Amino Acids and Proteins

There are 20 amino acids which are important in human nutrition. The side chain of the amino acid determines the properties of the amino acid which are classified by the chemistry of these side chains (R group). The carbon to which the carboxyl is attached is the a -carbon. Amino acids have four different groups around the a -carbon resulting in optically active l- or d-isomers or enantiomers. The l-forms are conjugated into proteins and biological systems.

Classification of amino acids —

Amino acids can be grouped in a number of ways. They can be classified chemically based on structure or nutritionally or increasing length of side chain. .

Chemical classification —

• Mono-amino, mono-carboxylic amino acids: glycine (Gly), alanine (Ala), valine (Val), leucine (Leu), isoleucine (Ileu)

• Hydroxy-amino acids: serine (Ser), threonine (Thr)

• Basic amino acids: lysine (Lys), arginine (Arg), histidine (His)

• Acidic amino acids and amides: aspartic acid (Asp), glutamic acid (Glu), asparagine (Asn), glutamine (Gln)

• Sulphur-containing amino acids: cysteine (Cys), methionine (Met)

• Aromatic amino acids: phenylalanine (Phe), tyrosine (Tyr), tryptophan (Trp)

• Imino acid: proline (Pro)

Functional classification

This separates the amino acids into four groups, polar, non-polar, acidic and basic. The polarity or non-polarity indicates how the amino acid will be incorporated into proteins, polar on the outside, non-polar in the interior of the protein. Amino acids may be charged or uncharged according to the pH of the environment.

Amino acids may undergo further reactions:

• Enzymatic acetylation and methylation, usually of lysine: this suppresses positive charges forming on the amino group.

• Phosphorylation: the addition of a phosphate group to the hydroxyl group of serine or tyrosine and occasionally threonine.

• Glycosylation: the addition of a carbohydrate to an amino acid. A sugar may be attached to the amino group of asparagine to form an N-linked oligosaccharide. Occasionally a sugar may link to the hydroxyl group of serine or threonine to form an O-linked oligosaccharide.

The side chain is the major factor in determining the transport system that is utilized by an amino acid. Among neutral amino acids bulk and lipophilic properties of the side chain are all important.

Humans can synthesise some non essential amino acids from glucose and ammonia, using the Krebs’ cycle or from free amino acids by transamination or reductive amination. There are nine amino acids for which humans have no amination capability and therefore cannot synthesise. These are essential amino acids which must therefore be provided in the diet and which were defined originally by Rose as those amino acids which must be included in the diet to ensure optimal growth.

Two other amino acids, tyrosine and cysteine, are facultatively essential. They are synthesized from essential amino acids and become essential only if there is a deficiency of their precursor essential amino acid.

Conditionally essential amino acids, require preformed carbon side chains and substituted groups from other amino acids. Glycine, serine and cysteine may well function as an inter-related group, with the need for adequate provision of each.

The following factors may complicate amino acid requirements:

• A lack of a primary amino acid may limit the utilization of other amino acids leading to equal loss of carbon and nitrogen.

• A lack of non-essential amino acids; could result in the deamination of essential amino acids to provide nitrogen.

• Lack of conditional essential amino acids, leads to problems in the balance of nitrogen and carbon substrates and the need for specific if not essential amino acids.

1. There are 20 amino acids which are important in human nutrition. The amino acids have a variety of side chains which provide a range of biological properties. The amino acids are classified by the nature of their side chain. The l-forms are conjugated into proteins and biological systems. The d-form is found in the walls of bacteria and in some antibiotics, but not found in mammals.

2. Humans can synthesise most of the amino acids from glucose and ammonia. These are called non-essential amino acids and can be synthesised via Krebs’ cycle or from free amino acids by transamination or reductive amination.

There are eight essential amino acids, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan and valine, which humans cannot synthesize. Hence, these amino acids must be provided in the diet.

3. Tyrosine and cysteine are facultatively essential. They are synthesised from essential amino acids and only become essential if there is a deficiency of their precursor essential amino acid.

4. Some amino acids are conditionally essential, requiring preformed carbon side chains and substituted groups from other amino acids, e.g. glycine, serine and cysteine may well function as a inter-related group, with the need for adequate provision of each. The requirements of the nitrogen cycles, e.g. glutamate cycle, may well increase the requirements for glutamate.

5. There are many other amino acids which are of plant origin which are at best not nutritional and which may be toxic.



Proteins are high molecular weight polyamides, consisting of one or more chains of amino acids which then fold into a form that gives that protein a particular function. Proteins vary in size (from 1000 to 1 000 000 Da) and length, with some extending to 2000 amino acid residues. ( the molecular weight of proteins are measured in kilodaltons , one dalton Da, is the mass of one hydrogen atom ie 1.6605 x 10 –24 g. The average protein has a molecular weight of between 24 000 and 37 500 Da, which is 200–280 amino acid residues long. Proteins differ in their amino acid sequence rather than the amino acid content.

Proteins are present in all living tissues and are the principal material of skin, muscle, tendons, nerves and blood; they form enzymes, antibodies and even have a supporting role in molecular biology. There are more than 100,000 different types of protein in the body, and these form half of the dry weight. Of the body. Proteins are involved in every one of the body’s processes.

The proteome, the pattern of proteins produced by and present in a cell under particular conditions, protein expression, protein function. This then will allow a data base of all the proteins to be constructed.

The enzymatic activity of purely protein enzymes, i.e. those which do not involve coenzymes, are dependent upon the chemical properties of the functional groups of the side chain of nine amino acids:

• imidazole ring of histidine

• carboxyl groups of glutamate and aspartate

• hydroxyl groups of serine, threonine and tyrosine

• amino groups of lysine

• guanidinium group of arginine

• sulphydryl group of cysteine

The groups act as general acids and bases and catalyse proton and group transfer reactions.

Metals, e.g. cobalt, iron, manganese, copper, zinc and molybdenum function as cofactors in enzyme reactions. They are points of positive charge, interact with two or more ligands and exist in two or more valency states.

Nutritional requirements of amino acids and protein

Protein intake is relatively constant at 10–12% of energy intake and diminishes in parallel with the fall in energy which accompanies age. This may be a factor in muscle loss with age. A safe intake of protein should not be lower than 0.75 g/kg/day (WHO/FAO/UNO, 1985). Dietary protein provides nitrogen in an organic form for the renewal of amino acids for their various functions including proteins in cell walls, plasma proteins, muscles, enzymes and collagen. The amino acids of protein can be deaminated and may act as an energy source in their own right.

Dietary amino acid requirements

Proteins differ in their biological quality, dependent upon the amounts and proportions of essential amino acids. A protein which is rich in all of the essential amino acids would score higher on the scale of biological quality than a protein deficient in one or more essential amino acids.

It is necessary to define protein and specific amino acid needs in diets both with abundant and also deficient amounts of nutrients, including protein and specific amino acids. The protein requirement of all age groups should be based on the recommendations in the report of the FAO/WHO/UNO Expert Consultation, where the values were based on estimates and the amounts of high quality egg or milk protein required for nitrogen (N) equilibrium as measured in nitrogen balance studies (Table 11.2). The estimated average intake of protein increases from 10.6 g/day at 4–6 months to 14.8 g/day at 4–6 six years and 22.8 g/ day at 7–10 years. In the male, protein requirement increases from 33.8 g/day in the 11–14-year-old male to 42.6 g/day in the 50+ year-old male. In the female, corresponding values were 33 g/day for 11–14-year-olds to 37 g/day for the over-50s. Athletes may require more dietary protein depending on the muscle power required in the sport. It was suggested that an addition should be made of 6 g/day for pregnancy and 11 g/day for lactation during the first 6 months and then 8 g/day required after 6 months as the protein content of the breast milk falls after this. For infants and children additions were made for growth and in pregnancy and lactation additions were made to account for the growth of the foetus and to allow adequate breast milk production. There is relatively little change with age in the requirement for protein for maintenance, values falling from 120 mg (N)/kg/day at 1 year to 96 mg (N)/kg/day for adults. This assumed, during growth, an efficiency of dietary utilisation of 70%.

In the case of the elderly, the recommended nitrogen intake is the same as for younger adults, 0.75 g protein/kg/day. Daily protein intakes in the United Kingdom have tended to increase, to figures of 84 g for men and 64 g for women. There has been concern that excessive intakes of protein may be associated with health risks.

Estimation of the biological value of a protein

Nitrogen excretion The nutritional value of a protein is measured by first establishing the rate of nitrogen excretion on a protein-free diet. Thereafter, known amounts of the protein being tested are added to the diet and the effect on nitrogen excretion measured.

Amino acid content An alternative approach is to measure the amino acids in the protein. The figure can be compared with that of the egg protein standard.

Amino acid regulation of protein turnover

Amino acid requirements include the maintenance of protein turnover above a certain limit, regardless of net protein retention. It is not yet clear whether protein turnover is regulated by the rate of supply of any amino acid or whether it is restricted to a limited number of amino acids. The physiological state of the subject may be a variable: age, growth, pregnancy or health.

Total body protein

This is a very important measurement as a reduction in values to under 80% of normal is a serious problem. Estimates of total body protein might be made by estimates based on the size of muscle masses eg arm and leg, or indirectly from serum proteins or albumin or by in vivo neutron activation analysis for total body nitrogen. These methods are either approximation or subject to substantial radiation risks. All such methods make assumptions, but a method which has some utility is the dual energy X-ray absorptiometer.

Protein turnover

Protein turnover is a measure of a continuous process.

One point measurements which give an indicator of protein status and separate what is regarded as normal from abnormal include somewhat old fashioned measurements. They have been used clinically and are approximations. If the result is abnormal then there is protein negative balance that is input is insufficient to meet the needs of the body. A normal result may not however mean that all is well

Key points

1. Proteins are high molecular weight polyamides, consisting of one or more chains of amino acids linked through covalent peptide bonds.

2. Proteins consist of a sequence of amino acids which is singular to that protein. The sequence is called the primary structure. Specific groupings of amino acids in one section of the protein gives biological properties individual to that protein, e.g. in an enzyme active centre.

3. When the primary structure is folded then a secondary structure results in a a -helix or b -sheet formation, created by free rotation around bonds.

4. A major factor in the conformation of proteins are non-covalent bonds. The non-covalent bonds between different side chains in different regions of the molecules especially proteins include Van der Waals, hydrophobic interactions, hydrogen bonds and ionic bonds.

5. The tertiary structure of a protein is the structure with the lowest free energy and therefore the most stable form. It is found in fibrous proteins, which provide structure in the cell or tissues. Globular proteins have an a -helical secondary structure, commonly found with most enzymes and proteins involved in gene expression and regulation.

7. A small molecule which binds to a protein is called a ligand. Such ligand arrangements are found with enzymes in which there is an active site with a catalytic reaction.

8. Some protein molecules are complexes of more than one polypeptide chain and form a larger protein molecule, the quaternary protein structure, e.g. allosteric proteins. There are a number of alternative conformations of this quaternary structure which have different biological properties, an important principle in metabolic and genetic regulation.

9. Different allosteric protein and enzyme shapes are dictated by the DNA of the gene encoding that enzyme. The metabolic characteristics of an individual are determined by the translation of RNA into different isoenzymes.

Further Reading

Carpenter, K.J. (1994) Protein and Energy, Cambridge University Press, Cambridge.
Cohen FE, Prusiner SB ( 1998) Pathological conformations of prion proteins . Annual Review of Biochemistry , 67, 793-819
Dean, PM. (ed.) (1995) Molecular Similarity in Drug Design, Blackie Academic and Professional, London.
Doolittle, R.F. (1995) The multiplicity of domains in proteins. Annual Review of Biochemistry, 64, 287–314.
Doolittle, RF, Feng, D-F, Tsang, S, Cho, G, Little E. ( 1996 ) Determining divergence times of the major kingdoms of living organisms with a protein clock. Science 271, 470-474
Food and Agriculture Organization/World Health Organization/United Nations (1985) Energy and Protein Requirements. Technical Report Series, no. 724, WHO, Geneva.
Food and Agriculture Organization/World Health Organization/United Nations (1989) Joint FAO/WHO expert consultation on protein quality evaluation. Rome
Frydman J ( 2001 ) Folding of newly translated proteins in vivo: the role of molecular chaperones. Annual Review Biochemistry 70, 603-49.
Fuller NJ, Wells JCK, Elia M ( 2001 ) Evaluation of a model for total body protein based on dual-energy X-ray absorptiometry : comparison with a reference four-component model. British Journal of Nutrition , 86, 45-52
Jeong H, Mason SP, Barabasi A-L, Oltvai ZN ( 2001) Lethality and centrality in protein networks Nature 411, 41
Lebman SW ( 2001 ) The shape of a species barrier Nature 410 161-2
Levitt M, Gerstein M, Huang E, Subbiah S, Tsai J ( 1997 ) Protein folding: the end game. Annual Review Biochemistry 66, 549-79.
Munro AW, Taylor P, Walkingshaw MD ( 2000) Structures of redox enzymes. Current Opinion in Biotechnology 11, 369-376
Perutz, M. (1990) Mechanisms of Cooperativity and Allosteric Regulation, Oxford University Press, Oxford.
Reeds, P.J. (1990) Amino acid needs and protein storing patterns. Proceedings of the Nutrition Society, 49, 489–97.
Rennie MJ, Edwards RH, Halliday D, Matthews DE, Wolman SL and Milward DJ ( 1982) Muscle protein synthesis measured by stable isotope techniquesin man: effects of feeding and fasting. Clin. Sci 63, 519-23.
Scheffner M , Whitaker NJ ( 2000 ) Proteolytic relay comes to an end Nature 410, 882-3
Stroud MA, Jackson AA, Waterlow JC ( 1996) Protein turnover rates of two human subjects during an unassisted crossing of Antarctica. British Journal of Nutrition , 76, 165-174.
Taylor W ( 2001) A “periodic table” for protein structures. Nature 416, 657-9
Waterlow JC ( 1995 ) Whole-body protein turnover in humans-past, present and future. Annual Review Nutrition 15, 57-92.
Welch WJ, Gambetti P ( 1998 ) Chaperoning brain diseases Nature 392, 23-4
Websites the human proteome organisation.


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