1. STRATEGY FOR GENE REGULATION 1.INFORMATION IN NUCLEIC ACID – CIS ELEMENT CIS = NEXT TO; ACTS ONLY ON THAT MOLECULE 2.TRANS FACTOR (USUALLY A PROTEIN) BINDS TO NUCLEIC ACID CIS ELEMENT. TRANS = ACROSS 3.SWITCH: REGULATES INTERACTION OF PROTEIN AND NUCLEIC ACID (OFTEN SMALL MOLECULE OR PROTEIN MODIFICATION) [RAPID RESPONSE] CAN BE SYNTHESIS OR DESTRUCTION OF TRANS FACTOR [SLOWER RESPONSE]

2. PROTEIN BINDING SITES IN DNA HAVE A CONSENSUS SEQUENCE

3. POSITIVE AND NEGATIVE CONTROL 1. Positive control means that the trans-acting factor binds to the target and the protein-nucleic acid complex stimulates expression of the gene. 2. Negative control means that the trans-acting factor binds to the target and the protein-nucleic acid complex represses expression of the gene.

4. STANDARD MODEL FOR GENE REGULATION Degradation of lactose by E.coli bacteria Enzymes made (gene transcribed) only when lactose is present Enzymes not made if glucose is present Rationale: lactose is degraded to make glucose; no need to go to trouble to degrade lactose if there is enough glucose

5. MORE THAN ONE MOLECULE OF A REGULATORY FACTOR CAN BIND DNA THE SEQUENCE OF THE DNA IS OFTEN A PALINDROME. A PALINDROME READS THE SAME BACKWARDS AND FORWARDS MADAM I’M ADAM IS A PALINDROME

6. BINDING SITE FOR THE LAC REPRESSOR RNA START SITE TWO PALINDROMIC BINDING SITES ON THE DNA

7. LACTOSE REPRESSOR (TRANS FACTOR) BINDS DNA AND BLOCKS TRANSCRIPTION (NEGATIVE REGULATION) IT PREVENTS RNA POLYMERASE FROM BINDING RNA START SITE

8. LACTOSE (SWITCH) BINDS REPRESSOR AND REPRESSOR COMES OFF DNA THIS IS HOW THE CELL TELLS IF LACTOSE IS PRESENT RNA START SITE LACTOSE

9. THE SECOND CIS ELEMENT IS ABOUT -40 TO -50 BEFORE THE START SITE A PROTEIN (CAP) BINDS THIS SITE AND HELPS THE RNA POLYMERASE BIND: IT IS NECESSARY FOR TRANSCRIPTION OF THIS GENE THIS IS POSITIVE CONTROL SWITCH: A HUNGER SIGNAL IS CYCLIC AMP (cAMP): cAMP BINDS TO THE CAP PROTEIN ALLOWS IT TO BIND DNA WITHOUT cAMP IT DOES NOT BIND DNA

10. REGULATION OF LACTOSE DEGRADATION IN E.COLI

11. 1.There is only one binding site for the lactose repressor in E.coli: It only regulates the synthesis of one mRNA. 2.There are many binding sites for the CAP protein upstream of the promoter of many genes encoding proteins that can help convert different compounds to glucose (other sugars, some amino acids). 3. Thus the same protein can regulate the expression of many genes since the consensus sequence for binding the regulatory protein is found in front of many promoters. ONE PROTEIN CAN REGULATE MULTIPLE GENES