Difference between revisions of "Team:NCKU Tainan/Model"

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                                       </div>
 
                                       </div>
 
                                     </div>
 
                                     </div>
 +
    <table>
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        　<tr>
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            　<th>Temperature</th>
 +
            　<th>Time</th>
 +
              <th></th>
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        </tr>
  
 +
        <tr>
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            　<td>94 ℃</td>
 +
            　<td>3 min.</td>
 +
              <td rowspan="3">25～30 cycles</td>
 +
        </tr>
 +
 +
        　<tr>
 +
            　<td>94 ℃</br>(Denaturation)</td>
 +
            　<td>40 sec</td>
 +
              <td></td>
 +
        </tr>
 +
 +
        <tr>
 +
            　<td>57.5 ℃</br>(Annealing)</td>
 +
            　<td>30 sec</td>
 +
              <td></td>
 +
        </tr>
 +
 +
        　<tr>
 +
            　<td>72 ℃</br>(Extension)</td>
 +
            　<td>Depend on sequence size</br>(2 kbp/min. for Taq)</td>
 +
              <td></td>
 +
        </tr>
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 +
        <tr>
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            　<td>72 ℃</td>
 +
            　<td>5 min.</td>
 +
              <td></td>
 +
        </tr>
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 +
        <tr>
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            　<td>4 ℃</td>
 +
            　<td>∞</td>
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              <td></td>
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        </tr>
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 +
    </table>
 
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                                     <div class="row">
 
                                         <div class="col-12" id="CO2_vs_xylose">
 
                                         <div class="col-12" id="CO2_vs_xylose">

Revision as of 17:35, 20 September 2018

Model

Achievement

Purpose

CO2 uptake

CO2 uptake Kf Kr
R1 $${[CO_2]_{air} \rightarrow [CO_2]_{uptake}}$$ 9.23E-04 4.78E-04
R2 $${[CO_2]_{uptake} + [H_2O] \rightarrow [H_2CO_3]}$$ 0.062 23.7
R3 $${[H_2CO_3] \rightarrow [H^+] + [HCO_3^-]}$$ 8000000 4.7E10
R4 $${[HCO_3^-] \rightarrow [H^+] + [CO_3^{2-}]}$$ 3 5E10
R5 $${[H^+] + [HCO_3^-] \longleftrightarrow [H_2O] + [CO_2]_{uptake}}$$ Vmax Km
0.47333 0.0062

CO2 Metabolism

E4P erythrose-4-phosphate
F6P fructose-6-phosphate
FBP fructose-1,6-bisphosphate
G6P glucose-6-phosphate
GAP glyceraldehyde-3-phosphate
PEP phosphoenol pyruvate
PYR pyruvate
R5P ribose-5-phosphate
Ru5P ribulose-5-phosphate
S7P sedoheptulose-7-phosphate
X5P xylulose-5-phosphate
6PG 6-phosphogluconate
DHAP Dihydroxyacetone phosphate
3PG 3-Phosphoglyceric acid
RuBP ribulose-1,5-bisphosphate
PRK Phosphoribulokinase
Rubisco Ribulose-1,5-bisphosphate carboxylase/ oxygenase
AcCoA Acetyl-CoA
CIT Citrate
ICIT Isocitrate
AKG Alpha-ketoglutarate
SUCCoA Succinyl-CoA
SUCC Succinate
FUM Fumarate
MAL Malate
OAA Oxaloacetic acid
GOX Glyoxylate

Pathway

CO2 bypass pathway Vmax (1/S) KM (mM)
A1 $${Xylose \rightarrow Xylulose}$$ $${Xylulose + ATP \rightarrow X5P}$$ 0.02456 124.55879
A2 $${X5P \rightarrow Ru5P}$$ 0.08 12.5
A3 $${Ru5P \xrightarrow{PRK} RuBP}$$ 225.81858 0.27
A4 $${RuBP + CO_2 \xrightarrow{RuBisCO} 3PG}$$ Vmax Krubp KCO2
333.33 53 2.7
Pentose Phosphate Pathway Vmax (1/S) KM (mM)
B1 $${Ru5P \rightarrow R5P}$$ 0.13672 12.5
B2 $${X5P + R5P \rightarrow S7P + GAP}$$
$${X5P \rightarrow S7P}$$ 58.27 4.96E-09
$${X5P \rightarrow GAP}$$ 58.27 48
$${R5P \rightarrow S7P}$$ 58.27 0.008
$${R5P \rightarrow GAP}$$ 58.27 3.05E-07
B3 $${S7P + GAP \rightarrow F6P + E4P}$$
$${S7P \rightarrow E4P}$$ 58.27 2.524
$${S7P \rightarrow F6P}$$ 58.27 6.10E-09
$${GAP \rightarrow E4P}$$ 58.27 1.73E-07
$${GAP \rightarrow F6P}$$ 58.27 8.23E-09
B4 $${E4P + X5P \rightarrow F6P + GAP}$$
$${E4P \rightarrow F6P}$$ 1 1
$${E4P \rightarrow GAP}$$ 5.827E-4 1.733E-7
$${X5P \rightarrow F6P}$$ 0.05827 1.733E-7
$${X5P \rightarrow GAP}$$ 0.005827 48.8
B5 $${FBP \rightarrow GAP}$$ 135.425 4
B6 $${DHAP \longleftrightarrow GAP}$$ Vmf Vmr KmDHAP KmGAP
0.2394 0.24 0.812 0.245
B7 $${FBP \rightarrow DHAP}$$ 0.0001247 0.04
B8 $${F6P + ATP \rightarrow FBP + ADP}$$ 88.2533 0.017
B9 $${F6P \rightarrow G6P}$$ 88.2353 0.017
B10 $${G6P + NADP^+ \rightarrow 6PG + NADPH}$$ Vmax KmG6P KmNADP
11.736 0.12 0.0123
B11 $${6PG + NADP^+ \rightarrow Ru5P + NADPH}$$ 1.0 0.044
B12 $${GAP + NADP^+ + ADP \rightarrow 3PGA + NADPH + ATP}$$ 0.4 0.013
B13 $${3PGA \rightarrow PEP}$$ 0.43478 0.23
B14 $${PEP \rightarrow PYR}$$ 0.23148 0.45
TCA cycle Vmf (mM/min) Vmr (mM/min) Ks (mM) Kp (mM)
C1 $${PEP + HCO_3^- + NAD^+ \rightarrow OAA + NADH}$$ 1 1 1 1
C2 $${AcCoA \rightarrow CIT}$$ 64.8 0.648 0.05 0.12
C3 $${CIT \rightarrow ICIT}$$ 31.2 0.312 1.7 0.7
C4 $${ICIT + NADP^+ \rightarrow AKG + NADPH + CO_2}$$ 10.2 0.102 0.03 0.3
C5 $${AKG + NAD^+ \rightarrow AKG + NADPH + CO_2}$$ 57.344 0.57344 0.1 1.0
C6 $${SUCCoA + ADP \rightarrow SUCC + ATP}$$ 6.54 0.0651 0.015 0.15
C7 $${SUCC + FAD \rightarrow FUM + FADH_2}$$ 1.02 1.02 0.12 0.15
C8 $${FUM \rightarrow MAL}$$ 887.7 87.7 0.25 2.38
C9 $${MAL + NAD^+ \rightarrow OAA + NADH}$$ 184 184 0.833 0.0443
C10 $${OAA \rightarrow CIT}$$ 64.8 0.648 0.012 0.12
C11 $${PYR \rightarrow NADH + AcCoA + CO_2}$$ Vmax (1/s) KM (mM)
0.00518 1.5
C12 $${ICIT \rightarrow GOX}$$ 1.172 0.01172 0.145 0.13
C13 $${GOX \rightarrow MAL}$$ 20 0.2 0.057 1.0
C14 $${ICIT \rightarrow SUCC + GOX}$$ Vmf (mM/min) Vmr (mM/min) Kicit (mM) Ksucc (mM) Kgox (mM)
1.172 0.012 0.145 0.59 0.13
　 　 　 　 　 　 　 　 　 　 　 　 　 　 　 　 　
TemperatureTime
94 ℃3 min. 25～30 cycles
94 ℃
(Denaturation)		40 sec
57.5 ℃
(Annealing)		30 sec
72 ℃
(Extension)		Depend on sequence size
(2 kbp/min. for Taq)
72 ℃5 min.
4 ℃∞

CO2 v.s. Xylose

Reference

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