Control of Gene Activity

1. Control of Gene Activity Chapter 18: Regulation of Gene Expression

2. Gene Regulation • Prokaryotes and eukaryotes alter gene expression in response to their changing environment • In multicellular eukaryotes, gene expression regulates development and is responsible for differences in cell types • RNA molecules play many roles in regulating gene expression in eukaryotes

3. Prokaryotic regulation • Gene expression in bacteria is controlled by the operon model • An operon is a cluster of functionally related genes can be under coordinated controlby a single on-off “switch” • Bacteria do not require same enzymes all the time • They produce just enzymes needed at the moment • The regulatory “switch” is a segment of DNA called an operator(positioned within the promoter)

4. Prokaryotic regulation • The operon can be switched off by a protein repressor • The repressor prevents gene transcription by binding to the operator and blocking RNA polymerase • The repressor is the product of a separate regulatory gene • The repressor can be in an active or inactive form, depending on the presence of other molecules • A corepressor is a molecule that cooperates with a repressor protein to switch an operon off

5. Operon Components • The operon includes the following: • 1) Regulatory gene • Located outside the operon • Codes for a repressor protein molecule
 • 2) Promoter • Sequence of DNA where RNA polymerase attaches • 3) Operator • A short sequence of DNA where repressor binds, preventing RNA polymerase from binding • 4) Structural genes • Code for enzymes of a metabolic pathway • Transcribed as a unit

6. E. coli & Tryptophan • E. coli is a bacteria that lives in your colon • It has a metabolic pathway that allows for the synthesis of the amino acid tryptophan (Trp) • This pathway starts with a precursor molecule and proceeds through five enzyme catalyzed steps before reaching the final product: tryptophan • It is important that E. coli be able to control the rate of Trp synthesis because the amount of Trp available from the environment varies considerably

7. E. coli & Tryptophan • If you eat a meal with little or no Trp, the E. coli in your gut must compensate by making more • If you eat a meal rich in Trp, E. coli doesn't want to waste valuable resources or energy to produce the amino acid because it is readily available for use • Therefore, E. coli uses the amount of Trp present to regulate the pathway • If levels are not adequate, the rate of Trp synthesis is increased • If levels are adequate, the rate of Trp synthesis is inhibited

8. trp Operon • The Trp operon has three components: • Five Structural Genes • These genes contain the genetic code for the five enzymes in the Trp synthesis pathway • One Promoter • DNA segment where RNA polymerase binds and starts transcription • One Operator • DNA segment found between the promoter and structural genes • It determines if transcription will take place

9. trp Operon

10. trp operon • When nothing is bonded to the operator, the operon is "on" • RNA polymerase binds to the promoter and transcription is initiated • The 5 structural genes are transcribed to one mRNA strand • The mRNA will then be translated into the 5 enzymes that control the Trp synthesis pathway

11. trp operon • The operon is turned "off" by a specific protein called the repressor • The repressor is inactive in this form and can not bind properly to the operator • To become active and bind properly, a corepressor must associate with the repressor • The corepressor for this operon is Tryptophan • This makes sense because E. coli does not want to synthesize Trp if it is available from the environment

12. trp operon

13. trp operon • An active repressor binds to the operator blocking the attachment of RNA polymerase to the promoter • Without RNA polymerase, transcription and translation of the structural genes can't occur and the enzymes needed for Tryptophan synthesis are not made • By default the trp operon is on and the genes for tryptophan synthesis are transcribed • When tryptophan is present, it binds to the trp repressor protein, which turns the operon off • The repressor is active only in the presence of its corepressor tryptophan; thus the trp operon is repressed if tryptophan levels are high

14. Repressible vs Inducible • The trp operon is a repressible operon • This type is one that is usually on • Binding of a repressor to the operator shuts off transcription • The end product, Trp, decreases or stops the transcription of the enzymes necessary for its production • The opposite is called an inducible operon • This type is one that is usually off • A molecule called an inducer inactivates the repressor and turns on transcription • An example of an inducible system is lac (lactose) operon

15. lac operon • The Lac operon has 3 components: • Three Structural Genes • Contain the genetic code for the 3 enzymes in the lactose catabolic pathway • One Promoter • DNA segment where RNA polymerase binds and starts transcription • One Operator • DNA segment found between the promoter and structural genes • It determines if transcription will take place • If the operator in turned "on", transcription will occur

16. lac operon • The lac operon is an inducible operon whose genes code for enzymes used in the hydrolysis and metabolism of lactose • By itself, the lac repressor is active and switches the lac operon off • The active repressor binds to the operator • This blocks RNA polymerase from transcribing the genes • Basically-- the lac operon is in the “off ” position and needs to be turned “on”

17. lac operon OFF

18. lac operon • A molecule called an inducerinactivates the repressor to turn the lac operon on • What inducer is used in the lac operon? Lactose • This makes sense because the cell only needs to make enzymes to catabolize lactose if lactose is present • When lactose enters the cell it binds to the repressor and changes its shape so that it can't bind to the operator • RNA polymerase can now start transcription of the 3 structural genes that will control lactose catabolism

19. lac operon ON

20. Eukaryotic Regulation • Eukaryotes lack a universal regulatory mechanism to control expression of genes coding proteins • In multicellular organisms gene expression is essential for cell specialization • DNA in eukaryotes is packaged as chromatin within a nucleus

21. Chromatin in Eukaryotes • Most chromatin is loosely packed in the nucleus during interphase and condenses prior to mitosis • Loosely packed chromatin is called euchromatin • The genes within this area are easily accessed, thus easily transcribed • During interphase a few regions of chromatin are highly condensed into heterochromatin • Genes within this area are difficult to access, thus they are usually not transcribed

22. Eukaryotic regulation • There are four primary levels of control of gene activity: • 1. Transcriptional Control • 2. Posttranscriptional Control • 3. Translational Control • 4. Posttranslational Control

23. Transcriptional Control • Takes place in nucleus, the site of transcription • Determines which structural genes are transcribed and the rate of transcription • Includes organization of chromatin • Includes the action of regulatory proteins that may activate or inhibit transcription (such as transcription factors)

24. Regulatory Proteins • General transcription factors are essential for the transcription of all protein-coding genes • Some transcription factors function as activators • An activator is a protein that binds to an enhancer and stimulates transcription of a gene • Enhancers are DNA sequences that may be far away from a gene or even located in an intron • Some transcription factors function as repressors • A repressor is a protein that prevents the expression of a particular gene • Some activators and repressors act indirectly by influencing chromatin structure to promote or silence transcription

25. Posttranscriptional control • Takes place in the nucleus or cytoplasm • Involves differential processing of pre-mRNA • Differential excision of introns and splicing of mRNA can vary type of mRNA • In alternative RNA splicing, different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns • Involves regulation of transport of mature mRNA • The life span of mRNA molecules in the cytoplasm is a key to determining protein synthesis • The mRNA life span is determined in part by sequences in the leader and trailer regions (cap and tail)

26. Translational control • Takes place in the cytoplasm, the site of translation • Life expectancy of mRNA molecules can vary, as well as their ability to bind ribosomes • Some mRNA's may need additional changes before they are translated • The initiation of translation of selected mRNAs can be blocked by regulatory proteins that bind to sequences or structures of the mRNA

27. Posttranslational control • Takes place in the cytoplasm after protein synthesis • May involve activation or degradation of the protein • After translation, various types of protein processing, including cleavage and the addition of functional groups, are subject to control • Proteasomesare giant protein complexes that bind protein molecules and degrade them • Eukaryotic Gene Control Animation

28. Review Questions Differentiate between prokaryotic and eukaryotic gene regulation. Explain the use of an operon as a prokaryotic form of gene regulation. Name and describe the four main parts of an operon. Define the following terms: operator, repressor, inducer, regulatory gene, and corepressor. Describe the functioning of the trp operon as a repressible operon and state its overall significance to E. coli. Differentiate between repressible and inducible operons. Describe the functioning of the lac operon as an inducible operon and state its overall significance to E. coli. Differentiate between euchromatin and heterochromatin in eukaryotes. Name and describe the important traits of the 4 primary levels of control of gene activity in eukaryotes. Differentiate between activators, enhancers, and repressors. Describe alternative RNA splicing and its significance to gene control. Define proteasome.