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Learning goals associated with 2020_Winter_Bis2a_Facciotti_Lecture_21
- Differentiate and convert between coding/noncoding, template/non-template strands.
- Define and explain the function and structure of an open reading frame (ORF).
- Create a model for a basic transcriptional unit that includes promoters, transcriptional regulatory sites for transcription factor binding, ribosome binding site, coding region,
stopcodon and transcriptionalterminator.
- Use the model of a transcriptional unit to discuss the roles of each of the structural elements of a transcriptional unit. Identify those that
are transcribed, those that may be translatedand those that serve other roles.
- Create a dynamic model (verbal, drawing, etc.)
ofthe process of transcription that includes the reactants, products, enzymes, the sites on the DNA required for transcription to take place, and how these components interact with the DNA template at different times during the process. Put your models intoaction!
The flow of genetic information
In bacteria, archaea, and eukaryotes, the primary role of DNA is to store heritable information that encodes the instruction set required for creating the organism in question. While we have gotten much better at quickly reading the chemical composition (the sequence of nucleotides in a genome and some chemical modifications that
to it), we still don't know how to decode reliably all the information within and all the mechanisms by which it
and ultimately expressed.
There are, however, some core principles and mechanisms associated with the reading and expression of the genetic code whose basic steps
and that need to be part of the conceptual toolkit for all biologists. Two of these processes are transcription and translation, which are the coping of parts of the genetic code written in DNA into molecules of the related polymer RNA and the reading and encoding of the RNA code into proteins, respectively.
In BIS2A, we focus on developing an understanding of theprocess
of transcription (recall that an Energy Story is a rubric for describing a process) and its role in the expression of genetic information. We motivate our discussion of transcription by focusing on functional problems (bringing in parts of our problem solving/design challenge rubric) that must
the process to take place. We then describe how the process
by Nature to create a variety of functional RNA molecules (that may have various structural, catalytic or regulatory roles) including so called messenger RNA (
) molecules that carry the information required to synthesize proteins. Likewise, we focus on challenges and questions associated with the process of translation, the process by which the ribosomes synthesize proteins.
We often depict the basic flow of genetic information in biological systems in a scheme known as "the central dogma" (see figure below). This scheme states that information encoded in DNA flows into RNA via transcription and ultimately translated to proteins. Processes like reverse transcription (the creation of DNA from and RNA template) and replication also represent mechanisms for propagating information in different forms. This scheme, however, says nothing per se about how information
Genotype to phenotype
An important concept in the following sections is the relationship between genetic information, the genotype, and the result of expressing it, the phenotype. These two terms and the mechanisms that link the two will
Genotype refers to the information stored in the DNA of the organism, the sequence of the nucleotides, and the compilation of its genes. Phenotype refers to any physical characteristic that you can measure, such as height, weight, amount of ATP produced, ability to metabolize lactose, and response to environmental stimuli. Differences in genotype, even
What is a gene? A gene is a segment of DNA in an organism's genome that encodes a functional RNA (such as
protein product (enzymes, tubulin, etc.). A generic gene contains elements encoding regulatory regions and a region encoding a transcribed unit.
Genes can gain mutations—defined as changes in the composition and or sequence of the nucleotides—either in the coding or regulatory regions. These mutations can lead to several outcomes: (1) nothing measurable happens as a result; (2) the gene is no longer expressed; or (3) the expression or behavior of the gene product
s) are different. In a population of organisms sharing the same
different variants of the gene
as alleles. Different alleles can lead to differences in phenotypes of individuals and contribute to the diversity in biology under selective pressure.
Start learning these vocabulary terms and associated concepts. You will then be
familiar with them when we dive into them in more detail over the next lectures.
Transcription always proceeds from the template strand, one of the two strands of the double-stranded DNA. The RNA product is complementary to the template strand and is almost identical to the nontemplate strand, called the coding strand, with the exception that RNA contains a uracil (U) in place of the thymine (T) found in DNA. During elongation, an enzyme called RNA polymerase proceeds along the DNA template, adding nucleotides by base pairing with the DNA template in a manner similar to DNA replication, with the difference being an RNA strand that
Figure 4. During elongation, RNA polymerase tracks along the DNA template, synthesizing mRNA in the 5' to 3' direction, unwinding and then rewinding the DNA as
Bacterial vs. eukaryotic elongation
In bacteria, elongation begins with the release of the
ahead of the core enzyme and rewound behind it. The base pairing between DNA and RNA is not stable enough to maintain the stability of the mRNA synthesis components. Instead, the RNA polymerase acts as a stable linker between the DNA template and the nascent RNA strands to ensure that elongation
In eukaryotes, following the formation of the preinitiation complex, the polymerase
from the other transcription factors, and
to proceed as it does in prokaryotes with the polymerase synthesizing pre-mRNA in the 5' to 3' direction. As discussed previously, RNA polymerase II transcribes the major share of eukaryotic genes, so this section will focus on how this polymerase accomplishes elongation and termination.
Possible NB Discussion Point
Compare and contrast the energy story for DNA replication initiation + elongation to the energy story for transcription initiation + elongation.
Once a gene
, the bacterial polymerase needs to dissociate from the DNA template and liberate the newly made mRNA. Depending on the gene being transcribed, there are two kinds of termination signals. One is
protein-based, and the other is RNA-based. Rho-dependent termination
protein, which tracks along the polymerase on the growing mRNA chain. Near the end of the gene, the polymerase encounters a run of G nucleotides on the DNA template and it stalls. As a result, the
protein collides with the polymerase. The interaction with rho releases the mRNA from the transcription bubble.
by specific sequences in the DNA template strand. As the polymerase nears the end of the gene being transcribed, it encounters a region rich in CG nucleotides. The mRNA folds back on itself, and the complementary CG nucleotides bind
. The result is a stable hairpin that causes the polymerase to stall as soon as it
a region rich in AT nucleotides. The complementary UA region of the mRNA transcript forms only a weak interaction with the template DNA. This, coupled with the stalled polymerase, induces enough instability for the core enzyme to break away and liberate the new mRNA transcript.
The termination of transcription is different for the different polymerases. Unlike in prokaryotes, elongation by RNA polymerase II in eukaryotes takes place
Termination of transcription in the archaea is far less studied than in the other two domains of life and
In bacteria and archaea
In bacteria and archaea, transcription occurs in the
In eukaryotes, the process of transcription
5' G-cap and 3' poly-A tail
Possible NB Discussion Point
Transcriptomics is a branch of “-omics” that involves studying an organism or population’s transcriptome or, the complete set of all RNA molecules. What kind of information can you obtain from studying the transcriptome(s)? Can you think of any cool scientific questions that a transcriptomic analysis might help resolve? What are some constraints to transcriptomic approaches one might keep in mind when conducting analyses?
Splicing occurs on most eukaryotic mRNAs in which introns