Janet B. Matsen:Key Ideas

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Notes for my project by date:
Notes for my project by date:
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2013/08/03:
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* '''synthase vs synthetase'''
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** they are both [http://en.wikipedia.org/wiki/Lyase lyases], enzymes that catalyze the breaking of various chemical bonds by means other than hydrolysis and oxidation, often forming a new double bond or a new ring structure".  (lyase = reverse rxn for ligase)
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** Historically, synthetase was reserved for reactions that use a high energy nucleoside triphosphate (such as ATP, GTP, CTP, TTP, UTP), whereas synthases do not.
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** Wikipedia says this has changed in 1984:
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*** However, the Joint Commission on Biochemical Nomenclature (JCBN) dictates that 'synthase' can be used with any enzyme that catalyzes synthesis (whether or not it uses nucleoside triphosphates), whereas 'synthetase' is to be used synonymously with 'ligase'.[1]
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** Summary: ''' just use synthase''' & note that [http://ecocyc.org/ECOLI/NEW-IMAGE?type=GENE&object=EG11448 EcoCyc] uses synthase for ACS.
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2013/07/05:
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* Rifamycin mode of action:  "inhibition of bacterial DNA-dependent RNA synthesis.[3]
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** This is due to the high affinity of rifamycins to prokaryotic RNA polymerase. Crystal structure data of the antibiotic bound to RNA polymerase indicates that rifamycin blocks synthesis by causing strong steric clashes with the growing oligonucleotide ("steric-occlusion" mechanism)." [http://en.wikipedia.org/wiki/Rifamycin wikipedia]
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* Rifamycin resistance mechanism:    cite: [http://pubs.acs.org/doi/pdf/10.1021/cr030112j RifamycinsMode of Action, Resistance, and Biosynthesis], 2005
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** could be one of several things.  Asked Marina.
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2013/07/02:
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* we don't measure [formaldehyde] b/c we don't believe the number will be accurate.  When you lyse a cell, there are a lot of things it can react with.
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* It is very difficult to engineer K<sub>m</sub> of enzymes compared to k<sub>kat</sub>
2013/06/19:  
2013/06/19:  
* ''' Why does formate --> formaldehyde conversion require ATP if it the reaction free energy is downhill? '''
* ''' Why does formate --> formaldehyde conversion require ATP if it the reaction free energy is downhill? '''

Current revision

Back to Janet

Notes for my project by date:

2013/08/03:

  • synthase vs synthetase
    • they are both lyases, enzymes that catalyze the breaking of various chemical bonds by means other than hydrolysis and oxidation, often forming a new double bond or a new ring structure". (lyase = reverse rxn for ligase)
    • Historically, synthetase was reserved for reactions that use a high energy nucleoside triphosphate (such as ATP, GTP, CTP, TTP, UTP), whereas synthases do not.
    • Wikipedia says this has changed in 1984:
      • However, the Joint Commission on Biochemical Nomenclature (JCBN) dictates that 'synthase' can be used with any enzyme that catalyzes synthesis (whether or not it uses nucleoside triphosphates), whereas 'synthetase' is to be used synonymously with 'ligase'.[1]
    • Summary: just use synthase & note that EcoCyc uses synthase for ACS.

2013/07/05:

  • Rifamycin mode of action: "inhibition of bacterial DNA-dependent RNA synthesis.[3]
    • This is due to the high affinity of rifamycins to prokaryotic RNA polymerase. Crystal structure data of the antibiotic bound to RNA polymerase indicates that rifamycin blocks synthesis by causing strong steric clashes with the growing oligonucleotide ("steric-occlusion" mechanism)." wikipedia
  • Rifamycin resistance mechanism: cite: RifamycinsMode of Action, Resistance, and Biosynthesis, 2005
    • could be one of several things. Asked Marina.

2013/07/02:

  • we don't measure [formaldehyde] b/c we don't believe the number will be accurate. When you lyse a cell, there are a lot of things it can react with.
  • It is very difficult to engineer Km of enzymes compared to kkat

2013/06/19:

  • Why does formate --> formaldehyde conversion require ATP if it the reaction free energy is downhill?
  • Why are we calling ADH AcDH now?
    • Ac is for "acylating," the process of adding an acyl group to a compound. An acyl group is

2013/06/19:

  • ATP for our pathway comes from the TCA cycle
  • the theoretical maximum of amino acid 13C labeling is 80-90% on our timescales
    • used 13C glycerol as a control for our tests
  • expect downstream metabolites to have a lag in 13C labeling relative to early metabolites in a pathway

2013/01/30:

  • should we have used His-tags in our pathway constructs?
    • tempting because then you can purify the enzymes and run them on SDS gels to make sure they are expressed, OR test them for enzyme activity.
    • bad because His-tags chelate metal, and may stick to things in the cell

2013/01/25:

  • Regulation is one of the first targets when you put an organism under selective pressure.
  • If you are trying to evolve an enzyme in a strain, you will first get many regulatory changes on the genome of the cell.

2013/01/11:

  • Regulation is combinatorial. You can't assume that knowledge of one regulator will allow you to change a enzyme activity however you want, as that gene may be regulated by several key regulatory elements. You might not even know the others exist. ** Often there are multiple promoters within a gene. RNAseq can be useful for identifying this scenario.
  • Synthetic biologists often think of the cell as they do about circuits. One of the key problems with this is that they are neglecting context. Cells are very complicated at every level and there are many interactions one will not know about. Thus it is important to investigate how an added pathway interacts with the rest of the cell. Of course this is difficult and expensive due to the required techniques, and won't necessarily give clear answers as there is a lot of nonlinearity.
  • Cells don't usually need regulation at steady state. Regulation is used to move from one steady state to the next.
  • Often transcript abundance correlates with metabolic flux, but this isn't always the case. Our lab often finds anticorrelation between the two, likely due to the necessity to keep the concentration of toxic intermediates low.

2012/08: when you have cells under starvation, it can look like they grow for two reasons:

  • 1. they start eating the proteins in the ribosomes
  • 2. they can divide, which increases OD
  • note: neither of these cause increases in dry cell weight, so this is a good way to measure growth.

2012/04: You can drive a few kb with LacI: naturally it drives ~4.9 kb (lacZ = 3075, lacY: 1254 bp, lacA: 612 bp) 2012/05: Do we have an easy (non enzymatic) assay for methanol? Betsy's Answer: Not that I'm aware of but you could probably come up with a bioassay using feeding experiments if it doesn't have to be quantitative. What are you trying to do?

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