11. Regulatory Mechanisms

• gene expression - which proteins are made
• enzyme activity - which proteins are on/off

• regulation of enzyme activity to determine which pathways are active by responding to product or substrate levels
• most efficient place is at the first enzymatic step specific to that pathway and no others

• enzyme has two sites:
• active site - binds the substrate and catalyzes reaction
• allosteric site - binds the end product, prevents catalysis at the active site

• Eukaryotic:
• transcription - nucleus, translation -cytoplasm
• introns are removed
• mature mRNA exported from the nucleus
• one protein per mRNA

• Bacterial:
• transcription - cytoplasm
• genes are organized in operons, creating polycistronic mRNAs
• translation occurs in same compartment and same time as transcription
• multiple genes on one RNA are translated separately

helps RNA polymerase core enzyme recognize and bind to the promoter region

strong promoter - better match with consensus sequence, yields more binding by the σ factor and more transcription of gene

weak promoter - worse match with consensus sequence, extra transcriptional activators are often needed to turn on transcription of these genes

• promote or repress transcription of specific genes
• often contain a DNA-binding domain and a separate regulatory domain that determines when the protein is active
• often act as dimers and bind to direct or inverted repeats on DNA

bind to specific DNA sequences and block transcription of downstream genes

• end product of biosynthetic pathways can act as corepressors
• - arginine is corepressor that binds repressor to prevent RNA poly from transcribing the operon

• specific enzyme substrates can act as inducers of transcription by blocking action of repressor
• - lac repressor stops transcription of lac operon unless lactose present, lactose is inducer that binds and inactivates repressor

• positive regulators recognize specific DNA sequences in the promoters
• can increase the affinity of RNA pol for the promoter by providing extra binding contacts for RNA pol
• - maltose operon activation requires maltose activator protein and maltose
• can act by bending the DNA to allow better contacts with the promoter
• can also bind hundreds of bases away and loop the DNA around to touch RNA pol at distant promoter