Chapters 1-3

WHY WE AREN'T ALONE

• The Human Body as an Ecosystem: we are an ecosystem of organs, cells, and trillions of our own cells interacting with trillions of microbes. Food is a bridge between our bodies and the world around us.
• Central questions: Why do you eat the food you do? How does it affect your body? These questions guide healthier, more sustainable choices.
• Information landscape: nutrition/health info is messy (advertising, labeling, guidelines). Understanding what happens when you consume foods helps you interpret labels and discern truth.
• Goals of the course: adopt sustainable, scientifically valid health habits; connect eating choices to personal health, mindset, and community well-being.
• Connectedness to food: understanding origin, how it is raised, where it comes from, and its environmental/world impact.
• Obesity and chronic diseases are linked to economic factors and education. Mindful eating can reduce health issues and influence communities.
• Essential definitions and framing:
  • Ecosystem: a defined space plus abiotic (nonliving) and biotic (living) factors; interactions and dependencies occur at multiple levels; input/output cycles studied by scientists.
  • Abiotic vs Biotic: abiotic = nonliving (water, gases, minerals); biotic = living organisms and their interactions.
  • Life attributes (basic criteria): made of cells; uses energy; grows/develops; responds to environment; maintains homeostasis; reproduces; DNA as universal inheritance molecule; evolution as a population-level process.
  • Cells and energy: energy comes in two main forms for life — light energy and chemical energy; cells import materials and export substances to maintain their environment (homeostasis).
  • DNA: universal inheritance molecule that dictates characteristics and reproduction; two reproductive strategies exist: sexual (DNA from two parents) and asexual (cloning).
  • Evolution: changes in populations over generations; driven by genetic variation and natural selection; evolution is a generational process, not a single individual's change.
  • Microbes: body hosts >200 human cell types, but for every human cell there are ~10 microbes on/in the body; bacteria are a major focus across the course.
  • Prokaryotes vs Eukaryotes: bacteria/archaea (prokaryotes) vs cells with nuclei and organelles (eukaryotes).
  • Biotic interactions with microbes: all interactions your body has with microbes are symbiotic to varying degrees.
• Four categories of biotic interaction (biotic relationships):
  • Commensalism: one species benefits, the other is unaffected (e.g., barnacles on an oyster). The oyster is not helped or harmed.
  • Mutualism: both species benefit (e.g., humans and gut microbes; we provide nutrients, microbes provide vitamins).
  • Exploitation (parasitism/herbivory/predation): one benefits at the expense of the other (harmful to the host).
  • Competition: two or more species compete for shared resources; often detrimental to all involved; can drive elimination or adaptation.
• Trophic levels and energy flow:
  • Producers (autotrophs) create organic molecules from inorganic carbon (CO₂).
  • Consumers (heterotrophs) obtain organic molecules by eating others.
  • Food web vs food chain: a web illustrates all feeding relationships; a chain is a single line of who eats whom.
  • Energy transfer across trophic levels is the backbone of ecosystem function; energy is stored as chemical energy in organic molecules and accounts for calories in nutrition.
  • Calorie vs Calorie: in nutrition, a Calorie (capital C) equals a kilocalorie; 1 Calorie = 1,000 calories. 1 ext{ Calorie} = 10^3 ext{ calories}
• Energy concepts in the body:
  • Kinetic energy: energy in use/change; Potential energy: energy stored for future use.
  • In biology, energy forms of interest include chemical energy (fuel stored in chemical bonds), thermal energy (heat), and electromagnetic energy (light).
  • Analogy for maintenance: like a car, the body needs regular maintenance and fueling; without it, systems deteriorate over time.
• Boil It Down / Study Prompts (examples):
  • 1.1: Guess how many elements make up the human body; list four most common elements with a bodily example.
  • 1.2: Understand life definitions and basic cellular criteria for living.
  • 1.3: Recognize that evolution is a population-wide process, not an individual event.
  • 1.4: List characteristics of life succinctly; understand prokaryotes vs eukaryotes; DNA and microbes.
  • 1.5: Summarize four biotic interactions with microbes via examples related to food.
  • 1.6: Distinguish energy types and calorie terminology; understand food energy transfer.
• Takeaway: Your body is a multi-ecosystem, intimately linked with innumerable microbes; understanding these interactions lays the foundation for healthier eating and living.

WHO IS THAT IN MY CHEESE PUFFS? The Organisms That Are Our Food

• Core idea: all food ultimately comes from living organisms; humans are chemoheterotrophs who consume organic molecules produced by other organisms.
• Key concepts:
  • Organisms are either prokaryotic or eukaryotic.
  • Prokaryotes (bacteria/archaea): single-celled, no nucleus; some are pathogenic, many are essential for nutrient cycling, digestion, and food production.
  • Eukaryotes: organisms with a nucleus and organelles (plants, fungi, animals, and many protists).
  • Microbes and food interactions: commensal, mutualistic, exploitative, and competitive relationships influence our digestion and health. Microbiome composition shifts with diet and antibiotics.
  • Life requires energy: autotrophs ( Producers ) vs heterotrophs ( Consumers ); four nutritional strategies:
  • Photoautotrophs: produce own organic molecules from light energy (e.g., many plants, cyanobacteria).
  • Chemoautotrophs: produce own organic molecules from chemical energy (oxidation of inorganic substances).
  • Photoheterotrophs: use light energy to help break down organic molecules.
  • Chemoheterotrophs: humans; rely on chemical energy to break down consumed organic molecules for energy.
• Prokaryotes we eat or interact with:
  • Decomposers (chemoheterotrophic prokaryotes) recycle dead matter and unlock essential elements like carbon and nitrogen; some nitrogen-fixers capture atmospheric N₂ for biological use.
  • Autotrophic prokaryotes use CO₂ to make organic compounds (e.g., cyanobacteria, the oldest known organisms; fossil records ~3.5 billion years).
  • Pathogenic bacteria: cause disease via exotoxins (secreted toxins) or endotoxins (cell components causing harm); common foodborne examples include E. coli, Salmonella; prevention via cooking/preservation techniques.
  • Good bacteria: lactic acid bacteria (Lactococcus, Streptococcus, Lactobacillus) in dairy, fermentation, pickling; part of the microbiome and food production; beneficial in vitamins production and digestion; antibiotic use can disturb microbiome balance.
• Eukaryotes we eat: protists, plants, fungi, and animals
  • Protists: diverse, many plant-like or animal-like; mostly food for other organisms rather than direct human staples.
  • Plants, fungi, animals form the main dietary lineages for humans.
  • Protist evolution and placement on the tree of life: still a focus of study; protists are not a single group but a broad collection of lineages.
• Plants we eat: anatomy and nutrition
  • Plant basics: roots, stems, leaves, flowers; photosynthesis is the central energy-generating process.
  • Leaves: main photosynthetic organs; CO₂ entry via stomata.
  • Flowers: hermaphroditic (often have both male and female parts) to promote genetic diversity via pollination; seeds form after fertilization and the ovary ripens to become fruit.
  • Fruit types: accessory fruit, simple fruit, aggregate fruit (many small fruits from one flower), multiple fruit (fusion of multiple flowers).
  • Vegetation we eat: leafy greens, root vegetables, tubers, bulbs; grains and endosperm are major energy sources. Grains store energy as starch; bran provides fiber; germ contains nutrients.
  • Grains anatomy: bran (fiber), endosperm (starch and gluten proteins), germ (embryo).
  • Vitamins produced by plant cells are often stored in vacuoles; photosynthesis basics: light reactions produce ATP and NADPH; the Calvin cycle/ dark reactions incorporate CO₂ to build sugars.
• Fruits, flowers, and photosynthesis in depth
  • Photosynthesis stages:
  • Light reactions (photo stage): generate ATP and NADPH; oxygen is released as a byproduct; chlorophyll a drives electron transfer via the photosystems and an electron transport chain.
  • Calvin cycle (synthesis stage): uses ATP and NADPH to fix carbon into sugars (e.g., glucose). Carbon fixation begins with CO₂ incorporation into an organic molecule, followed by ATP/NADPH-driven stabilization and sugar formation.
  • Pigments and chloroplasts: photosystems with pigments arranged to harvest light; chlorophyll a is central to electron donation.
• Fungi we eat: yeast and more
  • Yeast in bread, wine, beer; fermentation (anaerobic) yields CO₂ and ethanol in bread; different fungal roles in cheese and flavor development; fungi as decomposers recycle nutrients.
  • Fungi as recyclers (mycorrhizal associations) help plants acquire nutrients; mushrooms are the above-ground fruiting bodies used for dispersal of underground networks.
• Fungi and food safety: some mushrooms edible, some toxic; toxins prevent predation and have driven plant/mushroom coevolution.
• Animals we eat: invertebrates and vertebrates
  • Invertebrates: molluscs (bivalves like oysters, clams; cephalopods like octopus, squid; gastropods like snails) and arthropods (crustaceans like shrimp; insects like grasshoppers and crickets).
  • Vertebrates: meat and fish; endoskeletons (internal skeletons) distinct from plants or fungi; meat from poultry, beef, pork, lamb, etc.; fish vary in size and life stages (e.g., many fish begin as primary consumers and may become secondary or higher-level consumers as they grow).
  • CAFOs (Concentrated Animal Feeding Operations): industrial animal farming; concerns about animal welfare, sustainability, and diet quality; organic/free-range farming as alternatives.
  • Overfishing: impacts on food webs, including effects on lower trophic levels and predators; emphasizes interconnectedness of seafood choices with ecosystem balance.
• Summary of consumer choices and dietary patterns
  • Humans consume a wide range of organisms across all kingdoms, with plants and animals forming the core of most diets.
  • Different dietary patterns (omnivore, vegetarian, pescatarian, vegan) reflect cultural choices and bioavailability of nutrients.
  • The interaction between diet and microbial communities (microbiome) influences digestion, nutrient absorption, and overall health.

WHERE ARE THOSE TRANS FATS? What We Get from Other Organisms

• Core idea: nutrition is the bridge between what you eat and what your body does with those nutrients; nutrition labeling helps you manage intake of fats, carbohydrates, proteins, vitamins, and minerals.
• The nutrition facts label (key nutrients): fats, cholesterol, sodium, carbohydrates, protein, vitamins, minerals; labels assume a 2,000 calorie daily diet for reference; values vary by individual.
• Fats (lipids): essential components of membranes and energy storage; four fat types on labels: saturated, monounsaturated, polyunsaturated, and trans fats.
  • Fats basics: fats are hydrophobic (water-fearing) and part of the larger lipid family; fats transport in the blood via lipoproteins.
  • Saturated fats: typically dense in animal products; solid at room temperature; excessive intake linked to higher blood cholesterol (HDL/LDL balance).
  • Unsaturated fats: healthier fats; monounsaturated and polyunsaturated fats are usually from plants/seafood; they are bendable (not straight) chains that remain fluid; generally associated with better cardiovascular profiles.
  • Trans fats: artificially created by hydrogenating unsaturated fats to make them more solid; linked to worse cardiovascular outcomes; common in processed foods; many products can advertise 0 g trans fats even when small amounts remain unless >0.5 g per serving.
  • Function of fats: cell membranes are phospholipid bilayers; fats store energy as triglycerides in adipose tissue; white fat stores energy and hormones; brown fat burns energy to generate heat; lipolysis converts fat to usable energy; ketosis is fat-to-sugar conversion for energy when glucose is scarce.
• Cholesterol: a hydrophobic molecule essential for membranes, Vitamin D synthesis, and steroid hormones; cholesterol on a food label is the amount in that product, not the same as blood cholesterol measurements; LDL (low-density lipoprotein) and HDL (high-density lipoprotein) transport cholesterol in the body.
• Sodium: essential ion (Na⁺) for cellular processes; important for nerve signaling and fluid balance; excessive added salt can burden the circulatory system and harm health over time; many foods contain intrinsic sodium even without added salt.
• Carbohydrates: monosaccharides, disaccharides, and polysaccharides; primary energy source; plants and animals both rely on carbohydrates for energy storage and structure.
  • Monosaccharides: glucose and fructose; Disaccharides: sucrose (glucose + fructose);
  • Polysaccharides: starch (plant storage; including endosperm), glycogen (animal storage in liver and muscle), cellulose (plant fiber); fiber is undigestible and has health benefits; complex carbohydrates also include structural polysaccharides like cellulose and chitin (in exoskeletons).
  • Glycogen storage: liver and muscle tissues; energy needs over time.
  • The term “organic” in the nutrition context differs from the chemistry definition; organic foods must contain carbon-based compounds but the label’s meaning differs from the chemical sense of organic chemistry.
• Proteins: polymers of amino acids; 20 amino acids; 8 are essential (cannot be synthesized) and must be obtained from diet; sequence determines structure and function; proteins provide structure, transport, signaling, enzymes, and immune defense; membrane proteins (channels and transporters) enable selective import/export; insulin as an example of a protein signal requiring its receptor in the membrane; proteins also contribute to coloration and tissue structure.
• Vitamins: small organic molecules required for health; two classes: water-soluble and fat-soluble.
  • Water-soluble vitamins (B-complex and Vitamin C) are generally not stored and must be replenished regularly.
  • Fat-soluble vitamins (A, D, E, K) are stored in fat tissue and can accumulate to harmful levels if overconsumed; Vitamin D can be synthesized with sunlight exposure; vitamins help energy production, tissue maintenance, immune function, and antioxidant defense.
• Vitamins and antioxidants: vitamins help manage oxidative stress and support immune function; many colorful fruits and vegetables indicate the presence of vitamins.
• Minerals: inorganic elements required in small amounts; important for homeostasis, signaling, and structural roles (iron, iodine, fluorine, calcium, etc.); iron is crucial for oxygen transport; iodine supports thyroid function; minerals can be part of proteins or vitamins; imbalances can cause health issues (e.g., iron deficiency anemia, goiter from iodine deficiency).
• Food labeling and sourcing considerations:
  • Ingredients are listed from most to least abundant by weight; preservatives, processing aids, and fortification influence nutrition content.
  • Processed foods may include additives and added sugars; labels can obscure added sugar by listing it under various names (30+ aliases).
  • Organic labeling imposes standards on pesticide use and farming practices; CAFOs vs organic/free-range farming are debated for environmental and ethical reasons.
  • The microbiome can be influenced by diet and antibiotics; antibiotic use can reduce beneficial microbes; consumption of fermented foods (yogurt, kefir, certain cheeses) can support a balanced microbiome.
• Dietary patterns and ecological impact:
  • Plant-based foods form a cornerstone of many diets; plant photosynthesis sustains the food web by fixing carbon and releasing oxygen.
  • Overfishing and the removal of lower-level species can ripple through food webs, affecting predators and other organisms.
  • The choice of seafood and meat has broader environmental implications for ecosystems and biodiversity.
• Quick reference values and guidance:
  • Calorie terminology: 1 ext{ Calorie} = 10^3 ext{ calories}; nutritional labeling uses kilocalories (Calories).
  • Common dietary targets discussed include limits on saturated fats and trans fats, sodium intake, and added sugars; emphasis on fiber-rich carbohydrates and nutrient-dense foods.
  • The nutrition label highlights major nutrients (fats, cholesterol, sodium, carbohydrates, protein, vitamins, minerals) and provides a guide for daily values, often based on a 2,000 calorie diet.
• Get the Skinny (glossary-style emphasis):
  • Key terms covered include ATP, NADPH, glycogen, glucose, cellulose, chitin, lipolysis, ketosis, CAFOs, probiotics, prebiotics, endoskeleton, exoskeleton, and more; these terms provide quick anchors for understanding how the body processes nutrients and how foods relate to health and the environment.
• Practical takeaways:
  • Reading nutrition labels helps identify sources of fats (saturated vs unsaturated vs trans), sugars, and essential nutrients.
  • A balanced diet often emphasizes whole foods with natural fibers, essential amino acids, and a variety of micronutrients; processed foods may trade-off nutrient density for shelf life.
  • Understanding where foods come from and how they are produced fosters healthier and more sustainable choices for individuals and communities.

SECTION 3: WHERE ARE THOSE TRANS FATS? What We Get from Other Organisms (detailed nutrition overview)

• Fats (lipids): essential for membrane structure and energy storage; four major fat types on nutrition labels:
  • Saturated fats: typically from animal sources; solid at room temperature; materials that can raise LDL cholesterol if consumed in excess.
  • Monounsaturated fats: bendable, liquid at room temperature; generally considered healthier fats from plant sources.
  • Polyunsaturated fats: bendable, liquid; include omega-3 and omega-6 fats from fish, seeds, and certain oils; broadly associated with health benefits.
  • Trans fats: artificially hydrogenated fats; appear solid at room temperature; linked to worse cardiovascular outcomes; common in processed foods; labeling loophole allows 0 g trans fats if per-serving amount is <0.5 g.
• Fats’ roles and structures:
  • Phospholipids form the cell membrane with hydrophilic (water-loving) head groups and hydrophobic (water-repelling) tails; this arrangement creates a bilayer essential for cellular homeostasis and selective transport.
  • Triglycerides: three-fat molecules bound as energy storage in adipose tissue; white fat stores energy and hormones; brown fat burns stored fat to generate heat (thermogenesis).
  • Lipolysis and ketosis describe fat breakdown and fat-derived energy production in metabolism.
• Cholesterol:
  • A hydrophobic molecule essential for membranes, vitamin D synthesis, and steroid hormones; not the same as blood cholesterol; transported in the bloodstream by LDL and HDL lipoproteins.
  • Cholesterol’s inclusion in membranes helps adapt to temperature changes by maintaining membrane fluidity.
• Sodium (Na⁺):
  • An essential ion involved in nerve signaling, muscle contraction, and water balance; excess dietary sodium can stress the circulatory system.
• Carbohydrates:
  • Monosaccharides (e.g., glucose, fructose), disaccharides (e.g., sucrose), and polysaccharides (e.g., starch, glycogen, cellulose).
  • Glycogen stores energy in liver and muscle; starch stores energy in plants; fiber (cellulose) provides digestive benefits; chitin is a structural polysaccharide in arthropods.
  • Simple sugars provide quick energy; complex carbohydrates provide sustained energy and dietary fiber.
• Proteins:
  • Made of amino acids; 8 essential amino acids cannot be synthesized and must be obtained from food; the sequence of amino acids determines protein structure and function; proteins perform structural, transport, catalytic, signaling, and defense roles; enzymes accelerate digestion and metabolism.
• Vitamins:
  • Water-soluble vs fat-soluble vitamins; vitamins support energy production, tissue maintenance, immune function, and antioxidation.
  • Vitamin D can be synthesized with sun exposure; some vitamins act as cofactors for enzymes and participate in redox reactions; excess intake of fat-soluble vitamins can be harmful due to storage in adipose tissue.
• Minerals:
  • Involved in homeostasis, signaling, and energy production; essential components of proteins and vitamins; iron (oxygen transport), iodine (thyroid function), fluoride (teeth).
  • Imbalances can cause severe health issues (e.g., iron deficiency anemia, goiter from low iodine).
• Food systems and practices:
  • Processing and preservation methods (salt, pickling, drying, additives) help extend shelf life and reduce spoilage; cooking can kill pathogens and aid digestion.
  • Antibiotics can disrupt the gut microbiome; restoring balance often involves probiotics and fermented foods.
  • Dietary patterns influence microbial populations; a balanced microbiome supports digestion, immune function, and nutrient absorption.
• Practical exercises referenced in the text:
  • Boil It Down and Exercise Your Brain prompts to build deeper understanding of nutritional strategies, digestion, and the relationships among macronutrients and micronutrients.
  • Section 3 includes tasks to compare nutrient daily values across sources and to inspect ingredient lists for hidden sugars and hydrogenated fats.
• Get the Skinny (quick reference terms):
  • Terms include ATP, NADPH, cellulose, glycogen, LDL, HDL, lipolysis, ketosis, CAFOs, prebiotics, probiotics, and many others to help anchor memory of how nutrients, cells, and organisms interrelate.
• Takeaways for study and application:
  • The nutrient categories (fats, cholesterol, sodium, carbohydrates, proteins, vitamins, minerals) each have specific roles in cellular structure, energy metabolism, signaling, and health outcomes.
  • Understanding the chemistry and biology behind these nutrients improves diet quality, food choices, and awareness of environmental and public health implications.
  • The health impact of foods depends not only on macronutrient totals but also on nutrient quality, gut microbiome interactions, and chronic disease risk factors.

Glossary (selected terms you’ll encounter across the notes)

• ATP: universal energy carrier molecule; stores a phosphate group to energize reactions. ext{ATP}
• NADPH: energy carrier that donates electrons to energize reactions. ext{NADPH}
• Prokaryotes: single-celled organisms without a nucleus (e.g., bacteria, archaea).
• Eukaryotes: organisms with a nucleus and organelles.
• Autotrophs: organisms that produce their own organic molecules from inorganic sources.
• Heterotrophs: organisms that must consume other organisms to obtain organic molecules.
• Photoautotrophs: autotrophs that use light energy to fix carbon into organic molecules.
• Chemoautotrophs: autotrophs that use chemical energy to fix carbon into organic molecules.
• Photoheterotrophs: organisms that use light energy to acquire energy while consuming organic molecules.
• Chemoheterotrophs: organisms that use chemical energy to break down organic molecules; humans are in this group.
• Commensalism, Mutualism, Exploitation, Competition: four categories of biotic interactions.
• Food web vs food chain: food web maps all feeding relationships; a chain is a single line of who eats whom.
• Carbohydrates: monosaccharides, disaccharides, polysaccharides; primary energy source; fiber is a non-digestible carbohydrate.
• Fiber: non-digestible carbohydrate that contributes to digestive health.
• Glycogen: storage form of glucose in animals, stored mainly in liver and muscles.
• Starch: plant storage polysaccharide; major energy source in diets.
• Lipids/Phospholipids: fats and membrane components; phospholipids form the cell membrane’s bilayer with hydrophilic heads and hydrophobic tails.
• LDL/HDL: lipoprotein particles that transport cholesterol in the blood; LDL is often labeled as “bad” cholesterol, HDL as “good.”
• CAFOs: Concentrated Animal Feeding Operations; large-scale, industrial animal farming.
• Endoskeleton/Exoskeleton: skeleton inside the body vs outside; vertebrates have endoskeletons.
• Photosystems/Chloroplasts: components of the plant photosynthetic machinery; chlorophyll a is key for electron transfer and oxygen evolution.
• Phospholipid: a molecule with a phosphate head and two lipids tails forming the cell membrane; amphipathic nature enables membrane structure.