Molecular Chapter 26

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Molecular Chapter 26
2012-02-07 11:18:32

Chapter 26
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  1. Define regulator gene.
    It codes for a protein that controls transcription by binding to a particular site on DNA
  2. Define negative control
    A trans-acting repressor protein binds to the cis-acting operator to turn off transcription.
  3. Define positive regulation
    A trans-acting protein binds to the cis-acting site in order for RNA pol to initiate transcription at the promoter
  4. Define operon
    A unit of bacterial gene expression and regulation, including structural genes and control elements in DAN recognized by regulator gene products
  5. Define trans-acting factor
    A gene product that can diffuse to act on a target sequence
  6. Define cis-acting sequence
    A DNA sequence that function only as a sequence and affects only the DNA to which it is physically linked
  7. Define structural gene
    A gene that codes for a protein product
  8. Define inducible
    A genes ability to express due to the appearance of a protein product
  9. Define repressible
    A genes ability to be controlled by the amount of product made by the protein
  10. Define corepressor
    A molecule that prevents the production of enzymes that are able to synthesize them
  11. What are the combinations of gene regulation
    • - inducible
    • - repressible
    • + inducible
    • + repressible
  12. What is the lac operon
    • 1. lacI - encodes the lac repressor (diffusable) and has its own promoter and terminator
    • 2. Operator - lies between the promoter and lacZYA
    • 3. lacZYA - encodes polycistronic mRNA for products that digest B-galactosides (e.g. lactose)
  13. How does the lac repressor work
    • 1. The operator overlaps the promoter
    • 2. The repressor binds at the operator
    • 3. Repressor binding prevents RNA pol from initiating ranscription at the promoter
  14. What are the essential features of B-galactoside induction
    • 1. Addition of the inducer results in rapid induction of lac mRNA
    • 2. This is followed by enzyme synthesis
    • 3. Removal of the inducer is followed by rapid cessation of synthesis
  15. Why is the lac gene expressed in the absence of an inducer
    lac repressor is bound to the operator preventing RNA pol from initiating transcription
  16. How do B-galactosides induce transcription of the lac operon
    • 1. lac repressor is allosteric
    • 2. The inducer binds the lac repressor and changes the DNA binding site on the repressor such that it has a lower affinity for the DNA lac operator
    • 3. RNA pol binds the promoter and transcribes the operon
  17. Why are operator mutations constitutive
    • 1. The operator can't bind the repressor
    • 2. RNA pol has unrestricted access to the promoter
    • 3. Oc are cis-acting because they affect only the contiguous set of structural genes
  18. Why is lacI- a constitutive mutation
    • 1. lacI- mutations render the lac repressor inactive
    • 2. Inactive lac repressor can't bind the operator
    • 3. The operon is constitutively expressed
  19. Explain the dominant negative behavior of the lacI-d mutation
    • 1. A lacI-d mutant gene makes a monmer that has a damaged DNA binding site
    • 2. When present in the same cell with the WT gene, multimeric repressors are assembled at random from both types of monomeric subunits
    • 3. It only requires one of the subunits of the multimer to be of the lacI-d type to prevent repressor from binding the operator DNA
  20. What is the general structure of lac repressor monomer
    • 1. Helix-Turn-Helix - DNA binding domain
    • 2. Core - contains inducer binding site and multimerization binding sites
  21. What is the general structure of the lac repressor tetramer
    • 1. Consists of 2 dimers
    • 2. Dimers are held together by interactions between the core subdomains 1 and 2
  22. What are the 2 types of mutations in lac repressor
    • 1. lacI- - recessive and can't repress
    • 2. lacIs - dominant; either can't bind to DNA or can't be bound by inducer
    • 3. lacI-d - dominant negative; cna't bind DNA
  23. How does the repressor recognize the operator
    The operator is palindromic
  24. How is lac repressor regulated by an allosteric change in conformation
    • 1. The DNA binding domain of lac repressor has a conformation that makes it easy to bind to successive major groves of the operator DNA
    • 2. When the inducer binds lac repressor, it changes the orientation of the DNA binding domain and makes it harder for lac repressor to bind operator DNA
  25. What happens if both dimers in a repressor tetramer binds to DNA
    • 1. The DNA between the two binding sites forms a loop
    • 2. This is important to full repression
  26. How does comparing equilibruim constants for repressor/operator binding with inducer present and with inducer absent.
    • 1. The equilibrium constat for repressor/operator binding with inducer absent is 107
    • 2. The equilibrium constat for repressor/operator binding with inducer present is 104
    • 3. Repressor will bind 1000 times more easily when inducer is absent
  27. How does the operator compete with low affinity sites to bind repressor
    • 1. Active repressor stays bound to operator
    • 2. Repressor inactivated by inducer binds random low affinity DNA sites
    • 3. When inducer leaves, repressor becomes active and is attracted by operator
  28. How does cAMP work as an inducer in lac operon regulation
    • 1. cAMP activates inactive CRP
    • 2. Active CRP binds the lac promoter and assists RNA pol in initiating transcription
  29. How does glucose inhibit transcrition of operons that require CRP
    • 1. cAMP is synthesized by adenylate cyclase
    • 2. Glucose represses adenylate cyclase activity
    • 3. No cAMP = inactive CRP = no transcription
  30. What is the organization of the trp operon
  31. How is the trp operon negatively controlled
    • 1. It is controlled by the level of its product, tryptophan (autoregulation)
    • 2. Tryptophan activates an inactive repressor encoded by trpR
    • 3. The repressor will act on all 3 operator loci
  32. What is attenuation
    The regulation of bacerial operons by controlling termination via changes in RNA secondary structure due to ribosome movement
  33. How is the trp operon controlled by attenuation
    • 1. An attenuator controls the progression of RNA pol into the trp genes
    • 2. RNA pol initiates at the promoter and then proceeds before pausing at the attenuator
    • 3. In the absence of Trp, RNA pol continues transcribing the trp structural genes
    • 4. In the presence of Trp, RNA pol most likely terminates transcription
  34. What is a leader peptide
    • 1. The expression of a short sequence that is located between the operator and the attenuator on the trp operon
    • 2. The structure of mRNA at the attenuator depends on whether this reading frame is translated
    • 3. In the presence of Trp-tRNA, the leader is translated to the leader peptide, and the attenuator is able to from the hairpin that causes termination
  35. What conformation must the mRNA trp leader region exist in order to terminate transcription
    Regions 3 and 4 must be paired
  36. How does the position of the ribosome on the mRNA determine the mRNA structure during trp transcription
    • 1. In the absence of Trp, the ribosome stalls at the leader sequence
    • 2. Regions 2:3 pair
    • 3. RNA pol continues to the trp genes
    • 4. In the presence of Trp, the ribosome translates the leader sequence and disrupts the 2:3 pairing
    • 5. Regions 3:4 pair forming a hairpin
    • 6. Termination
  37. How can translation be regulated by a regulator protein
    • 1. A regulator protein binds to the ribosome binding site
    • 2. Ribosome can't bind to mRNA
    • 3. No translation
  38. How is r-Protein synthesis controlled by autoregulation
    The product of a first initiation site changes the mRNA secondary structure such that the second initiation site is blocked and translation stops
  39. How is translation of the r-protein operon autogenously controlled
    • 1. When rRNA is available, the r-proteins associate with it and translation of mRN continues
    • 2. When no rRNA is available, r-proteins accumulate and begins to bind to mRNA and prevents translation