in eukaryotes that influence the efficiency or the rate of transcription initiation by RNAP II from the core-promoter element
enhancers and silencers
proteins that facilitate RNAP II binding and thus the initiation of transcription
trans-acting / transcription factors
trans-acting factors bind to cis-acting DNA elements to influence gene expression
type of transcription factor in eukaryotes that are required for RNAP II-mediated transcription
general transcription factors (GTFs)
examples: TFIIA, TFIIB, TFIID
type of transcription factors in eukaryotes that influence the efficiency or rate of RNAP II transcription initiation as they bind to enhancer and silencer elements
transcriptional activators and repressors
stages of transcription
(1) promoter recognition
(2) local unwinding
(3) chain initiation
(4) chain elongation
(5) chain termination
what happens in the first stage: promoter recognition?
sigma factor recognizes promoter and initiation site
what happens in second stage: local unwinding?
🔸RNA pol begins to unwind the DNA double helix at the promoter region
🔸this unwinding creates an open promoter complex where the DNA strands are separated which exposes the template strand
🔸RNA pol then locates and recognizes the transcription start site (TSS) which is close to the initial binding site
what happens in the third stage: chain initiation?
🔸RNAP begins reading the DNA template strand
🔸using free nucleoside triphosphates (NTPs), RNAP starts synthesizing a complementary RNA strand
what happens to the sigma factor once a short sequence of RNA has been formed during chain initiation?
dissociates from the holoenzyme; RNA chain continues to grow
how does initiation of transcription go about in eukaryotes?
requires chromatin remodelling, which involves the use of ATP-dependent chromatin remodelers and histone-modifying enzymes to uncoil compact chromatin fibers and make the DNA helix accessible to RNA polymerase and other regulatory proteins
what happens in the fourth stage: chain elongation?
🔸during elongation, RNAP moves along the 3’ to 5’ template strand in 5’ to 3’ direction by adding nucleotides to the 3’ OH of the growing RNA chain
what happens in the fifth stage: chain termination?
🔸when the termination site is reached, chain growth stops.
🔸polymerase and RNA are released
🔸governed by specific base sequences on the DNA
mechanisms of termination in bacteria
(1) rho-dependent termination
(2) rho-independent termination
explain rho-dependent termination
(1) rho (ρ) protein recognizes and binds to a rho dependent termination site, called rho utilization or rut site, on the mRNA
(2) after binding, rho moves down the chain in the 3’ direction chasing after the RNA polymerase-DNA complex
(3) RNA polymerase pauses at a specific sequence in the DNA which allows rho to catch up
(4) once rho catches up, it uses its helicase activity to unwind the RNA-DNA hybrid, causing both the RNA transcript and RNA polymerase to be released from the DNA
(5) transcriptions is terminated
rho protein is a large hexameric protein with RNA helicase activity–it can dissociate RNA hairpins and DNA-RNA interactions
explain rho-independent termination
(1) the DNA template has G-C rich sequence with inverted repeats and a central nonrepeating segment
(2) inverted repeats cause the newly formed RNA to fold into a stem-loop structure via intra-strand base pairing
(3) after the hairpin, the DNA template has a sequence of adenines, resulting in uracils in the RNA
(4) RNA forms weak U-A base pairs with the DNA
(5) hairpin causes the RNAP to pause
(6) the weak U-A bonds allow the RNA to dissociate from the DNA, terminating transcription
true or false : unlike prokaryotes, eukaryotes do not have a single and specific sequence that signals transcription termination.
true
how does transcription termination occur in eukaryotes?
involves sequence-specific cleavage fo the transcript
🔸incorporation of polyadenylation signal sequence AAUAAA
🔸cleavage roughly 10 - 35 bases downstream in the 3’ direction
🔸leads to eventual dissociation of RNA polymerase from the DNA template
cleavage of the transcript destabilizes RNAP II which leads to dissociation of both dna and rna
initial or primary transcripts of protein-coding mRNA found in eukaryotes that undergo “processing” to produce a mature RNA; post-transcriptional modification
pre-mRNA
post-transcriptional modifications
(1) addition of 7-methylguanosine cap
(2) poly-A tailing
(3) RNA splicing
explain the addition of 7-methylguanosine cap at 5’end. when is it added? what is/are its significance?
🔸cap is added shortly after synthesis of the initial RNA transcript has begun
🔸cap stabilizes the mRNA by protecting the 5’ end of the molecule from nuclease attack
🔸facilitates transport of mRNAs across nuclear membrane
🔸facilitates initiation of translation
a post-transcriptional modification that involves the addition of 250 adenylic acid residues at the 3’ end’ contributes to mRNA stability
poly-A tailing
what enzyme facilitate poly-A tailing?
poly-A polymerase
this enzyme catalyzes the addition of a poly-A tail to the free 3’ OH group at the end of the transcript
what proteins bind to poly-A tails, preventing the mRNA to be degraded?
poly-A binding protein
they bind to poly-A tails and prevent nucleases from degrading the 3’ end of the mRNA
removal of intervening sequences
RNA splicing
introns are removed from a pre-mRNA; exons are joined together
true or false : introns are non-coding.
true
what type of introns are capable of self-splicing?
group I introns (rRNA) and
group II introns (organelle mRNA and tRNA)
group I introns are found in rRNA; group II are found in organelle mRNA and tRNA
the removal of introns in nuclear-derived eukaryotic pre-mRNA are mediated by ___.
spliceosome
