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A kinetic model for the synthesis of proteins in prokaryotes is ..

A mathematical model for prokaryotic protein synthesis

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Mechanisms of Protein Synthesis: In prokaryotes, the RNA synthesis ..

Both data sets show that protein synthesis capacity influences the assembly strategy of protein synthesis and hence the genomic organization of genes. A sequential synthesis, caused by a low protein synthesis capacity, leads to smaller operon sizes. On the other hand, if protein synthesis capacity is high, the optimality of a simultaneous synthesis leads to larger operon sizes. Hence, also on the level of protein complexes protein biosynthetic capacities are an important factor in the formation and dissolution of operons. This observation is further emphasized by a recent study about the optimal genomic organization of the nitrogen fixation gene cluster of Klebsiella oxytoca []. Our results provide an explanation for the unexpected result that the disruption of operons leads to a higher production rate of active forms of nitrogenase in Klebsiella oxytoca and the transferred cluster in Escherichia Coli.

In bacteria protein is synthesized at the rate of about 20 amino acids per second.

To validate our hypotheses about the influence of protein synthesis on the genomic structure, we used data of protein complexes in many organisms with known operon structure and protein synthesis capacity. For protein complexes we used two independent data sets. The first was retrieved from the EcoCyc database [] covering all protein complexes with at least three protein entities present in E. coli. The same was done for the gathered protein complexes from the protein structure database PDB [], which is the second data set.

Why is protein synthesis different in prokaryotes and eukaryotes

Given these parameters, we were able to calculate a cell's material and energy expenditures for protein synthesis using a flux balance approach.

As in our previous work on metabolic pathways [], the overall synthesis rate of protein is constrained. Therefore a total maximum synthesis capacity dtotal is introduced:

These results are comparable with our previous results for metabolic pathways, which show the same strategies and their impact on the operonic structure of prokaryotes. Both results extend our understanding of evolutionary forces driving operon formation and dissolution. Most hypotheses explain why operons have an advantage like better co-regulation or easier horizontal gene transfer (selfish operons). In contrast, through our work we were able to identify factors that lead to the optimality of arranging co-regulated proteins in separate operons. Moreover, our findings also provide guidelines for metabolic engineering to optimally design operons containing protein complexes of interest when transferred from one species into a production strain.

by John Hopfield for protein synthesis.

The protein synthesis network exhibited one extreme pathway per messenger RNA synthesized and one extreme pathway per protein synthesized.

The solutions of optimizations are analyzed in a first step by visualizing the time course of protein concentrations and synthesis rates. Additionally, the advantage of the optimal solution to a simultaneous synthesis strategy is calculated and possible correlations with the randomized parameters are investigated. The simultaneous strategy was chosen as a reference and is defined by a constant synthesis rate usimultan(t) = 0.25. If the individual synthesis capacity di of a subunit is lower than 0.25, the synthesis rate usimultan of this subunit is limited to di and the remaining free synthesis capacity is equally distributed over the other subunits. The advantage of an optimal synthesis strategy uoptimal is calculated as:

Under these constraints the objective is to maximize the production of the final protein complex ABCD x7(t) over a fixed time span Tmax by finding the optimal program for protein synthesis and assembly:

The fundamental protein synthesis network described by this formalism was analysed via extreme pathway and flux balance analyses.
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  • The rate of protein synthesis is higher in ..

    What is the difference between Protein Synthesis in Prokaryotic and Eukaryotic

  • it must have had a prior function before protein synthesis

    Which of the following is a characteristic of protein synthesis in prokaryotes ..

  • They must find the correct starting point for protein synthesis

    The feedback system is responsible for balancing the ribosome synthesis rate with the need for protein ..

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Protein synthesis rate is the predominant regulator of

2011):
Coding RNAs
RNAi
Prokaryotes
In prokaryotes, transcription and translation happen simultaneously (they are "coupled")

Prokaryotes regulate gene expression (and therefore their metabolism) almost entirely by regulating transcription.

The lack of a nucleus makes this very efficient.
Refer to organized clusters of genes that all contribute to a particular metabolic task.

Prokaryotes only!!!

2 Major Flavors:
Inducible
and
Repressible
Operons:
Inducible:
Repressible:
"Up Regulation":
Precursor
Enzyme 1
Enzyme 2
Enzyme 3
-
-
Gene 1
Gene 2
Gene 3
Gene 4
Gene 5
Product
Inhibition of
enzyme activity
Inhibition of
transcription
Francois Jacob & Jacques Monod
Nobel Prize: 1965
For metabolic pathways that are usually "off".

Ex: The
Lac
Operon
(digests lactose)
For metabolic pathways that are usually "on".

Ex: The
Trp
Operon
(synthesizes tryptophan)
When Lactose is absent:
The repressor protein (made by the
LacI

gene) is able to attach to the
operator
(a region of the promoter)
RNA polymerase cannot transcribe the
structural genes
(
LacZ
,
LacY
and
LacA
) that the cell needs to be able to digest lactose, since it can not attach to the promoter.
This is how things remain in the cell as long as there is no lactose present.
When Lactose is present:
The
inducer
molecule (
allolactose
, a form of lactose) binds to the repressor protein.

Protein Synthesis Post Workout - Workout Routines


RNA polymerase can not transcribe the structural genes that the cell uses to synthesize tryptophan.
This is how things remain in the cell until tryptophan is no longer present.
What kind of feedback?
A way to increase the rate of transcription of an operon

Ex: The
CAP/cAMP
System
When Lactose is present and glucose is low:
Low glucose means the amount of
cyclic AMP
(
cAMP
) is high
cAMP binds to the
Catabolite Activator Protein
(
CAP
), activating it
The Activated
cAMP/CAP complex
increases the rate of transcription of the lac operon (and ~100 other catabolic operons), boosting the rate of transcription several fold.
When Glucose and Lactose are both present:
Normal glucose level means the amount of cyclic AMP (cAMP) is low
cAMP is not bound to CAP
CAP is inactive.
Very little lac structural gene transcription occurs.
What kind of feedback?
What kind of logic?
What kind of logic?
What kind of logic?
Polyribosomes demonstrating the coupling of transcription and translation in prokaryotes:
Prokaryotic control of metabolism through control of transcription:

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In this work, we investigate optimality principles behind synthesis strategies for protein complexes using a dynamic optimization approach. We show that the cellular capacity of protein synthesis has a strong influence on optimal synthesis strategies reaching from a simultaneous to a sequential synthesis of the subunits of a protein complex. Sequential synthesis is preferred if protein synthesis is strongly limited, whereas a simultaneous synthesis is optimal in situations with a high protein synthesis capacity. We confirm the predictions of our optimization approach through the analysis of the operonic organization of protein complexes in several hundred prokaryotes. Thereby, we are able to show that cellular protein synthesis capacity is a driving force in the dissolution of operons comprising the subunits of a protein complex. Thus, we also provide a tested hypothesis explaining why the subunits of many prokaryotic protein complexes are distributed across several operons despite the presumably less precise co-regulation.

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