rna polymerase is able to open the dna double helix as it moves down the template. what type of enzymatic activity does this mean rna polymerase must possess?
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From DNA to RNA
Transcription and translation are the means by which cells read out, or express, the genetic instructions in their genes. Because many identical RNA copies can be made from the same gene, and each RNA molecule can direct the synthesis of many identical protein molecules, cells can synthesize a large amount of protein rapidly when necessary. But each gene can also be transcribed and translated with a different efficiency, allowing the cell to make vast quantities of some proteins and tiny quantities of others (Figure 6-3). Moreover, as we see in the next chapter, a cell can change (or regulate) the expression of each of its genes according to the needs of the moment—most obviously by controlling the production of its RNA.Figure 6-3Genes can be expressed with different efficienciesGene A is transcribed and translated much more efficiently than gene B. This allows the amount of protein A in the cell to be much greater than that of protein B.
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Molecular Biology of the Cell. 4th edition.
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From DNA to RNA
Transcription and translation are the means by which cells read out, or express, the genetic instructions in their genes. Because many identical RNA copies can be made from the same gene, and each RNA molecule can direct the synthesis of many identical protein molecules, cells can synthesize a large amount of protein rapidly when necessary. But each gene can also be transcribed and translated with a different efficiency, allowing the cell to make vast quantities of some proteins and tiny quantities of others (Figure 6-3). Moreover, as we see in the next chapter, a cell can change (or regulate) the expression of each of its genes according to the needs of the moment—most obviously by controlling the production of its RNA.
Figure 6-3
Genes can be expressed with different efficiencies. Gene A is transcribed and translated much more efficiently than gene B. This allows the amount of protein A in the cell to be much greater than that of protein B.
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Portions of DNA Sequence Are Transcribed into RNA
The first step a cell takes in reading out a needed part of its genetic instructions is to copy a particular portion of its DNA nucleotide sequence—a gene—into an RNA nucleotide sequence. The information in RNA, although copied into another chemical form, is still written in essentially the same language as it is in DNA—the language of a nucleotide sequence. Hence the name transcription.
Like DNA, RNA is a linear polymer made of four different types of nucleotide subunits linked together by phosphodiester bonds (Figure 6-4). It differs from DNA chemically in two respects: (1) the nucleotides in RNA are —that is, they contain the sugar ribose (hence the name nucleic acid) rather than deoxyribose; (2) although, like DNA, RNA contains the bases adenine (A), guanine (G), and cytosine (C), it contains the base uracil (U) instead of the thymine (T) in DNA. Since U, like T, can base-pair by hydrogen-bonding with A (Figure 6-5), the complementary base-pairing properties described for DNA in Chapters 4 and 5 apply also to RNA (in RNA, G pairs with C, and A pairs with U). It is not uncommon, however, to find other types of base pairs in RNA: for example, G pairing with U occasionally.
Figure 6-4
The chemical structure of RNA. (A) RNA contains the sugar ribose, which differs from deoxyribose, the sugar used in DNA, by the presence of an additional -OH group. (B) RNA contains the base uracil, which differs from thymine, the equivalent base in DNA, (more...)
Figure 6-5
Uracil forms base pairs with adenine. The absence of a methyl group in U has no effect on base-pairing; thus, U-A base pairs closely resemble T-A base pairs (see Figure 4-4).
Despite these small chemical differences, DNA and RNA differ quite dramatically in overall structure. Whereas DNA always occurs in cells as a double-stranded helix, RNA is single-stranded. RNA chains therefore fold up into a variety of shapes, just as a polypeptide chain folds up to form the final shape of a protein (Figure 6-6). As we see later in this chapter, the ability to fold into complex three-dimensional shapes allows some RNA molecules to have structural and catalytic functions.
Figure 6-6
RNA can fold into specific structures. RNA is largely single-stranded, but it often contains short stretches of nucleotides that can form conventional base-pairs with complementary sequences found elsewhere on the same molecule. These interactions, along (more...)
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Transcription Produces RNA Complementary to One Strand of DNA
All of the RNA in a cell is made by DNA transcription, a process that has certain similarities to the process of DNA replication discussed in Chapter 5. Transcription begins with the opening and unwinding of a small portion of the DNA double helix to expose the bases on each DNA strand. One of the two strands of the DNA double helix then acts as a template for the synthesis of an RNA molecule. As in DNA replication, the nucleotide sequence of the RNA chain is determined by the complementary base-pairing between incoming nucleotides and the DNA template. When a good match is made, the incoming ribonucleotide is covalently linked to the growing RNA chain in an enzymatically catalyzed reaction. The RNA chain produced by transcription—the —is therefore elongated one nucleotide at a time, and it has a nucleotide sequence that is exactly complementary to the strand of DNA used as the template (Figure 6-7).
Figure 6-7
DNA transcription produces a single-stranded RNA molecule that is complementary to one strand of DNA.
Transcription, however, differs from DNA replication in several crucial ways. Unlike a newly formed DNA strand, the RNA strand does not remain hydrogen-bonded to the DNA template strand. Instead, just behind the region where the ribonucleotides are being added, the RNA chain is displaced and the DNA helix re-forms. Thus, the RNA molecules produced by transcription are released from the DNA template as single strands. In addition, because they are copied from only a limited region of the DNA, RNA molecules are much shorter than DNA molecules. A DNA molecule in a human chromosome can be up to 250 million nucleotide-pairs long; in contrast, most RNAs are no more than a few thousand nucleotides long, and many are considerably shorter.
QUESTIONS
ANSWERS to Questions from Part ThreeAnswers, Chapter 10. Transcription: RNA polymerases
10.1 The sigma factor (s) causes RNA polymerase to bind to the correct sites on DNA to initiate transcription (i.e. promoters). s destabilizes the complex between core polymerase and non-promoter DNA and decreases the amount of time it is bound. It enhances the affinity and increases the amount of time that holoenzyme (a2bb's) is bound to promoter, i.e. it facilitates a random search for promoters.
10.2 Statements 2 and 4 are correct.
10.3 Elongation of transcription by RNA polymerase proceeds at about 50 nucleotides per sec. Therefore, the rRNA primary transcript would be synthesized in 6500 nucleotides /50 nucleotides per sec = 130 sec, or slightly over 2 min.
10.4 0.83 initiations per sec. (50 nt/sec)(3.4 Angstroms/nt) = 170A/sec. 204A/170A sec-1 = 1.2 sec per initiation, or 0.83 initiations per sec.
10.5 a) True
b) False c) True d) True
10.6 Common features include:
a. All are template directed, synthesizing a sequence complementary to the template.
b. Synthesis occurs in a 5' to 3' direction.
c. All catalyze the addition of a nucleotide via the formation of a phosphodiester bond.
d. All release pyrophosphate as a product.
Distinctive features include:
a. The substrates: DNA polymerase, reverse transcriptase, and telomerase use deoxyribonucleoside triphosphates as a substrate, whereas RNA polymerase uses ribonucleoside triphosphates.
b. The templates: DNA polymerase and RNA polymerase use DNA as a template, whereas telomerase copies an RNA template that is part of the enzyme. Reverse transcriptase uses RNA as a template in the life cycle of retroviruses and retrotransposons, but it can use either DNA or RNA as a template.
c. Primer requirements: DNA polymerase, reverse transcriptase and telomerase require primers provided by some other activity or protein (primase, an tRNA or the 3’ end of a DNA strand, respectively), whereas RNA polymerase can begin synthesis of RNA internally to the template without a primer.
In general, the chemistry of the enzyme reaction is similar for all four, but the specific substrates, templates and primers differ.
Answers, Chapter 11. Transcription: Promoters and Terminators11.1 a) Right to left
b) 1800 c) 400
5' end label: The lack of protection of the labeled 500 nucleotide fragment tells you that the mRNA is synonymous with the bottom strand, and thus the top strand is the template strand. The top strand is labeled at the 5' end of the 1500 nucleotide * fragment, and hybridization of this probe with mRNA gives protection of a 1300 nt fragment. This indicates that transcription proceeds from right to left (on the map as given), and the 5'' end of the transcript is 1300 nts to the right of the II site. In the coordinates of the map, this would be 500 (position of II) + 1300 = 1800.
5' 500 1500
---------------------> *--------------------------------------->
<--------------------* <---------------------------------------ß ¯
no protection 5'
*--------------------------------------->
| | | | | | | | | | | | | | | | | | | | | | | | |
<~~~~~~~~~~~~~~~~~~~~~~~~~•cap¯ S1 ¯ gel
*--------------------------->
1300 nt protected fragment
When the 5' end label is at the RI site, a similar result is obtained, but one can map the 5' end with greater accuracy. The protected fragment is from the top strand and is 100 nts (a size that can be measured more accurately than the 1300 nt fragment on the polyacrylamide gels used in this analysis).
1700 300
*--------------------------------------------> *----------------->
<--------------------------------------------* ------------------<~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~•¯ *-----------------> | | | | | ¯ S1,..etc. 100 nt *------->
3' end label: When the DNA fragments are labeled at the 3' end, again the top strand will be protected by hybridization to mRNA, thus reaffirming the conclusions above that the top strand is the template strand. The 500 nt * fragment generates a 100 nt protected fragment, showing that the 3' end of the mRNA is 100 nts to the left of the II site, or at 500 - 100 = 400 on the coordinates of the map.
5' 500 3' 1500
----------------->* ------------------------------------>
----------------- *------------------------------------
¯ ß
5' -----------------* no protection
<~~~~~~~~~~~~~~~~~~~~•| | | | ¯ S1, gel,..etc. -----* 100 nt
11.2 a) Left to right.
b) 400
c) Cannot be determined.
11.3 a) It will increase expression of the gene.
b) It has no effect.
c) It will increase expression of the gene.
d) The -50 to -1 fragment is acting like a promoter. In the first set of experiments, it is needed for promotion of transcription and it is needed to respond to upstream activating sequences. In the second set of experiments, the heterologous promoter will substitute for it.
RNA polymerase
RNA polymerase
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Compare RNA-dependent RNA polymerase.
DNA-Directed RNA Polymerase
RNA Polymerase hetero27mer, Human
Identifiers EC no. 2.7.7.6 CAS no. 9014-24-8 Databases IntEnz IntEnz view BRENDA BRENDA entry
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RNA polymerase (purple) unwinding the DNA double helix. It uses one strand (darker orange) as a template to create the single-stranded messenger RNA (green).
In molecular biology, RNA polymerase (abbreviated RNAP or RNApol), or more specifically DNA-directed/dependent RNA polymerase (DdRP), is an enzyme that synthesizes RNA from a DNA template.
Using the enzyme helicase, RNAP locally opens the double-stranded DNA so that one strand of the exposed nucleotides can be used as a template for the synthesis of RNA, a process called transcription. A transcription factor and its associated transcription mediator complex must be attached to a DNA binding site called a promoter region before RNAP can initiate the DNA unwinding at that position. RNAP not only initiates RNA transcription, it also guides the nucleotides into position, facilitates attachment and elongation, has intrinsic proofreading and replacement capabilities, and termination recognition capability. In eukaryotes, RNAP can build chains as long as 2.4 million nucleotides.
RNAP produces RNA that, functionally, is either for protein coding, i.e. messenger RNA (mRNA); or non-coding (so-called "RNA genes"). At least four functional types of RNA genes exist:
Transfer RNA (tRNA)
Transfers specific amino acids to growing polypeptide chains at the ribosomal site of protein synthesis during translation;
Ribosomal RNA (rRNA)
Incorporates into ribosomes;
Micro RNA (miRNA)
Regulates gene activity; and,
Catalytic RNA (ribozyme)
Functions as an enzymatically active RNA molecule.
RNA polymerase is essential to life, and is found in all living organisms and many viruses. Depending on the organism, a RNA polymerase can be a protein complex (multi-subunit RNAP) or only consist of one subunit (single-subunit RNAP, ssRNAP), each representing an independent lineage. The former is found in bacteria, archaea, and eukaryotes alike, sharing a similar core structure and mechanism.[1] The latter is found in phages as well as eukaryotic chloroplasts and mitochondria, and is related to modern DNA polymerases.[2] Eukaryotic and archaeal RNAPs have more subunits than bacterial ones do, and are controlled differently.
Bacteria and archaea only have one RNA polymerase. Eukaryotes have multiple types of nuclear RNAP, each responsible for synthesis of a distinct subset of RNA:
RNA polymerase I synthesizes a pre-rRNA 45S (35S in yeast), which matures and will form the major RNA sections of the ribosome.
RNA polymerase II synthesizes precursors of mRNAs and most sRNA and microRNAs.
RNA polymerase III synthesizes tRNAs, rRNA 5S and other small RNAs found in the nucleus and cytosol.
RNA polymerase IV and V found in plants are less understood; they make siRNA. In addition to the ssRNAPs, chloroplasts also encode and use a bacteria-like RNAP.
Contents
1 Structure 2 Function 3 Action 3.1 Initiation 3.2 Promoter escape 3.3 Elongation 3.3.1 Fidelity 3.4 Termination 4 Other organisms 4.1 Bacteria 4.2 Eukaryotes 4.3 Archaea 4.4 Viruses 5 History 6 Purification 7 See also 8 References 9 External links
Structure[edit]
RNA polymerase core (PDB: 1HQM).
Yeast RNA polymerase II core (PDB: 1WCM).
Homologous subunits are colored the same:[1]
orange: α1/RPB3, yellow: α2/RPB11, wheat: β/RPB2, red: β′/RPB1, pink: ω/RPB6.
The 2006 Nobel Prize in Chemistry was awarded to Roger D. Kornberg for creating detailed molecular images of RNA polymerase during various stages of the transcription process.[3]
In most prokaryotes, a single RNA polymerase species transcribes all types of RNA. RNA polymerase "core" from E. coli consists of five subunits: two alpha (α) subunits of 36 kDa, a beta (β) subunit of 150 kDa, a beta prime subunit (β′) of 155 kDa, and a small omega (ω) subunit. A sigma (σ) factor binds to the core, forming the holoenzyme. After transcription starts, the factor can unbind and let the core enzyme proceed with its work.[4][5] The core RNA polymerase complex forms a "crab claw" or "clamp-jaw" structure with an internal channel running along the full length.[6] Eukaryotic and archaeal RNA polymerases have a similar core structure and work in a similar manner, although they have many extra subunits.[7]
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