Help
Options
Didn't know it?
click below
click below
Knew it?
click below
click below
Don't Know
Remaining cards (0)
Know
retry
shuffle
restart
0:00
Embed Code - If you would like this activity on your web page, copy the script below and paste it into your web page.
Normal Size Small Size show me how
Normal Size Small Size show me how
Gene Regulation
| Question | Answer |
|---|---|
| Microbial Regulatory Systems Overview: | the amount of protein synthesized can be regulated by transcription or translation, by translating or not translating the mRNA. After the protein has been synthesized, post-regulatory processes can further the activity of proteins. |
| Repression Site: | blocks transcription |
| Activation Site: | helps transcription start |
| Operator: | control region in the DNA (the operator controls expression of the operon) |
| Repression & Induction: | repression turns genes off, induction turns genes on |
| Four General Models of Transcription Regulation: | negative repressible control, negative inducible control, positive inducible control, positive repressible control |
| Negative Repressible Control (turns OFF): | Protein: Repressor/Aporepressor Chemical: Corepressor Example: Arginine biosynthesis Logic: When end product (arginine) is abundant, shut down synthesis genes. Transcript is on, repressor is off, corepressor activates it and transcription is turned off |
| Negative Inducible Control (turns ON): | Protein: Repressor Chemical: Inducer Example: Lactose utilization (lac operon) Logic: When substrate (lactose) is present, turn on utilization genes. Default state: The gene is off. A repressor protein is active and bound to the operator site, presence |
| Positive Inducible Control (turns ON): | Protein: Activator/Apoactivator Chemical: Inducer (or coactivator) Example: Maltose utilization Logic: When substrate (maltose) is present, activate utilization genes. Off first. An activator protein is normally unable to bind to the promoter to star |
| Positive Repressible Control (turns OFF): | Protein: Activator Chemical: Inhibitor In positive repressible control, an operon is normally ON because an activator protein is bound to a DNA sequence, promoting transcription. Transcription is turned OFF when a signal molecule (or "repressor" in this |
| DNA Binding Proteins & Transcription Regulation: | DNA binding proteins functioning in transcription regulation often 1) act as dimers, 2) bind to two inverted sequences — same sequence on opposite DNA sides, 3) bind to each other |
| Helix-turn-helix: | most common DNA-binding motif, two α-helices separated by short turn. Other possibilities are the zinc finger (common in eukaryotes) and the leucine zipper. |
| What are the helix-turn-helix binding proteins? | The recognition helix and the stabilization helix. |
| Recognition helix: | interacts with specific sequences in DNA |
| Stabilization helix: | stabilizes the recognition helix through hydrogen bonds |
| Magic Number in Regards to DNA Binding Proteins: | 10, Spacing between helices = 10 bp (one helical turn!) |
| Bonus Exam Question. Why is the lac operon the professor’s favorite operon? | It contains ZYA proteins — lacZ, lacY, and lacA, matching his name. |
| Catabolite Repression: | mechanism of global control that controls the use of carbon sources if more than one is present. This ensures that the best carbon source is used first. In E. coli, the best carbon source is glucose. |
| Result of Catabolite Repression: Diauxic growth (two growth phases): | First phase: Rapid growth on glucose Lag phase: Switching metabolism Second phase: Slower growth on alternative sugar (e.g., lactose) |
| Signal Molecule for Catabolite Repression: | Enzyme Adenylate Cyclase makes cAMP from ATP. It's cAMP |
| Regulation of adenylate cyclase: | High glucose → Inhibits adenylate cyclase → Low cAMP Low glucose → Active adenylate cyclase → High cAMP |
| Key Principle of cAMP: | cAMP concentration is inversely proportional to glucose concentration cAMP goes UP when glucose goes DOWN |
| Catabolite Repression Is Actually Activation! | cAMP binds to CAP → CAP-cAMP complex CAP-cAMP binds DNA in front of promoter Helps RNA polymerase bind correctly Acts in Positive Inducible manner (like maltose system) |
| Catabolite Repression Example: | the lac operon needs BOTH CAP-cAMP and Lacl-lactose to allow transcription to begin. CAP-cAMP HELPS RNA polymerase bind the correct position. Lacl-allolactose UNBLOCKS the promoter. |
| Can the Lac Operon Perform Transcription with Just Glucose? | No |
| Can the Lac Operon Perform Transcription with Glucose + Lactose? | No |
| Can the Lac Operon Perform Transcription with Just Lactose? | Yes. Both controls are met. Lactose enters the cell and is converted to allolactose, which binds to and deactivates the repressor protein. With glucose absent, cyclic AMP (cAMP) levels are high, which activates the Catabolite Activator Protein (CAP). |
| Signal Transduction: | Mechanism for cells to sense and respond to environmental signals. Signals: Temperature, pH, oxygen, osmolarity, phosphate, nitrate, light, etc. Very common in bacteria and archaea. |
| Why Is Signal Transduction Called a Two Component Regulatory System? | Because it has two components → first, the sensor kinase protein senses the condition (normally in the cell membrane). Then the response regulator protein transmits to the DNA target. |
| Signal Transduction General Mechanism: | Signal triggers sensor kinase → autophosphorylation → phosphate transferred to response regulator → regulator-P binds DNA → phosphatase removes phosphate → regulator released, cycle resets. |
| Example of Signal Transduction: E.Coli Outer Membrane Protein Pores: | senses osmotic pressure, needs to regulate the flow of chemicals from outside the cell to the periplasm. Osmotic pressure LOW then needs more OmpF. Osmotic pressure HIGH then needs more OmpC (and less OmpF). |
| OmpC: | small pore, creating smaller pores to restrict solute flow and maintain osmotic balance. |
| OmpF: | big pore, forms larger pores to allow more solutes into the periplasm. |
| When would osmotic pressure be low or high? | “Environment” vs. “intestine.” |
| Quorum Sensing: | a regulatory mechanism that assesses a population density (measures how many bacteria are in a particular environment). A way that bacteria “talk” to each other either within a species or cross-species. |
| Why Perform Quorum Sensing? | Bacteria need a quorum to make toxins or light—one cell can’t produce enough. E.g., the squid’s Aliivibrio fischeri glow collectively so the host matches moonlight and avoids sharks. |
| Quorum Sensing Mechanism: | individual cells produce a specific signal molecule called an autoinducer that diffuses in and out of the cell. When the concentration of the autoinducer is high, the regulatory proteins turn on transcription of the target genes. |
| Quorum Sensing Autoinducer Example: | acyl homoserine lactone (AHL). This family of chemicals were the first autoinducers introduced. |
| sRNAs can control translation of mRNA by two mechanisms: | sRNAs can bind to mRNA in an antisense manner at the RBS → inhibit translation sRNAs can bind to mRNA and uncover the RBS by disrupting inhibitory structure → stimulate translation |
| When does translation occur and not occur? | Translation occurs until the sRNA blocks the RBS on the mRNA “turns off” translation. Translation does not occur until the sRNA unblocks the RBS by alternative folding of the mRNA “turns on” translation. |
| sRNAs can control degradation of mRNA by two mechanisms: | sRNAs bind mRNA antisense to either: Promote degradation by forming double-stranded RNA recognized by ribonucleases. Prevent degradation by blocking ribonuclease access to specific mRNA sites. |
| Riboswitches: | Riboswitches inhibit translation when metabolite binds to a specific region of an mRNA, causing the RNA to fold into a new structure that hides Shine-Dalgarno sequence. This prevents the ribosome from binding, effectively blocking protein synthesis. |
| Riboswitch General Mechanism | Sequence 1 can bind to 2, Sequence 2 can bind to 3, Sequence 1 can bind to a small molecule, Sequence 3 contains the RBS, if RBS is free, translation can occur. |
| What Riboswitch Sequences Bond when Translation is On? | 1 & 2 bind, stem loop, RBS is free |
| What Riboswitch Sequences Bond when Translation is Off? | Molecule binds 1, 2 is free from 1, 2 & 3 bind, RBS is blocked |
| Riboswitch Attenuation: | Transcriptional control that terminates transcription prematurely. Depends on transcription termination by the structure of the mRNA. |
| Riboswitch Best Model: | the tryptophan operon is the best studied and is the model system. |
| Leader Sequence: | essential to riboswitch inhibition, the leader sequence contains multiple codons for the amino acid whose synthesis is to be controlled. Attenuation depends on a leader sequence that can fold in two possible confirmations. |
| Riboswitch & High Amino Acid Concentration: | high tRNA-AA, fast translation, terminates transcription |
| Riboswitch & Low Amino Acid Concentration: | low tRNA-AA, slow translation, does not terminate transcription |
| Attenuation: High Tryptophan (Turn OFF): | ribosome covers 2, Sequence 2 cannot pair with 3, Sequences 3 & 4 pair → Terminator forms, Transcription terminates, No synthesis enzymes made. Logic: "If Trp is abundant, don't make more" |
| Attenuation: Low Tryptophan (Turn ON): | ribosome covers sequence 1, sequences 2 and 3 pair → antiterminator, no terminator forms, tryptophan synthesis enzymes made, logic: “if Trp is scarce, make more.” |
| Very Simple Summary of RNA Regulation: | effects translation (sRNA and riboswitch), effects RNA degradation (sRNA), effects transcription (attenuation). |
| Exam Tip | Make sure you watch a video about riboswitch! It’s likely to be on the exam! |
| Feedback Inhibition: | Reversible regulation where pathway’s end product binds an enzyme’s allosteric site, disrupts its active site & stops activity. Ex, high isoleucine inhibits threonine deaminase, and low restores it. |
| Arginine | When arginine is abundant, it acts as a corepressor that activates a repressor protein to block transcription of genes for its own synthesis. Negative repressible |
| Lactose | When lactose is present, it binds to and inactivates the repressor, allowing transcription of enzymes needed to metabolize lactose. Negative inducible |
| Maltose | When maltose is present, it activates an activator protein that promotes transcription of genes for maltose metabolism. Maltose is a coactivator, not inducer. No maltose, no transcription. Positive inducible |
| Dummy Terms | Riboswitch: RNA itself senses a molecule and flips a “switch” to turn genes on or off. Attenuation: RNA folding + ribosome speed act like a “traffic light” that tells RNA polymerase to stop or go depending on metabolite levels. |
Created by:
smurtab