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 11.2 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.

11. 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.

12. 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.

13. 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.

14. 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. The operator is a repressor binding site. • Inducible operon—turned off unless needed • Repressible operon—turned on unless not needed

15. Figure 11.7 The lac Operon of E. coli

16. 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.

17. http://www.highschool.bfwpub.com/launchpad/pol2e/2764206 -

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

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

20. The gene for the 3 lactose metabolizing enzymes are called structural genes, whilst the gene for the lac operon repressor protein is called a regulatory gene because it encodes for a protein that regulates the transcription of other genes. http://bcs.whfreeman.com/pol2e/default.asp - 940573__943481__

21. Concept 11.2 Many Prokaryotic Genes Are Regulated in Operons • Like an inducible operon, 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.

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

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

24. Trp operon http://bcs.whfreeman.com/pol2e/default.asp - 940573__943482__

25. 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.(lac Operon) Default setting is Off, unless lactose is present to induce it. • In repressible systems—a metabolic product (co-repressor) binds to regulatory protein, which then binds to the operator and blockstranscription. (trp operon. Default setting is on unless the coreprssor (tryp) deactivates it.

26. 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

27. In the previous slides we saw related genes stacked conveniently alongside each other in an operon. • Global gene regulation • Genes that encode for proteins with related functions may have different locations on the genome, yet they have the same promoter sequence, so they can be transcribed at the same time when the environment demands it.

28. Concept 11.2 Many Prokaryotic Genes Are Regulated in Operons • Sporulation occurs when nutrients in their environment are depleted. Bacteria stop growing and enter into a dormant state where metabolic activity slows and a tough protein shell assembled around them. The process requires certain genes to be expressed sequentially. Each class of genes has a specific promoter, each with a corresponding Sigma factor—other proteins that bind to RNA polymerase and direct it to specific promoters so that gene expression is sequential coordinated.

29. Eukaryotic genes are regulated by transcription factors. • In eukaryotes, some genes are constitutive (expressed most of the time), such as those that code for metabolic enzymes. Others are inducible and expressed only as needed, or, as is the case with keratin and haemoglobin proteins, in certain specialized cells. • Eukaryotic cells employ conceptually similar mechanisms for regulating gene expression. There are some significant differences, largely reflecting their greater complexity.

30. Concept 11.3 Eukaryotic Genes Are Regulated by Transcription Factors and DNA Changes • Transcription factors act at eukaryotic promoters. Eukaryotic cells also have promoters at the 5’ end of the gene on the DNA • 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.

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

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

33. 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.

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

35. 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.

36. Figure 11.11 A Transcription Factor Protein Binds to DNA

37. Concept 11.3 Eukaryotic Genes Are Regulated by Transcription Factors and DNA Changes • Gene expression can be coordinated, even if genes are far apart or 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.

38. Figure 11.12 Coordinating Gene Expression

39. EPIGENETICS Ep.i.ge.net.ics Altering gene function without altering DNA Gene regulation through transcription factors involves sections of DNA at or near the gene's promoter region. Epigenetic regulation can occur as reversible, non-sequence-specific alterations to DNA or chromosomal proteins. It is typically pre transcription. The DNA changes can be passed on to daughter cells during mitosis or meiosis

40. 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 that package DNA in the nucleus. • Alterations can be passed on to daughter cells. • These epigenetic changes are different from mutations, because they are reversible changes which do not alter N.base sequencing in the DNA.

41. METHYLATION Methylated DNA binds specific proteins that are involved in the repression of transcription, so heavily methylated DNA tends to be silenced

42. Concept 11.3 Eukaryotic Genes Are Regulated by Transcription Factors and DNA Changes • Some cytosine N.bases in DNA are modified by adding a methyl group covalently to the 5′ carbon—forms 5′-methylcytosine • DNA methyltransferase catalyzes the reaction—usually in C lying adjacent G. • Some regions are rich in C and G sequences and are called CpG islands—often in promoters. They are particularly succeptible to methylation.

43. Concept 11.3 Eukaryotic Genes Are Regulated by Transcription Factors and DNA Changes • Effects of DNA methylation: • Methylated DNA binds proteins that are involved in repression of transcription—genes tend to be inactive (silenced). • Patterns of DNA methylation may include large regions or whole chromosomes. • In some cases, large sequences and even entire chromosomes are methylated and silenced.

44. Figure 11.13 DNA Methylation: An Epigenetic Change (Part 1)

45. Concept 11.3 Eukaryotic Genes Are Regulated by Transcription Factors and DNA Changes • This covalent change in DNA is heritable: • When DNA replicates, a maintenance methylase catalyzes formation of 5′-methylcytosine in the new strand. • However, methylation pattern may be altered—demethylase can catalyze the removal of the methyl group. • When and why methylization or demethylization occur seems to be linked to chemical exposure (cigarettes) diet (folic acid) and stress.

46. FIGURE THIS ONE OUT???? • The x chromosome contains the same genetic info in males as it does in females. With twice as many x chromosomes, one might expect females to have the potential to produce twice the proteins coded on the x cromosome as males. Yet for 75% of x chromo genes, mRNA production levels are similar in males and females. Why is this the case?

47. The ARSE gene is located on the short arm of the human x chromosome. It codes for an enzyme called arylsulfatase, which is active in the golgi app. Arylsulfatase plays an important role in cartiledge and bone formation

48. Concept 11.3 Eukaryotic Genes Are Regulated by Transcription Factors and DNA Changes • Two kinds of chromatin are visible during interphase: • Euchromatin—diffuse and light-staining; contains DNA for mRNA transcription • Heterochromatin—condensed, dark-staining; contains genes not transcribed. They may me silenced due to methylation.

49. Concept 11.3 Eukaryotic Genes Are Regulated by Transcription Factors and DNA Changes • A type of heterochromatin is the inactive X chromosome in mammals. • Males (XY) and females (XX) contain different numbers of X-linked genes, yet for most genes transcription, rates are similar. • Early in female development, one of the X chromosomes is inactivated—this Barr bodyis identifiable during interphase and can be seen in cells of human females.

50. https://www.youtube.com/watch?v=BD6h-wDj7bw&feature=youtu.be Why women are stripey.