1. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings PowerPoint ® Lecture Presentations for Biology Eighth Edition Neil Campbell and Jane Reece Lectures by Chris Romero, updated by Erin Barley with contributions from Joan Sharp Click to add text Chapter 18 Regulation of Gene Expression

2. Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings Overview: Conducting Gene Expression 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. Regulation of gene expression trpE gene trpD gene trpC gene trpB gene trpA gene (b) Regulation of enzyme production (a) Regulation of enzyme activity Enzyme 1 Enzyme 2 Enzyme 3 Tryptophan Precursor Feedback inhibition

4. Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings Operons : The Basic Concept A cluster of functionally related genes can be under coordinated control by a single on-off “switch.” The regulatory “switch” is a segment of DNA called an operator usually positioned within the promoter. An operon is the entire stretch of DNA that includes the operator, the promoter, and the genes that they control.

5. Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings The operon can be switched off by a protein repressor - blocks transcription. The repressor prevents gene transcription as it binds to the operator and blocks RNA polymerase. The repressor is the product of a separate regulatory gene.

6. Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings 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. For example, E. coli can synthesize the amino acid tryptophan

7. Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings By default the trp operon is on and the genes for tryptophan synthesis are transcribed. When tryptophan is abundantly present, it binds to the trp repressor protein, which turns the operon off. The trp operon is a repressible operon: turned off, repressed, if tryptophan levels are high.

8. Polypeptide subunits that make up enzymes for tryptophan synthesis (b) Tryptophan present, repressor active, operon off. Tryptophan (corepressor) (a) Tryptophan absent, repressor inactive, operon on. No RNA made Active repressor mRNA Protein DNA mRNA 5 Protein Inactive repressor RNA polymerase Regulatory gene Promoter trp Operon - Repressible trp operon Genes of operon Operator Stop codon Start codon mRNA trpA 5 3 trpR trpE trpD trpC trpB ABC D E

9. Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings Repressible and Inducible Operons: Two Types of Negative Gene Regulation A repressible operon is one that is usually on; binding of a repressor to the operator shuts off transcription. The trp operon is a repressible operon. An inducible operon is one that is usually off; a molecule called an inducer inactivates the repressor and turns on transcription. The lac operon is an inducible operon.

10. lac Operon - inducible (b) Lactose present, repressor inactive, operon on. (a) Lactose absent, repressor active, operon off. mRNA Protein DNA mRNA 5 Protein Active repressor RNA polymerase Regulatory gene Promoter Operator mRNA 5 3 Inactive repressor Allolactose inducer 5 3 No RNA made RNA polymerase Permease Transacetylase lac operon  -Galactosidase lacY lacZ lacAlac I lacZ

11. Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings Inducible enzymes usually function in catabolic pathways; their synthesis is induced by a chemical signal. Repressible enzymes usually function in anabolic pathways; their synthesis is repressed by high levels of the end product. Regulation of the trp and lac operons involves negative control of genes because operons are switched off by the active form of the repressor. Negative Gene Regulation

12. Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings Positive Gene Regulation Some operons are also subject to positive control through a stimulatory protein, such as catabolite activator protein (CAP), an activator of transcription. When glucose (a preferred food source of E. coli) is scarce, CAP is activated by binding with cyclic AMP. Activated CAP attaches to the promoter of the lac operon and increases the affinity of RNA polymerase -- accelerating transcription. When glucose levels increase, CAP detaches from the lac operon, and transcription returns to a normal rate.

13. Positive Gene Regulation (b) Lactose present, glucose present (cAMP level low): little lac mRNA synthesized cAMP DNA Inactive lac repressor Allolactose Inactive CAP lac I CAP-binding site Promoter Active CAP Operator lacZ RNA polymerase binds and transcribes Inactive lac repressor lacZ Operator Promoter DNA CAP-binding site lac I RNA polymerase less likely to bind Inactive CAP (a) Lactose present, glucose scarce (cAMP level high): abundant lac mRNA synthesized

14. Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings Eukaryotic Differential Gene Expression Almost all the cells in an organism are genetically identical. Differences between cell types result from differential gene expression, the expression of different genes by cells with the same genome. Errors in gene expression can lead to diseases including cancer. Gene expression is regulated at many stages.

15. Eukaryotic Differential Gene Expression DNA Signal Gene NUCLEUS Chromatin modification Chromatin Gene available for transcription Exon Intron Tail RNA Cap RNA processing Primary transcript mRNA in nucleus Transport to cytoplasm mRNA in cytoplasm Translatio n CYTOPLASM Degradation of mRNA Protein processing Polypeptide Active protein Cellular function Transport to cellular destination Degradation of protein Transcription

16. Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings Regulation of Chromatin Structure: Histone Modifications Affect Transcription Chemical modifications to histones and DNA of chromatin influence both chromatin structure and gene expression. In histone acetylation, acetyl groups are attached to positively charged lysines in histone tails. This loosens chromatin structure, thereby promoting the initiation of transcription. The addition of methyl groups is called DNA methylation. Methlylation tends to condense chromatin thereby restricting transcription. The addition of phosphate groups (phosphorylation) next to a methylated amino acid can loosen chromatin.

17. Histone Modifications Acetylation Promotes Transcription Histone tails DNA double helix (a) Histone tails protrude outward from a nucleosome. Acetylated histones Amino acids available for chemical modification (b) Acetylation of histone tails promotes loose chromatin structure that permits transcription. Unacetylated histones

18. Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings DNA Methylation - Reduces Transcription DNA methylation, the addition of methyl groups to certain bases in DNA, is associated with reduced transcription in some species. DNA methylation can cause long-term inactivation of genes in cellular differentiation. In genomic imprinting, methylation regulates expression of either the maternal or paternal alleles of certain genes at the start of development.

19. Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings Epigenetic Inheritance Although the chromatin modifications just discussed do not alter DNA sequence, they may be passed to future generations of cells. The inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence is called epigenetic inheritance.

20. Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings Organization of a Typical Eukaryotic Gene Chromatin-modifying enzymes provide initial control of gene expression by making a region of DNA either more or less able to bind the transcription machinery. Associated with most eukaryotic genes are control elements, segments of noncoding DNA that help regulate transcription by binding certain proteins. Control elements and the proteins they bind are critical to the precise regulation of gene expression in different cell types.

21. Control Elements = Transcription Factors Enhancer distal control elements Proximal control elements Poly-A signal sequence Termination region Downstream Promoter Upstream DNA Exon Intron Exon Intron Cleaved 3 end of primary transcript Primary RNA transcript Poly-A signal Transcription 5 RNA processing Intron RNA Coding segment mRNA 5 Cap 5 UTR Start codon Stop codon 3 UTR Poly-A tail 3

22. Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings Proximal control elements are located close to the promoter. Distal control elements, groups of which are called enhancers, may be far away from a gene or even located in an intron. An activator is a protein that binds to an enhancer and stimulates transcription of a gene. Bound activators cause mediator proteins to interact with proteins at the promoter. Enhancers and Specific Transcription Factors

23. Enhancer TATA box Promoter Activators DNA Gene Distal control element Group of mediator proteins DNA-bending protein General transcription factors RNA polymerase II RNA polymerase II Transcription initiation complex RNA synthesis

24. Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings Coordinately Controlled Genes in Eukaryotes Unlike the genes of a prokaryotic operon, each of the coordinately controlled eukaryotic genes has a promoter and control elements. These genes can be scattered over different chromosomes, but each has the same combination of control elements. Copies of the activators recognize specific control elements and promote simultaneous transcription of the genes.

25. Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings Mechanisms of Post-Transcriptional Regulation Transcription alone does not account for gene expression. Regulatory mechanisms can operate at various stages after transcription. These mechanisms allow a cell to rapidly response to environmental changes by using:  Alternative RNA Processing  mRNA Degradation  Initiation of Translation  Protein Processing and Degradation

26. Alternative RNA Processing or RNA splicing mRNA Primary RNA transcript Troponin T gene Exons DNA

27. Proteasome - Protein Degradation Proteasome and ubiquitin to be recycled Proteasome Protein fragments (peptides) Protein entering a proteasome Ubiquitinated protein Protein to be degraded Ubiquitin

28. Modifiers of Translation miRNA- protein complex (a) Primary miRNA transcript Translation blocked Hydrogen bond (b) Generation and function of miRNAs Hairpin miRNA Dicer 3 mRNA degraded 5

29. Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings The inhibition of gene expression by RNA molecules is called RNA interference (RNAi). RNAi is caused by small interfering RNAs (siRNAs). siRNAs play a role in heterochromatin formation and can block large regions of the chromosome. Small RNAs may also block transcription of specific genes.

30. Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings A program of differential gene expression leads to the different cell types in a multicellular organism During embryonic development, a fertilized egg gives rise to many different cell types. Cell types are organized successively into tissues, organs, organ systems, and the whole organism. Gene expression orchestrates the developmental programs of animals. Embryonic Development: The transformation from zygote to adult results from cell division, cell differentiation, and morphogenesis.

31. Fig. 18-14 (a) Fertilized eggs of a frog (b) Newly hatched tadpole

32. Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings Cytoplasmic Determinants and Inductive Signals Affect Gene Expression An egg’s cytoplasm contains RNA, proteins, and other substances that are distributed unevenly in the unfertilized egg. Cytoplasmic determinants are maternal substances in the egg that influence early development. As the zygote divides by mitosis, cells contain different cytoplasmic determinants, which lead to different gene expression.

33. Differential Gene Expression (b) Induction Signals by nearby cells (a) Cytoplasmic determinants in the egg Two different cytoplasmic determinants Unfertilized egg cell Sperm Fertilization Zygote Mitotic cell division Two-celled embryo Signal molecule (inducer) Signal transduction pathway Early embryo (32 cells) Nucleus NUCLEUS Signal receptor

34. MyoD Protein - Muscle Cell Differentiation Embryonic precursor cell Nucleus OFF DNA Master regulatory gene myoD Other muscle-specific genes OFF mRNA MyoD protein (transcription factor) Myoblast (determined) mRNA Myosin, other muscle proteins, and cell cycle– blocking proteins Part of a muscle fiber (fully differentiated cell) MyoD Another transcription factor

35. Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings Pattern Formation: Setting Up the Body Plan Pattern formation is the development of a spatial organization of tissues and organs. In animals, pattern formation begins with the establishment of the major axes. Positional information, the molecular cues that control pattern formation, tells a cell its location relative to the body axes and to neighboring cells.

36. Pattern Formation in Drosophila fruit fly Thorax HeadAbdomen 0.5 mm Dorsal Ventral Right Posterior Left Anterior BODY AXES Follicle cell (a) Adult Nucleus Egg cell Nurse cell Egg cell developing within ovarian follicle Unfertilized egg Fertilized egg Depleted nurse cells Egg shell Fertilization Laying of egg Body segments Embryonic development Hatching 0.1 mm Segmented embryo Larval stage (b) Development from egg to larva 1 2 3 4 5

37. Tail Head Wild-type larva T1T1 T2T2 T3T3 A1 A2 A3 A4 A5 A6 A7 A8 A7 A6 A7 A8 Mutant larva (bicoid) EXPERIMENT RESULTS CONCLUSION Fertilization, translation of bicoid mRNA Bicoid protein in early embryo Anterior end Bicoid mRNA in mature unfertilized egg 100 µm bicoid mRNA Nurse cells Egg Developing egg Bicoid mRNA in mature unfertilized eggBicoid protein in early embryo Biocid Protein Affects Polarity Development

38. Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings The bicoid research is important for three reasons: –It identified a specific protein required for some early steps in pattern formation. –It increased understanding of the mother’s role in embryo development. –It demonstrated a key developmental principle that a gradient of molecules can determine polarity and position in the embryo.

39. Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings Types of Genes Associated with Cancer The gene regulation systems that go wrong during cancer are the very same systems involved in embryonic development. Cancer can be caused by mutations to genes that regulate cell growth and division. Tumor viruses can cause cancer in animals including humans.

40. Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings Oncogenes and Proto-Oncogenes Oncogenes are cancer-causing genes. Proto-oncogenes are the corresponding normal cellular genes that are responsible for normal cell growth and division. Conversion of a proto-oncogene to an oncogene can lead to abnormal stimulation of the cell cycle.

41. Proto-ongogene to Ongogene Normal growth- stimulating protein in excess New promoter DNA Proto-oncogene Gene amplification: Translocation or transposition: Normal growth-stimulating protein in excess Normal growth- stimulating protein in excess Hyperactive or degradation- resistant protein Point mutation: Oncogene within a control element within the gene

42. Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings Tumor-Suppressor Genes Tumor-suppressor genes help prevent uncontrolled cell growth. Mutations that decrease protein products of tumor-suppressor genes may contribute to cancer onset. Tumor-suppressor proteins: Repair damaged DNA & control cell adhesion. Inhibit the cell cycle in the cell-signaling pathway.

43. Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings The Multistep Model of Cancer Development Multiple mutations are generally needed for full-fledged cancer; thus the incidence increases with age. At the DNA level, a cancerous cell is usually characterized by at least one active oncogene and the mutation of several tumor-suppressor genes.

44. Multi-Step Model of Cancer Development EFFECTS OF MUTATIONS Malignant tumor (carcinoma) Colon Colon wall Loss of tumor- suppressor gene APC (or other) Activation of ras oncogene Loss of tumor-suppressor gene DCC Loss of tumor-suppressor gene p53 Additional mutations Larger benign growth (adenoma) Small benign growth (polyp) Normal colon epithelial cells 5 4 2 3 1

45. Review Promoter Genes Genes not expressed Active repressor: no inducer present Inactive repressor: inducer bound Genes expressed Operator Fig. 18-UN2

46. Regulation of Gene Expression Genes in highly compacted chromatin are generally not transcribed. Chromatin modification DNA methylation generally reduces transcription. Histone acetylation seems to loosen chromatin structure, enhancing transcription. Chromatin modification Transcription RNA processing Translation mRNA degradation Protein processing and degradation mRNA degradation Each mRNA has a characteristic life span, determined in part by sequences in the 5 and 3 UTRs. Protein processing and degradation by proteasomes are subject to regulation. Protein processing and degradation Initiation of translation can be controlled via regulation of initiation factors. Translation ormRNA Primary RNA transcript Alternative RNA splicing: RNA processing Coordinate regulation: Enhancer for liver-specific genes Enhancer for lens-specific genes Bending of the DNA enables activators to contact proteins at the promoter, initiating transcription. Transcription Regulation of transcription initiation: DNA control elements bind specific transcription factors.

47. Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings You should now be able to: 1.Explain the concept of an operon and the function of the operator, repressor, and corepressor. 2.Explain the adaptive advantage of grouping bacterial genes into an operon. 3.Explain how repressible and inducible operons differ and how those differences reflect differences in the pathways they control.

48. Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings 4.Explain how DNA methylation and histone acetylation affect chromatin structure and the regulation of transcription. 5.Define control elements and explain how they influence transcription. 6.Explain the role of promoters, enhancers, activators, and repressors in transcription control.

49. Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings 7. Explain how maternal effect genes affect polarity and development in Drosophila embryos. 8. Explain how mutations in tumor-suppressor genes can contribute to cancer.