Chapter 16 Outline

1. Chapter 16 Outline • 16.4 Some Operons Regulate Transcription Through Attenuation, the Premature Termination of Transcription, 442 • 16.5 Antisense RNA Molecules Can Affect the Translation of mRNA, 445 • 16.6 Riboswitches Function as Regulatory Elements in mRNAs, 446

2. 16.2 Many Aspects of Gene Regulation Are Similar in Bacterial and Eukaryotes

3. Genes and Regulatory Elements • Structural genes: encoding proteins • Regulatory genes: encoding products that interact with other sequences and affect the transcription and translation of these sequences • Regulatory elements: DNA sequences that are not transcribed but play a role in regulating other nucleotide sequences

4. Genes and Regulatory Elements • Constitutive expression: continuously expressed under normal cellular conditions • Positive control: stimulate gene expression • Negative control: inhibit gene expression

5. Level of Gene Regulation • Many levels at which gene expression may be regulated • DNA access • Transcription • RNA modification and stability • Translation • Post-translational modification

7. DNA-Binding Proteins • Domains: 60 ~ 90 amino acids, responsible for binding to DNA, forming hydrogen bonds with DNA • Distinctive types of DNA-binding proteins based on the motif • Motif: within the binding domain, a simple structure that fits into the major groove of the DNA

13. Concept Check 1 How do amino acids in DNA-binding proteins interact with DNA? • By forming covalent bonds with DNA base • By forming hydrogen bonds with DNA base • By forming covalent bonds with sugars

14. Concept Check 1 How do amino acids in DNA-binding proteins interact with DNA? • By forming covalent bonds with DNA base • By forming hydrogen bonds with DNA base • By forming covalent bonds with sugars

15. 16.3 Operons Control Transcription in Bacterial Cells • Operon: promoter + additional sequences that control transcription (operator) + structure genes • Regulator gene: DNA sequence encoding products that affect the operon function, but are not part of the operon

16. Negative and Positive Control; Inducible and Repressible Operons • Inducible operons: Transcription is usually off and needs to be turned on. • Repressible operons: Transcription is normally on and needs to be turned off.

17. Negative and Positive Control; Inducible and Repressible Operons • Negative inducible operons: The control at the operator site is negative. Molecule binding is to the operator, inhibiting transcription. Such operons are usually off and need to be turned on, so the transcription is inducible. • Inducer: small molecule that turns on the transcription

20. Negative and Positive Control; Inducible and Repressible Operons • Negative repressible operons: The control at the operator site is negative. But such transcription is usually on and needs to be turned off, so the transcription is repressible. • Corepressor: a small molecule that binds to the repressor and makes it capable of binding to the operator to turn off transcription

22. Negative and Positive Control; Inducible and Repressible Operons • Positive inducible operon • Positive repressible operon

25. The lac Operon of E. coli • A negative inducible operon • Inducer: allolactose • lacI: repressor encoding gene • lacP: operon promoter • lacO: operon operator

26. The lac Operon of E. coli • Structural genes • lacZ: encoding β-galactosidases • lacY: encoding permease • lacA: encoding transacetylase • The repression of the lac operon never completely shuts down transcription.

30. Concept Check 4 In the presence of allolactose, the lac repressor . • binds to the operator • binds to the promoter • cannot bind to the operator • binds to the regulator gene

31. Concept Check 4 In the presence of allolactose, the lac repressor . • binds to the operator • binds to the promoter • cannot bind to the operator • binds to the regulator gene

32. Positive control and catabolite repression • Catabolite repression: using glucose when available, and repressing the metabolite of other sugars • This is a positive control mechanism: The positive effect is activated by catabolite activator protein (CAP). cAMP is binded to CAP, together CAP–cAMP complex binds to a site slightly upstream from the lac gene promoter.

33. Positive control and catabolite repression • cAMP – adenosine-3′,5′-cyclic monophosphate • The concentration of cAMP is inversely proportional to the level of available glucose.

35. Concept Check 4 What is the effect of high levels of glucose on the lac operon? • Transcription is stimulated. • Little transcription takes place. • Transcription is not affected. • Transcription may be stimulated or inhibited, depending on the levels of lactose.

36. Concept Check 4 What is the effect of high levels of glucose on the lac operon? • Transcription is stimulated. • Little transcription takes place. • Transcription is not affected. • Transcription may be stimulated or inhibited, depending on the levels of lactose.

37. The trp Operon of E. coli • A negative repressible operon • Five structural genes • trpE, trpD, trpC, trpB, and trpA – five enzymes together convert chorismate to typtophane.

39. 16.4 Some Operons Regulate Transcription Through Attenuation, the Premature Termination of Transcription • Attenuation: affects the continuation of transcription, not its initiation. This action terminates the transcription before it reaches the structural genes.

40. Attenuation in the trp Operon of E. coli • Four regions of the long 5′ UTR (leader) region of trpE mRNA • When tryptophan is high, region 1 binds to region 2, which leads to the binding of region 3 and region 4, terminating transcription prematurely.

43. Attenuation in the trp Operon of E. coli • Four regions of the long 5′ UTR (leader) region of trpE mRNA • When tryptophan is low, region 2 binds to region 3, which prevents the binding of region 3 and region 4, and transcription continues.

45. Concept Check 6 Attenuation results when which regions of the 5′ UTR region pair? • 1 and 3 • 2 and 3 • 2 and 4 • 3 and 4

46. Concept Check 6 Attenuation results when which regions of the 5′ UTR region pair? • 1 and 3 • 2 and 3 • 2 and 4 • 3 and 4

47. 16.5 Antisense RNA Molecules Can Affect the Translation of mRNA • Antisense RNA: • Complementary to targeted partial sequence of mRNA

48. 16.6 Riboswitches Function as Regulatory Elements in mRNAs • Riboswitch: the regulatory sequence of mRNA molecules where molecules can bind and affect gene expression by influencing the formation of secondary structure in the mRNA