1. DNA-PROTEIN INTERACTIONS AN IN-CLASS PROJECT

2. DNA-PROTEIN INTERACTIONS NONSPECIFIC NONSPECIFIC LOOSE LOOSE BETWEEN PROTEIN FUNCTIONAL GROUPS AND DNA BACKBONE BETWEEN PROTEIN FUNCTIONAL GROUPS AND DNA BACKBONE IONIC IONIC H-BONDS H-BONDS VANDERWAALS VANDERWAALS SPECIFIC (SEQUENCE-SPECIFIC) SPECIFIC (SEQUENCE-SPECIFIC) TIGHT BINDING TIGHT BINDING DIRECT H-BONDING DIRECT H-BONDING INDIRECT H-BONDING INDIRECT H-BONDING “INDIRECT READOUT” “INDIRECT READOUT”

3. PROKARYOTIC CONTROL MOTIFS STUDY THE FOLLOWING MOTIFS STUDY THE FOLLOWING MOTIFS 434 PHAGE REPRESSOR WITH TARGET DNA (PDBid 2OR1) 434 PHAGE REPRESSOR WITH TARGET DNA (PDBid 2OR1) E.coli Trp REPRESSOR-OPERATOR COMPLEX E.coli Trp REPRESSOR-OPERATOR COMPLEX (PDBid 1TRO) (PDBid 1TRO) E.COLI Met REPRESSOR-SAM OPERATOR COMPLEX E.COLI Met REPRESSOR-SAM OPERATOR COMPLEX (PDBid 1CMA) (PDBid 1CMA) ANSWER ALL QUESTIONS ANSWER ALL QUESTIONS FILL OUT THE SUMMARY SHEET FILL OUT THE SUMMARY SHEET

4. EUKARYOTIC TRANSCRIPTION CONTROL FACTORS LOOK AT THE FOLLOWING CONTROL FACTORS LOOK AT THE FOLLOWING CONTROL FACTORS Cys 2 – His 2 ZINC FINGER BINDING MOTIFS Cys 2 – His 2 ZINC FINGER BINDING MOTIFS (PDBidS 1ZNF AND 1AIF) (PDBidS 1ZNF AND 1AIF) Cys 4 ESTROGEN RECEPTOR (PDBid 1HCQ) Cys 4 ESTROGEN RECEPTOR (PDBid 1HCQ) Cys 6 YEAST TRANSCRIPTION FACTOR GAL4 (PDBid 1D66) Cys 6 YEAST TRANSCRIPTION FACTOR GAL4 (PDBid 1D66) GCN4 LEUCINE ZIPPER MOTIF (PDBid 1YSA) GCN4 LEUCINE ZIPPER MOTIF (PDBid 1YSA) ANSWER ALL QUESTIONS ANSWER ALL QUESTIONS FILL OUT THE SUMMARY SHEET FILL OUT THE SUMMARY SHEET

5. IN-CLASS PROJECT ON TRANSCRIPTION FACTORS WORK TOGETHER IN SMALL GROUPS OF 2 OR 3 STUDENTS WHEN LOOKING AT THE STRUCTURES AND ANSWERING THE QUESTIONS WORK TOGETHER IN SMALL GROUPS OF 2 OR 3 STUDENTS WHEN LOOKING AT THE STRUCTURES AND ANSWERING THE QUESTIONS EACH STUDENT IN EACH GROUP WILL FILL OUT EACH OF THE TWO “SUMMARY SHEETS” AND HAND THEM IN FOR GRADING NO LATER THAN MONDAY, APRIL 20, 2009 AT 2:00 PM IN CLASS. EACH STUDENT IN EACH GROUP WILL FILL OUT EACH OF THE TWO “SUMMARY SHEETS” AND HAND THEM IN FOR GRADING NO LATER THAN MONDAY, APRIL 20, 2009 AT 2:00 PM IN CLASS. BEFORE HANDING IN THE SHEETS, PUT THE NAME OF EACH GROUP MEMBER ON THEM. THERE SHOULD BE NO COLLABORATION AMONG GROUPS WHEN FILLING THESE OUT. BEFORE HANDING IN THE SHEETS, PUT THE NAME OF EACH GROUP MEMBER ON THEM. THERE SHOULD BE NO COLLABORATION AMONG GROUPS WHEN FILLING THESE OUT. THIS WILL COUNT FOR 25 POINTS OF YOUR LAST EXAM. THIS WILL COUNT FOR 25 POINTS OF YOUR LAST EXAM.

6. CONCLUSIONS NATURE USES A NUMBER OF DEVICES WHICH CAN BE VARIED TO MAXIMIZE DIVERSITY BUT MINIMIZE COMPLEXITY OF DNA-PROTEIN INTERACTIONS: NATURE USES A NUMBER OF DEVICES WHICH CAN BE VARIED TO MAXIMIZE DIVERSITY BUT MINIMIZE COMPLEXITY OF DNA-PROTEIN INTERACTIONS: MOTIF TYPE MOTIF TYPE DIMERIZATION DIMERIZATION PALINDROMIC DNA SEQUENCES PALINDROMIC DNA SEQUENCES BONDING TYPES BONDING TYPES CONTACT SITE ON DNA CONTACT SITE ON DNA NEED FOR ADDITIONAL SUBSTRATE NEED FOR ADDITIONAL SUBSTRATE