Guide to Protein Quality, Digestion and Absorption

It’s frequently claimed that different proteins vary in quality and that some are more beneficial than others. This is true, but only to a point. There are a number of factors which may affect the protein quality from food, including:

  • The amino acid profile of the protein
  • The structure of the protein
  • The digestibility of the protein
  • The amount of protein consumed in one meal
  • Other nutrients and food constituents present in the meal, e.g. fibre, carbohydrate
  • How the food has been prepared
  • Recent intake of protein
  • The metabolic state of the individual, e.g. exercise and sleep
  • The individual's age, weight, sex and general health

We also need to consider the reason why we want protein; obviously, we all need adequate protein for good health, but bodybuilders, for example, will be looking at protein for muscle growth, so the quality may be more important to them.

Protein Digestion and Absorption

Before we look at protein quality, let’s first look at the way proteins are digested and absorbed. Digestion of food begins in the mouth and continues until all nutrients have been absorbed in the intestines. Several digestive enzymes are involved in the digestion process which break down – or hydrolyse – protein into short-chain oligopeptides or amino acids. The simplest units of proteins are amino acids of which there are 20-odd different types. Two amino acids linked together are called dipeptides, a few amino acids in a peptide chain are called oligopeptides and long chains of them are called polypeptides.

Amino acids are absorbed in their basic form by an active transport process, where they are pumped across the cell membranes and then into the blood. However, there is a second process which happens simultaneously to the active transport mechanism where oligopeptides can be taken up in their current form and, when inside the cells of the intestine, are then further broken down to free amino acids. The process of this is a cell enzyme-related system that relies on a chemical ion gradient.

As there are two independent protein absorption systems in operation, this allows for more protein absorption at times when it’s required as the second system only comes into play when there are oligopeptides present. In a high-protein meal with more than one protein source (i.e. the majority of meals), both systems come into play at similar rates.

Methods of Determining Protein Quality

There are different methods for assessing the quality of protein sources which look at the amino acid profile and how readily the protein is digested and absorbed.

1) Amino Acid Scoring (AAS) aka Chemical Scoring (CS)

AAS is fast and cheap. It measures the essential amino acids (EAAs) – also known as indispensable amino acids (IAAs) – present in a protein and compares the values with a reference protein[1]. The rating of the protein being tested is based upon the most limiting EAAs. Obviously, this has real-world limitations.

2) Protein Efficiency Ratio (PER)

PER measures the ability of a protein to support the growth of a weanling rat. It represents the ratio of weight gain to the amount of protein consumed[2]. The main limitation is obvious: it’s based on rats, but also that PER measures growth and not maintenance and exercise requirements[3].

3) Nitrogen Protein Utilisation (NPU)

This is the ratio of the nitrogen used for tissue formation versus the amount of nitrogen digested[4]. This method doesn’t account for the amino acid profile[3].

4) Biological Value (BV)

BV is the most commonly used and well-known protein scoring system. It measures the amount of nitrogen retained in comparison to the amount of nitrogen absorbed[5, 6]. It looks at how similar the amino acid profile is to that of human requirements. Proteins are grouped into those of high BV (HBV) and low BV (LBV).

BV is significantly flawed, yet it still seems to be favoured as a reference guide when comparing protein, especially in sports nutrition. BV studies are in rats, and rats have different digestive systems to humans and their protein requirements differ indicating that the reliability of BV in humans is questionable. Also, BV does not take into consideration several key factors that influence the digestion and interaction of protein with other foods before absorption; it only measures a protein's maximal potential quality and not its estimate at requirement amounts[3]. As more of an HBV protein is consumed, the actual amount of that protein retained decreases, and BV doesn’t account for this.

Another limitation is that proteins which are missing one EAA can still have a BV of up to 40. This is because of our ability to conserve and recycle EAAs as an adaptation of inadequate intake of the amino acid in malnutrition[3].

5) Protein Digestibility-Corrected Amino Acid Score (PDCAAS)

PDCAAS takes into account the profile of IAAs of the protein in question, as well as its digestibility in humans; it is the AAS with an added digestibility component. Scores are from 0.1 to 1.0, with 1.0 being a high-quality protein. PDCAAS is the current accepted measure of protein quality, and is the method adopted by the World Health Organization / Food and Agriculture Organization (WHO/FAO) and the US Food and Drug Administration (FDA)[7-9], because it’s both simple to test and has a direct relationship to human protein requirements[10].

Although more up to date and accurate, PDCAAS isn’t without its shortfalls. All proteins of a score greater than 1.0 are rounded down to 1.0 as scores above are considered to indicate that the protein contains IAAs in excess of human requirements[7]. This obviously limits the validity of comparisons between proteins.

Another flaw of PDCAAS is that the scores are based on that of a 2 to 5-year-old child (considered to be nutritionally the most demanding group[7]). Adults have a proportionally larger maintenance : growth ratio and this is not considered when using PDCAAS[7, 9]. As PDCAAS doesn’t account for certain factors influencing the digestion of the protein, the PDCAAS of a single protein source is of limited use for application to human protein requirements. This is because what is measured is the maximal potential of quality and therefore it’s not a true estimate of the quality at requirement level[10].

PDCAAS is also limited by the fact that it doesn’t account for conditionally essential amino acids, and these contribute to the nutritional value of a protein[9]. For example, a good intake of non-essential cysteine – a sulphur-containing amino acid – reduces the requirement for the essential sulphur-containing methionine, and tyrosine reduces the need for the EAA phenylalanine. Arginine is also considered conditionally essential as in certain population sub-groups and at times of high demand, an insufficient amount may be synthesised within the body[11].

Another crucial limitation of PDCAAS is the fact that human diets are generally comprised of varied protein sources, even in a single meal. This means the total amino acid profile of a meal is improved and there are other food constituents that may affect protein hydrolysis, digestion and absorption. In order to assess the true PDCAAS of a meal, all individual amino acids need to be taken into account. Fortunately, PDCAAS can be adapted to account for this in order to evaluate the protein quality of a meal more reliably.

The protein from rice has a PDCAAS of 0.4-0.5, limited only by the fact that it’s significantly low in the EAA lysine. However, it’s abundant in methionine and cysteine; the high content of these two key amino acids is a point that PDCAAS doesn’t account for when looking at a single food. The PDCAAS of pulses ranges from 0.4-0.8, depending on the pulse, and pulse proteins are low in methionine and cysteine but abundant in lysine. So, when beans and rice are consumed together in a meal, their combined constituent PDCAAS is 1.0: an ideal protein source.

Despite its limitations, PDCAAS is currently the most widely adopted protein scoring system as it provides a valid method of assessing protein quality as long as the cumulative score of the different protein sources in a meal is accounted for. Indeed, in US labelling regulations, the protein quality of a food using PDCAAS needs to be considered when labelling the total protein content of a food[12].

6) Digestible Indispensable Amino Acid Score (DIAAS)

DIAAS is much like PDCAAS in that it determines the digestibility of the amino acids as well as the protein’s contribution to human amino acid and nitrogen requirements. However, DIASS is shown as a percentage and doesn’t limit to scoring the protein to a maximum value; instead, proteins can have a higher score. It has been suggested that DIAAS should be the adopted scoring method for the US FAO[13, 14], but as yet hasn’t been adopted as the preferred protein scoring method.

An advantage of DIASS over PDCAAS is that proteins with greater amounts of IAAs have a higher score that may be more reflective of the amino acid profile with relevance for those with higher protein requirements. However, while this may have relevance to single foods, the combination of protein sources in a meal still needs to be considered[14].

Bioavailability of Protein

Bioavailability is the amount of protein we actually absorb, and both BV and PDCAAS in part account for this. Bioavailability is affected by a number of factors including the total amount of types of protein consumed within one meal as well as other constituents of the meal.

Proteins are not simply a long chain of amino acids; the amino acid chain wraps around itself (known as the secondary structure of protein), and these double chains wrap around themselves again (tertiary structure) and then bonds form between amino acids as the chain’s folded over into a protein molecule forming its quaternary structure. The structure of proteins vary and this can have a bearing on bioavailability.

We’ve discussed the limitations of both BV and PDCAAS above, yet BV is often cited as a reference for protein bioavailability. Indeed, plant proteins are often indicated to be inferior to animal proteins and, while this is partly true, it doesn’t account for the fact that meals often contain a combination of proteins.

Whey protein – the number-one protein choice of bodybuilders – has a very high bioavailability. Indeed, it’s considered to be so quickly digested and absorbed that a good amount of it goes to the liver after absorption where it’s converted to carbohydrate by gluconeogenesis for energy, indicating that the fate of whey is not as retained nitrogen, but for energy, i.e. not the reason why the protein was consumed in the first place.

One study compared the effects of supplementation with rice protein isolate and whey protein isolate post resistance workout and found both to have an equally positive effect on body composition and exercise performance[15]; i.e. whey was no better than rice protein.


  1. Mitchell HH, et al. Some relationships between the amino acid contents of proteins and their nutritive values for the rat. J Biol Chem. 1946; 163:599-620.
  2. Chapman DG, et al. Evaluation of protein in foods. I. A method for the determination of protein efficiency ratios. Can J Biochem Physiol. 1959; 37(5):679-86.
  3. Pellett P. Amino Acid Scoring Systems and their Role in the Estimation of the Protein Quality of Cereals. In: Lásztity R., Hidvégi M. (eds) Amino Acid Composition and Biological Value of Cereal Proteins.: Springer, Dordrecht; 1985.
  4. Eckfeldt GA, et al. The pepsin-digest-residue (PDR) amino acid index of net protein utilization. J Nutr. 1956; 60(1):105-20.
  5. Chick H, et al. The biological values of proteins: A method for measuring the nitrogenous exchange of rats for the purpose of determining the biological value of proteins. Biochem J. 1930; 24(6):1780-2.
  6. Mitchell HH. A method of determining the biological value of protein. J Biol Chem. 1924; 58:873.
  7. Food and Agriculture Organization of the United Nations. Protein Quality Evaluation. Report of Joint FAO/WHO Expert Consultation. 1989.
  8. Boutrif E. Food Quality and Consumer Protection Group, Food Policy and Nutrition Division, FAO, Rome: "Recent Developments in Protein Quality Evaluation" Food, Nutrition and Agriculture. Food, Nutrition and Agriculture. 1991; (2/3).
  9. Schaafsma G. The protein digestibility-corrected amino acid score. J Nutr. 2000; 130(7):1865S-7S.
  10. Schaafsma G. Advantages and limitations of the protein digestibility-corrected amino acid score (PDCAAS) as a method for evaluating protein quality in human diets. Br J Nutr. 2012; 108 Suppl 2:S333-6.
  11. Tapiero H, et al. L. Arginine. Biomed Pharmacother. 2002; 56(9):439-45.
  12. U.S. Food & Drug Administration. CFR - Code of Federal Regulations Title 21 2018. Date Accessed: 19/08/16. [Available from:].
  13. Institute of Food Technologists. FAO proposes new protein quality measurement. Date Accessed: 19/08/16. [Available from:].
  14. Food and Agriculture Association. Dietary protein quality evaluation in human nutrition: Report of an FAO Expert Consultation. FAO Food and Nutrition paper 92. 2011.
  15. Joy JM, et al. The effects of 8 weeks of whey or rice protein supplementation on body composition and exercise performance. Nutr J. 2013; 12:86.

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