Term
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Definition
| Enzymes synthesized at a more or less constant rate all the time -- house keeping enzymes (e.g. glycolidic enzymes) |
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Term
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Definition
| Enzymes synthesized depending on need and in response to cellular or environmental cues; regulated by protein activators and repressors |
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Term
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Definition
| Transcription of a protein is quantitatively increased by the presence of a specific activator protein (or by the inactivation of a specific repressor protein). |
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Term
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Definition
| Transcription of a gene is quantitatively decreased by the presence of a repressor (or by the inactivation of an activator). |
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Term
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Definition
| A sequence of DNA that affects the activity of adjacent sequences. This DNA does not encode a protein. (e.g. the repressor binding site upstream of an operator) |
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Term
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Definition
| Refers to a diffusible product the affects the activity of DNA. (e.g. the repressor protein binding to an operator) |
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Term
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Definition
- Bacteria use glucose first
- Use lactose if no glucose is available
- Lactose genes are clustered in the lac operon, allowing coordinated expression of all genes for lactose utilization (more efficient)
- Lacl gene product (Lacl) is the lac repressor
- Operator is between the promoter and initiation site
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Term
| Describe how lactose acts as an inducer by way of allolactose. |
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Definition
| When lactose enters the cell, a small fraction is isomerized to allolactose, which binds to the lactose repressor. This causes a change in conformation of the repressor protein, causing it to dissociate from the operator DNA. |
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Term
| Mutually exclusive binding |
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Definition
| Either repressor or RNA polymerase can bind to the promoter-operator region. |
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Term
| What is the catabolite gene activator protein (CAP)? |
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Definition
| Because the lac promoter is intrinsically weak, binding of the CAP to the promoter increases binding strength to RNA polymerase, increasing transcription rate; CAP activity is regulated by cAMP. |
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Term
| How does cAMP affect CAP? |
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Definition
Acts as a "barometer" for glucose levels. High glucose levels = low cAMP.
Low glucose = high cAMP.
Glucose inhibits adenylate cyclase which is necessary for ATP breakdown to cAMP. |
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Term
| How does CAP regulate binding of RNA polymerase to lac promoter? |
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Definition
- cAMP binds to CAP and changes CAP's tertiary structure, allowing it to fit in the major grooves of its conjugate DNA site
- CAP binding causes a 94 degree bend in promoter DNA, facilitating interaction with RNA polymerase
- Three domains of CAP: ligand binding; DNA binding; protein-protein interactions
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Term
| How are AA levels attenuated in prokaryotes (e.g. trp)? |
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Definition
- Bacteria obtain AAs from nutrient medium because biosynthesis is energetically expensive.
- AA levels modify the RNA structure of the leader RNA in the 5' end of the polycistronic mRNA to form either:
- transcriptional terminator - stem-loop structure followed by poly U
- anti-terminator - stem loop to allow RNA polymerase to proceed
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Term
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Definition
| Virus that infects bacteria. |
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Term
| What are the 2 phases of infx by Lambda phage? |
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Definition
- Infective phase: viral genes expressed, leading to lysis of the bacterial host and release of progeny viral particles.
- Dormant phase: Viral DNA covalently inserted into host DNA; the cI repressor gene is activated, cI suppresses transcription of all other viral genes; viral genome is dormant.
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Term
| Describe the differential binding strengths of the lambda repressor to operator sequences. |
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Definition
- When repressor levels are low, repressor binds to Or1 site (high affinity) and blocks transcription of cro gene.
- The 1st repressor recruits binding of a 2nd repressor to the weaker Or2 site, which recruits RNA polymerase to stimulate transcription of its own gene (cI gene).
- As the repressor levels increase, a 3rd repressor binds to Or3, inhibiting transcription of the cI repressor gene.
- As repressor levels drop, Or3 becomes unoccupied and cI gene is activated, synthesizing more repressor to maintain equilibrium in Or1,2,3
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Term
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Definition
| Prevent the enhancer of a gene domain from activating the genes in the neighboring domains and protects the resident gene from inadvertant transcriptional activation by the heterologous enhancers in the neighboring domains. |
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Term
| Ligand binding domain (in eukaryotic transcription factors) |
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Definition
| Binds inducers, repressors, hormones, etc. |
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Term
| Activating domain (eukaryotic transcription factors) |
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Definition
| binds to other transcription factors and RNA pol II to activate transcription |
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Term
| DNA binding domain (eukaryotic transcription factors) |
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Definition
| bands to specific DNA motifs in the promoters, enhancers, and LCRs |
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Term
Helix-turn-helix: Homeodomain proteins
What do they regulate? |
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Definition
Two alpha-helices separated by a tight turn interact with DNA in the major groove;
Regulate genes involved in development. |
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Term
Helix-loop-helix
What do they regulate? |
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Definition
Both helix-loop-helix and basic-leucine zipper proteins are dimeric transcription factors containing ␣- helices with hydrophobic (leucine, isoleucine, valine, methionine) residues. The hydrophobic residues are alternatively spaced (every 3 and 4 position) so that the side chain of each residue are positioned toward one side of the helix to form a hydrophobic interacting surface. Two ␣-helical monomers dimerize through hydrophobic residues (looped helices or leucine zipper). They have basic a. a. regions for interaction with the cognate DNA motifs. Dimerization of bHLH or bZIP is required for function. Both bHLH and bZIP can form heterodimers.
Regulate immune system genes.
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Term
Basic-leucine zipper (bZIP)
What do they regulate? |
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Definition
Both helix-loop-helix and basic-leucine zipper proteins are dimeric transcription factors containing ␣- helices with hydrophobic (leucine, isoleucine, valine, methionine) residues. The hydrophobic residues are alternatively spaced (every 3 and 4 position) so that the side chain of each residue are positioned toward one side of the helix to form a hydrophobic interacting surface. Two ␣-helical monomers dimerize through hydrophobic residues (looped helices or leucine zipper). They have basic a. a. regions for interaction with the cognate DNA motifs. Dimerization of bHLH or bZIP is required for function. Both bHLH and bZIP can form heterodimers.
Regulate cell division genes. |
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Term
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Definition
| Spans 30 or more AA that are held in 'finger' arrangement through zinc coordination; Finger 1 dimerizes with Finger 2 |
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