Biology Homework Chapter 11: Gene Expression
Textbook assignment: Chapter 11: The Control of Gene Expression, sections 1-11.
In chapter 10, we looked at the structure of DNA and the process by which it is duplicated during mitosis. That process occurs only once during each cell's creation. Now we look at the real reason for the DNA in the cell: to direct and control the cell's processes in gene expression. For each step, we want to know what conditions are necessary before the step can procede and what conditions cause it to stop.
Much of this chapter was rewritten for this edition of the text, reflecting research in the last decade that challenges some of our "accepted wisdom" about genes and proteins. If you have studied biology before in other texts, read this section carefully! You may find that theories you learned two years ago has already undergone change.
- 11.1 Prokaryotic Genes We start by looking at the simplest case. The DNA of bacteria (prokaryotic cells) is a single loop floating in the cell's cytoplasm. This makes such strands easy to study. One of the earliest sets of bacterial genes to be identified and studied is the bacteria Escherichia coli (E. coli) operon for the digestion of lactose. Operons (found mostly in prokaryotes) have three sections: the promoter, the operator, and the gene section, which can contain one or more genes. The promoter region is where the RNA polymerase attaches if not otherwise inhibited by a repressor molecule.
Gene expression is controlled by "always on" repressors, "always off" repressors, and activators which limit gene activity to situations where gene expression is needed, and leaves the gene inactive when it is not needed, conserving resources.
- The lac operon breaks down lactose and is controlled by a repressor that is "on" (in repression mode) by default so that the gene is usually turned off. When lactose is present, it interferes with the repressor, so the gene switches on and produces enzymes to break down the lactose.
- The try operon manufactures tryptophan and is controlled by a repressor that is "off" (not repressing gene expression) by default, so that the gene is usually turned on and making tryptophan. But when tryptophan is present in the environment, it activates the repressor, so the gene switches off, and the cell uses environmentally-available sources rather than wasting energy making even more tryptophan.
- Some sequences don't rely on repressors for the promoter, but use activators which help RNA polymerase attach to the operator strand.
- 11.2 Eukaryotic Genes and differentiation. In eukaryotic cells, things are more complicated. All multicellular organisms start as a single cell (the zygote formed from the gametes). In mitosis, cells are cloned; the daughters and parent cell all have exactly the same DNA. During embryonic stage, genes in different cells are switched on or off, providing different functions for different tissues, organs, and organ systems.
DNA packing provides one method of deactivating gene sequences by wrapping the DNA helix around proteins called histones to compact DNA that isn't required for cell functionality.
Methylation occurs when methyl units attach to the DNA base (often cytosine) and deactivate a gene.
DNA packing and methylation are not considered mutations because the DNA sequence is not changed, but the pattern of packing and methylation can lead to epigenetic inheritance, where gene expression patterns are inherited by offspring. DNA mutations are usually permanent, but epigenetic changes can be reversed.
In mammals, females inherit two X chromosomes. For cells to function properly, one of the chromosomes must be deactivated (becoming a Barr body). The early selection of which X chromosome to deactivate is random, leading some embryonic cells to express the allele inherited on the male parent X chromosome, and embryonic cells to express the allele inherited on the female parent X chromosome. Once chromosome deactivation has occurred, all cells produced through mitosis with that parent will have the same X chromosome deactivated -- an example of epigenetic inheritance.
- 11.3 Eukaryotic transcription is far more complex than prokaryotic transcription. Most eukaryotic genes are turned of by default. Regulatory molecules called transcription factors bind to enhances located at some distance from the gene, and form protein complexes that bend the DNA sequence to allow RNA polymerase attachment for gene expression. In much rarer situations, silencer repressors may work to prevent RNA polymerase attachment to the promoter and prevent gene expression.
- 11.4 mRNA formation. Once transcribed, RNA is spliced to remove intron (unexpressed) sequences of base pairs. The same RNA sequence may be spliced different ways at different times, yielding variations in the finam mRNA which will be transported out of the nucleus.
- 11.5 MicroRNA complexes are small RNA segments around 20 nucleotides that do not program for proteins but instead appear to attach to mRNA sequences and alter their function, providing yet another gene expression control mechanism.
- 11.6 Gene expression is also controlled by mechanisms acting after mRNA is fully manufactured and leaves the nucleus.
- mRNA breaks down, within minutes in prokaryotic cells, but within hours or days for eukaryotic cells. Cells must constantly manufacture the mRNA sequences needed for different situations.
- Initiation of protein synthesis (translation) may depend on the presence of necessary resources.
- The cell may use enzymes to control the rate of post-translation packaging, when the amino-acid sequence or polypeptide is folded its secondary, tertiary, and quaternary structures, to meet cell needs.
- Cells may enforce protein breakdown to assure that "tired" proteins are removed from processes before they mis-function and create problems.
- 11.7 [Summary]: Gene expression can therefore be controlled by mechanisms during transcription inside the nucleus, translation outside the nucleus, and activation in the cell. Responses to immediate conditions allow a cell to meet specific needs at different times in its own life cycle, and (in multi-celled organisms) in the life pattern of the entire organism.
- 11.8 Cascading gene expression is the process where the expression of one gene leads to the expression of certain other genes. In the early stages of embryonic development, a homeotic gene can create a sequence of gene expression that result in the development of a major complex structure, such as a leg or antennae. A mutation in such a gene can have grave consequences (creating a leg instead of an antenna).
- 11.9 DNA microarrays allow researches to test fragments of single-stranded DNA from individual genes. When fluorescent cDNA is added to the strand environments, active binding DNA marks where transcription is occurring.
- 11.10 In signal-transduction, signal molecules or hormones produced by one cell are transported to other cells, where they reaction with proteins on the surface of the cell. These receptor proteins start a chain reaction of protein generation that eventually triggers RNA transcription of DNA in the target cell.
- 11.11 There is some evidence that these cell signaling mechanisms exist in very similar forms in widely diverse species (for example, yeast and humans). Evolutionists consider this an indication that such systems were in effect very early in the evolution of life forms.
Read the following weblecture before chat: Control of Gene Expression
Take notes on any questions you have, and be prepared to discuss the lecture in chat.
Perform the study activity below:
Use the Interactive Exercise at Learn Genetics to Translate and Transcribe a Gene.
- Click to start the interactive session.
- Watch the short introduction. When prompted to choose a gene, hover over the cell DNA and pick one of the three gene options.
- When prompted, match each of the the designated DNA bases with the appropriate RNA base.
- Watch the explanation describing how the cell builds the ribosome complex to produce the protein sequence from the RNA information.
- See if you can determine the matching codon sequences and the amino acid each identifies to build the amino acid peptide chain.
- Watch the final summary.
- If you have time, process a different gene to review and verify what you have learned.
- No quiz yet: the Chapter Quiz opens when we finish the chapter.
Read through the lab for this week; bring questions to chat on any aspect of the lab, whether you intend not perform it or not. If you decide to perform the lab, be sure to submit your report by the posted due date.
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