BIOL 2201 Study Guide - Final Guide: Active Transport, Cloning, Mutagen

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7 Feb 2016
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Final Exam Review
Final exam covers Chapters 7, 8, 15, 18 and 20 (Stem Cell and Cancer).
Chapter 7
Transcription, polymerase, prokaryotic transcription components, eukaryotic
transcription component, promoter, sigma factor, ribozymes, ribosome, Exon,
Intron, RNA capping, Poly-A, polyosome, tRNA synthase, spliceosome, genetic
code
Prokaryotic Transcription.
-The initiation of transcription is an especially critical process because it is the
main point at which the cell selects which proteins or RNAs are to be produced.
-To begin transcription, RNA polymerase must be able to recognize the start of a
gene and bind firmly to the DNA at this site.
-When an RNA polymerase collides randomly with a DNA molecule, the enzyme
sticks weakly to the double helix and then slides rapidly along its length. RNA
polymerase latches on tightly only after it has encountered a gene region called a
promoter, which contains a specific sequence of nucleotides that lies
immediately upstream of the starting point for RNA synthesis. Once bound tightly
to this sequence, the RNA polymerase opens up the double helix immediately in
front of the promoter to expose the nucleotides on each strand of a short stretch
of DNA.
-One of the two exposed DNA strands then acts as a template for complementary
base pairing with incoming ribonucleoside triphosphates, two of which are
joined together by the polymerase to begin synthesis of the RNA chain. Chain
elongation then continues until the enzyme encounters a second signal in the
DNA, the terminator (or stop site) where the polymerase halts and releases
both the DNA template and the newly made RNA transcript. This terminator
sequence is contained within the gene and is transcribed into the 3 end of the ʹ
newly made RNA.
(mRNAs) code for proteins
(rRNAs) form the core of the ribosome’s structure and catalyze protein synthesis
(miRNAs) regulate gene expression
(tRNAs) serve as adaptors between mRNA and amino acids during protein synthesis
other noncoding RNAs used in RNA splicing, gene regulation, telomere maintenance,
and many other processes
-Bacterial RNA polymerase contains a subunit called sigma factor that recognizes
the promoter of a gene.
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-Each base presents unique features to the outside of the double helix, allowing
the sigma factor to find the promoter sequence without having to separate the
entwined DNA strands.
How RNA polymerase determines which of the two DNA strands to use as a template
for transcription:
-Each strand has a different nucleotide sequence and would produce a different
RNA transcript.
-Every promoter has a certain polarity: it contains two different nucleotide
sequences upstream of the transcriptional start site that position the RNA
polymerase, ensuring that it binds to the promoter in only one orientation.
-Because the polymerase can only synthesize RNA in the 5′-to-3′ direction, once
the enzyme is bound it must use the DNA strand oriented in the 3′-to-5′ direction
as its template. This selection of a template strand does not mean that on a given
chromosome, transcription always proceeds in the same direction. With respect
to the chromosome as a whole, the direction of transcription varies from gene to
gene. But because each gene typically has only one promoter, the orientation of
its promoter determines in which direction that gene is transcribed and therefore
which strand is the template strand.
Eukaryotic Transcription
Many of the principles we just outlined for bacterial transcription also apply to
eukaryotes. However, transcription initiation in eukaryotes differs in several important
ways from that in bacteria:
-The first difference lies in the RNA polymerases themselves (1vs3). RNA
polymerases I and III transcribe the genes encoding transfer RNA, ribosomal
RNA, and various other RNAs that play structural and catalytic roles in the cell
(Table 7–2). RNA polymerase II transcribes the vast majority of eukaryotic genes,
including all those that encode proteins and miRNAs. Our subsequent discussion
will therefore focus on RNA polymerase II.
-A second difference is that, whereas the bacterial RNA polymerase (along with its
sigma subunit) is able to initiate transcription on its own, eukaryotic RNA
polymerases require the assistance of a large set of accessory proteins. Principal
among these are the general transcription factors, which must assemble at each
promoter, along with the polymerase, before the polymerase can begin
transcription.
-A third distinctive feature of transcription in eukaryotes is that the mechanisms
that control its initiation are much more elaborate than those in prokaryotes. In
bacteria, genes tend to lie very close to one another in the DNA, with only very
short lengths of nontranscribed DNA between them. But in plants and animals,
including humans, individual genes are spread out along the DNA, with stretches
of up to 100,000 nucleotide pairs between one gene and the next. This
architecture allows a single gene to be controlled by a large variety of regulatory
DNA sequences scattered along the DNA, and it enables eukaryotes to engage
in more complex forms of transcriptional regulation than do bacteria.
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-Last but not least, eukaryotic transcription initiation must take into account the
packing of DNA into nucleosomes and more compact forms of chromatin
structure.
Eukaryotic RNA Polymerase Requires General Transcription Factors
-These accessory proteins assemble on the promoter, where they position the
RNA polymerase and pull apart the DNA double helix to expose the template
strand, allowing the polymerase to begin transcription.
-Thus the general transcription factors have a similar role in eukaryotic
transcription as sigma factor has in bacterial transcription.
-The assembly process typically begins with the binding of the general
transcription factor TFIID to a short segment of DNA double helix composed
primarily of T and A nucleotides; because of its composition, this part of the
promoter is known as the TATA box. Upon binding to DNA, TFIID causes a
dramatic local distortion in the DNA double helix (Figure 7–13), which helps to
serve as a landmark for the subsequent assembly of other proteins at the
promoter.
-The TATA box is a key component of many promoters used by RNA polymerase
II, and it is typically located 25 nucleotides upstream from the transcription start
site.
-Once TFIID has bound to the TATA box, the other factors assemble, along with
RNA polymerase II, to form a complete transcription initiation complex.
-After RNA polymerase II has been positioned on the promoter, it must be
released from the complex of general transcription factors to begin its task of
making an RNA molecule.
-A key step in liberating the RNA polymerase is the addition of phosphate groups
to its “tail”. This liberation is initiated by the general transcription factor TFIIH,
which contains a protein kinase as one of its subunits. Once transcription has
begun, most of the general transcription factors dissociate from the DNA and
then are available to initiate another round of transcription with a new RNA
polymerase molecule. When RNA polymerase II finishes transcribing a gene, it
too is released from the DNA; the phosphates on its tail are stripped off by
protein phosphatases, and the polymerase is then ready to find a new promoter.
Only the dephosphorylated form of RNA polymerase II can initiate RNA
synthesis.
Eukaryotic mRNAs Are Processed in the Nucleus
Although the templating principle by which DNA is transcribed into RNA is the same in
all organisms, the way in which the RNA transcripts are handled before they can be
used by the cell to make protein differs greatly between bacteria and eukaryotes.
-Bacterial DNA lies directly exposed to the cytoplasm, which contains the
ribosomes on which protein synthesis takes place. As an mRNA molecule in a
bacterium starts to be synthesized, ribosomes immediately attach to the free 5′
end of the RNA transcript and begin translating it into protein.
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