DEPARTMENT OF BIOCHEMITRY

FACULTY OF LIFE SCIENCES

UNIVERSITY OF BENIN
BENIN-CITY
A UNDERGRADUATE SEMINAR PRESENTATION
BY

OKOLIE UGONNA STANLEY

LSC2006838

ON

BIOCHEMICAL FLUX AND CONFUSION

MAY, 2024
 Introduction
• Biochemical flux is defined as the rate of metabolic
reactions in living systems (Noguchi et al., 2021).

• Understanding biochemical flux is crucial for gaining

insights into cellular metabolism and its regulation.

• However, there are many sources of confusion

surrounding the analysis of biochemical fluxes.
Challenges in Measuring Flux
• Directly measuring intracellular fluxes is difficult due to
technical limitations (McCloskey et al., 2015).

• Measuring fluxes relies on costly techniques such as

stable isotope labeling and nuclear magnetic resonance
(NMR) spectroscopy.

• Alternative computational approaches for estimating

fluxes also have significant limitations.
Flux Balance Analysis
• Flux balance analysis is a widely used constraint-based
modeling approach for studying metabolic fluxes (Orth et
al., 2010).

• This approach assumes that the metabolic network is at

steady-state and that the flux distribution is optimal for a
given objective function.

• The results obtained from flux balance analysis can be

confusing due to the inherent assumptions and the
selection of the objective function (Chen and Vitkup, 2021).
13C Metabolic Flux Analysis
• 13C metabolic flux analysis tracks the redistribution of
13C isotopes to determine in vivo metabolic fluxes
(Nargund and Sriram, 2021).

• While powerful, this technique involves a complicated

experimental and computational workflow.

• It is prone to errors arising from measurements, modeling,

and underdetermined systems.
Kinetic Modeling
• Kinetic modeling aims to predict the dynamic behavior
of metabolic fluxes based on kinetic rate laws (Saa and
Nielsen, 2016).

• This approach is extremely data-intensive, requiring in

vivo kinetic parameters for all enzymes in the network.

• The estimation of kinetic parameters is challenging, and

uncertainties can compound, leading to confusing
results (Srinivasan et al., 2015).
Accounting for Regulation

• Metabolic fluxes are influenced by various regulatory

mechanisms, including gene expression, protein levels,
and enzymatic regulation (McCloskey et al., 2022).

• Integrating these different layers of regulation into flux

models is crucial but also a source of confusion.

• Such integration requires multi-omics data and the

development of complex integrated models (Opdam et
al., 2017).
Metabolic Channeling

• Metabolic channeling refers to the temporary

sequestration of metabolic intermediates away from the
bulk metabolism (Sweetlove and Fernie, 2018).

• This phenomenon challenges our understanding of steady-

state assumptions commonly made in flux analysis.

• Modeling and quantifying the effects of metabolic

channeling on flux distributions is difficult (Islam and
Petre, 2020).
Spatial Organization
• Metabolic reactions are compartmentalized within
different organelles and subcellular structures in cells
(Scharlemann et al., 2021).

• The transport of metabolites between these

compartments can create bottlenecks and affect
metabolic fluxes.

• Accounting for spatial constraints and

compartmentalization in flux models is complex and
often overlooked (Castellanos et al., 2017).
Experimental Evolution
• Experimental evolution studies provide a systems-level
view of how metabolic fluxes are regulated in response to
different selective pressures (Rowland and Deleniv, 2022).

• However, linking genotypic changes to observed flux

phenotypes remains a confusing task (Charubin et al.,
2022).

• Inconsistencies between experimental observations and

computational predictions of flux distributions are
common.
Conclusion
Understanding biochemical flux is a key challenge in
metabolic engineering and systems biology, but the field
is rife with confusion.
Addressing this confusion requires integrating multi-
scale data, carefully dealing with assumptions, and
developing interdisciplinary approaches.
Collaborative efforts from researchers with diverse
expertise are needed to untangle the complexity of
biochemical flux analysis.