Midterm exam #1 - Fall 1995

1. List the main evolutionary groups (i.e. Kingdoms) of living things, and indicate which are prokaryotic and which eukaryotic. (5 points) .

2. What can we conclude from the observation that all living things are very much alike? (5 points) .

3. Describe membrane lipids in Archaea. (5 points) .

4. Briefly describe why the 'Evolutionary Ladder' theory is clearly false. (5 points) .

5. How was it shown that mitochondria and chloroplasts evolved from bacterial symbionts rather than as part of the eukaryote? (5 points) .

6. What is the difference between taxonomy and phylogeny? (5 points) .

7. Align the RNAs below: (10 points)

(note - you dont necessarily have to use all of the blanks above) .

8. Answer the following questions about this tree: (2 points each, 10 points total)

• Which is the outgroup sequence? _____
• Which 2 sequences are most closely related? _____
• Which 2 sequences are least similar? _____
• Which sequence (other than perhaps the outgroup) is the most primative? _____
• Which sequence (excluding the outgroup) separated from the others earliest in their evolution? _____

9. Align the following sequences. (10 points)

    Seq A AGGCCUUCGGGCC     __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __
    Seq B GACCUUCGGGUC      __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __
    Seq C UAGACCUUUGGGUC    __ __ __ __ __ __ __ __ __ __ __ __ __ __ __ __

(note - you dont necessarily have to use all of the blanks above)

10. Given the unknown RNA from a methanogen, the reference structure, and the table of signature nucleotides, what group does the methanogen belong to? (15 points)

 Reference structure (Methanoocus vannielii)               Unknown

             

     Position   Unknown Methanococcales Methanobacteriales  Methanosarcina  Methanopyrus
    ------------------------------------------------------------------------------------
        4       ____            A               A                   G           C
        7       ____            U               R                   U           A
        12      ____            G               A                   A           A
        21      ____            G               Y                   G           G
        29      ____            G               G                   G           A
        31      ____            A               G                   A           G
        48      ____            G               A                   G           G
        53      ____            G               A                   C           C
        59      ____            A               R                   G           G
        62      ____            U               C                   U           U
        66      ____            A               R                   C           A
        69      ____            A               A                   U           U
        77      ____            U               U                   U           G
        81      ____            U               U                   C           N
    ------------------------------------------------------------------------------------
        (R = A or G; Y = U or C; N = A,G,U or C)

11. Please complete the similarity matrix: (2 points each, 10 points total)

                                    A       B       C       D
    Seq A   AUCGAUCGAU      A       X       X       X       X 
    Seq B   ACCGACCGAU      B       0.8     X       X       X 
    Seq C   AGCGAGCGAU      C       ___     ___     X       X 
    Seq D   AACAGACGGU      D       ___     ___     ___     X

12. Describe the conversion of sequence similarity to evolutionary distance, and why it is necessary. (10 points)

13. In what way is the comic tree below fundamentally flawed? (5 points) .