COLLEGE OF NATURAL SCIENCES

DEPARTMENT OF PLANT SCIENCES, MICROBIOLOGY & BIOTECHNOLOGY

BIOCHEMICAL PROCESSES IN ORGANISMS

WAYS WE STUDY METABOLIC PATHWAYS

GROUP 1

AWORI ANNA 23/U/07080/PS

AYELLA JOHNATHAN BONGOMIN 23/U/07171/PS
JJUKO LARRY ABRAHAM 23/U/08447/PS
NANYANGE CHRISTINE ANGELL 23/U/15342/PS
MWASE JOSHUA MARK 23/U/24242/PS
RUHANGARIYO EVELYN 23/U/17112/PS
NAMBALIRWA BENITAH 23/U/1104
KWEHAYO PRAISE 23/U/0657
ABUBAKARI FAHAD SSEMPEWO 22/U/22544
JEMIMAH RUTH ETIANG 20/U/11835/PS
Ways We Study Metabolic Pathways

Metabolic pathways are networks of biochemical reactions that occur within living
organisms, enabling them to convert molecules into energy, synthesize essential
molecules, and eliminate waste products. A comprehensive understanding of these
pathways is crucial for elucidating disease mechanisms, designing therapeutic
interventions, and enhancing biotechnological applications.

1. Genetic Approaches.
Genetic techniques, such as gene knockout or RNA interference, allow researchers to
selectively perturb specific genes involved in metabolic pathways. For instance, by
inactivating a gene encoding an enzyme within the glycolysis pathway, we can elucidate
the consequences of its absence, allowing a deeper comprehension of its function.

2. Proteomics and Metabolomics.

Using mass spectrometry-based techniques, such as liquid chromatography-mass
spectrometry (LC-MS), researchers can identify and quantify the abundance of proteins
and metabolites, respectively. These approaches help comprehend the dynamic changes
occurring within metabolic pathways under various conditions. One illustrative example
is the analysis of the Krebs cycle intermediates to unravel the metabolic effects of a drug
or a disease.

3. Enzyme Kinetics.
Analyzing enzyme kinetics provides insights into the rates of metabolic reactions and
enzyme activities within a pathway. This approach involves measuring the change in
reactant or product concentration over time. By quantitatively characterizing the enzyme
kinetics of a specific reaction, we can deduce its role within the metabolic network.

4. Isotope Tracing.
Stable isotope tracing involves incorporating non-radioactive isotopes into metabolites
and tracking their fate. This technique allows researchers to determine metabolic fluxes,
identify branching points, and evaluate pathway connectivity. For instance, by feeding
^13C-labeled glucose to cells, we can trace its incorporation into different metabolic
intermediates and comprehend carbon flow within the pathways.

5. Computational Modeling.
Mathematical modeling of metabolic pathways provides a powerful tool to uncover their
behavior and predict system dynamics. This approach combines biochemical data with
theoretical frameworks to simulate pathway behavior and identify key regulatory
components. Examples include Boolean modeling to analyze signal transduction pathways
or kinetic models simulating large-scale metabolic networks.

6. High-Throughput Screening.
High-throughput screening methods enable the rapid analysis of large compound libraries
for identifying enzymatic inhibitors or activators. By applying these techniques to
metabolic pathways, researchers can identify lead compounds for drug development.
These techniques have been instrumental in discovering novel drugs targeting metabolic
diseases, such as type 2 diabetes.

7. Flux Balance Analysis (FBA).

FBA is a computational approach that quantifies metabolic fluxes through a stoichiometric
model of metabolic pathways, considering constraints such as nutrient availability. By
integrating experimental data and mathematical modeling, FBA predicts cellular behavior
and aids in metabolic engineering applications. For instance, FBA has been used to design
optimized microbial strains for biofuel production.

8. Omics Integration.
Integrating data from genomics, transcriptomics, proteomics, and metabolomics allows a
holistic understanding of metabolic pathways. This comprehensive approach enables the
identification of regulatory elements, understanding system-level responses, and
predicting metabolic states under specific conditions. Notably, omics integration has
greatly contributed to personalized medicine and cancer metabolism research.

9. Metabolic Flux Analysis (MFA).

MFA uses isotopic tracers to quantify metabolic fluxes within a pathway or an entire
organism. By combining isotopic labeling experiments with mathematical models, MFA
estimates flux distributions under different physiological or environmental conditions.
MFA has been pivotal in understanding host-microbiome interactions and elucidating
metabolic shifts in cancer cells.

10. Functional Genomics.

Studying metabolic pathways through functional genomics involves systematic gene
perturbation or over-expression in a high-throughput manner. Techniques like CRISPR-
Cas9 enable targeted genetic modifications at scale, unveiling the role of specific genes in
the regulation of metabolic pathways. Functional genomics approaches have elucidated
novel drug targets and therapeutic strategies for various metabolic disorders.

The study of metabolic pathways encompasses a diverse array of techniques and

methodologies. By employing a combination of genetic approaches, proteomics,
metabolomics, computational modeling, and other emerging tools, researchers can gain
a deeper understanding of the intricate nature of metabolic pathways. This knowledge
not only enhances our comprehension of fundamental biological processes but also
provides valuable insights for therapeutic interventions, biotechnology.