3.1.1.3.1.1. etfl.data.ecoli¶
3.1.1.3.1.1.1. Module Contents¶
3.1.1.3.1.1.1.1. Functions¶
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ATP synthesis rate of F1F0 ATP synthase |
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# Ribosome |
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# RNAP |
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# RNAP |
Read table with data on Π, the fraction of RNAP holoenzyme. We define Π: |
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We are given the active RNAP ratio Π, which we approximate to be |
3.1.1.3.1.1.1.2. Attributes¶
- etfl.data.ecoli.get_atp_synthase_coupling(atps_name)[source]¶
ATP synthesis rate of F1F0 ATP synthase Range at room temperature ∼0.060-0.10 μmol/min/mg of membrane protein : at 37°C 0.20 μmol/min/mg of membrane protein Organism Bacteria Escherichia coli Reference Tomashek JJ, Glagoleva OB, Brusilow WS. The Escherichia coli F1F0 ATP synthase displays biphasic synthesis kinetics. J Biol Chem. 2004 Feb 6 279(6):4465-70 DOI: 10.1074/jbc.M310826200 p.4467 right column bottom paragraphPubMed ID14602713 Primary Source [18] Etzold C, Deckers-Hebestreit G, Altendorf K. Turnover number of Escherichia coli F0F1 ATP synthase for ATP synthesis in membrane vesicles. Eur J Biochem. 1997 Jan 15 243(1-2):336-43.PubMed ID9030757 Method Luciferase assay Comments P.4467 right column bottom paragraph: “Previously, Etzold et al. (primary source) used the luciferase assay to measure the turnover number of the ATP synthase during synthesis by membrane vesicles of E. coli. They measured ATP synthesis rates of ∼0.060-0.10 μmol/min/mg of membrane protein at room temperature and 0.20 μmol/min/mg of membrane protein at 37 °C.” Entered by Uri M ID 115175 :return:
- etfl.data.ecoli.get_dna_polymerase(dna_pol_name='DNAPol3')[source]¶
https://en.wikipedia.org/wiki/DNA_polymerase_III_holoenzyme
The replisome is composed of the following:
- 2 DNA Pol III enzymes, each comprising α, ε and θ subunits. (It has been proven that there is a third copy of Pol III at the replisome.[1])
the α subunit (encoded by the dnaE gene) has the polymerase activity. the ε subunit (dnaQ) has 3’→5’ exonuclease activity. the θ subunit (holE) stimulates the ε subunit’s proofreading.
2 β units (dnaN) which act as sliding DNA clamps, they keep the polymerase bound to the DNA. 2 τ units (dnaX) which act to dimerize two of the core enzymes (α, ε, and θ subunits). 1 γ unit (also dnaX) which acts as a clamp loader for the lagging strand Okazaki fragments, helping the two β subunits to form a unit and bind to DNA. The γ unit is made up of 5 γ subunits which include 3 γ subunits, 1 δ subunit (holA), and 1 δ’ subunit (holB). The δ is involved in copying of the lagging strand. Χ (holC) and Ψ (holD) which form a 1:1 complex and bind to γ or τ. X can also mediate the switch from RNA primer to DNA.[2] :return:
- etfl.data.ecoli.get_rib()[source]¶
# Ribosome
rRNA: b3851: K01977 16S ribosomal RNA | (RefSeq) rrsA; 16S ribosomal RNA of rrnA operon b3854: K01980 23S ribosomal RNA | (RefSeq) rrlA; 23S ribosomal RNA of rrnA operon b3855: K01985 5S ribosomal RNA | (RefSeq) rrfA; 5S ribosomal RNA of rrnA operon # rPeptides: See file ribosomal_proteins_ecoli.tsv
- Returns
- etfl.data.ecoli.get_rnap()[source]¶
# RNAP
b3295: K03040 DNA-directed RNA polymerase subunit alpha [EC:2.7.7.6] | (RefSeq) rpoA; RNA polymerase, alpha subunit b3649: K03060 DNA-directed RNA polymerase subunit omega [EC:2.7.7.6] | (RefSeq) rpoZ; RNA polymerase, omega subunit b3987: K03043 DNA-directed RNA polymerase subunit beta [EC:2.7.7.6] | (RefSeq) rpoB; RNA polymerase, beta subunit b3988: K03046 DNA-directed RNA polymerase subunit beta’ [EC:2.7.7.6] | (RefSeq) rpoC; RNA polymerase, beta prime subunit
- Returns
- etfl.data.ecoli.read_growth_dependant_rnap_alloc()[source]¶
Read table with data on Π, the fraction of RNAP holoenzyme. We define Π: Π = holoRNAP / RNAP_total = holoRNAP / (holoRNAP + RNAP_free) :return:
- etfl.data.ecoli.get_growth_dependant_transformed_rnap_alloc()[source]¶
We are given the active RNAP ratio Π, which we approximate to be
Π = holoRNAP / RNAP_total = holoRNAP / (holoRNAP + RNAP_free)
For our calculations, we are interested in q = holoRNAP / RNAP_free
Π = holoRNAP / (holoRNAP + RNAP_free) <=> 1/Π = 1 + 1/q <=> 1/Π - 1 = 1/q <=> Π/(1 - Π) = q
- Returns