week 6 Flashcards
promoter
is located at the start of the gene (recognition/binding site for RNAP/Oreinets polymerase)
coding region
- produces codon AUG and ends with stop codon
leader sequence
- in DNA transcribed into mRNA but not amino acids (folding)
- gives rise to SD (helps facilitate translation)
operon
- found predominantly in bacteria and archeal genes, encoding proteins involved in related processes are transcribed by a single promoter (not common in euk - monocistronic)
mono= start codon, coding region ,and stop codon - transcription can yield mRNA consisting of a leader, coding region, spacer, and a second coding region (polycistronic)
What are the two kinds of regulation mechanisms in bacteria?
- constitutive genes - housekeeping genes) - constant supply needed (central metabolic pathway ) - always on
= give off basal expression - expression is regulated - some enzymes are only needed during specific conditions/environments.
What are regulatory proteins that control transcription initiation? what structure is involved?
- initiation = when sigma subunit position RNAP at a promoter
- Transcription factors - regulatory proteins that bind at promoter
- helix-turn-helix motif, which allows them to interact with the grooves of the DNA, similar to a “cowboy on a horse.” This interaction can alter the DNA’s topology or flip regions to either promote or inhibit transcription
What protein is used by negative control? positive control?
- repressor protein - The protein binds to the operators to block RNAP binding (lac)
- activator protein -The protein binds upstream of the promoter and encourages RNAP binding
what are the enzymes that repress and induce enzyme synthesis?
- inducer- small effector molecule that stimulates gene expression, inducible genes- encode inducible enzymes - required only when their substrates are available (lac)
- co-repressor- small effector molecule, irrepressible genes - genes for enzyme involved in biosynthetic pathways - generally present unless the end PDT is available
How does the lac repressor regulate transcription in the presence and absence of lactose?
- absence: the lac repressor binds to the operator and creates DNA loops to prevent RNAP and sigma factors from accessing the promoter, inhibiting transcription. (negative control - repressor prevents gene expression )
- lactose is present, lactose permease brings lactose into the cell, and β-galactosidase converts lactose to allolactose, which will bind to the repressor, preventing the repressor form from binding to the operator = allowing transcription from happening (induces the expression of the operon)
what are the three genes for lactose uptake and metabolism?
- lacZ - encodes for an enzyme that cleaves disaccharides to release two monomers for consumption
- B-galactosidase - hydrolyzes lactose into galactose and glucose
- Lac repressor (lacL) binds the operator and inhibits transcription when no lactose
What is repressible control? How does the presence of tryptophan regulate transcription in the trp operon? operon function when?
- Turns transcription OFF by the presence of specific molecules
- In the trp operon, tryptophan acts as a co-repressor (when present), meaning that when tryptophan is abundant, it binds to the repressor protein, enabling it to bind to the operator and block transcription.
- When tryptophan levels are low, the repressor is inactive, allowing transcription of the genes responsible for synthesizing tryptophan to occur.
- open only functions in the absence of trp
How can the transcription elongation step be regulated? example
- attenuation: Is the termination of transcription within the leader region
- happens through a stem-loop structure in the leader RNA depending on the level of trp (high trp means that there is one and stops transcription)
What is used to regulate transcription elongation?
- riboswitch - It is a specialized form of transcription attenuation that is found in bacteria and archaea.
- Folding of the RNA leader sequence determines if transcription will occur or terminate and is a response to the effector molecule binding to teh RNA
What is used to regulate translation?
- RNA thermometers are RNA secondary structures located in the leader sequence of mRNA that regulate translation in a temperature-dependent manner.
- The RNA thermometer folds into a structure to prevent access of the ribosome to the Shine-Dalgarno (SD) sequence within the mRNA at lower temperatures.
What is the global regulatory system? how do they help bacteria adapt to changing conditions? regulon?
- are regulatory networks that can simultaneously affect many genes, operons, and pathways, allowing bacteria to adapt to changing environmental conditions.
- regulon genes or operons controlled by a common global regulatory protein
what are the four types of regulations that global regulatory systems use?
Two-component signal transduction systems
Phophorelays system
Sigma factors
Second messengers
What is the two-component system? Sensor kinase?
- Direct line for a bacterial system
- a sensor kinase (e.g., EnvZ) spans the plasma membrane, so a part of it is exposed to the external environment, and the other part is in the cytoplasm, detecting environmental changes such as osmolarity.
- The sensor kinase phosphorylates itself and then transfers the phosphate to a response regulator in the cytoplasm.
- The response regulator undergoes a conformational change, which triggers transcriptional changes, allowing the bacteria to respond to the detected environmental signal.
what are alternate sigma factors? What do these help with?
- these change the expression of many genes, directing RNAP to specific subsets of bacteria promoters.
- These help bacteria control which genes should be turned on or off in response to different conditions
- differ in consensus binding sites and protein subunits
