Week 13 (NOT FINISHED0

Regulated Promoters

Promoters that allow for transcription only when certain conditions are met

• Gene expression can be controlled by this

Gene Expression

The process that heritable information in a gene is made into a functional gene product, such as protein or RNA

Gene Regulation

The process of controlling gene expression

• The mechanisms of this can occur during any part of gene expression → transcription, RNA processing, translation, post-translational modifications

Constitutive Expression

A gene that is expressed at a constant level

Lac Operon

A set of genes in E. coli and other bacteria that control lactose metabolism

lacZ Gene

Encodes β-galactosidase

Initiation Energy Cost

1 GTP

Elongation Energy Cost

2 GTPs per aa incorporation

1 ATP per charged tRNA

Termination Energy Cost

1 GTP

Constitutive Expression

A gene that is expressed at a constant level, at all times

β-galactosidase

An enzyme that converts lactose into allolactose → gets cleaved into glucose and galactose

lacY

Gene that encodes for lactose permease

Lactose Permease

Enzyme that allows lactose to enter cell 

Lac Repressor Protein

A DNA-binding protein that regulates the operon’s expression

LacI

Gene that encodes for the repressor protein

Lactose

Inducer → induces lac operon expression

Lactose Absent

LacI repressor binds to operator sequence → prevents transcription

• Blocks RNA polymerase from transcribing ZYA genes needed for breaking down lactose

Lactose Present

Converts to allolactose → allows for transcription 

• Allolactose binds to the lac repressor and has it detach from the operator 

Allolactose

Acts as the lac operon inducer

• Converted from lactose

Glucose Absent 

Means high levels of cyclic AMP (cAMP)

Glucose Present

Means low levels of cyclic AMP (cAMP)

Cyclic AMP (cAMP)

Regulates the lac operon in bacteria by activating CAP when glucose is low

Catabolite Activator Protein (CAP)

A regulatory protein that acts as a positive control mechanism

• Activates the transcription of the lac operon when glucose levels are low

cAMP-CAP Complex

A regulatory mechanism in bacteria where this binds to specific DNA sequences to regulate the transcription of genes

• Positive regulator: Low glucose levels raises cAMP → activates CAP → increase in transcription

CAP Binding Site

Binds to a specific DNA sequence located upstream of the promoter region for certain genes

• Positive regulation

• Presents the promoter high up for RNA polymerase to see (like a flag attendant in a packed parking lot) 

Promoter

A DNA sequence where RNA polymerase binds to initiate transcription of the lac genes 

Operator

DNA sequence in the lac operon that acts as a binding site for the lac repressor protein

LacA

Gene that we are unsure of what the function is

Leaky Expression

There is some basal, very low level of expression 

• Occurs when there is no lactose nor glucose present

IPTG

A mimic of allolactose → causing lacI to fall off the operator sequence

• Biotech use of the lac operon

X-Gal

A colorless lactose mimic in which β-galactosidase can convert into a blue pigment

Negative Regulation

When binding of a regulatory protein to the DNA blocks transcription, preventing a gene from being expressed

• Lac Repressor example 

Inducer

A small molecule that activates/promotes gene expression

• Like a like switch

• Allolactose example

Positive Regulation

When binding of a regulatory protein to the DNA activates transcription, causing a gene to be expressed

• CAP example

Activator

A regulatory protein that promotes gene expression

Repressor 

A regulatory protein that prevents gene expression 

Co-repressor

A small molecule that prevents gene expression (typically works with a repressor)

Signaling Molecule

A small molecule that transmits signals to regulatory systems (cell communication)

Regulatory Sequence

Sequences on DNA/RNA that control gene expression

• Promoters, operators, CAP binding site

Tryptophan

An essential amino acid

• In E. coli, enzymes that synthesize this are found in the the Trp Operon

Trp Operon

A set of genes in bacteria that work together to synthesize tryptophan 

• Expression through negative regulation and attenuation 

Trp Repressor

A DNA binding protein that negatively regulates the trp operon in bacteria

• High levels of tryptophan → low levels of transcription

• Not part of the trp operon

Trp Leader Peptide 

A short sequence in the trp operon that controls gene expression

Trp EDCBA

Genes encoding enzymes needed for tryptophan biosynthesis

Chorismate

A vital intermediate/precursor in the biosynthesis of a few amino acids (like tryptophan)