1. How is gene expression regulated?
    Tightly. May be modified to counteract environmental changes or gene expression can change to change cell function
  2. What are constitutive proteins
    Proteins that are expressed all the time
  3. What are inducible genes
    Expressed only when they are needed to be ‘induced’
  4. At what level can genes be regulated?
  5. Gene expression begins when?
    At the promoter, where the transcription is initiated
  6. What happens in selective gene transcription
    A ‘decision’ is made about which genes to activate. And transcription factors control whether a gene is active
  7. What are transcription factors
    Regulatory proteins that bind to specific dna sequences near promoter
  8. What are two types of regulation
    Negative and positive
  9. What is negative regulation
    a repressor protein preventing transcription
  10. what is positive regulation
    an activator protein binding to stimulate transcription
  11. how do acellular viruses use gene regulation to take over host?
    They inject host cell with nucleic acid that takes over synthesis. New viral particles (virions) appear rapidly and are soon released from the now lysed cell
  12. What is the lytic cycle
    A typical viral reproductive cycle in a lysogenic phase. The viral genome is incorporated into the host genome and is replicated too
  13. A bacteriophage may contain what two things
    DNA and RNA and may not have a lysogenic phase.
  14. What are the two stages of the lytic cycle?
    Early stage and Late stage
  15. What happens during the early stage of the lytic cycle
    Promoter in the viral genome binds to host RNA polymerase and the nearby viral genes are ranscribed. Early genes shut down transcription and begin replicating themselves. Posttranscriptional mechanism shuts down host gene. The viral nucleus digests the host’s chromosome.
  16. What happens during the late stage of the lytic cycle
    It takes about 30 minutes, viral genes are now transcribe and they encode the viral capsid proteins and enzymes to lyse the host cell and release new virions
  17. What is a retrovirus
    HIV, a virus that encloses itself in the host cell. Fuses with its membrane and through reverse transcriptase, DNA synthesis directs RNA. Two strands of DNA are synthesized and they chill in the host’s chromosome as provirus.
  18. Can some host cells reject invaders?
    Some can. One such system is transcription terminator. Proteins that interfere with RNA polymerase but HIV counteracts this negative regulation with TAT.
  19. What is TAT
    Transactivator of transcription. It allows RNA polymerase to transcribe the viral genome
  20. How do prokaryotes conserve energy?
    They only make proteins when needed
  21. At what level is the most efficient gene regulation
  22. What does E. coli need to do
    Adapt quickly to food supply changes. Glucose or lactose may be present
  23. If lactose is predominant, what happens?
    Then glucose is low and E. coli synthesizes all 3 enzymes
  24. If lactose is removed, what happens?
    The synthesis stops
  25. What is an inducer
    A compound that induces protein synthesis
  26. What are two ways to regulate a metabolic pathway?
    Gene expression and regulating enzyme activity
  27. What are structural genes
    They specify primary protein structure – the amino acid sequence.
  28. Tell me about the 3 structural genes for lactose enzymes.
    They are adjacent on the chromosome, they share a promoter, and they are transcribed together. Their synthesis is ALL OR NONE
  29. What is an operon
    It is a gene cluster with a single operon; a short stretch of DNA near the promoter that controls transcription of structural gene. Lac operon encodes for lactose enzymes
  30. How does an inducible operon work?
    It is off unless needed (unless it needs to be induced)
  31. How does a repressible operon work?
    It is on until it needs to be repressed (off)
  32. When is the lac operon transcribed
    When B- galactoside predominates in the cell
  33. What happens to the repressor in the presense of B-galactoside?
    It detatches and allows RNA polymerase to initiate transcription.
  34. What is the key to the lac operon regulatory system?
    The repressor protein.
  35. What happens when the repressor is bound to its operator
    The repressible operon is OFF. But it only binds in the presence of a co-repressor
  36. What is a co-repressor?
    It causes a repressor to change shape in order to bind to the protmoter and inhibit transcription.
  37. What is significant about tryptophan in regards to co-repressors?
    It acts as its own repressor in the trp Operon.
  38. What are two different types of operons
    Inducible and repressible
  39. How doe inducible systems work?
    A metabolic substrate (inducer) interacts with a regulatory protein (repressor) the repressor then cannot bind and allows for transcription
  40. How does a repressible system work
    A metabolic product (co-epressor) binds to regulatory protein which then binds to operator and blocks transcription.
  41. How do inducible systems control catabolic pathway
    They are turned on when the substrate is available
  42. How do repressive systems control anabolic pathways
    They are turned on UNTIL the product concentration becomes excessive
  43. What are sigma factors
    Other proteins that bind to RNA polymerase and direct it to specific promoters
  44. What are two kinds of sigma factors
    Global gene regulation and sporulation
  45. What is global gene regulation
    Genes that encode protein relate functions may have different locations but they hav the same promoter sequence- they are on at the same time
  46. What is sporulation
    This occurs when nutrients are depleted and genes are expressed sequentially, directed by a sigma factor.
  47. What are eukaryotic promoters
    Transcription factors. Each promoter contains a core promoter sequence where RNA polymerase binds.
  48. Name a common core promoter sequence.
    TATA box. Rich in a-t base pairs. Only after general transcription factors bind to the core promoter, RNA polymerase II bind and initiate transcription
  49. What are enhancers?
    DNA sequences that bind activators.
  50. What are silencers. Those DNA sequences that bind repressors
  51. What determines the rate of transcription
    The combination of factors present
  52. What are NFAT’s
    Nucear factors of activated t-cells. They are transcription factors and they control genes in the immune system.
  53. How can gene expression be coordinated?
    Even if the genes are far apart on different chromosomes. They have regulatory sequences that bind the SAME transcription factors.
  54. How do plants use coordinated gene expression?
    They use the dehydration response element. A transcription factor changes shape and binds to this element during a drought
  55. How can gene transcription be regulated by reversal alterations
    Reversal alterations to DNA or chromosomal proteins can be passed on to daughter cells. These epigenetic changes are different from mutations because they are reversible
  56. How can DNA be modified with methyl group
    In cytosine, methyl group is covalently added to 5’ carbon to form 5’-methylcytosine. DNA methyltransferase catalyzes this reaction.
  57. What kind of DNA change is heritable
    A covatlent one.
  58. Tell me about methylase and demethylase
    When dna replicates, maintenance methylase catalyzes formation of 5’ methylcytosine in new strand and demethylase catalyzes the removal of this extra methyl group
  59. What are the effects of DNA methylation
    Can bind proteins involved in repression of transcription and genes tent to be silenced (inactive); patterns of DNA methylation can include large regions or whole chromosomes.
  60. Two kinds of chromatin that are visible during interphase
    Euchromatin and heterochromatin
  61. What is euchromatin
    It is diffuse and light staining; contains DNA and mRNA transcription
  62. What is Heterochromatin
    It is condensed, dark staining; and containes genes not transcribed
  63. What is a type of hetero chromatine
    Inactive X chromosome in mammals. The barr body is identifiable during interphase and can be seen in cells of human females.
  64. What is chromatin remodeling
    A mechaninism for epigenetic regulation; it is the lalteration of the chromatin structure.
  65. What happens in chromatin remodeling
    Histones acetyltransferases change charge by adding acetyl groups and histone loses affinity for DNA. It can activate transcription
  66. What is histone deactylase
    Another kind of chromatin remodeling protein that can remove acetyl groups from histones thurs, repressing transcription
  67. What plays an important role in epigenetic modifications?
    Environment; twins can show different methylation after living in different environments.
  68. What can alternative splicing do
    It can make different mRNAs from the same gene.
  69. Can gene expression be regulated?
    Yep! After the initial gene transcript is made.
  70. What are microRNAs
    Small molecules of noncoding RNA. They are important regulators of gene expression
  71. What role do lin-14 mutations have iin C. elegans
    They cause larvae to skip the first step; normally, they would be involved in it
  72. What does lin 4 mutation do
    It causes the cell to repeat stage one events.
  73. How come mRNA transcriptions can be regulated
    Protein and mRNA concenrations are not consistently related- they are governed by factors after mRNA is made. They can be blocked or altered as to how long they persist in cell
  74. What are 3 ways to regulate mRNA translation
    Inhibition of translation with miRNAs, modification of 5’cap end of mRNA or repressor proteins can block translation (translational repressors).
  75. How does Creb regulate the expression of many genes?
    Creb fam of transcription factors can activate or repress genes by binding to cAMP response element (CRE). It has been linked to addiction and memory tasks as well as metabolism.
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ch 11 principles of life