Carbohydrates

A carbohydrate (ˌkɑːrboʊˈhaɪdreɪt) is a biomolecule consisting of carbon (C), hydrogen (H) and oxygen (O) atoms, usually with a hydrogen–oxygen atom ratio of 2:1 (as in water) and thus with the empirical formula (where m may or may not be different from n), which does not mean the H has covalent bonds with O (for example with , H has a covalent bond with C but not with O). However, not all carbohydrates conform to this precise stoichiometric definition (e.g., uronic acids, deoxy-sugars such as fucose), nor are all chemicals that do conform to this definition automatically classified as carbohydrates (e.g. formaldehyde and acetic acid). The term is most common in biochemistry, where it is a synonym of saccharide (), a group that includes sugars, starch, and cellulose. The saccharides are divided into four chemical groups: monosaccharides, disaccharides, oligosaccharides, and polysaccharides. Monosaccharides and disaccharides, the smallest (lower molecular weight) carbohydrates, are commonly referred to as sugars. While the scientific nomenclature of carbohydrates is complex, the names of the monosaccharides and disaccharides very often end in the suffix -ose, which was originally taken from the word glucose (), and is used for almost all sugars, e.g. fructose (fruit sugar), sucrose (cane or beet sugar), ribose, lactose (milk sugar), etc. Carbohydrates perform numerous roles in living organisms. Polysaccharides serve as an energy store (e.g. starch and glycogen) and as structural components (e.g. cellulose in plants and chitin in arthropods). The 5-carbon monosaccharide ribose is an important component of coenzymes (e.g. ATP, FAD and NAD) and the backbone of the genetic molecule known as RNA. The related deoxyribose is a component of DNA. Saccharides and their derivatives include many other important biomolecules that play key roles in the immune system, fertilization, preventing pathogenesis, blood clotting, and development. Carbohydrates are central to nutrition and are found in a wide variety of natural and processed foods.

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ENG-436: Food biotechnology

The course will deliver basic knowledge on the principles of food fermentation and enzyme technology. The course will also present benefits that food biotechnology can bring in terms of Nutrition & He

Α-Amylase

α-Amylase is an enzyme (; systematic name 4-α-D-glucan glucanohydrolase) that hydrolyses α bonds of large, α-linked polysaccharides, such as starch and glycogen, yielding shorter chains thereof, dextrins, and maltose: Endohydrolysis of (1→4)-α-D-glucosidic linkages in polysaccharides containing three or more (1→4)-α-linked D-glucose units It is the major form of amylase found in humans and other mammals. It is also present in seeds containing starch as a food reserve, and is secreted by many fungi.

Prandial

Prandial relates to a meal. Postprandial (from post prandium) means after eating a meal, while preprandial is before a meal. The term postprandial is used in many contexts. Refers to activities performed after a meal, such as drinking cocktails or smoking. A common use is in relation to blood sugar (or blood glucose) levels, which are normally measured 2 hours after and before eating in a postprandial glucose test. This is because blood glucose levels usually rise after a meal.

Glucose

Glucose is a sugar with the molecular formula . Glucose is overall the most abundant monosaccharide, a subcategory of carbohydrates. Glucose is mainly made by plants and most algae during photosynthesis from water and carbon dioxide, using energy from sunlight, where it is used to make cellulose in cell walls, the most abundant carbohydrate in the world. In energy metabolism, glucose is the most important source of energy in all organisms. Glucose for metabolism is stored as a polymer, in plants mainly as starch and amylopectin, and in animals as glycogen.

Developing structure-oriented models for enzymatic hydrolysis of lignocellulosic biomass

Jessica Charlène Rohrbach

With the unsustainable use of fossil fuels increasing strains on human institutions and ecosystems, the development of a renewable energy alternative is of paramount importance. Second generation biorefineries, based on the production of fuels and chemicals from lignocellulosic biomass, appear as attractive alternative to their non-renewable counterparts. Within the multiplicity of existing valorisation routes, enzymatic hydrolysis of lignocellulosic biomass into its constituent sugars has generated considerable interest, notably in the context of biofuels production. However, major hurdles stemming from the intricate structure of the lignocellulosic feedstocks still impede large-scale deployment of this process. The multiplicity of highly intertwined spatiotemporal factors impacting the enzymatic hydrolysis of lignocellulosic biomass represents a challenge to rationally design efficient hydrolysis process. Here, we propose a theory-based modelling framework relying on pore-diffusion and surface reaction to explore the effects of recognised bottlenecks on the enzymatic hydrolysis of lignocellulosic substrates. The model is based on a set of partial differential equations describing the evolution of the substrate morphology to investigate the interplay between experimental conditions and the physical characteristics of biomass particles as the reaction proceeds. The overall quantity of cellulase present in the hydrolysis mixture is carefully considered to investigate its interplay with the available accessible cellulose surface. Also, non-uniformity in terms of cellulose accessibility and cellulose digestibility are introduced in the model to weight their influence on observed hydrolysis rates. Finally, deactivation mechanisms are considered through unproductive adsorption of cellulases on both cellulose and lignin fractions, with the existence of such phenomena alleged to be critical in the efficiency of the hydrolysis process. Based on predictions of our model, we were able to confirm the critical role of cellulose accessibility, as defined by the combination of particle size, porosity and accessible cellulose surface, in dictating early reaction rates for a range of pretreated beech wood substrates. While high biomass loading should be favoured to improve enzyme penetration in the substrates, high enzyme loadings going beyond the initial number of cellulose adsorption appeared beneficial in notably two cases: (i) to promote internal diffusion in large particles and (ii) counteract undesired enzyme adsorption on lignin. For the latter, a relatively low increase in enzyme loading was sufficient to offset the resulting slowdown. We also showed that the existence of structural heterogeneities, and in particular non-uniform pore volume distribution within the lignocellulosic samples, contribute to the rate slowdown observed at later stage of the hydrolysis, while not explaining it in its entirety. Unproductive adsorption to cellulose, coupled to decrease in the cellulase efficiency at the cellulose surface, appeared as major contributor to the rate slowdown. Overall, we show how the use of a theory-based model can help decouple and evaluate the effects of key factors in the enzymatic hydrolysis of lignocellulosic biomass. As such, our model can help pave the way towards efficient integrated rational design strategies for enzyme process engineering for biomass conversion.

EPFL2021

Development of novel tools for imaging of metabolic fluxes in vivo

Tamara Maric

Bioluminescent imaging is a powerful technique that enables imaging in living organisms with high sensitivity, low background signal, low cost and without the need for radioactivity. The emitted photons are produced in the oxidation reaction of luciferin catalyzed by luciferase. In the caged luciferin approach, the bioluminescent readout is used for measuring the activity of a specific biochemical process. Luciferin is caged in order to prevent catalysis by luciferase, and only when the cage is removed by a specific biochemical event of interest, luciferin is released and becomes a substrate of luciferase. Hence, emitted photons are proportional to the amount of free luciferin, thus allowing to monitor the dynamics of the investigated process. Recent progress in the development of bioorthogonal reactions enabled to answer several fundamental biological questions, improve clinical diagnosis, and to better evaluate therapy efficacy. For example, one of the most robust biorthogonal reactions is the Staudinger ligation, which occurs between a properly tuned azide and a phosphine. In this work, we have used the caged luciferin approach combined with the Staudinger ligation to monitor metabolite uptake in living animals. We have successfully applied this method for the monitoring uptake of two metabolites â glucose and nicotinamide riboside (NR). Glucose is a major source of energy for most living organisms and its aberrant uptake is linked to many pathological conditions. On the other hand, NR is a form of vitamin B3 and represents one of the salvageable NAD+ precursors. Low NAD+ level inside of cells is strongly linked to numerous metabolic and age-related disorders. Despite of their importance, in both cases our understanding of disease-associated glucose or NR flux is limited due to a lack of robust tools. To date, positron emission tomography (PET) imaging remains the gold standard for measuring glucose uptake and no optical tools exist for non-invasive longitudinal imaging of neither of the two metabolites in in vivo settings. Here we report the development of a novel bioluminescent glucose uptake probe (BiGluc) and bioluminescent NR uptake probe (BiNR) for real-time, non-invasive longitudinal imaging of glucose and NR absorption both in vitro and in vivo. The new imaging reagents enable a wide range of applications in the field of metabolism and drug development.

EPFL2020

Role of metabolism and mitochondria during glucose sensing and glucose-induced dysfunction in human pancreatic beta-cells

Isabelle Chareyron

Glucose sensing and regulation of insulin secretion are the two main functions performed by the pancreatic beta-cell. Together these processes contribute to the tight control of blood glucose in our body. Compromising the ability of the beta-cells to properly secrete insulin can lead to the development of Type 2 diabetes. Mitochondria play an important role in beta-cell function, by integrating nutrients signals and modulating insulin secretion. In this thesis, we aimed at better understanding the role of metabolism and mitochondria during glucose sensing and glucose-induced dysfunction in human pancreatic beta-cells. To that end, we designed three studies looking at different aspects of beta-cell mitochondrial function. In the first one, we developed an in vitro model of glucose overload in human islet. We report an over activation of the mitochondria when returned to basal conditions after a 4 day culture in elevated glucose. Additionally, these mitochondria only poorly responded to nutrient stimulation. Impaired metabolism secretion coupling and insulin secretion indicated a partial loss of beta-cell function, despite the increased mitochondrial activity. After 4 days of elevated glucose treatment, unusually high levels of glycerol-3-phosphate and pyruvate, even in sub-stimulatory extracellular glucose concentrations, were observed. We propose that the accumulation of these metabolites renders beta-cells blind to subsequent glucose stimulation. After removing the glucose stress for 24 hours the mitochondrial energy metabolism was fully restored and metabolism-secretion coupling was normalized. In the second approach, we measured for the first time the matrix pH in primary human pancreatic beta-cells. We showed that the mitochondrial pH in beta-cell is more acidic than in other cell types. Furthermore, in response to glucose, the beta-cell mitochondrial matrix slightly acidifies, possibly due to uptake and metabolism of pyruvate. Lastly, we observed that adenoviruses used to deliver the genetically encoded pH sensor can have an intrinsic impact on mitochondrial pH and calcium signaling. It must be used at low infection units per cell in the study of primary beta-cells. In the third project, we tried to modify the mitochondrial energy metabolism in beta-cells by inhibiting mitochondrial protein synthesis. We used different antibiotics to achieve this, in particular chloramphenicol, known to interfere with the activity of the mitochondrial ribosome. Surprisingly, we observe that when mitochondrial protein synthesis is inhibited, the respiration of insulin-secreting cells (INS-1E cells, human islets) is not affected. Expression of mtDNA encoded respiratory chain subunits is reduced and a mitochondrial unfolded protein response initiated without reducing respiratory rates. This raises the possibility that limited activation of unfolded protein response has a positive effect on the cells. This doctoral thesis provides novel insights into various aspects of mitochondrial behavior in pancreatic beta-cells, both during physiological and pathophysiological conditions. Additional work is needed to better understand the molecular mechanisms underlying the mitochondrial adaptation to nutrient overload and the associated beta-cell dysfunction leading to the accelerated impairment of glucose homeostasis during the development of Type 2 diabetes.

EPFL2019

Food Biotechnology: Enzymes and Protein Sources ENG-436: Food biotechnology

Covers the use of enzymes in food processing, protein sources, and their environmental impact.

Inclusion of Fermented Foods in Food Guides ENG-436: Food biotechnology

Discusses the inclusion of fermented foods in global food guides, exploring their benefits and risks, enzyme kinetics, and the history of food enzymes.

Fermented Foods: Microbial Transformations and Health Benefits ENG-436: Food biotechnology

Explores the microbial transformations and health benefits of fermented foods, emphasizing their potential as delivery vehicles for probiotics to underserved communities.

Metabolism (məˈtæbəlɪzəm, from μεταβολή metabolē, "change") is the set of life-sustaining chemical reactions in organisms. The three main functions of metabolism are: the conversion of the energy in food to energy available to run cellular processes; the conversion of food to building blocks for proteins, lipids, nucleic acids, and some carbohydrates; and the elimination of metabolic wastes. These enzyme-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, and respond to their environments.

Nutrition is the biochemical and physiological process by which an organism uses food to support its life. It provides organisms with nutrients, which can be metabolized to create energy and chemical structures. Failure to obtain sufficient nutrients causes malnutrition. Nutritional science is the study of nutrition, though it typically emphasizes human nutrition. The type of organism determines what nutrients it needs and how it obtains them.

In chemistry, many authors consider an organic compound to be any chemical compound that contains carbon-hydrogen or carbon-carbon bonds, however, some authors consider an organic compound to be any chemical compound that contains carbon. The definition of "organic" versus "inorganic" varies from author to author, and is a topic of debate. For example, methane () is considered organic, but whether some other carbon-containing compounds are organic or inorganic varies from author to author, for example halides of carbon without carbon-hydrogen and carbon-carbon bonds (e.