Biology Reference
In-Depth Information
Fig. 1. Abstract model of biochemical reactions.
MODELING AND SIMULATION
Biochemical networks
The metabolism is based on biochemical reactions. To understand the behavior of biochemical
networks, modeling and simulation are important [3]. In the case of genes, enzymes, and biochemical
reactions, database systems are available, which represent the analyzed molecular data. Several models
have been developed, but the main gap in this area of modeling and simulation is the development of
an integrative model and simulation shell [12], which allows the dynamic representation of biochemical
networks. The meaning of “integrative” is that this model enables discussion of biosynthetic processes,
gene regulation processes, and cell communication processes. Therefore, integrative models allow the
discussion of regulatory metabolic networks.
The genetic information (DNA) controls metabolism indirectly. The protein synthesis of structural
genes produces specific enzymes which catalyze biochemical reactions. The transcription of these genes
has to be regulated by enzymatic mechanisms. The fundamental model of gene regulation is based on
the model of Jacob and Monod [13] for the synthesis of the Lactose operon. The primary unit of the gene
regulation is the operon, which consists of the promoter, the operator, the gene(s), and the terminator
sequence. The RNA polymerase identifies the promoter sequence of the operon and carries out the
transcription process. The affinity of the promoter/RNA polymerase complex is defined by specific DNA
signal structures, which are called the Pribnow box and the
−
35 box of the promoter (prokaryotes).
Homeotic genes, transposons, enhancers and silencers demonstrate that gene regulation is a complex
process. The metabolic control of a cell is defined by biochemical reactions, which change substrates
into products (S
→
P). This can be done spontaneously or catalyzed by specific enzymes (S-E
→
P).
Most of the biochemical reactions are 2-way processes, which are catalyzed by enzymes (S
←
E
→
P). Therefore, concentration rates are important. In some cases specific molecules, which are called
inhibitors (I), are able to reduce the flux. However, the flux of biosynthetic processes is controlled by
enzyme affinity, enzyme concentration, and reaction rate (p).
These parameters can be modified by
proteins and enzymes, which are called influence proteins.
In the case of 2-way biochemical reactions, the enzyme will catalyze biochemical reactions from
the higher to the lower level of the concentration rates. Moreover, kinetic effects are important [14].
Most biochemical reactions follow the Michaelis-Menten kinetic scheme, which is characterized by the
following equation:
V
=
−
dS/dt
=
V
max
∗
S
/
S
+
K
m
