Term
| Why do cells need to regulate gene expression? |
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Definition
1. Save energy
2. Respond to environmental changes
=aka you don't need the Lac operon if there's no lactose around
3. Differentiation
=Only express genes specific to their cell type
4. Tissue specific functions
=Toe cells don't need to do the same stuff as liver cells |
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Term
| Where regulation can happen in prokaryotes. |
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Definition
1. Transcription
2. Translation
3. Protein folding
4. Modification (acetylation, methylation, ect.) |
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Term
| Where regulation can happen in eukaryotes. |
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Definition
1. Transcription
2. RNA splicing
3. How well it can leave the nucleus
4. Stability in cytoplasm
5. translation
6. Post translational modification |
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Term
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Definition
| Under most conditions, it's expressed at the same level |
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Term
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Definition
| Pretty much the lowest level that a gene can be expressed at. |
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Term
| Protein domains used to interact with DNA. |
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Definition
1. Leucine zipper
2. Helix-loop-helix
3. Zinc Finger |
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Term
Helix-Turn-Helix motif
What are the functions of the two helixes? |
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Definition
1. Scaffolding helix= holds the recog. helix in postition. Supports it
2. Recognition helix= interacts with DNA
3. Turn= allows flexibility. |
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Term
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Definition
| When proteins bind together a dimers, they get increased affinity to their binding sites. This is because if one feels like letting go, the other can keep it on. It's like having two dice to roll instead of one. There's a higher probability of getting greater than 3 and winning! |
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Term
| Covalent bonds and gene switching on and off. |
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Definition
| The interactions between proteins and DNA must be non-covalent so that they can be turned off and on. |
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Term
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Definition
1. LacZ= beta-galactosidase; cleaves lactose into glucose and galactose
2. LacY= lactose permease
3. LacA= Nobody knows
4. Promoter= where RNA pol binds
5. Operator= Where Lac I binds
6. LacI= repressor for lac operon |
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Term
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Definition
| A group of genes who are coordinatly controlled. Usually in a polycistronic RNA |
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Term
| Types of constitutive mutants |
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Definition
Express genes at high levels all the time.
Trans recessive= caused by a mutant protein. Can be fixed by adding a plasmid with the fixed gene on it.
Cis dominant= Caused by a mutation in DNA. Cannot be fixed by adding a new copy on a plasmid. |
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Term
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Definition
| The operator of the Lac operon. Is downstream from the promoter. LacI tetramer binds there and prevents RNA polymerase from binding to the promoter. |
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Term
| Constitutive mutants in Lac Operon |
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Definition
cis-dominant mutant= operator is mutated
trans-recessive mutant= mutant LacI cannot bind to operator
trans-dominant= LacS, can make tetramers |
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Term
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Definition
Can form tetramer
Can bind to operator
Cannot bind to inducer
So, even if you add WT LacI, it won't work because the LacIs keep holding on. |
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Term
| How does lacI bind to the operator? |
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Definition
| LacI is a tetramer, more accurately, a homodimer-dimer. There are three different operators with three different sequences with different affinities for LacI (O1>O2>O3). One dimer binds to one operator and the other binds to a different one. Then, they bind to each other to make a tetramer and they make a loop where the promoter is. Thus, RNA Pol can't bind. |
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Term
| What is an inducer? What is the inducer for the Lac operon |
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Definition
| An inducer is something that turns on expression of a gene. The inducer for the Lac operon is allolactose. It is an isomer of lactose that is made by enzymes. |
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Term
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Definition
1. DNA binding domain
2. Dimer domain
3. Tetramer domain
4. Allolactose binding domain |
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Term
| How does the Trp operon work? |
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Definition
The repressor is a dimer and only works when bound by Trp.
Aporepressoro= no ligand bound, low affinity to operator, no repression
Repressor= Trp ligand is bound, high affinity to operator, represses expression |
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Term
| Allostery and its importance |
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Definition
Allostery= the change in the tertiary structure of a protein caused by ligand binding.
This is important because it changes the affinity of repressors and activators for their binding sites. Activates and represses genes. |
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Term
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Definition
| Represses a gene by preventing the RNA polymerase from opening and transcripting the gene. |
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Term
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Definition
When a mutation give a phenotype without gene expression and it cannot be corrected by giving them another copy of the gene on a plasmid.
Example: LacI that can dimerize, but cannot bind to the promoter, even if it's bound to WT LacI. |
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Term
| Positive control elements characteristics verses repressors |
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Definition
1. They're both genetic switches
=Controls expression of gene sets
=Respond to cell needs or changing conditions
Different:
=Positive control elements are necessary for complete expression of gene
=If you knock out the positive control factor, genes won't be fully expressed. |
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Term
| Two major types of positive control factors in prokaryotes. |
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Definition
1. Transcriptional activators: help RNA polymerase initiate transcription
2. Alternative sigma factors: alter teh specificity of RNA pol for specific promoters |
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Term
| Positive Control Element of Lac operon |
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Definition
Catabolite Activator Protein or CAP
Needs cAMP to be able to activated and bind with high affinity to the promoter region.
CAP/cAMP makes a dimer and binds to the activator site upstream of the promoter with a helix-turn-helix motif. It interacts with the C-terminal of the alpha subunit of the RNA polymerase. |
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Term
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Definition
| Levels of cAMP go up when levels of glucose go down. So, the Lac Operon is only expressed a lot when glucose is not around. |
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Term
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Definition
Glucose phase and lactose phase
There's two phases when bacteria are grown with glucose and lactose. First, the bacteria grow exponentially while eating glucose. Then, they run out of glucose, they stop growing so much and switch over to the lac operon. Then, they start growing exponentially again by eating lactose. |
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Term
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Definition
| When the genes for the expression of an alternate carbon source are turned off when glucose is present. |
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Term
| Three Mechanisms of Activators recruiting RNA polymerase |
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Definition
1. Pre-recruitment= activator and RNA pol bind before attaching to the promoter
2. Recruitment= activator binds to the DNA and helps RNA pol bind to the promoter
3. Post-Recruitment= RNA polymerase binds, then the activator binds to the DNA and stablizes it |
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Term
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Definition
| Changes the distance between the -10 and -35 promoter sequences so that RNA polymerase can bind well. |
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Term
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Definition
Sigma factor is the piece of RNA polymerase that identifies the promoter. Different sigma factors have different
Screw this I know it. |
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Term
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Definition
Plasmids that can be used to monitor the expression of a gene.
Example: LacZ is fused in frame to the gene of interest. Transcriptional fusion= LacZ has its own RBS. Translational fusion= LacZ doesn't have its own RBS. |
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Term
| Genes that control lysogeny |
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Definition
1. cI- Repressor protein represses genes from promoters PL and PR.
2. cII- activator of early genes required for lysogeny (including cI)
3. Cro- repressor of cI |
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Term
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Definition
If cII wins, cI is expressed and lytic functions are repressed by cI
If Cro wins, cI remains repressed and lytic functions are imporessed.
For lysogeny keep Cro off and keep cI on. |
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Term
| What factors influence the Cro/CI race? |
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Definition
| FtsH degrades cII which activates cI. FtsH is maximally active in a healthy cell. Thus, healthy cells tend to do lysis. |
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Term
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Definition
DNA damage
1. DNA is damaged
2. RecA is expressed
3. RecA activates cI's autoproteolysis activity.
4. cI deactivates itself
5. Cro is expressed and the virus enters the lytic cycle |
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Term
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Definition
| Salmonella can make H2 flagella or H1 flagella. When they express H2, they make an H1 repressor. But, when Hin flips it sequence around in the gene, the promoter is facing in the wrong direction. The H1 repressor is not made and H1 is expressed. H2 is not expressed because it doesn't have its own promoter. |
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Term
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Definition
| mRNA forms the right kind of stem loop pattern and transcription is halted prematurely. |
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Term
| Attenuation for Trp Operon |
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Definition
Ribosome continues translating, and prevents 2-3 stem loop. terminator 3-4 stem loop forms. Transcription is terminated.
Without trp, ribosome stalls at trp codons and waits to find some, 2-3 antiterminator stem loop forms. Trp operon is expressed. |
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Term
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Definition
Two forms: control transcription or control translation
Riboswitches are when a ligand binds to the mRNA and changes its stem loops.
Antiterminator + ligand = anti-antiterminator and terminator stem loops
Antisequestor +ligand= anti-antisequestor and sequestor stem loops |
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Term
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Definition
| Binds to mRNA and makes it unstable. Makes it easy to degrade. |
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Term
| How small RNAs affect gene expression |
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Definition
Positively activating:
1. unmask RBS so ribosome can bind
2. stablize mRNA binding to 3' end and preventing degredation
Negatively acting
1. Hide (occlude) RBS
2. Stimulate mRNA degredation |
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Term
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Definition
ATP-dependent protease
Segregates protein for degredation
Multimeric barrel shape
heximeric and heptimeric ring, I don't really know |
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Term
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Definition
| DNA sequences in Euks that are necessary for transcription. Transcription factors can bind to them and recruit RNA polymerase. |
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Term
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Definition
| Where proteins bind and bring in the preinitiator complex of the RNA polymerase. The polymerase opens and begins transcription. |
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Term
| Activation methods in Euks |
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Definition
Euks mostly do activation of genes.
1. Nucleosome remodeling
2. Recruitment of RNA polymerase |
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Term
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Definition
| 10 nm fibers are expressed. 30 nm fibers are not expressed. To promote expression make the gene be 10 nm. |
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Term
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Definition
Histone remodeling complex = HRC
HRC + HATs = Acetylates histones so that it's a 10 nm fiber and is expressed
HRC + HDACs= deacetylated it and makes DNA 30 nm fiber and it's not |
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Term
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Definition
| Enhancers are DNA sequences that attract activators. The activators are proteins that recruit HRCs. The HRCs decondense the histones. HRCs also recruit HATs and HATs acetylate the histones to prevent them from being condensed again. |
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