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Gene Regulation _ DNA Replication

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					     Bio 221 Discussion # 5 – Prokaryotic Gene Regulation & DNA Replication



I. Operons -- Review Questions & Animated Views

Repressors & Operators
       1) Which of these (repressor/operator) is a protein?

       2) Which of these (repressor/operator) is the DNA region to which the protein
       binds?

       3) How do the repressor & operator recognize (bind to) each other?

       4) What is the effect of repressor binding on RNA polymerase's ability to bind &
       carry out transcription?

           ** See Animation**

       5) Under what conditions does Trp repressor bind DNA?

       6) Under what conditions does Lac repressor bind DNA?

       7) Do these responses to Trp & Lac make good energetic sense?


cAMP-CAP as an Example of an Activator
     1) What molecule binds to CAP and influences the ability of CAP to bind DNA?

       2) What is the relationship between glucose levels and cAMP concentration?

       3) Given your answers to the prior 2 questions, what is the relationship between
       glucose levels and the ability of CAP to bind DNA?

               ** See Animation and Figure**


II. Operon practice problems

The attached page contains several examples of mutations in the various DNA sequences
involved in lac operon function. In some cases, bacteria can be made to be “partial
diploids”, that is, contain two alleles for a given sequence. Those situations are indicated
by a slash separating the different version of those sequences.

Each group should work on two or three of the problems on the attached lac operon
worksheet, as assigned by your instructor. You should be prepared to present your
conclusions and reasoning to the class.
III. DNA REPLICATION

        On each table you will find large sheet of newsprint and a package of colored
pencils. With the other members of your group, draw out the process of replication as it is
occurs going in one direction from the origin. Draw a large replication fork on the paper in
the orientation of shown below. Label the unlabelled ends of the DNA in the diagram as 3‟
or 5„ as appropriate. Then begin to add the elements below in a logical sequence (not in the
order listed) as they participate in replication. As each element is added, take turns
explaining its function in the replication process.




Elements to include in your drawing:
      Okazaki Fragments
      Single-Stranded DNA Binding Proteins
      DNA Polymerase I
      DNA Ligase
      RNA Primers
      Gyrase
      DNA Polymerase III – subunit 1
      DNA Polymerase III – subunit 2
      Helicase
      Primase (primasome)

Other items to label:
        Parental DNA Helix
        Leading Strand
        Lagging Strand
        All 5‟ ends
        All 3‟ ends
Bio 221        Discussion # 5                                        lac operon worksheet
Indicate how each operon is regulated and what, if any, enzyme is made.
       Symbols: + = normal allele; - = mutant (non-functional) allele; s = "super" allele (product can't be inactivated)


                                                                              Functional Nonfunctional   No
                                                                               Enzyme      Enzyme      Enzyme
                    Genotype                          Medium contains:          Made        Made        Made    Explanation
                    +       +       +       +
Example             I P O Z                         No Lactose No Glucose
                    +       +       +       +
                    I P O Z                         No Lactose    Glucose
                    +       +       +       +
                    I P O Z                          Lactose     No Glucose
                    +       +       +       +
                    I P O Z                          Lactose      Glucose
                    +       -       +       +
   1                I PO Z                          No Lactose No Glucose
                    +       -       +       +
                    I PO Z                          No Lactose    Glucose
                    +       -       +       +
                    I PO Z                           Lactose     No Glucose
                    +       -       +       +
                    I PO Z                           Lactose      Glucose
                    -       +       +       +
   2                IP O Z                          No Lactose No Glucose
                    -       +       +       +
                    IP O Z                          No Lactose    Glucose
                    -       +       +       +
                    IP O Z                           Lactose     No Glucose
                    -       +       +       +
                    IP O Z                           Lactose      Glucose
                    +       +       -       +
   3                I P O Z                         No Lactose No Glucose
                    +       +       -       +
                    I P O Z                         No Lactose    Glucose
                    +       +       -       +
                    I P O Z                          Lactose     No Glucose
                    +       +       -       +
                    I P O Z                          Lactose      Glucose
                -       +       +       +       +
   4           I P O Z /I                           No Lactose No Glucose
                -       +       +       +       +
               I P O Z /I                           No Lactose    Glucose
                -       +       +       +       +
               I P O Z /I                            Lactose     No Glucose
                -       +       +       +       +
               I P O Z /I                            Lactose      Glucose
                    s       +       +       +
   5                I P O Z                         No Lactose No Glucose
                    s       +       +       +
                    I P O Z                         No Lactose    Glucose
                    s       +       +       +
                    I P O Z                          Lactose     No Glucose
                    s       +       +       +
                    I P O Z                          Lactose      Glucose
               s        +       +       +       +
   6           I P O Z /I                           No Lactose No Glucose
               s        +       +       +       +
               I P O Z /I                           No Lactose    Glucose
               s        +       +       +       +
               I P O Z /I                            Lactose     No Glucose
               s        +       +       +       +
               I P O Z /I                            Lactose      Glucose
Indicate how each operon is regulated and what, if any, enzyme is made.
      Symbols: + = normal allele; - = mutant (non-functional) allele; s = "super" allele (product can't be inactivated)

                                                                                             Functional Nonfunctional   No
                                                                                              Enzyme      Enzyme      Enzyme
                       Genotype                                       Medium contains:         Made        Made        Made    Explanation
                       +       +           +       -
  7                    I P O Z                                     No Lactose   No Glucose
                       +       +           +       -
                       I P O Z                                     No Lactose    Glucose
                       +       +           +       -
                       I P O Z                                      Lactose     No Glucose
                       +       +           +       -
                       I P O Z                                      Lactose      Glucose
           +       +       -   +               +       +       +
  8     I P O Z /P O Z                                             No Lactose   No Glucose
           +       +       -   +               +       +       +
        I P O Z /P O Z                                             No Lactose    Glucose
           +       +       -   +               +       +       +
        I P O Z /P O Z                                              Lactose     No Glucose
           +       +       -   +               +       +       +
        I P O Z /P O Z                                              Lactose      Glucose
                   +    +          -       +           +
  9            I P O Z /O                                          No Lactose   No Glucose
                   +    +          -       +           +
               I P O Z /O                                          No Lactose    Glucose
                   +    +          -       +           +
               I P O Z /O                                           Lactose     No Glucose
                   +    +          -       +           +
               I P O Z /O                                           Lactose      Glucose
                   +       -       -       +           +
 10            I P O Z /O                                          No Lactose   No Glucose
                   +       -       -       +           +
               I P O Z /O                                          No Lactose    Glucose
                   +       -       -       +           +
               I P O Z /O                                           Lactose     No Glucose
                   +       -       -       +           +
               I P O Z /O                                           Lactose      Glucose
       -       +       +       +           +       -       +   +
 11    I P O Z /I P O Z                                            No Lactose   No Glucose
       -       +       +       +           +       -       +   +
       I P O Z /I P O Z                                            No Lactose    Glucose
       -       +       +       +           +       -       +   +
       I P O Z /I P O Z                                             Lactose     No Glucose
       -       +       +       +           +       -       +   +
       I P O Z /I P O Z                                             Lactose      Glucose
                   +       +           +       +       S
 12            I P O Z /I                                          No Lactose   No Glucose
                   +       +           +       +       S
               I P O Z /I                                          No Lactose    Glucose
                   +       +           +       +       S
               I P O Z /I                                           Lactose     No Glucose
                   +       +           +       +       S
               I P O Z /I                                           Lactose      Glucose

				
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