Lesson 1: Overview of metabolism

Table of Contents


Welcome to Lesson 1. Before discussing the specifics of healthy nutrition and weight management, it is very helpful to understand the basics of metabolism. This is where calories come into play, and this is crucial for understanding what influences body weight (“BW”). So, let’s talk about burning calories.

Note: Technically, 1 Calorie = 1000 calories = 1 kilocalorie, but I will use “calorie” and “kilocalorie” (which I will shorthand with “kcal”) interchangeably, as almost all people do when talking about food. You will likely never need to convert these for any practical reason.

Any given day you burn some total number of calories. If you consume the same number of calories as you burn, your weight should be stable. Fluctuations can occur due to:Balance showing when calories in = calories out weight is maintained

  • retaining more or less water (due to variations in carbohydrate and sodium intake, stress levels, going through a menstrual cycle, etc)
  • undigested food in your gut
  • stool retention
  • obvious factors such as wearing different clothing when you step on the scale

Total daily energy expenditure (“TDEE”)

The total amount of calories burned in any given day is referred to as the “total daily energy expenditure” (“TDEE”). This is comprised of multiple components(Melanson, 2017):

  • There are the calories you burn at complete rest doing nothing, which is called either the “basal metabolic rate” (“BMR”) or “resting metabolic rate” (“RMR”). BMR is generally measured first thing in the morning while in the awake state but lying still in a dark, temperature-controlled environment after having fasted overnight. RMR can be measured under other conditions and thus will generally be higher, but these terms are often used interchangeably.
  • There are the calories you burn in the process of digesting and absorbing food you eat, frequently called the “thermic effect of feeding” (“TEF”) or “dietary induced thermogenesis” (“DIT”).
  • There are the calories you burn while you purposefully exercise, called different things but I will go with “exercise activity thermogenesis” (“EAT”).
  • Additionally, there are calories you burn with unplanned activity, which includes rolling over in bed, fidgeting in a chair, pacing, alterations in energy utilization of different organs, etc. This is called “non-exercise activity thermogenesis” (“NEAT”).

Putting all of this together:


Note: Not included here, as technically this is not energy we utilize, are calories lost in urine and feces. It’s estimated that ~1% of calories we consume are lose in urine and ~2-9% of calories we consume are lost in stool.(Lund, 2020) There can be a wide variability between individuals, it is possible that people who lose fewer calories in stool have a more difficult time with weight loss.

In general if we consume fewer calories than our TDEE we lose BW while if we consume more calories than our TDEE we gain BW. scales showing calories in greater than out leads to weight gainscales showing calories in less than out leads to weight loss



Remember, energy cannot be created or destroyed. As calories are a unit of energy, at the end of the day all calories must be accounted for.


There are many different components that contribute to BW (bones, skin, other organs, fat, water, muscle, etc). These can be divided into “body fat” (“BF”) and “lean body mass” (“LBM” – everything other than BF).

Tip: While eating fewer calories than our TDEE is the key for losing BW, another consideration is what proportion of the weight we lose is LBM vs BF. A caloric deficit alone will yield weight loss and many health benefits (if our starting weight is too high), but incorporating appropriate exercise is important to help maintain our LBM.(Broskey, 2019) Maintaining LBM (particularly skeletal muscle) is beneficial for overall health and is likely helpful to prevent weight regain long term.(Dulloo, 2018; Stubbs, 2021) Briefly, avoiding too rapid weight loss (discussed in Lesson 3), keeping protein intake sufficiently high (discussed in Lesson 4) and engaging in resistance training (see the general exercise course on this site) are the key steps to ensure LBM retention while BF is lost.

Now we will go through the components of TDEE in more detail.

Resting Metabolic Rate (“RMR”)

RMR is the largest contributor to TDEE & is primarily due to LBM.(Heymsfield, 2018) Total BF also contributes. Age and gender can contribute (higher in males, decreasing with age) but this seems mediated by alterations in LBM. Skeletal muscle burns more calories than BF (roughly 6 kcal/lb of skeletal muscle vs. 2 kcal/lb of BF per day), so if there are two people at the same BW but one has more LBM and the other has more BF, the former will likely burn more calories. Due to variations in organ size and possibly other unaccounted factors (ie, genetics), two people of the same size, age, and body composition can still have different RMRs. Approximate values for different organs are shown in the table below:

table showing contribution of different organs to resting metabolic rate
Residual includes intestines, pancreas, thyroid, etc. This example sums to 1685 kcal for a 71 kg person. Of note, as these are approximate values that change with age, gender, and BW, these numbers are not directly applicable to any one specific person. Values primarily taken from (Heymsfield, 2018) & (Müller, 2013).

If you compare two people with different RMRs and they eat the same number of calories with no other differences between them, the person with the lower RMR will move to a higher BW than the person with the higher RMR. In practice there are other considerations (see discussion regarding NEAT below).

When we diet to lose weight, our RMR tends to decrease. This occurs in part due to the loss of LBM and BF. When losing a significant amount of BW some of our organs (which are very metabolically active) may decrease in size, further leading to a decrease in RMR. This is less likely to occur if we start dieting from a non-obese state, though it may occur to a degree in the liver.(Shen, 2021) On the other hand, exercise has at most a minimal impact on RMR, and possibly has no impact.(MacKenzie-Shalders, 2020)

Additionally, there is an adaptive component frequently termed adaptive thermogenesis that leads to a further decrease in RMR while actively losing weight (you can think of this as the body trying to fight to maintain its current BW); this is variable between people. Thus, some will have their RMR drop more than others in response to dieting. Of note, adaptive thermogenesis typically disappears once one is maintaining their new lower BW; when you are not actively dieting it will trend back to what you expect from your overall new LBM and BF.(Ostendorf, 2018; Martins, 2020; Müller, 2021; Nunes, 2021)

Example: You may have read that a 3,500 kcal deficit equates to losing 1 pound of BF. So if you normally eat 2,000 kcal/day with a TDEE of 2,000 kcal/day and decrease your calories by 500 kcal per day (500 per day = 3,500 per week) to 1,500 kcal per day, you may expect to lose 1 pound of BF in 1 week. However, if your RMR drops by say 150 kcal/day, your new TDEE is 1,850 kcal/day. With your current 1,500 kcal/day diet your caloric deficit is actually 350 kcal/day. So instead of taking 7 days to lose 1 pound of BF we may expect it to take 10 days (350 kcal/day * 10 days = 3,500 kcal). However, other changes also occur (see further examples below).

Note: A 2021 analysis quantified the change in TDEE (using >6,000 subjects) & basal expenditure (using >2,000 subjects, basal expenditure is similar to BMR and RMR) across the lifespan. The authors found(Pontzer, 2021):

  • In the first month of life the size-adjusted TDEE & basal expenditure are similar to that of young adults.
  • Throughout the remainder of the first year these energy expenditures increase such that they are ~50% higher than that of young adults (when adjusting for body size) by age 9-15 months.
  • They then steadily decline at ~2.8% per year until age ~20 years and thereafter remain stable until age ~60 years.
  • Subsequently, they decline by ~0.7% per year for the remainder of the lifespan.
  • Of note, these results incorporate age-related changes in physical activity as well as age-related changes in tissue-specific metabolism.
  • Lastly, there was significant individual variability within the data sets.

They note there are no gender differences and also that during pregnancy there are no differences; thus even neonates not-yet-born have a metabolism similar to that of adults (when adjusting for body size).

The two key takeaways here in my opinion are:

  • In young and middle-age adulthood metabolism does not decrease beyond that expected for changes in body size and composition. Weight gain commonly observed during this time period is more likely due to increases in caloric intake, decreases in physical activity, or changes in body composition as opposed to innate slowing of one’s metabolism.
  • There is significant variability at the individual level with respect to TDEE and basal expenditure. I will comment on this more in the example at the end of this lesson as well as in the next lesson.

Thermic Effect of Feeding (“TEF”)

You will commonly read that 1 gram of fat has 9 kcals, 1 gram of carbohydrate has 4 kcals, 1 gram of protein has 4 kcals, and you will less commonly read that 1 gram of alcohol has 7 kcals while 1 gram of fiber has ~0-2 kcals. Fiber and alcohol are discussed in lessons 7 & 8. The numbers for fats, carbohydrates, and proteins are general ballpark figures and some sources of these nutrients will have greater or fewer calories. If curious about these differences, there is an excellent overview here. However, this variability is generally quite small and it is typically fine to just use the 9/4/4 numbers, though there are some exceptions (see the tip below).

Tip: If you are looking at a nutrition label and the overall calories on the label do not match up with the stated grams of carbohydrates, protein, and fat when using the 9/4/4 numbers, this is likely due to fiber, sugar alcohols, or the 9/4/4 numbers not being accurate for that specific food. As one extreme example, let’s look at 92% cacao:


*The numbers for the adjusted kcals are taken from the Atwater factors specific for cocoa.

Most foods are not this extreme, but here it is clear that there is a difference of almost 40 kcals per serving when using the adjusted vs unadjusted numbers. Importantly, the nutrition label lists the corrected total calories. In general, when looking at nutrition labels the total calories should be trusted more than the sum of the components.

What these numbers do not consider is how much energy we have to use to actually digest nutrients we consume. It turns out we use little energy to digest fats (likely 2-3% of the kcals in fats are needed to digest them), more for carbohydrates (5-10%), and considerably more for protein (20-30%). For an overall diet, a lot of people average all three components to roughly 10%, meaning that the equivalent of 10% of the calories we consume are used in the process of absorbing & digesting food.(Westerterp, 2004) In addition to macronutrient content there are other contributing factors leading to variability, such as(Calcagno, 2019):

  • insulin resistance tends to decrease one’s TEF, likely due to the body not processing nutrients to the same degree in an insulin resistant state (as less glucose will enter cells) – this is likely the largest determining factor in interindividual variability of the TEF
  • as one ages a handful of studies indicates our TEF decreases
  • a few studies indicate that both physical activity as well as an increase in meal size seem to increase our TEF
  • of note, most of the studies evaluating this are small and there are few in number

For dieting purposes, if you eat less food your TEF will go down, so instead of having a TEF of 200 kcal while eating 2,000 kcal/day, it will drop to 150 kcal while eating 1,500 kcal/day.

Example: Back to the prior example, by going from 2,000 kcal/day to 1,500 kcal/day your TDEE drops not only to 1,850 kcal/day due to a reduction in RMR but an additional 50 kcal/day due to a reduction in TEF. Thus, your TDEE is now 1,800 kcal/day. Not a huge difference but worth knowing about, and because the total deficit is now 300 kcal/day, you may expect it to take 11-12 days to lose 1 pound of fat (300 kcal/day * 12 days = 3,600 kcal). However, other changes also occur (see further examples below).

Exercise Activity Thermogenesis (“EAT”)

There are really two components here:

  • the amount of calories you burn during exercise
  • the amount of calories you burn after exercise (termed “excess post-exercise oxygen consumption” (“EPOC”))

Figure illustrating physiologic rationale for EPOC

A figure describing excess post exercise oxygen consumptionFrom: Clark, M., Lucett, S. McGill, E., Montel, I., Sutton, B. National Academy of Sports Medicine. (2018). NASM essentials of personal fitness training. 6th edition. Jones & Bartlett Learning.

A: Prior to exercise. B: When running on a treadmill an oxygen deficit develops as anaerobic pathways are utilized first. C: With continued exercise aerobic pathways turn on and oxygen utilization eventually meets demand. D: After exercise stops excess oxygen is still consumed to make up the deficit;  this declines rapidly as the initial deficit is mostly replaced. E: For an extended period of time there is still a slight increase in oxygen consumption until the body returns to a physiologic resting state.

Total calories burned during exercise is hard to predict. This varies considerably depending on exercise modality, duration, intensity, individual level of fitness(Levine, 2003), and efficiency of movement. In general, resistance training without a cardiovascular component will burn considerably fewer calories than cardiovascular training. See the tip below regarding cardio machines.

In regards to EPOC, this is generally not a big contributor unless you do a lot of intense exercise (getting your heart rate up pretty high) for extended periods of time; you need to be in rather good shape to get a decent-sized contribution from EPOC.(Moniz, 2020; Panissa, 2020)

Tip: When using cardio machines do not trust the calorie counts they provide without careful thought. These generally overestimate and can do so by a factor of 2-3x.(Glave, 2018) They also do not necessarily subtract your RMR; the calories they state may include the calories you would have burned at rest plus the additional calories burned with exercise rather than just the calories burned with exercise. Regardless, you can still compare the calorie counts from one session to another to reasonably track progress.

Example: Back to the prior examples, you started at 2,000 kcal/day intake with a TDEE of 2,000 kcal/day, decreased your intake to 1,500 kcal/day and had a drop in RMR and TEF resulting in a new TDEE of 1,800 kcal/day. If you don’t exercise at all you may expect to lose 1 pound of fat in 11-12 days. If you do exercise, any calories you burn with the exercise get added to your TDEE. So if you do any form of additional exercise that burns 300 kcal/day while starting your diet, your TDEE goes up to 2,100 kcal/day, and thus your daily deficit is now 2,100 – 1,500 = 600 kcal/day. You now may expect to lose 1 pound of fat in 6 days (600 kcal/day * 6 days = 3,600 kcal). However, this ignores the last factor in the equation, which is NEAT (see the next example below).

Non-Exercise Activity Thermogenesis (“NEAT”)

NEAT helps explain why some people have so much more trouble losing or gaining weight than others.(Levine, 2003) This varies considerably between people at least in part due to genetics. When eating an excess of food, some people naturally tend to move around a lot more, and these people will put on less weight. Others will move around less and put on more weight. When losing weight this can manifest by making people feel more sluggish. If you have ever tried to lower your caloric intake to lose weight and find yourself feeling more “lazy”, that is most likely NEAT working against you. There is also evidence that as more weight is lost NEAT decreases further.(Rosenbaum, 2016) Counteracting NEAT can be a key factor in ensuring successful dieting (see tip below).

Of interest, a 2018 systematic review evaluating 36 articles of dietary, exercise, or dietary + exercise interventions found that many of them did not result in a decrease in NEAT or NEPA (NEPA is non-exercise physical activity – distinct from NEAT which is the actual energy expenditure associated with the physical activity).(Silva, 2018) Only 63%, 27%, and 23% of the articles found a decrease in NEAT/NEPA with dietary, exercise, or dietary + exercise interventions, respectively. Of particular interest, none of the interventions that incorporated resistance training found a downregulation of NEAT/NEPA.

However, the interventions in this latter review that led to greater amounts of weight loss (~10kg vs 5kg) had significantly greater amounts of downregulation of NEAT/NEPA. The authors also acknowledged many trials were underpowered and potentially had other methodologic issues. Thus, it is likely that downregulation of NEAT/NEPA is more significant as individuals lose more weight, and we need larger and better-designed trials to more formally evaluate the characteristics of the downregulation.

Tip: Lifestyle choices can be made to attempt to counteract a decrease in NEAT when dieting.(Villablanca,2015) Examples include:

  • take the stairs instead of the elevator and park further away from buildings
  • wear a step counter of some sort (or use a smart phone) and set a minimum step count to aim for daily
  • stand up and walk during commercials, march in place or pace while watching things on screens
  • dance to music while relaxing
  • set up a standing desk for work or obtain a pedal exerciser to use when sitting
  • set a 5 or 10 minute timer on repeat and get up & move around when it goes off

Example: Back to our example; you are eating 1,500 kcal/day with a TDEE of 1,800 kcal/day (with no exercise) or 2,100 kcal/day (with exercise). Let’s say your NEAT decreases by 100 kcal/day without exercise and 150 kcal/day with exercise. This makes your new TDEE 1,700 kcal/day (with no exercise) or 1,950 kcal/day (with exercise). This makes your final caloric deficit either 200 kcal/day (with no exercise) or 450 kcal/day (with exercise). Thus you may expect it to take 18 days to lose 1 pound of fat without exercise (200 kcal/day * 18 days = 3,600 kcal) or 8 days to lose 1 pound of fat with exercise (450 kcal/day * 8 days = 3,600 kcal).

Below is a visual depiction of the above example using the same numbers. Scenario 1 is at baseline when you are eating 2,000 kcal/d, which matches your TDEE, and thus your weight is stable. Scenario 2 is when you eat 1,500 kcal/d without additional exercise, decreasing your TDEE to 1,700 kcal/d for a deficit of 200 kcal/d. Scenario 3 is when you eat 1,500 kcal/d & add in 300 kcal/d of exercise, yielding a 450 kcal deficit.

figure showing the magnitude that various aspects of metabolism change when dieting

Tip: It is generally easier to maintain a larger caloric deficit by including exercise. This also generally makes it easier to maintain weight loss. Increasing one’s “energy flux”, which has different definitions but essentially means the total amount of energy we consume and expend while maintaining our body weight, seems to be an effective strategy to help keep weight off after weight loss.(Melby, 2019)

The basic idea is that we live in an “obesogenic environment” where there is lots of easy access to tempting calories, and it is difficult to continuously utilize willpower to fight these temptations. By increasing activity levels we are allowed to indulge a bit more with caloric intake, and this may help stave off cravings and feelings of hunger. This also may have additional health benefits given the increased exercise, but one consideration if using this strategy is whether or not you will be able to maintain higher activity levels long-term; if not then this may set you up for weight regain once your activity levels decrease.(Bosy-Westphal, 2021)

However, this only works to a point. A 2021 analysis shows at baseline (meaning with normal daily activities, not with adding in additional physical activity) there is an energy compensation of 28% (this implies for more active people their RMR &/or NEAT may decrease by 28% of the additional calories they would burn by being more active); this compensation increases to 49% for individuals at the 90th percentile of the BMI distribution (in the obesity range).(Careau, 2021) Again, that is for individuals at baseline without adding in additional activity. There are other lines of evidence that support this and additionally show that with continued increases in physical activity (via natural lifestyle or planned exercise) one’s TDEE may not increase substantially due to these various compensatory mechanisms as well as increases in skeletal muscle efficiency.(Pontzer, 2016; Westerterp, 2018; Hand, 2020; Fernández-Verdejo, 2021)

Thus, adding in exercise is helpful for the various health benefits, and will likely provide some benefit to one’s TDEE, but generally it will not make as much of a difference as one may expect. So how much physical activity should one perform? Due to individual variability in the metabolic adaptations described above it is difficult to provide a specific recommendation for this purpose. The general exercise course on this site goes into much greater detail regarding how much exercise and activity to perform for overall health benefits.

Example: One final example in this lesson. I am reproducing images from a recent publication where the authors performed a very careful assessment of energy expenditure in individuals during a 24 hour fast and during 5 different overfeeding diets (at ~200% of their TDEE).(Hollstein, 2021).  Compensatory exercise was not allowed in this trial. The point of showing these images is to highlight the significant variability in energy expenditure between individuals in these different conditions.

In the below image each circle represents a participant. FST = fasting, the other columns correspond to diets. LPF = (3% protein, 51% carbohydrate, 46% fat), HPF = (30% protein, 26% carbohydrate, 44% fat), FNP = (20% protein, 20% carbohydrate, 60% fat), CNP = (20% protein, 75% carbohydrate, 5% fat), and BOF = (20% protein, 50% carbohydrate, 30% fat). The Y axis shows the change in TDEE measured over 24 hours. The median change in TDEE while fasting was -177 kcal. People with a decrease of a greater magnitude than this were considered to have a “thrifty” phenotype while people with a decrease of lesser magnitude (or a positive change) were considered to have a “spendthrift” phenotype.

Note the large variability in change in energy expenditure and the mostly consistent placement of the most spendthrift and thrifty participants in each trial. This indicates individual variability is consistent across dramatically different dietary conditions.

Reproduced from: Hollstein T, Basolo A, Ando T, Krakoff J, Piaggi P. Reduced adaptive thermogenesis during acute protein-imbalanced overfeeding is a metabolic hallmark of the human thrifty phenotype. Am J Clin Nutr. 2021 Jul 5:nqab209. doi: 10.1093/ajcn/nqab209. Epub ahead of print. PMID: 34225360.

The image below shows the specific data for the low-protein overfeeding (LPF) and high-protein overfeeding (HPF) trials, but splits up the subjects into the spendthrift and thrifty phenotypes described above. Of note, the thrifty phenotypes have a higher baseline TDEE when in energy balance (the height of the black bars, this denotes their TDEE when eating in energy balance to maintain their weight). The gray bars indicate the increase in TDEE when overfeeding with the specified diets. While the thrifty phenotypes have a higher TDEE when in energy balance, with overfeeding the spendthrift phenotypes have a larger increase in their TDEE (seen by the larger size of their gray bars).

Reproduced from: Hollstein T, Basolo A, Ando T, Krakoff J, Piaggi P. Reduced adaptive thermogenesis during acute protein-imbalanced overfeeding is a metabolic hallmark of the human thrifty phenotype. Am J Clin Nutr. 2021 Jul 5:nqab209. doi: 10.1093/ajcn/nqab209. Epub ahead of print. PMID: 34225360.

Thus, individuals with a spendthrift phenotype, which was defined by a smaller decrease in TDEE when fasting, have a greater increase in TDEE with overfeeding. Therefore, people with a spendthrift phenotype have an easier time losing weight when decreasing caloric intake (as they have a smaller decrease in their TDEE) and a harder time gaining weight when in a caloric surplus (as they have a greater increase in their TDEE). This is likely a key factor in why some people can more easily maintain a healthy body weight than others.

Note: As seen throughout this lesson, there are many aspects of physiologic adaptations to weight loss, but they impact people to different degrees.(Martínez-Gómez, 2021) Given so much individual variability in the various aspects of metabolism and energy expenditure, it is tempting to think that some day we will be able to measure these individual qualities to yield personalized interventions. Unfortunately we are still far away from being able to do this on a regular basis.(Löffler, 2021)

Thus, throughout this course and the general exercise course I provide general advice that applies to most people, but keep in mind there will frequently be exceptions and it is difficult to predict for whom these exceptions will occur. As discussed in the next couple of lessons, monitoring progress and then making adjustments when indicated is a key component to an effective dietary strategy.


Hopefully it is clear why trying to lose weight solely by eating fewer calories can be problematic. RMR, TEF, and NEAT all decrease, slowing weight loss significantly, as your body fights your efforts to lose the weight. Without exercise it is hard to counteract these changes and the only way to continue losing weight at a faster rate is to further reduce calories, making it harder to get in all of the nutrients your body needs to live healthily. You can counteract this with increased exercise; this will increase your caloric deficit and if employing resistance training will help you maintain your LBM as you lose BF, a potential key factor in staving off weight regain in the long run.

Thus, while nutrition is key for weight loss, exercise is still very helpful even beyond the health benefits it confers. Additionally, while there can be significant individual variability in the above aspects of metabolism, the same basic concepts apply to everyone.

Now with this basic understanding of metabolism, in the next lesson we will begin to discuss more practically how to determine what your caloric intake should be, and if you even need to track calories in the first place.

Click here to proceed to Lesson 2


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