Gene Expression Regulation in Bacteria and Eukaryotes

In bacteria, genes are frequently organized into operons with coordinate regulation, and genes with operons can be transcribed as on a single long mRNA. Eukaryotic genes are not organized into operons and are singly transcribed from their own promoters. In eukaryotes, nucleosome structure of the DNA is remodeled prior to transcription occurring. Essentially, the chromatin must assume a more open configuration state, allowing for access by transcription-associated factors. Activator and repressor molecules function in both eukaryotic and bacterial cells. However, in eukaryotic cells activators appear to be more common than in bacterial cells. In bacteria, transcription and translation can occur concurrently. In eukaryotes, the nuclear membrane separates transcription from translation both physically and temporally. This separation results in a greater diversity of regulatory mechanisms that can occur different points during gene expression.

Changes in chromatin structure can result in repression or stimulation of gene expression. As genes become more transcriptionally active, DNA shows increased sensitivity to DNase I digestion, suggesting that the chromatin structure is more open. Acetylation of histone proteins by acetytransferase proteins results in the destabilization of the nucleosome structure and increases transcription as well as hypersensitivity to DNase I. The reverse reaction by deacetylases stabilizes nucleosome structure and lessens DNase I sensitivity. Other transcription factors and regulatory proteins, called chromatin remodeling complexes, bind directly to the DNA altering chromatin structure without acetylating histone proteins. The chromatin remodeling complexes allow for transcription to be initiated by increasing accessibility to the promoters by transcription factors. DNA methylation is associated with decreased transcription. Methylated DNA sequences stimulate histone deacetylases to remove acetyl groups from the histone proteins, thus stabilizing the nucleosome and repressing transcription. Demethylation of DNA sequences is often followed by increased transcription, which may be related to the deacetylation of the histone proteins.

Transcriptional activator proteins stimulate transcription by binding DNA at specific base sequences such as an enhancer or regulatory promoter and attracting or stabilizing the basal transcription factor apparatus. Repressor proteins bind to silencer sequences or promoter regulator sequences. These proteins may inhibit transcription by either blocking access to the enhancer sequence by the activator protein, preventing the activator from interacting with the basal transcription apparatus, or preventing the basal transcription factor from being assembled.

<p>Enhancers are DNA sequences that are the binding sites of transcriptional activator proteins. Transcription at a distant gene is affected when the DNA sequence located between the gene's promoter and the enhancer is looped out, allowing for the interaction of the enhancer-bound proteins with proteins needed at the promoter, which in turn stimulates transcription. Additionally, the transcription of short enhancer (e)RNA molecules from an enhancer template may be involved in transcriptional activation, but a precise mechanism for such activation has not been determined.</p> Signup and view all the answers

<p>An insulator or boundary element is a sequence of DNA that inhibits the action of regulatory elements called enhancers in a position dependent manner.</p> Signup and view all the answers

<p>Response elements are regulatory DNA sequences consisting of short specific sequences located at various distances from the genes that they regulate. Under conditions of stress, a transcription activator protein binds to the response element and stimulates transcription. If the same response element sequence is located in the control regions of different genes, then these genes will be activated by the same stimuli, thus producing a coordinated response.</p> Signup and view all the answers

<p>Sex development in fruit flies depends on alternative splicing as well as a cascade of genetic regulation. Early in the development of female fruit flies, a female-specific promoter is activated stimulating transcription of the sex-lethal (Sxl) gene. Splicing of the pre-mRNA of the transformer (tra) gene is regulated by the Sxl protein. The mature mRNA produces the Tra protein. In conjunction with another protein, the Tra protein stimulates splicing of the pre-mRNA from the doublesex (dsx) gene. The resulting Dsx protein is required for the embryo to develop female characteristics. Male fruit flies do not produce the Sxl protein, which results in the tra pre-mRNA in male fruit flies being spliced at an alternate location. The alternate Tra protein is not functional, resulting in the dsx pre-mRNA splicing at a different location as well. Protein synthesis from this mRNA produces a male-specific doublesex protein, which causes development of male-specific traits.</p> Signup and view all the answers

<p>The total amount of protein synthesized is dependent on how much mRNA is available for translation. The amount of mRNA present is dependent on the rates of mRNA synthesis and degradation. Less-stable mRNAs will be degraded faster so there will be fewer copies available to serve as templates for translation. The presence of the 5' cap, 3' poly(A) tail, the 5' UTR, 3' UTR, and the coding region in the mRNA molecule are features that can affect the stability of the mRNA molecule. Poly(A) binding proteins (PABP) bind at the 3' poly(A) tail. These proteins contribute to the stability of the tail and protect the 5' cap through direct interaction. Once a critical number of adenine nucleotides have been removed from the tail, the protection is lost and the 5' cap is removed. The removal of the 5' cap allows for 5' to 3' nucleases to degrade the mRNA. AU-rich sequence elements in the 3' UTR can also increase degradation of the mRNA.</p> Signup and view all the answers

<p>(1) Through cleavage of mRNA sequences through “slicer activity”: The binding of RISCs containing either siRNA or miRNA to complementary sequences in mRNA molecules stimulates cleavage of the mRNA through “slicer activity.” This is followed by further degradation of the cleaved mRNA. (2) Through binding of complementary regions with the mRNA molecule by miRNAs to prevent translation: The miRNAs as part of RISC bind to complementary mRNA sequences preventing either translation initiation or elongation, which results in premature termination. (3) Through transcriptional silencing due to methylation of either histone proteins or DNA sequences: The siRNA binds to complementary DNA sequences within the nucleus and stimulates methylation of histone proteins. Methylated histones bind DNA more tightly preventing transcription factors from binding the DNA. The miRNA molecules bind to complementary DNA sequences and stimulate DNA methylases to directly methylate the DNA sequences, which results in transcriptional silencing. (4) Through slicer-independent mRNA degradation stimulated by miRNA binding to complementary regions in the 3' UTR of the mRNA: A miRNA binds to the AU rich element in the 3' UTR of the mRNA stimulating degradation using RISC and dicer.</p> Signup and view all the answers

<p>Similarities: Bacterial and eukaryotic gene regulation involves the action of protein repressors and protein activators. Cascades of gene regulation in which the activation of one set of genes affects another set of genes take place in both eukaryotes and bacteria. Regulation of gene expression at the transcriptional level is also common in both types of cells. Both have coordinated expression, although, through different mechanisms. Bacterial genes are often clustered in operons and are coordinately expressed through the synthesis of a single polygenic mRNA. Eukaryotic genes are typically separate, with each containing its own promoter and transcribed on individual mRNAs. Coordinate expression of multiple genes is accomplished through the presence of common [shared] response elements. Genes sharing the same response element will be regulated by the same regulatory factors. Differences: In eukaryotic cells, gene-coding regions are interrupted by introns, which are generally longer than exons. An individual intron may be much longer than the entire coding region. Gene expression requires the proper splicing of the pre-mRNA to remove these noncoding regions. In prokaryotic cells, gene-coding regions are usually not interrupted. In eukaryotic cells, chromatin structure plays a role in gene regulation. Chromatin that is condensed inhibits transcription. Therefore, for expression to occur, the chromatin must altered to allow for changes in structure. Acetylation of histone proteins and DNA methylation are important in these changes. At the level of transcription initiation, the process is more complex in eukaryotic cells. In eukaryotes, initiation requires a complex machine involving RNA polymerase, general transcription factors, and transcriptional activators. Bacterial RNA polymerase is either blocked or stimulated by the actions of regulatory proteins. Finally, in eukaryotes the action of activator proteins binding to enhancers may take place at a great distance from the promoter and structural gene. These distant enhancers occur much less frequently in bacterial cells.</p> Signup and view all the answers

<p>It is likely that flowering will not occur if the flowering locus D is deleted. The protein encoded by FLD is a deacetylase enzyme. This deacetylase enzyme normally removes acetyl groups from histones surrounding the flowering locus C (FLC). Once the acetyl groups are removed, the chromatin structure within this region is restored to be transcriptionally repressed. The restored chromatin inhibits transcription from the FLC locus. FLC codes for a transcriptional activator whose expression activates other genes that suppress flowering. If FLC transcription is active due to a deletion in FLD, then flowering will not occur.</p> Signup and view all the answers

<p>In bacteria, repressors that bind to the operator block RNA polymerase from binding to the promoter, and thus, directly block transcription. On the other hand, repressors that bind to silencers in eukaryotes block transcriptional activator proteins from binding at an activator site, thus eliminating transcriptional activation.</p> Signup and view all the answers

<p>Transition (more common) purine -&gt; purine or pyr -&gt; pyr; transversion (less common) pyr-&gt;purine or purine -&gt; pyr</p> Signup and view all the answers

<p>3 base insertion/trinucleotide repeats and gets worse with generation; more copies very bad; add more copies of amino acid to make faulty proteins</p> Signup and view all the answers

<p>Missense -&gt; diff codon/amino acid Nonsense -&gt; changes to stop codon Silent -&gt; changes but same result/amino acid Neutral -&gt; codes for new amino acid but function doesn't change</p> Signup and view all the answers

<p>To test mutagenesis or carcinogenicity of compounds; his- strain is plated so only the mutants that revert the change to be his+ can grow (no his on plate)</p> Signup and view all the answers

<p>Base excision – remove base, create AP site, remove sugar and phosphate, DNA poly/ligase Direct – revert changed nucleotides back to normal structure; photolyase</p> Signup and view all the answers

<p>There are two possible codons for glutamic acid, GAA and GAG. Single-base substitutions at the second position in both codons can produce codons that encode valine: GAA--------&gt; GUA (Val) GAG--------&gt; GUG (Val) Both substitutions are transversions. However, in the gene encoding the ẞ chain of hemoglobin, the GAG codon is the wild-type codon and the mutated GUG codon results in the sickle-cell phenotype.</p> Signup and view all the answers

<p>Spontaneous deamination of 5-methylcytosine produces thymine. If the subsequent repair of the GT mispairing is repaired incorrectly or, more likely, not repaired at all because the thymine is a normal base, then a GC to AT transition will result. Over time, the incorrect repairs will lead to an increase in the number of AT base pairs.</p> Signup and view all the answers

<p>The chemical tested is not mutagenic and likely not carcinogenic. The number of colonies on each plate represents the number of bacterial cells that underwent a mutation. Because the number of cells undergoing mutation on the control plate, without the tested chemical, was the same as the number undergoing mutation on the plate treated with the chemical, there is no evidence that the chemical elevates the mutation rate or is potentially carcinogenic.</p> Signup and view all the answers

<p>Exposure of DNA to UV light results in the formation of pyrimidine dimers in the DNA molecule. Often the repair of these dimers leads to mutations. Because the SOS repair system is error-prone and leads to an increased accumulation of mutations, UV light produces more mutations in bacteria when the SOS repair system is activated to repair the damage caused by the UV light. However, many species of bacteria have a direct DNA repair system that can repair pyrimidine dimers by breaking the covalent linkages between the pyrimidines that form the dimer. The enzyme that repairs the DNA is called photolyase and is activated and energized by light. The photolyase is a very efficient repair enzyme and typically makes accurate repairs of the damage. If the bacteria in the UV radiation experiment are exposed to light, then the photolyase will be activated to repair the damage, resulting in fewer mutations in the irradiated bacteria.</p> Signup and view all the answers

<p>Somatic arise in somatic tissues which do not produce gametes. When a somatic cell with a mutation divides by mitosis, the mutation is passed on to the daughter cells leading to a population of genetically identical cells. Germ line mutations- arise in cells that ultimately produce gametes. A germ line mutation can be passed to future generations producing offspring that carry the mutation in there somatic and germ line cells.</p> Signup and view all the answers

<p>Anticipation is the increase in the severity of a disease over subsequent generations. In diseases influenced by expansion of polynucleotide repeats, the numbers of repeats increase in subsequent generations, leading to increases in the severity of the diseases in those progenies.</p> Signup and view all the answers

<p>Bacterial genes are often organized into operons.</p> Signup and view all the answers

<p>They alter chromatin structure to improve access for transcription factors.</p> Signup and view all the answers

<p>It destabilizes nucleosome structure, increasing transcription.</p> Signup and view all the answers

<p>It stabilizes nucleosomes, leading to transcription repression.</p> Signup and view all the answers

<p>Eukaryotic activators can enhance transcription more effectively.</p> Signup and view all the answers

<p>In eukaryotes, transcription occurs in the nucleus, while translation occurs in the cytoplasm.</p> Signup and view all the answers

<p>It suggests more open chromatin, allowing for increased transcription.</p> Signup and view all the answers

<p>To modify chromatin structure, promoting gene access for transcription.</p> Signup and view all the answers

<p>Flowering will not occur.</p> Signup and view all the answers

<p>Eukaryotic repressors block transcriptional activators.</p> Signup and view all the answers

<p>A change within the same category of bases.</p> Signup and view all the answers

<p>Transitions are more common.</p> Signup and view all the answers

<p>Worsening effects across generations.</p> Signup and view all the answers

<p>It strengthens the binding of histones to DNA.</p> Signup and view all the answers

<p>Incorporation of an incorrect amino acid.</p> Signup and view all the answers

<p>By stimulating degradation of the mRNA using RISC.</p> Signup and view all the answers

<p>The occurrence of introns in eukaryotic genes.</p> Signup and view all the answers

<p>Creation of a truncated protein.</p> Signup and view all the answers

<p>Bacterial genes are clustered in operons.</p> Signup and view all the answers

<p>Does not change the amino acid sequence.</p> Signup and view all the answers

<p>Proper splicing of pre-mRNA.</p> Signup and view all the answers

<p>Operon structures.</p> Signup and view all the answers

<p>Altered chromatin structure facilitates transcription.</p> Signup and view all the answers

<p>They regulate genes that share common regulatory factors.</p> Signup and view all the answers

<p>The tra pre-mRNA is spliced at an alternate location.</p> Signup and view all the answers

<p>5' cap.</p> Signup and view all the answers

<p>It causes degradation of the mRNA.</p> Signup and view all the answers

<p>It protects the mRNA from degradation.</p> Signup and view all the answers

<p>Exposure to degradation by 5' to 3' nucleases.</p> Signup and view all the answers

<p>It produces a non-functional Dsx protein.</p> Signup and view all the answers

<p>By cleaving complementary mRNA sequences.</p> Signup and view all the answers

<p>They increase mRNA degradation rates.</p> Signup and view all the answers

<p>Nonsense mutation</p> Signup and view all the answers

<p>The production of valine</p> Signup and view all the answers

<p>Strand slippage</p> Signup and view all the answers

<p>To cause mismatches during replication</p> Signup and view all the answers

<p>Base excision repair</p> Signup and view all the answers

<p>Lack of histidine</p> Signup and view all the answers

<p>It does not change the amino acid sequence.</p> Signup and view all the answers

<p>Missense mutation in the beta chain</p> Signup and view all the answers

<p>Production of thymine</p> Signup and view all the answers

<p>A transition from GC to AT</p> Signup and view all the answers

<p>The chemical does not affect mutation rate.</p> Signup and view all the answers

<p>To avoid exposure to light that can cause damage.</p> Signup and view all the answers

<p>They can distort the DNA structure, leading to errors.</p> Signup and view all the answers

<p>It increases mutation accumulation.</p> Signup and view all the answers

<p>Error-prone repairs frequently result in mutations.</p> Signup and view all the answers

<p>Spontaneous deamination.</p> Signup and view all the answers