Regulation of Gene Expression

1. 11 Regulation of Gene Expression

2. Chapter 11 Regulation of Gene Expression • Key Concepts • 11.1 Several Strategies Are Used to Regulate Gene Expression • 11.2 Many Prokaryotic Genes Are Regulated in Operons • 11.3 Eukaryotic Genes Are Regulated by Transcription Factors and DNA Changes • 11.4 Eukaryotic Gene Expression Can Be Regulated after Transcription

3. Chapter 11 Opening Question How does CREB regulate the expression of many genes?

4. Concept 11.1 Several Strategies Are Used to Regulate Gene Expression • Gene expression is tightly regulated. • Gene expression may be modified to counteract environmental changes, or gene expression may change to alter function in the cell. • Constitutiveproteins are actively expressed all the time. • Inducible genes are expressed only when their proteins are needed by the cell.

5. Figure 11.1 Potential Points for the Regulation of Gene Expression

6. Concept 11.1 Several Strategies Are Used to Regulate Gene Expression • Genes can be regulated at the level of transcription. • Gene expression begins at the promoter where transcription is initiated. • In selective gene transcription a “decision” is made about which genes to activate. • Two types of regulatory proteins—also called transcription factors—control whether a gene is active.

7. Concept 11.1 Several Strategies Are Used to Regulate Gene Expression • These proteins bind to specific DNA sequences near the promoter: • Negative regulation—a repressor protein prevents transcription • Positive regulation—an activatorprotein binds to stimulate transcription

8. Figure 11.2 Positive and Negative Regulation (Part 1)

9. Figure 11.2 Positive and Negative Regulation (Part 2)

10. Concept 11.1 Several Strategies Are Used to Regulate Gene Expression • Acellular viruses use gene regulation to take over host cells. • A phage injects a host cell with nucleic acid that takes over synthesis. • New viral particles (virions) appear rapidly and are soon released from the lysed cell. • This lytic cycle is a typical viral reproductive cycle—in a lysogenic phase, the viral genome is incorporated into the host genome and is replicated too.

11. Concept 11.1 Several Strategies Are Used to Regulate Gene Expression • A bacteriophage may contain DNA or RNA and may not have a lysogenic phase. • The lytic cycle has two stages: • Earlystage—promoter in the viral genome binds host RNA polymerase and adjacent viral genes are transcribed • Early genes shut down transcription of host genes, and stimulate viral replication and transcription of viral late genes. • Host genes are shut down by a posttranscriptional mechanism. • Viral nucleases digest the host’s chromosome for synthesis in new viral particles.

12. Concept 11.1 Several Strategies Are Used to Regulate Gene Expression • Latestage—viral late genes are transcribed • They encode the viral capsid proteins and enzymes to lyse the host cell and release new virions. • The whole process from binding and infection to release of new particles takes about 30 minutes.

13. Figure 11.3 A Gene Regulation Strategy for Viral Reproduction

14. Concept 11.1 Several Strategies Are Used to Regulate Gene Expression • Human immunodeficiency virus (HIV) is a retrovirus with single-stranded RNA. • HIV is enclosed in a membrane from the previous host cell—it fuses with the new host cell’s membrane. • After infection, RNA-directed DNA synthesis is catalyzed by reverse transcriptase. • Two strands of DNA are synthesized and reside in the host’s chromosome as a provirus.

15. Figure 11.4 The Reproductive Cycle of HIV

16. Concept 11.1 Several Strategies Are Used to Regulate Gene Expression • Host cells have systems to repress the invading viral genes. • One system uses transcription “terminator” proteins that interfere with RNA polymerase. • HIV counteracts this negative regulation with Tat (Transactivator of transcription), which allows RNA polymerase to transcribe the viral genome.

17. Figure 11.5 Regulation of Transcription by HIV (Part 1)

18. Figure 11.5 Regulation of Transcription by HIV (Part 2)

19. Concept 11.1 Several Strategies Are Used to Regulate Gene Expression Where is gene expression regulated? Working with a partner, draw a diagram summarizing the different points at which gene’s expression can be regulated. Then answer the following questions: 1. What is the difference between a constitutive gene and an inducible gene? Give an example of a protein made by each type. 2. What is a transcription factor and how can it regulate gene expression? Do transcription factors always activate gene expression? 3. How do viruses subvert a cell’s genetic machinery for their own purposes? Present your diagram and answers to the class and discuss why so much effort has gone into understanding the bases of gene regulation in eukaryotes.

20. Concept 11.1 Several Strategies Are Used to Regulate Gene Expression Reverse transcriptase a. is an enzyme that makes a DNA strand complementary to an RNA. b. is an enzyme that makes an RNA strand complementary to a DNA. c. is important in certain retroviruses, such as HIV. d. Both a and c e. Both b and c

21. Concept 11.2 Many Prokaryotic Genes Are Regulated in Operons • Prokaryotes conserve energy by making proteins only when needed. • In a rapidly changing environment, the most efficient gene regulation is at the level of transcription. • E. coli must adapt quickly to food supply changes. Glucose or lactose may be present.

22. Concept 11.2 Many Prokaryotic Genes Are Regulated in Operons • Uptake and metabolism of lactose involve three proteins: • -galactoside permease—a carrier protein that moves sugar into the cell • -galactosidase—an enzyme that hydrolyses lactose • -galactoside transacetylase—transfers acetyl groups to certain -galactosides • If E. coli is grown with glucose but no lactose present, no enzymes for lactose conversion are produced.

23. Concept 11.2 Many Prokaryotic Genes Are Regulated in Operons • If lactose is predominant and glucose is low, E. coli synthesizes all three enzymes. • If lactose is removed, synthesis stops. • A compound that induces protein synthesis is an inducer. • Gene expression and regulating enzyme activity are two ways to regulate a metabolic pathway.

24. Figure 11.6 Two Ways to Regulate a Metabolic Pathway

25. Concept 11.2 Many Prokaryotic Genes Are Regulated in Operons • Structural genes specify primary protein structure—the amino acid sequence. • The three structural genes for lactose enzymes are adjacent on the chromosome, share a promoter, and are transcribed together. • Their synthesis is all-or-none.

26. Concept 11.2 Many Prokaryotic Genes Are Regulated in Operons • A gene cluster with a single promoter is an operon—the one that encodes for the lactose enzymes is the lac operon. • An operator is a short stretch of DNA near the promoter that controls transcription of the structural genes. • Inducible operon—turned off unless needed • Repressible operon—turned on unless not needed

27. Figure 11.7 The lac Operon of E. coli

28. Concept 11.2 Many Prokaryotic Genes Are Regulated in Operons • The lac operon is only transcribed when a -galactoside predominates in the cell: • A repressor protein is normally bound to the operator, which blocks transcription. • In the presence of a -galactoside, the repressor detaches and allows RNA polymerase to initiate transcription. • The key to this regulatory system is the repressor protein.

29. Figure 11.8 The lac Operon: An Inducible System (Part 1)

30. Figure 11.8 The lac Operon: An Inducible System (Part 2)

31. Concept 11.2 Many Prokaryotic Genes Are Regulated in Operons • A repressible operon is switched off when its repressor is bound to its operator. • However, the repressor only binds in the presence of a co-repressor. • The co-repressor causes the repressor to change shape in order to bind to the promoter and inhibit transcription. • Tryptophan functions as its own co-repressor, binding to the repressor of the trp operon.

32. Figure 11.9 The trp Operon: A Repressible System (Part 1)

33. Figure 11.9 The trp Operon: A Repressible System (Part 2)

34. Concept 11.2 Many Prokaryotic Genes Are Regulated in Operons • Difference in two types of operons: • In inducible systems—a metabolic substrate (inducer) interacts with a regulatory protein (repressor); the repressor cannot bind and allows transcription. • In repressible systems—a metabolic product (co-repressor) binds to regulatory protein, which then binds to the operator and blockstranscription.

35. Concept 11.2 Many Prokaryotic Genes Are Regulated in Operons • Generally, inducible systems control catabolic pathways—turned on when substrate is available • Repressible systems control anabolic pathways—turned on until product concentration becomes excessive

36. Concept 11.2 Many Prokaryotic Genes Are Regulated in Operons • Sigma factors—other proteins that bind to RNA polymerase and direct it to specific promoters • Global gene regulation: Genes that encode proteins with related functions may have a different location but have the same promoter sequence—they are turned on at the same time. • Sporulation occurs when nutrients are depleted—genes are expressed sequentially, directed by a sigma factor.

37. Table 11.1 Transcription in Bacteria and Eukaryotes

38. Concept 11.2 Many Prokaryotic Genes Are Regulated in Operons The lac operon of E. coli The lac operon provides a clear model for regulation of gene expression. To understand it, assemble a group of ten classmates. Seven people should line up as the functionally relevant genes. Another individual will act as the repressor protein; another individual will represent the inducer, allolactose; and the last individual will be the RNA polymerase. (Use Figures 11.7 and 11.8 in the textbook as your guide.) Start by having gene Pi promote synthesis of the repressor protein by activating gene i (a handshake will do). Once the repressor has been synthesized, have that person hold one hand of the operator gene, o. Next, have the inducer come in, take the repressor’s other hand, and separate the repressor from o. Now the RNA polymerase can move along the genes for the three enzymes, transcribing each with a handshake, so that the enzymes needed for lactose metabolism can be made.

39. Concept 11.2 Many Prokaryotic Genes Are Regulated in Operons The lac operon of E. coli is expressed a. continuously. b. only at night when photosynthesis is not possible. c. when a suitable sugar substrate such as lactose is present in the medium. d. to generate -galactosidase and other enzymes needed to break down lactose. e. Both c and d

40. Concept 11.3 Eukaryotic Genes Are Regulated by Transcription Factors and DNA Changes • Transcription factors act at eukaryotic promoters. • Each promoter contains a core promoter sequence where RNA polymerase binds. • TATA box is a common core promoter sequence—rich in A-T base pairs. • Only after general transcription factors bind to the core promoter, can RNA polymerase II bind and initiate transcription.

41. Figure 11.10 The Initiation of Transcription in Eukaryotes (Part 1)

42. Figure 11.10 The Initiation of Transcription in Eukaryotes (Part 2)

43. Concept 11.3 Eukaryotic Genes Are Regulated by Transcription Factors and DNA Changes • Besides the promoter, other sequences bind regulatory proteins that interact with RNA polymerase and regulate transcription. • Some are positive regulators—activators; others are negative—repressors. • DNA sequences that bind activators are enhancers, those that bind repressors are silencers. • The combination of factors present determines the rate of transcription.

44. In-Text Art, Ch. 11, p. 216

45. Concept 11.3 Eukaryotic Genes Are Regulated by Transcription Factors and DNA Changes • Transcription factors recognize particular nucleotide sequences: • NFATs (nuclear factors of activated T cells) are transcription factors that control genes in the immune system. • They bind to a recognition sequence near the genes’ promoters. • The binding produces an induced fit—the protein changes conformation.

46. Figure 11.11 A Transcription Factor Protein Binds to DNA

47. Concept 11.3 Eukaryotic Genes Are Regulated by Transcription Factors and DNA Changes • Gene expression can be coordinated, even if genes are far apart on different chromosomes. • They must have regulatory sequences that bind the same transcription factors. • Plants use this to respond to drought—the scattered stress response genes each have a specific regulatory sequence, the dehydration response element. • During drought, a transcription factor changes shape and binds to this element.

48. Figure 11.12 Coordinating Gene Expression

49. Concept 11.3 Eukaryotic Genes Are Regulated by Transcription Factors and DNA Changes • Gene transcription can also be regulated by reversible alterations to DNA or chromosomal proteins. • Alterations can be passed on to daughter cells. • These epigenetic changes are different from mutations, which are irreversible changes to the DNA sequence.

50. Concept 11.3 Eukaryotic Genes Are Regulated by Transcription Factors and DNA Changes • Some cytosine residues in DNA are modified by adding a methyl group covalently to the 5′ carbon—forms 5′-methylcytosine • DNA methyltransferase catalyzes the reaction—usually in adjacent C and G residues. • Regions rich in C and G are called CpG islands—often in promoters