Nutrition Science Explained: How Food Actually Works in Your Body

Nutrition science is not wellness marketing. It’s the study of how food molecules become energy, tissue, and chemical signals inside your body. The gap between those two things matters.

A superfood claim on a package is marketing. A named study in a peer-reviewed journal is the beginning of evidence. They’re not the same thing. Knowing the difference helps you cut through most of what you read about food online.

The Three Macronutrients

Your body needs energy and raw materials. The macronutrients provide both.

Carbohydrates are your body’s preferred fuel. During digestion, starches and complex carbohydrates break down into glucose. Your small intestine absorbs that glucose, which enters the bloodstream. From there, insulin helps cells take it up and use it for energy or store it as glycogen in the liver and muscle.

Sugar is also a carbohydrate. Table sugar is glucose bonded to fructose. Your body splits them apart and processes them separately. Fructose goes to the liver first, which is why very high fructose intake (mainly from added sugars, not whole fruit) can stress the liver differently than glucose. The [Mozaffarian, 2016] review in Circulation lays out the evidence on dietary carbohydrate quality and its link to cardiovascular disease and metabolic risk.

Proteins are chains of amino acids, and amino acids are the raw materials for building nearly everything in your body. Enzymes, antibodies, structural proteins like collagen, signaling molecules like insulin, muscle fibers. Your digestive system breaks dietary proteins down into individual amino acids and short peptide chains. Those get absorbed in the small intestine and used to build whatever the body needs.

There are 20 amino acids. Nine of them are called “essential” because your body can’t make them, so they have to come from food. Animal proteins contain all nine in adequate proportions. Many plant proteins are missing or low in one or more, which matters for muscle building and some other functions. This is covered in detail in the plant vs. animal protein article.

Fats have three main jobs. Energy storage (fat tissue holds far more energy per gram than glycogen). Structural roles (every cell membrane in your body is built from a phospholipid bilayer). And hormone production (sex hormones, cortisol, and others are made from cholesterol, a type of fat).

Dietary fats also carry fat-soluble vitamins (A, D, E, K). That’s why eating fat with vegetables isn’t optional if you want to absorb those nutrients. A salad with fat-free dressing poorly absorbs fat-soluble compounds like beta-carotene compared to the same salad with olive oil. This is a documented, measurable effect, not nutritional folklore.

Think of fats like a delivery truck. The truck carries important cargo (fat-soluble vitamins, anti-inflammatory omega-3s, essential fatty acids) to where it needs to go. Cut the truck and the cargo doesn’t arrive.

Micronutrients: Small Amounts, Large Consequences

Vitamins and minerals don’t provide energy directly. They run the machinery that converts food into energy and keeps every organ system functioning.

Vitamins split into two categories based on how they dissolve:

Fat-soluble vitamins (A, D, E, K) dissolve in dietary fat, are absorbed alongside fat in the small intestine, and can be stored in body fat and the liver. This means you can build up toxic levels with very high supplementation, and deficiency develops more slowly because stored reserves exist. Vitamin D is technically a hormone precursor, not a vitamin in the classical sense. The full synthesis pathway is in the vitamin D metabolism article.

Water-soluble vitamins (all eight B vitamins plus vitamin C) dissolve in water. They’re not stored in meaningful quantities, which means regular intake matters more. Excess is excreted in urine, making toxicity rarer. B vitamins are involved in energy metabolism at almost every step. Vitamin C is needed for collagen synthesis and iron absorption.

Minerals include calcium (bones, nerve signaling, muscle contraction), iron (oxygen transport in blood), zinc (immune function, enzyme activity), magnesium (hundreds of enzymatic reactions), and many others. Getting them from food is generally more effective than supplements because the food matrix affects how they’re absorbed.

Digestion: A Series of Chemical Handoffs

Food doesn’t enter your bloodstream intact. It gets dismantled first.

The breakdown starts in your mouth. Salivary amylase begins splitting starch. Your teeth mechanically break food into smaller pieces to increase surface area for enzymes. Swallowing moves the bolus into your esophagus and then your stomach.

Your stomach is a churning acid bath with a pH of around 1.5 to 3.5. Hydrochloric acid denatures (unfolds) proteins, making them accessible to digestive enzymes. Pepsin starts breaking protein chains. The stomach holds food for 2-4 hours, mixing it into a liquid called chyme.

The small intestine is where most absorption happens. It’s about 6 meters long, coiled up in your abdomen, and lined with finger-like projections called villi that increase surface area dramatically. Pancreatic enzymes continue breaking down carbohydrates, proteins, and fats. Bile from the gallbladder emulsifies fats so they can be absorbed. The absorptive cells of the small intestine pull nutrients into the bloodstream.

Your large intestine (colon) handles what the small intestine couldn’t absorb. Mostly water, some minerals, and the fiber your own enzymes can’t break down. This is where your gut microbiome takes over.

The Gut Microbiome

Your colon contains trillions of bacteria, archaea, fungi, and viruses. The bacteria outnumber your own cells at roughly the same order of magnitude. They’re not passengers. They’re metabolically active.

When gut bacteria ferment dietary fiber, they produce short-chain fatty acids (SCFAs), primarily butyrate, propionate, and acetate. Butyrate is the main energy source for colonocytes (the cells lining your colon). It also has anti-inflammatory effects and plays a role in regulating immune function. The gut microbiome basics article covers this in detail.

The practical implication: dietary fiber isn’t just roughage for bowel regularity. It feeds a community of organisms that produce compounds your body can actually use. A low-fiber diet starves those organisms, which shifts microbial community composition in ways associated (in observational research) with inflammation and metabolic disease.

Bioavailability: The Gap Between Label and Reality

A food contains nutrients on paper. Your body absorbs a fraction of them. That fraction is bioavailability.

Iron is a clear example. Spinach looks iron-rich on a nutrition label. But spinach iron is non-heme iron, and spinach contains oxalates that bind iron and prevent absorption. The iron in spinach is poorly bioavailable. Meat iron (heme iron) absorbs at 15-35%. Non-heme plant iron absorbs at 2-20% depending on what you eat with it. Vitamin C doubles or triples non-heme iron absorption. This matters enormously for people eating plant-heavy diets.

Fat-soluble vitamins require dietary fat for absorption. Calcium absorption is inhibited by iron, and vice versa, so taking both supplements at once wastes one of them. Cooking increases the bioavailability of some nutrients (lycopene in tomatoes, beta-carotene in carrots) and destroys others (vitamin C, some B vitamins).

The full breakdown of what affects bioavailability is in the bioavailability article.

Why “Eating Healthy” Is More Complex Than Macros

Tracking protein, carbs, and fat tells you something, but not everything. Food is not just the sum of its macros and micros.

The food matrix matters. Almonds on paper have a certain calorie and fat content. But a 2012 study by Novotny et al. found people absorbed roughly 32% fewer calories from almonds than the nutrition label predicted, because the cellular structure of the nut kept fat trapped inside cells that passed through digestion intact. Eating whole almonds is metabolically different from consuming almond oil with the same fatty acid profile.

Processing matters too. Ultra-processed foods are engineered to be digested quickly and easily. This affects satiety signals, how fast glucose enters the bloodstream, and what your gut microbiome gets to ferment. A calorie from white bread and a calorie from intact whole grain have different effects because the food matrix is different.

Antinutrients like phytates in legumes and grains bind minerals and reduce their absorption. Fermentation, soaking, and cooking can reduce antinutrient levels significantly.

How Nutrition Research Actually Works

Most nutrition research is observational. Researchers ask people what they eat, track health outcomes over years, and look for correlations. These studies are valuable for generating hypotheses. They don’t establish causation.

Randomized controlled trials (RCTs) are the gold standard for causation, but they’re difficult for diet. You can’t blind people to what they’re eating. You can’t control everything they eat for years at a time. So most diet RCTs are short-term, underpowered, and test specific nutrients rather than whole dietary patterns.

Walter Willett’s “Nutritional Epidemiology” (3rd edition, 2012) is the methodological foundation for this field, and it’s honest about these limitations. The WHO’s dietary guidelines acknowledge the same issues, noting that recommendations are based on the best available evidence, which is still imperfect.

This is why nutrition advice seems to contradict itself over decades. It’s not because scientists are incompetent. It’s because the research tools available are imperfect for studying something as complex as diet over a lifetime.

What this means practically: when you see a single study overturning decades of established nutrition guidance, be skeptical. Nutritional consensus shifts slowly and for good reason. On the other hand, some well-established nutritional effects (vitamin C prevents scurvy, folate prevents neural tube defects, iodine prevents goiter) are so strongly supported that they’re settled science.

How Evidence Quality Works on This Site

Every article on this site carries an evidence quality rating: strong, moderate, emerging, or mixed.

Strong means multiple high-quality trials and consistent expert consensus support the claim. Moderate means good evidence exists but questions remain. Emerging means early or preliminary findings without sufficient replication. Mixed means the evidence is genuinely contradictory or contested between credible researchers.

The ratings aren’t a substitute for reading the references. They’re a shortcut for how much confidence you should have before making dietary changes based on what you read.

All factual claims on this site cite named studies. “Research suggests” without a citation is not evidence. “The [Mozaffarian, 2016] review found…” is. That distinction matters.

This article is for educational purposes only and does not constitute medical advice. Consult a qualified health professional before making changes to your diet or health regimen.