Control of Gene Expression Chapter 16

2 Control of Gene Expression Initiation of Transcription is controlled by controlling gene expression. Regulatory proteins bind to DNA to either block or stimulate transcription, depending on how they interact with RNA polymerase Prokaryotic organisms are able to respond to changes in their environment by regulating gene expression. Eukaryotic cells are able to maintain homeostasis by regulating gene regulation

3 Regulatory Proteins Binding of regulatory proteins to specific DNA sequences results in controlling gene expression. –regulatory proteins gain access to the bases of DNA at the major groove via their DNA-binding motifs DNA-binding motifs are regions of regulatory proteins which bind to DNA –helix-turn-helix motif –homeodomain motif –zinc finger motif –leucine zipper motif

4 Prokaryotic Regulation Control of transcription initiation can be: –positive control – increases transcription when activators bind DNA –negative control – reduces transcription when repressors bind to DNA regulatory regions called operators

5 Prokaryotic Regulation Prokaryotic cells often respond to their environment by changes in gene expression. Genes involved in the same metabolic pathway are organized in operons. Some operons are induced when the metabolic pathway is needed. Example: Lactose utilization Some operons are repressed when the metabolic pathway is no longer needed. Example: Tryptophan utilization

6 Prokaryotic regulation The lac operon contains genes for the use of lactose as an energy source. Regulatory regions of the operon include the CAP binding site, promoter, and the operator. The coding region contains genes for 3 enzymes: –b-galactosidase, permease, and transacetylase

7 Respression of lac operon lac repressor binds to the operator to block transcription

8 How lac operon is induced? In the presence of lactose, an inducer molecule binds to the repressor protein repressor can no longer bind to operator transcription proceeds

9 How the presence of glucose prevents induction of lac operon? In the presence of both glucose and lactose, bacterial cells prefer to use glucose. Glucose prevents induction of the lac operon. –binding of CAP – cAMP complex to the CAP binding site is required for induction of the lac operon –high glucose levels cause low cAMP levels –high glucose  low cAMP  no induction

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11 Prokaryotic Regulation The trp operon encodes genes for the biosynthesis of tryptophan. The operon is not expressed when the cell contains sufficient amounts of tryptophan. The operon is expressed when levels of tryptophan are low.

12 Trp operon is controlled by trp respressor The trp operon is negatively regulated by the trp repressor protein –trp repressor binds to the operator to block transcription –binding of repressor to the operator requires a corepressor which is tryptophan –low levels of tryptophan prevent the repressor from binding to the operator

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15 Eukaryotic Regulation Controlling the expression of eukaryotic genes requires transcription factors. –general transcription factors are required for transcription initiation required for proper binding of RNA polymerase to the DNA –specific transcription factors increase transcription in certain cells or in response to signals

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17 Eukaryotic Transcription General transcription factors bind to the promoter region of the gene. RNA polymerase II then binds to the promoter to begin transcription at the start site (+1). Enhancers are DNA sequences to which specific transcription factors (activators) bind to increase the rate of transcription.

18 Eukaryotic Transcription Coactivators and mediators are also required for the function of transcription factors. –coactivators and mediators bind to transcription factors and bind to other parts of the transcription apparatus

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20 Eukaryotic Chromosome Structure Eukaryotic DNA is packaged into chromatin. Chromatin structure is directly related to the control of gene expression. Chromatin structure begins with the organization of the DNA into nucleosomes. Nucleosomes may block RNA polymerase II from gaining access to promoters.

21 Eukaryotic Chromosome Structure Methylation (the addition of –CH 3 ) of DNA or histone proteins is associated with the control of gene expression. Clusters of methylated cytosine nucleotides bind to a protein that prevents activators from binding to DNA. Methylated histone proteins are associated with inactive regions of chromatin.

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23 Posttranscriptional Regulation Control of gene expression usually involves the control of transcription initiation. But gene expression can be controlled after transcription, with mechanisms such as: –RNA interference –alternative splicing –RNA editing –mRNA degradation

24 Posttranscriptional Regulation RNA interference involves the use of small RNA molecules The enzyme Dicer chops double stranded RNA into small pieces of RNA –micro-RNAs bind to complementary RNA to prevent translation –small interfering RNAs degrade particular mRNAs before translation

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26 Posttranscriptional Regulation Introns are spliced out of pre-mRNAs to produce the mature mRNA that is translated. Alternative splicing recognizes different splice sites in different tissue types. The mature mRNAs in each tissue possess different exons, resulting in different polypeptide products from the same gene.

27 Posttranscriptional Regulation RNA editing creates mature mRNA that are not truly encoded by the genome. For example – –apolipoprotein B exists in 2 isoforms –one isoform is produced by editing the mRNA to create a stop codon –this RNA editing is tissue-specific

28 Posttranscriptional Regulation Mature mRNA molecules have various half- lives depending on the gene and the location (tissue) of expression. The amount of polypeptide produced from a particular gene can be influenced by the half- life of the mRNA molecules.

29 Protein Degradation Proteins are produced and degraded continually in the cell. Proteins to be degraded are tagged with ubiquitin. Degradation of proteins marked with ubiquitin occurs at the proteasome

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31 This project is funded by a grant awarded under the President’s Community Based Job Training Grant as implemented by the U.S. Department of Labor’s Employment and Training Administration (CB ). NCC is an equal opportunity employer and does not discriminate on the following basis: against any individual in the United States, on the basis of race, color, religion, sex, national origin, age disability, political affiliation or belief; and against any beneficiary of programs financially assisted under Title I of the Workforce Investment Act of 1998 (WIA), on the basis of the beneficiary’s citizenship/status as a lawfully admitted immigrant authorized to work in the United States, or his or her participation in any WIA Title I-financially assisted program or activity. This product was funded by a grant awarded under the President’s High Growth Job Training Initiative, as implemented by the U.S. Department of Labor’s Employment & Training Administration. The information contained in this product was created by a grantee organization and does not necessarily reflect the official position of the U.S. Department of Labor. All references to non-governmental companies or organizations, their services, products, or resources are offered for informational purposes and should not be construed as an endorsement by the Department of Labor. This product is copyrighted by the institution that created it and is intended for individual organizational, non-commercial use only.

32 Helix-Turn-Helix Motif

33 Homeodomain Motif

34 Zinc Finger Motif

35 Leucine Zipper Motif

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38 This project is funded by a grant awarded under the President’s Community Based Job Training Grant as implemented by the U.S. Department of Labor’s Employment and Training Administration (CB ). NCC is an equal opportunity employer and does not discriminate on the following basis: against any individual in the United States, on the basis of race, color, religion, sex, national origin, age disability, political affiliation or belief; and against any beneficiary of programs financially assisted under Title I of the Workforce Investment Act of 1998 (WIA), on the basis of the beneficiary’s citizenship/status as a lawfully admitted immigrant authorized to work in the United States, or his or her participation in any WIA Title I-financially assisted program or activity. “This workforce solution was funded by a grant awarded under the President’s Community-Based Job Training Grants as implemented by the U.S. Department of Labor’s Employment and Training Administration. The solution was created by the grantee and does not necessarily reflect the official position of the U.S. Department of Labor. The Department of Labor makes no guarantees, warranties, or assurances of any kind, express or implied, with respect to such information, including any information on linked sites and including, but not limited to, accuracy of the information or its completeness, timeliness, usefulness, adequacy, continued availability, or ownership. This solution is copyrighted by the institution that created it. Internal use by an organization and/or personal use by an individual for non-commercial purposes is permissible. All other uses require the prior authorization of the copyright owner.”