Here is a hypothetical set of reactions required to produce a molecule of mRNA for the protein product X:
| Reaction number (Probability) (Duration) | Reactants | Catalysts | Products |
|---|---|---|---|
| 0 ( .7 ) ( 1 ) |
D TBP |
D/TBP | |
| Join TFIID with the Transcription Binding Protein. | |||
| 1 ( .7 ) ( 1 ) |
D/TBP TATA:Gene.X-1 ATP |
D/TBP/TATA:Gene.X-1 ADP PO4 | |
| Bind to the TATA box of Gene.X, Segment 1. | |||
| 2 ( .7 ) ( 1 ) |
D/TBP/TATA:Gene.X-1 ABF EH ATP |
PolyII |
D/TBP/TATA:Gene.X-1/ABF/PolyII/EH ADP PO4 |
| Build the transcription initiation complex. | |||
| 3 ( .7 ) ( 1 ) |
D/TBP/TATA:Gene.X-1 ABF EH ATP Gene.XActivator |
PolyII |
D/TBP/TATA:Gene.X-1/ABF/PolyII/EH ADP PO4 Gene.XActivator |
| Build the transcription initiation complex under enhancement. | |||
| 4 ( .7 ) ( 1 ) |
D/TBP/TATA:Gene.X-1/ABF/PolyII/EH ATP |
D/TBP/TATA:Gene.X-1/ABF/PolyII/EH/PO4 ADP | |
| Phosphorylate the Polymerase to activate it. | |||
| 5 ( .7 ) ( 1 ) |
D/TBP/TATA:Gene.X-1/ABF/PolyII/EH/PO4 mRNAPrecursor Gene.X-2 |
D/TBP/TATA:Gene.X-1 ABF PolyII/EH/PO4/Gene.X-2 mRNAX-1 ADP PO4 | |
| Transcribe the first mRNA segment for Gene X | |||
| 6 ( .7 ) ( 1 ) |
PolyII/EH/PO4/Gene.X-2 Gene.X-3 mRNAX-1 mRNAPrecursor ATP |
PolyII/EH/PO4/Gene.X-3 mRNAX-1.2 ADP PO4 Gene.X-2 | |
| Transcribe the second mRNA segment for Gene X | |||
| 7 ( .7 ) ( 1 ) |
PolyII/EH/PO4/Gene.X-3 mRNAPrecursor mRNAX-1.2 TermII |
PolyII/EH/PO4/Gene.X-3/TermII mRNAX ADP PO4 | |
| Transcribe the final mRNA segment for Gene X, add the termination complex, and release the transcript. | |||
| 8 ( .7 ) ( 1 ) |
PolyII/EH/PO4/Gene.X-3/TermII ATP |
PolyII EH PO4 Gene.X-3 TermII ADP PO4 | |
| Break up the transcription complex. | |||
| 9 ( .1 ) ( 1 ) |
mRNA.X ATP |
mRNAPrecursor mRNAPrecursor mRNAPrecursor ADP PO4 | |
| This reaction degrades mRNA to force an equilibrium. | |||
Note that Gene X is assumed to be composed of 3 separate segments (X-1, X-2, X-3) and produces mRNA.X in a segmented fashion. This is done to allow multiple Polymerase II molecules to operate on the same Gene in the usual transcription "pipeline". There are other ways to simulate such parallel activity, but this one is relatively simple.
And here are the reactions that translate mRNA.X to ProteinX:
| Reaction number (Probability) (Duration) | Reactants | Catalysts | Products |
|---|---|---|---|
| 10 ( .7 ) ( 1 ) |
Gene.tRNA tRNAPrecursor ATP |
PolyIII |
tRNA Gene.tRNA PolyIII ADP PO4 |
| Make a tRNA molecule. | |||
| 11 ( .7 ) ( 1 ) |
Gene.rRNA5S rRNAPrecursor ATP |
PolyIII |
Gene.rRNA5S rRNA5S PolyIII ADP PO4 |
| Make a 5S rRNA. | |||
| 12 ( .7 ) ( 1 ) |
Gene.rRNA5.8-18-28S rRNAPrecursor rRNAPrecursor rRNAPrecursor ATP |
PolyI |
Gene.rRNA5.8-18-28S rRNA5.8-18-28S PolyI ADP PO4 |
| Make the large transcript for rRNA5.8-18-28S. | |||
| 13 ( .7 ) ( 1 ) |
rRNA5.8-18-28S ATP |
ribonucleaseMRP |
rRNA5.8S rRNA18S rRNA28S ADP PO4 |
| Cut the large transcript into 5.8, 18 and 28S rRNAs | |||
| 14 ( .7 ) ( 1 ) |
rRNA5S rRNA5.8S rRNA28S |
LargeRibosomeUnit | |
| Make the large ribosomal unit | |||
| 15 ( .7 ) ( 1 ) |
eIF-2-Protein1 eIF-2-Protein2 eIF-2-Protein3 |
eIF-2 | |
| Make translation initiation factor 2. | |||
| 16 ( .7 ) ( 1 ) |
rRNA18S tRNAmet eIF-2 GTP |
rRNA18S/tRNAmet/eIF-2/GTP | |
| Begin the translation initiation complex | |||
| 17 ( .7 ) ( 1 ) |
eIF-4A eIF-4E eIF-4G |
eIF-4 | |
| Assemble eIF-4. | |||
| 18 ( .7 ) ( 1 ) |
rRNA18S/tRNAmet/eIF-2/GTP PADP mRNA.X eIF-4 |
rRNA18S/tRNAmet/eIF-2/GTP/PADP/mRNA.X/eIF-4 | |
| More translation inititiation complex. | |||
| 19 ( .7 ) ( 1 ) |
rRNA18S/tRNAmet/eIF-2/GTP/PADP/mRNA.X/eIF-4 LargeRibosomeUnit |
rRNA18S/tRNAmet/eIF-2/GDP/PADP/mRNA.X/eIF-4/LargeRibosomeUnit PO4 | |
| Add the Large Ribosome subunit to the initiation complex. | |||
| 20 ( .7 ) ( 1 ) |
rRNA18S/tRNAmet/eIF-2/GDP/PADP/mRNA.X/eIF-4/LargeRibosomeUnit tRNA ProteinPrecursor ATP |
rRNA18S/tRNAmet/eIF-2/GDP/PADP/mRNA.X/eIF-4/LargeRibosomeUnit/ProteinPrecursor ADP PO4 tRNA | |
| Begin adding amino acids. | |||
| 21 ( .7 ) ( 1 ) |
rRNA18S/tRNAmet/eIF-2/GDP/PADP/mRNA.X/eIF-4/LargeRibosomeUnit/ProteinPrecursor CRF GTP |
rRNA18S tRNAmet eIF-2 GDP PADP mRNA.X eIF-4 LargeRibosomeUnit StraightProtein.X CRF GDP PO4 | |
| Release the protein and break up the translation complex. | |||
| 22 ( .7 ) ( 1 ) |
StraightProtein.X |
Chaperone |
Protein.X |
| Fold Protein X into proper configuration. | |||
| 23 ( .2 ) ( 1 ) |
Protein.X Ubiquitin ATP |
Protein.X/Ubiquitin ADP PO4 | |
| Begin process to degrade Protein X molecule | |||
| 24 ( .3 ) ( 1 ) |
Protein.X/Ubiquitin ATP |
Proteasome |
ProteinPrecursor Ubiquitin ADP PO4 |
| Degrade a Protein X molecule | |||
Note that Gene X is assumed to be composed of 3 separate segments (X-1, X-2, X-3) and produces mRNA.X in a segmented fashion. This is done to allow multiple Polymerase II molecules to operate on the same Gene in the usual transcription "pipeline". There are other ways to simulate such parallel activity, but this one is relatively simple.