Chapter 16 Transcription
prokaryotes only have one type of polymerase and three types of RNA, what are they?
RNA polymerase which transcribes mRNA, tRNA, and rRNA which are the only three types of RNA in prokaryotes
what is a consensus sequence?
a sequence that describes the nucleotides most often present in a segment of interest ex. -10 sequence (prokaryotes) and TATA box (eukaryotes)
guide RNA (gRNA)
in eukaryotes, helps in RNA editing
small cytoplasmic RNA (scRNA)
in eukaryotes, unknown functions, catch all classification. Prosomes have scRNAs and apparently repress expression of mRNA. It is a catch-all class (eukaryotes only)
wont find I in
mRNA, I can only be found in tRNA
RNA polymerase II
mRNA, snoRNA (in introns), and most snRNA
miRNA or micro RNA
miRNA or micro RNA is used to reduce the rate of translation. They are only in eukaryotes and help reduce gene expression by either inhibiting translation or suppressing transcription.
n and c?
n is start, c is stop
termination of RNA polymerase III in eukaryotes during transcription
poly-U sequence on RNA has poor binding strength and transcription derails
promotion in prokaryotes short version
pribnow box (-10 region), -35 region, a sigma enzyme attaches to the polymerase core enzyme and "finds" the -10 and -35 regions, positive control
Transcription initiation comparison between prokaryotes and eukaryotes
prokaryotic: sigma factor helps polymerase find gene, uses same RNA polymerase, but sigma factor can be different eukaryotic: cis element signal TFs to attach. Initiation complex is built on DNA, uses three different RNA polymerases depending on RNA type
difference between promoters and enhancers
promoters are related to the physical attachment of the RNA polymerase to the DNA, while enhancers are related to the regulatory nature of initiation
trans-acting
proteins from genes elsewhere, proteins recognize cis elements and help polymerase start
ribosomal RNA (rRNA)
rRNA is RNA found in the ribosome. They have control function, helping to translate the mRNA. Most of the RNA in the cell is rRNA, prokaryotic has 3 types ranging from 1700-3700 bases, while eukaryotice has 4 types ranging from 500-5000 bases
non-template strand
sense strand, coding strand
how is transcription terminated in RNA polymerase III genes
similar to rho-independent termination, a sequence of poly-Us are unstable when being transcribes and the RNA falls off
small nuclear RNA (snRNA)
snRNA is found only in eukaryotes in the nucleus. They are generally small in size, and are found in protein complexes that are responsible for pre-mRNA splicing and polyadenylation. They make up spliceosomes
transfer RNA (tRNA)
tRNA is used in translation. Each tRNA is charged with an amino acid and brings this amino acid to the ribosome during the building of the protein. They are very small, less than 100 bases in lenght, but many copies are transcribed together (multiple copy gene)
RNA polymerase III
tRNA, some snRNA, & 5S rRNA
differences in transcription for eukaryotes
the basic process for transcription is the same in eukaryotes. There are some major differences due to the call for increased regulatory control. For example, while prokaryotes use a single generalized RNA polymerase for transcription, eukaryotes use specialized polymerases for the different types of transcripts , messenger RNA , ribosomal RNA, and transfer RNA and other small RNAs. The regulation in eukaryotes involves a different signaling process than found in prokaryotes. There are basically two types, cis-elements and trans-acting factors.
mitochondrial transcription
the control region controls all transcription, both strands are transcribed into polycistronic transcripts - apparently related to replication. RNA is then spliced into individual genes. Protein-coding genees have poly-A tail. Unlike the nucleus, some genes in the mitochondria are overlapping.
trans-acting factors
trans-acting factors (also called transcription factors) are enzymes or RNAs that bind o the DNA, acting as signals for the initiation of transcription. The trans-acing factors are transcribed from other genes elsewhere in the genome. The genes creating the trans-acting factors also have cis-acting elements and trans-acting factors. Trans-acting factors (Transcription factors) are proteins from genes elsewhere, attach to cis-elements or other TFs, and recruit RNA polymerase.
Eukaryotic transcription - initiation with RNA polymerase I
transcribes long multiple copy genes, less regulatory control - they are mostly always on (no TATA, upstream control in two sections), polymerase is designed for fast transcription of long segments, this is because RNA polymerase I transcribes the larger of the rRNAs
Eukaryotic transcription - initiation with RNA polymerse III
transcribes small RNAs, less regulatory control - they are mostly always on, polymerase is designed for fast transcription of small segments, ICR (internal control region). Typically, RNA polymerase III-transcribing genes have enhancers that are internal (inside the gene), promoters are upstream often include portions of the transcript.
initiation in prokaryotes (initates the transcription process)
-10 and -35 regions + sigma factor, DNA dependent RNA polymerase separates the DNA strands and attaches to the templae strand. The RNA polymerase doesn't require a 3'end to start transcription. The polymerase moves along the template strand from 3' to 5' creating an RNA strand that is the complement of the template strand.The RNA polymerase has a subunit that often attaches during initiation. The subunit, called the sigma factor, detaches after transcription has been initiated. There are at least four different sigma subunits found in prokaryotes: general housekeeping, nitrogen metabolism, heat-shock, flagellum synthesis and chemotaxis
Transcription is the process of creating RNA and DNA
1) RNA synthesis is complementary and antiparallel to the template strand. 2) new nucleotides are added to the 3'-OH group of the growing RNA; so transcription proceeds in a 5' to 3' direction. 3) the nontemplate strand is not usually transcribed
promotion in prokaryotes:
1) promotion: Promotion tells cells where genes are and when they are expressed. the promoter is an upstream portion of the DNA involved with initiating transcription. the initiation involves two parts, identifying to the cell there is a cistron and helping the RNA polymerase to attach and begin to transcribe. Tehre are several consensus sequences in this area, including: 1) Pribnow Box or -10 region - the -10 refers to the location of the sequence, it is 10 bases before the start of transcription, termed upstream 2) -35 region - another promoter region 35 bases upstream from the start of transcription
RNA polymerase I transcribes what kind of RNA
28S, 18S, 5.8S rRNA (all, except 5S rRNA)
how is transcription terminated in RNA polymerase I genes
A DNA-binding protein blocks the RNA polymerase
Difference between timing and location of transcription for prokaryotes v. eukaryotes
For prokaryotes, the translation machinery (in particular, the ribosme) is located alongside the DA, and translation and transcription can occur simultaneously. Eukaryotes have a nuclear membrane separating the two events. For this reason, eukaryotes have evolved an additional step between transcription and translation, where the RNA is processed. Prokaryotes also have RNA processing for those RNAs that are used as RNAs, such as transfer and ribosomal RNA.
termination of RNA polymerase I in eukaryotes during transcription
Polymerase I requires a termination factor. this protein binds to the DNA and "blocks" transcription from continuing
upstream consensus sequences for eukaryotic protein-coding genes (promoters)
TATA box, CAAT box, GC elements, Octomer, kB, ATF
cis-elements
actual sequences in the DNA
messenger RNA (mRNA)
an RNA copy of the DNA information for a protein coding gene, size of the protein determines size of the mRNA, some eukaryotic transcripts are >1 million bases. The information that will eventually be translated into protein is found here. The mRNA in eukaryotes is called pre-mRNA while it is still in the nucleus
arrangment of genes in prokaryotes
an operon is a basic regulatory unit (a transcript). Not all operons in prokaryotes have all parts. Each operon may have several cistrons, in which case the operon is called polycistronic. A cistron is a sequence that will eventually be translated as protein. usually the cistrons in an operon are related to each other, as they will be turned on or off as a unit.
template strand
anti-sense strand
arrangement of genes in eukaryotes
as with the prokaryotes, not all genes have all parts. The biggest difference is hat tehre is only one protein-coding gene per transcript. For eukaryotes, each individual gene must be turned on and off separately form each other. The terms cistron and operon are not used for eukaryotic genes.
how is transcription terminated in RNA polymerase II genes
as yet largely unknown process that starts with cutting the pre-mRNA after the AAUAAA signal (poly-A attachment signal)
cis-acting elements
cis-acting elements are DNA sequences that signal transcription, or are used in the physical attachment of the RNA polymerase. They can be upstream, downstream, or internal (within the transcribed region). OFTEN, the cis-acting elements are attachment sites for otehr enzymes, the trans-acting factors. cis-Elements are sequences that are "near' the gene that help the cell to determine when to transcribe a gene. Binding spots for proteins - transcription factors.
DNA binding domains
helix-turn-helix, zinc finger, leucine zipper, they are different shapes that proteins will take to clamp onto and bind to DNA
small nucleolar RNA (snoRNA)
found in eukaryotes in the nucleus, used in the processing of rRNA, mainly by modifying nomal nucleotides and splicing. Some are also found in telomerases (eukaryotes only)
Prokarytoic Elongation
elongation in transcription is very similar to elongation along the leading strand in replication. A ribonucleoside triphosphate (RNA) is attached to the 3' end of the growing RNA strand, releasing two phosphates. The ribonucleotide is the complement of the base on the template strand. Tehre is some error checking before the polymerase moves down the template strand, repeating the process until terminated. Unlike replication, there is no error checking after the strand has been created. in short: elongation is 3' elongation, uses DNA dependent RNA polymerase, and the bubble moves with polymerase.
elongation during transcription between prokaryotes and eukaryoties
essentially the same
small interfering RNA (siRNA)
found in eukaryotes and turn off expression of viral genes, RNA is from infection and not in the genome. siRNA is used to degrade mRNA, inhibiting translation. They are one way to defend cells against viral attacks (eukaryotes only). Together, miRNA and siRNA comprise a system of "silencing." While this is a natural process, we can use it in the laboratory with both eukaryotic and prokaryotic systems.
Transcription
transcription is the process of producing RNA from a DNA template. DNA dependent RNA polymerases mediate this process, mimicing the replication process. Teh basic process is the same as in DNA replication, although it creates an RNA strand, and only uses one of the two strands as template. 3' elongation, the same as replication, 3' of transcript facing into the fork, template strand has the transcript.
prokaryotic termination
two ways to terminate transcripton: 1) rho dependent termination - the RNA polymerase may detach itself from the strand with the help of the rho subunit in rho dependent termination or 2) the shape of the RNA created may itself to be a signal to terminate transcription in rho-independent termination. The shape of the RNA is a hairpin, caused by base pairing of the RNA with itself. The base pairs holding the hairpin together are GC pairs, with three hydrogen bonds, and the bases on the 3' end are U, a weaker bond with the template strand. It should be reemphasized that this is a structure found on the RNA during transcription. Inverted repeat leads to hairpin on the RNA during transcription. Transposons use inverted repeats when moving.
termination of RNA polymerase II in eukaryotes during transcription
unstable DNA/RNA binding, AAUAAA attracts a binding complex that "eventually" terminates transcription
eukaryotic transcription - initiation with RNA polymerase II
uses promoters TATA box, CAAT box, GC elements
