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Chapter 16

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RNA polymerase enzymes responsible for synthesizing mRNA
NTP like dNTPs except that they contain sugar ribose instead of deoxyibose
RNA polymerase produces a sequence that is complementary to the DNA strand
The strand that is read by the enzyme is called the template strand
The other strand is called the coding strand or nontemplate strand
RNA polymerase does not require a primer to begin transcription
One one RNA polymerase in bacteria but three in eukaryotes
oEach transcribe only certain types of RNA
oRNA pol II is the only one that transcribes genes that code for
proteins and produce mRNA
oRNA pol I: transcribes genes that code for most of the large RNA
molecules found in ribosomes
oRNA pol II: transcribes genes that code for proteins and produce mRNA
oRNA pol III: transcribes genes that code for transfer RNA (tRNA), non
coding RNA, one of the small RNA found in ribosomes
The initiation phase tells RNA polymerase where to start transcription on the
DNA template
RNA polymerase cannot begin transcription on its own, instead a protein subunit
called sigma must bind to the polymerase before transcription
A holoenzyme (whole enzyme) an RNA polymerase and sigma
Researchers found that the holoenzyme bound tightly to specific regions of DNA,
these are called the promoter regions
DNA located in the direction that RNA polymerase moves is called downstream,
the opposite is upstream
Many eukaryotic promoters include a uniqe 30 base pair sequence called the
TATA box upstream from transcription site
Sigma makes initial contact with RNA polymerase meaning it is the regulatory
For eukaryotes, proteins known as basal transcription factors bind to the
appropriate promoter region and initiate transcription
Basal transcription factors not a part of the holoenzyme, assembled at promoter
first then RNA polymerase follows
Initiation Transcription in Bacteria
oSigma bind to promoter region of DNA
oSigma opens up DNA helix, transcription begin, NTPs bind to comp bases
on DNA strand
oSigma is released, mRNA synthesis continues
Once RNA polymerase begins moving along DNA in 3’ to 5 but synthesizing
RNA in 5 to 3’ elongation phase has started
The termination phase occurs mostly when the RNA polymerase reaches a DNA
sequence that function as a transcription termination signal
When these transcription termination signals are reached two shapes can be
formed in the mRNA
oHairpin loop where it fold in on itself
oOr it completely is removed from the holoenzyme
Different sigma proteins have different amino acid sequences therefore they are
able to bind to different DNA stretches that differ in base sequence
NTPS are required because three phosphate groups raise the monomers potential
energy high enough to make the reaction exergonic
In eukaryotes, in contrast to bacteria, DNA is not converted to mRNA completely
When the eukaryotic gene is transcribed, the product is an immature primary
RNA transcript. Before these are transcribe, they must go through complex steps
Non-coding regions of DNA are extra sections of DNA that do not have an
equivalent sequence of mRNA.
Non-coding sections must be removed before translation
Regions of final mRNA be referred to as mRNA while sections not in te mRNA
be referred to as introns (because they intervene)

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• RNA polymerase enzymes responsible for synthesizing mRNA • NTP like dNTPs except that they contain sugar ribose instead of deoxyibose • RNA polymerase produces a sequence that is complementary to the DNA strand • The strand that is read by the enzyme is called the template strand • The other strand is called the coding strand or nontemplate strand • RNA polymerase does not require a primer to begin transcription • One one RNA polymerase in bacteria but three in eukaryotes o Each transcribe only certain types of RNA o RNA pol II is the only one that transcribes genes that code for  proteins and produce mRNA o RNA pol I: transcribes genes that code for most of the large RNA  molecules found in ribosomes o RNA pol II: transcribes genes that code for proteins and produce mRNA  o RNA pol III: transcribes genes that code for transfer RNA (tRNA), non  coding RNA, one of the small RNA found in ribosomes • The initiation phase tells RNA polymerase where to start transcription on the  DNA template • RNA polymerase cannot begin transcription on its own, instead a protein subunit  called sigma must bind to the polymerase before transcription • A holoenzyme (whole enzyme) an RNA polymerase and sigma • Researchers found that the holoenzyme bound tightly to specific regions of DNA,  these are called the promoter regions • DNA located in the direction that RNA polymerase moves is called downstream,  the opposite is upstream • Many eukaryotic promoters include a uniqe 30 base pair sequence called the  TATA box upstream from transcription site • Sigma makes initial contact with RNA polymerase meaning it is the regulatory  protein • For eukaryotes, proteins known as basal transcription factors bind to the  appropriate promoter region and initiate transcription • Basal transcription factors not a part of the holoenzyme, assembled at promoter  first then RNA polymerase follows • Initiation Transcription in Bacteria o Sigma bind to promoter region of DNA o Sigma opens up DNA helix, transcription begin, NTPs bind to comp bases  on DNA strand  o Sigma is released, mRNA synthesis continues • Once RNA polymerase begins moving along DNA in 3’ to 5’ but synthesizing  RNA in 5’ to 3’ elongation phase has started • The termination phase occurs mostly when the RNA polymerase reaches a DNA  sequence that function as a transcription termination signal • When these transcription termination signals are reached two shapes can be  formed in the mRNA o Hairpin loop where it fold in on itself o Or it completely is removed from the holoenzyme • Different sigma proteins have different amino acid sequences therefore they are  able to bind to different DNA stretches that differ in base sequence • NTPS are required because three phosphate groups raise the monomers potential  energy high enough to make the reaction exergonic • In eukaryotes, in contrast to bacteria, DNA is not converted to mRNA completely • When the eukaryotic gene is transcribed, the product is an immature primary  RNA transcript.  Before these are transcribe, they must go through complex steps • Non­coding regions of DNA are extra sections of DNA that do not have an  equivalent sequence of mRNA. • Non­coding sections must be removed before translation • Regions of final mRNA be referred to as mRNA while sections not in te mRNA  be referred to as introns (because they intervene) • Introns are the reason that eukaryotic genes are much longer than their  corresponding mature RNA trasncripts • RNA splicing  o As transcription proceeds, the introns are removed from the growing RNA  strand by a process known as splicing • When introns and removed and the exons are joined together, they make mature  mRNA/mRNA o snRNPs (small nuclear ribonucleoproteins) bind to the start of the intron  and a key Adenine base o snRNPs assemble to form the splicesosome  o intron is cut and the loop forms where 5’end of intron is covalently  attached to the adenine base o intron is released exons join together • the spliced intron usually degraded into ribonucleotide monophosphates • as soon as a 5’end comes out of the RNA polymerase enzymes add a structure  called the 5’ cap to it which consists of the molecule 7­methyl­guanylate and three  phosphate groups • an enzyme cleaves the 3’ end of most RNA once transcription is complete and  another enzyme adds 100­250 adenine nucleotides not encoded c
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