Digestion of proteins, absorption of amino acids, synthesis of amino acids, catabolism of amino acids and synthesis of specialised non-protein compounds from amino acids for undergraduates

1. R. C. Gupta
Professor and Head
Department of Biochemistry
National Institute of Medical Sciences
Jaipur, India
Metabolism
of
Amino Acids

2. Carbohydrates, lipids and proteins are
energy-giving nutrients
Hence they are known as proximate
principles of diet
Carbohydrates and lipids are used
mainly as energy source
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3. EMB-RCG
Provision of energy is not the primary
purpose of amino acid metabolism
Amino acids are used mainly to:
Synthesize various
proteins
Form some specialized
non-protein products

4. EMB-RCG
Amino acids can be used as a source
of energy if:
Availability of carbohydrates and
lipids is low
Availability of amino acids exceeds
their requirement

5. Amino acids are obtained from:
Digestion of dietary proteins
Breakdown of body proteins
Endogenous synthesis
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6. Amino acids are used for:
Synthesis of body proteins
Synthesis of non-protein
specialized products
Provision of energy
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7. In plasma as well as in tissues, there is
an amino acid pool
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Amino acids are continuously added to
and removed from the pool

9. Nitrogen balance
Proteins are the main nitrogenous
constituent of our diet
Proteins are broken down into amino
acids
Catabolism of amino acids results in the
release of their amino groups in the
form of ammonia

10. In human beings and other mammals,
ammonia is converted into urea which
is excreted in urine
Urea is the main nitrogenous compound
excreted from the body

11. Thus, nitrogen is taken in mostly as
proteins and excreted mainly as urea
The relative intake and excretion of
nitrogen is known as the nitrogen
balance

12. In healthy adults, nitrogen excretion equals
nitrogen intake
The person is said to be in nitrogen
equilibrium
Nitrogen equilibrium

13. In growing age, amino acids are used to
form tissue proteins
Therefore, nitrogen excretion is less than
the intake
The individual is said to be in a positive
nitrogen balance
Positive nitrogen balance

14. In starvation and wasting diseases, there
is excessive breakdown of body proteins
Nitrogen excretion exceeds the intake
The individual is said to be in negative
nitrogen balance
Negative nitrogen balance

15. Proteins are synthesized from twenty
L-amino acids (standard amino acids) in
living organisms
All these amino acids are equally
important for protein synthesis
Essential and non-essential amino acids

16. However, the presence of all these amino
acids in diet is not imperative
Some of these can be synthesized in
human beings
Amino acids that cannot be synthesized by
human beings are nutritionally essential
Their presence in diet is imperative

17. The essential amino acids are:
• Valine
• Leucine
• Isoleucine
• Threonine
• Methionine
• Lysine
• Phenylalanine
• Tryptophan

18. Two amino acids, arginine and histidine,
are said to be semi-essential
Their endogenous synthesis cannot meet
the requirements in growing age
The remaining amino acids can be
synthesized in adequate amounts
They are considered to be nutritionally
non-essential or dispensable

19. Our study of amino acid
metabolism will comprise:
• Digestion of proteins and absorption
of amino acids
• Synthesis of non- and semi-
essential amino acids
• Catabolism of amino acids
• Synthesis of non-protein specialized
products from amino acids
• Inborn errors of amino acid
metabolism

20. Proteins are macromolecules
They cannot be absorbed from the
alimentary tract as such
Dietary proteins have to be hydrolysed
into amino acids before their absorption
Digestion and absorption

21. Proteins are hydrolysed by the proteolytic
enzymes present in digestive juices
The number of proteins present in the
diet is large
But the number of proteolytic enzymes in
digestive secretions is very small

22. The proteolytic enzymes present in
digestive juices are group-specific
They are specific for peptide bonds but
not for the actual substrate
Some are endopeptidases and some are
exopeptidases

23. The proteolytic enzymes are generally
secreted in the form of inactive proenzymes
The catalytic site is concealed by a portion of
the polypeptide chain in proenzymes
Removal of the covering peptide reveals the
catalytic site
This converts the proenzyme into active
enzyme

24. Proenzyme
Active site
revealed
Enzyme
Masking
sequence

25. Conversion of proenzymes into enzymes
occurs only upon entry of food
This protects the structural proteins of
mucosa against proteolysis by digestive
enzymes

26. Digestive secretions taking part in the
digestion of proteins are:
Gastric juice
Pancreatic juice
Intestinal secretion
(succus entericus)
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27. Gastric juice
The proteolytic enzyme present in
gastric juice is pepsin
It is secreted as a proenzyme, pepsinogen
Gastric hydrochloric acid splits a peptide
off pepsinogen to convert it into pepsin
Pepsin, once formed, can convert further
molecules of pepsinogen into pepsin
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28. Pepsin is an endopeptidase
It hydrolyses internal bonds of proteins to
convert them into peptides
It acts preferentially on peptide bonds
formed by aromatic and dicarboxylic
amino acids

30. Another enzyme, rennin is present in the
gastric juice of infants
It acts on casein of milk, and converts it
into calcium paracaseinate
Calcium paracaseinate is hydrolysed by
pepsin into peptides

32. Pancreatic juice
Pancreatic juice contains the
proenzymes:
Trypsinogen
Chymotrypsinogen
Proelastase
Procarboxypeptidase
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33. Pancreatic proenzymes
are converted into:
Trypsin
Chymotrypsin
Elastase
Carboxypeptidase
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34. Trypsinogen is converted into trypsin
by enterokinase
Trypsin can convert further molecules
of trypsinogen into trypsin
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36. Trypsin also converts:
Chymotrypsinogen into
chymotrypsin
Proelastase into elastase
Procarboxypeptidase
into carboxypeptidase

38. Trypsin, chymotrypsin and elastase are
endo-peptidases
They hydrolyse proteins and polypeptides
into small peptides

39. Trypsin acts preferentially on peptide bonds
formed by basic amino acids
Chymotrypsin acts preferentially on peptide
bonds in which the carboxyl group is
contributed by aromatic amino acids

40. Elastase acts preferentially on peptide
bonds in which the carboxyl group is
contributed by glycine, alanine or serine
Carboxypeptidase is an exopeptidase
which removes amino acids one by one
from the carboxyl end of proteins
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41. Intestinal secretion
Intestinal secretion contains an amino-
peptidase and some dipeptidases
Aminopeptidase removes amino acids
one by one from the amino end
Dipeptidases hydrolyse dipeptides into
amino acids

43. The final products of digestion of proteins
are L-amino acids
These are absorbed by the mucosal
cells of the small intestine
The absorption is active and energy-
consuming

44. There are several active transport
systems for absorption of different groups
of amino acids
Some of these are linked with sodium
pump in the same way as the active
transport system for glucose (SGLT 1)

45. Glucose Amino acids
Intestinal lumen

46. Synthesis of non- and semi-essential
amino acids
These amino acids can be
synthesized in human beings from:
Amphibolic
intermediates
Some other
amino acids

47. Amino acids synthesized from
amphibolic intermediates are:
• Glycine
• Alanine
• Serine
• Aspartate
• Glutamate

49. Alanine can be synthesized from
pyruvate by a transamination reaction
The reaction is catalysed by glutamate
pyruvate transaminase (GPT)
Pyridoxal phosphate is required as a
coenzyme
Alanine

51. Aspartate can be synthesized from
oxaloacetate by transamination
The reaction is catalysed by glutamate
oxaloacetate transaminase (GOT)
Pyridoxal phosphate is required as a
coenzyme
Aspartate

53. Serine can be synthesized from 3-phospho-
glycerate
3-Phosphoglycerate is an intermediate of
glycolysis
Serine

55. Glutamate can be synthesized from a-keto-
glutarate
The reaction is catalysed by glutamate
dehydrogenase
NADPH is required as a coenzyme
Glutamate

57. Amino acids synthesized from other
amino acids are:
• Glycine
• Asparagine
• Serine
• Glutamine
• Cysteine
• Tyrosine
• Proline
• Hydroxyproline
• Hydroxylysine
• Arginine
• Histidine

61. Glutamine can be synthesized from
glutamate and free ammonia
Energy is provided by hydrolysis of ATP
into ADP and Pi
Glutamine

63. Cysteine can be synthesized from
methionine and serine
These are converted into homoserine and
cysteine respectively
Cysteine

64. S-Adenosyl methionine (SAM; active
methionine) is formed as an intermediate
during the reactions
SAM is a donor of labile methyl groups,
and provides methyl groups for several
methylation reactions

67. Tyrosine can be synthesized by
hydroxylation of phenylalanine
The reaction is catalysed by phenyl-
alanine hydroxylase, a mono-oxygenase
One atom of O2 is incorporated in phenyl-
alanine; the other is reduced to water
Tyrosine

68. The hydrogen atoms are provided by
tetrahydro-biopterin (H4-biopterin)
This is oxidized to dihydrobiopterin
(H2-biopterin)
H4-Biopterin is regenerated at the
expense of NADPH

70. Hydroxylation of phenylalanine is an
irreversible reaction
Therefore, phenylalanine cannot be
synthesized from tyrosine

71. Proline can be synthesized from
glutamate
All the reactions are reversible
Therefore, glutamate can also be
synthesized from proline
Proline

73. Hydroxyproline is found in large
amounts in collagen
There is no codon or anticodon for
hydroxyproline
Hence preformed hydroxyproline cannot
be incorporated in proteins
Hydroxyproline

74. Proline is incorporated in the growing
polypeptide chain
The prolyl residues are later hydroxylated
by prolyl hydroxylase
This enzyme cannot act on free proline

75. Prolyl hydroxylase is a mono-oxygenase
It requires a-ketoglutarate as a second
substrate
It also requires molecular oxygen,
ascorbic acid and Fe++

77. Hydroxylysine is also present in
collagen
Like proline, lysine is incorporated in the
growing polypeptide chain
Then, the lysine residues are
hydroxylated by lysyl hydroxylase
The reaction is analogous to
hydroxylation of proline residues
Hydroxylysine

79. Arginine is formed by cleavage of
argininosuccinate
Argininosuccinate is an intermediate in
urea cycle
Arginine

81. The reactions by which histidine is
synthesized in human beings are not
fully known
Some authorities believe that human
beings cannot synthesize histidine
Histidine

82. The proteins in our body are in a constant
state of flux
A protein is degraded when its life-span is
over
Protein turnover

83. Some abnormal and harmful
proteins are promptly degraded e.g.:
Newly-synthesized proteins that are
defective due to errors in translation
Proteins that become defective
due to oxidative damage
Exogenous proteins that enter as
components of bacteria, viruses etc

84. There are two pathways for
degradation of proteins:
Lysosomal
degradation
Cytosolic
degradation
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85. Lysosomes contain hydrolytic enzymes
These include proteolytic enzymes also
The lysosomal proteolytic enzymes are
known as cathepsins
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Lysosomal degradation

86. The cathepsins hydrolyse:
Proteins having long half-lives
Circulating proteins
Membrane proteins
Exogenous microbial proteins
residing in endosomes

87. No energy is required for lysosomal
hydrolysis of proteins
Loss of sialic acid from the prosthetic group
of circulating glycoproteins destines them for
destruction
These proteins are taken up by hepatocytes
with the help of asialoglycoprotein receptors
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88. Cytosolic degradation
Proteins degraded in the cytosol are:
Proteins having short half-lives
Defective proteins
Exogenous proteins of most
viruses and some bacteria
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89. EMB-RCG
Cytosolic degradation:
Is ubiquitin-dependent
Is ATP-dependent
Requires 26 S protease complex
(proteasome)
Requires three other enzymes
(ENZ1, ENZ2 and ENZ3)

90. Ubiquitin is a ubiquitous protein found in
all organisms
It is made up of 76 amino acids, and has a
molecular weight of 8,500
Primary structure of ubiquitin is remarkably
similar in different species
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91. Glycine is the C-terminal amino acid residue
of ubiquitin
It forms a peptide bond with e-amino group
of a lysine residue of the target protein
If there are more than one lysine residues in
the target protein, a number of ubiquitin
molecules may attach to it
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92. C-terminal glycine of ubiquitin forms a thio-
ester bond with the ‒SH group of ENZ1
This reaction is driven by hydrolysis of ATP
into AMP and PPi
In the second reaction, ENZ1 is replaced by
ENZ2
In the presence of ENZ3, ENZ2 is replaced
by the target protein

94. Once the target protein is tagged with
ubiquitin, it is destined for destruction
The 26S protease complex hydrolyses
the target protein
Ubiquitin is not hydrolysed and is
recycled

95. Half-lives of proteins vary over a wide range
Regulatory enzymes usually have half-lives
of minutes
Circulating proteins have half-lives of weeks
Structural proteins have half-lives of years
Half-lives of proteins

96. Half-life of a protein is determined by its N-
terminal amino acid
Proteins having Met, Val, Gly, Thr or Ser at
their N-terminus have long half-lives
Proteins having Arg, His, Lys, Phe or Asp at
their N-terminus have short half-lives
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97. A protein is degraded when its life-span is
over
ENZ3 recognizes the N-terminal amino acid
of the protein and targets it for degradation
In adult human beings, the daily protein
turnover is 1-2%
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98. Three-fourths of the amino acids released
from breakdown of proteins are reutilized
The remaining amino acids are catabolized

99. Catabolism of amino acids
Catabolism of amino acids comprises
catabolism of their:
Amino groups Carbon skeletons
Carbon skeletons of different amino acids
have different fates
The fate of their amino groups is the same

100. The amino groups of amino acids are
removed as ammonia
Since ammonia is very toxic, it has to be
converted into a non-toxic metabolite
In ureotelic organisms, e.g. mammals,
ammonia is converted into urea

101. Though amino acids are catabolized in
several tissues, urea is synthesized only
in liver
Liver releases urea in circulation from
where it extracted by the kidneys, and is
excreted in urine

102. Fate of carbon skeletons
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The carbon skeletons of amino
acids are converted into:
Pyruvate or Acetyl CoA or
Intermediates
of citric acid
cycle

103. Pyruvate and intermediates of citric acid
cycle (CAC) are substrates for gluconeo-
genesis
Therefore, amino acids which form
pyruvate or CAC intermediates are
known as glycogenic amino acids

105. Carbon skeletons of leucine and lysine
are converted into acetyl CoA
Acetyl CoA can form fatty acids
Hence, these two amino acids are known
as ketogenic amino acids

106. Some amino acids can form:
Acetyl CoA and
Pyruvate/CAC
intermediates
Their carbon skeletons can form glucose
as well as fatty acids
These are known as glyco- and keto-
genic amino acids

107. The glyco- and keto-genic
amino acids are:
Isoleucine
Phenylalanine
Tyrosine
Tryptophan

108. Amino acids forming pyruvate are: (i)
threonine, (ii) glycine, (iii) serine, (iv)
alanine, (v) cysteine and (vi) hydroxyproline
Some of these amino acids may have
additional fates also
Amino acids forming pyruvate

110. Glycine, besides forming pyruvate, may
also be cleaved into ammonia, carbon
dioxide and a methylene moiety
Glycine + H4-Folate + NAD+
Methylene-H4-Folate + NH3 + CO2 +NADH + H+
The methylene moiety is taken up by
tetrahydrofolate

111. Conversion of alanine into pyruvate occurs
by a simple transamination reaction:
Alanine + a-Ketoglutarate
Pyruvate + Glutamate
Glutamate pyruvate
transaminase, PLP

113. Hydroxyproline
Hydroxyproline is catabolised to
pyruvate and glyoxylate via:
D1-Pyrroline-3-hydroxy-5-carboxylic acid
g-Hydroxyglutamate g-semialdehyde
g-Hydroxyglutamate
a-Keto-g-hydroxyglutarate

115. Intermediates of citric acid cycle
formed from amino acids are:
a-Ketoglutarate
Succinyl CoA
Fumarate
Oxaloacetate

116. Histidine, proline, arginine, glutamine and
glutamate form a-ketoglutarate
The first four are converted into
glutamate which is transaminated to
a-ketoglutarate
Amino acids forming a-ketoglutarate

117. Histidine is converted into N-formimino-
glutamic acid (FIGLU)
The conversion occurs via urocanic acid
and 4-imidazolone-5-propionic acid
FIGLU transfers its formimino group to H4-
folate, and is converted into glutamic acid

119. If H4-folate is not available, FIGLU will not
be converted into glutamic acid and urinary
FIGLU excretion will be increased
Therefore, measurement of urinary FIGLU
after a test dose of histidine is an important
test for diagnosis of folic acid deficiency

120. Arginine is hydrolysed into urea and
ornithine by arginase
Ornithine is transaminated to glutamate g-
semialdehyde
Glutamate g-semialdehyde is oxidised
to glutamate
The latter is converted into a-keto-
glutarate by transamination

122. Proline is oxidised to D1-pyrroline-5-
carboxylic acid
D1-Pyrroline-5-carboxylic acid is converted
into glutamate g-semialdehyde
The latter is oxidised to glutamate

124. Glutamine is converted into glutamate by
glutaminase
Glutamate is converted into a-keto-
glutarate by transamination
a-Ketoglutarate enters the citric acid
cycle

126. Methionine, isoleucine and valine are
catabolised to form succinyl CoA
Methionine is converted into S-adenosyl
methionine (SAM)
SAM acts as a donor of labile methyl
groups for various methylation reactions
Amino acids forming succinyl coenzyme A

127. Conversion of methionine into homo-
serine has been seen earlier
Homoserine is deaminated to a-keto-
butyrate by homoserine deaminase
a-Ketobutyrate is converted into propionyl
CoA
Propionyl CoA is then converted into
succinyl CoA as seen earlier

129. Valine, isoleucine and leucine are branched-
chain amino acids
The first three reactions in their catabolic
pathways are similar
The first two reactions are catalysed by
common enzymes
First, these three are converted into their a-
keto acid derivatives by transamination

130. The a-keto acids undergo oxidative
decarboxylation to their CoA derivatives
with one carbon atom less
The CoA derivatives are oxidised by
removal of two hydrogen atoms
From this reaction onwards, the pathways
differ

131. Valine is converted into methylmalonyl
CoA
Methylmalonyl CoA forms succinyl CoA

134. Isoleucine is glyco- and keto-genic
Its carbon skeleton is converted into one
molecule of propionyl CoA and one
molecule of acetyl CoA
Propionyl CoA can be converted into
succinyl CoA
Acetyl CoA can form fatty acids

137. A part of the carbon skeletons of phenyl-
alanine and tyrosine is converted into
fumarate as will be seen later
The major portion of the carbon
skeletons is converted into acetyl CoA
Amino acids forming fumarate

138. Asparagine and aspartate are catabolized
to oxaloacetate
Asparagine is first converted into
aspartate by a reaction analogous to the
conversion of glutamine into glutamate
Amino acid forming oxaloacetate

139. Aspartate is transaminated to oxalo-
acetate
Oxaloacetate is a citric acid cycle
intermediate

141. Amino acids forming acetyl coenzyme A
Acetyl CoA is
formed from:
Phenylalanine
Tyrosine
Tryptophan
Lysine
Leucine

142. Phenylalanine is converted into tyrosine by
phenylalanine hydroxylase as seen earlier
The subsequent pathway for catabolism of
these amino acids is common
Carbon skeletons of phenylalanine and
tyrosine are catabolised to fumarate and
acetyl CoA
Phenylalanine and tyrosine

145. Tryptophan is catabolised to acetoacetyl
CoA which can be converted into acetyl
CoA
The side chain of tryptophan is removed
as alanine which can be converted into
pyruvate
Tryptophan

149. In pyridoxine deficiency, 3-hydroxykyn-
urenine is not converted into 3-hydroxy-
anthranilic acid
3-Hydroxykynurenine is converted into an
alternate metabolite, xanthurenic acid
Xanthurenic acid is excreted in urine

150. Laboratory diagnosis of pyridoxine
deficiency can be made by:
Giving a test dose of tryptophan
Measuring urinary excretion of
xanthurenic acid

151. Lysine is catabolised to a-ketoadipic acid
a-Ketoadipic acid is converted into acetyl
CoA via glutaryl CoA and acetoacetyl CoA
Lysine

155. Leucine is catabolised to acetyl CoA and
acetoacetate
The latter is converted into acetyl CoA via
acetoacetyl CoA

158. Synthesis of non-protein specialized products
Hormones
PorphyrinsPurines
Pigments
Specialized
products synthesized
from amino acids

159. The amino acids forming specialized
products are:
• Glycine
• Methionine
• Cysteine
• Glutamate
• Arginine
• Histidine
• Tyrosine
• Tryptophan

160. Glycine acts as a neurotransmitter in brain
Many specialized products are formed
from glycine
For example, the entire glycine molecule
is incorporated in the purine nucleus
Glycine

162. Glycine also forms a part of the porphyrin
nucleus
Porphyrin synthesis begins with
condensation of glycine with succinyl CoA
The bile acid, glycocholic acid is formed by
conjugation of glycine with cholic acid

163. Glycine is used to synthesize glutathione
Glycine can provide a one-carbon unit to
tetrahydrofolate
It can be converted into serine
It can combine with benzoyl CoA to form
hippuric acid

164. Glycine is used in the synthesis of
creatine also
Creatine plays an important role in
energy-transfer reactions in muscles
It acts as a reservoir of energy in muscles

167. For muscle contraction, energy is provided
by hydrolysis of ATP to ADP
Continued muscle contraction can cause
depletion of ATP
Creatine phosphate transfers its high-energy
phosphate to ADP to regenerate ATP

168. When muscles are relaxing, creatine
phosphate is regenerated
ATP transfers a high-energy phosphate
to creatine forming creatine phosphate
This is a reversible reaction catalysed by
creatine kinase (CK)

170. The biologically important compound
formed from methionine is S-adenosyl
methionine
S-adenosyl methionine acts as a donor of
labile methyl groups for various
methylation reactions
Methionine

172. Cysteine forms taurine which acts as a
neuro-transmitter in brain
Taurine also conjugates with cholic acid
to form taurocholic acid, a bile acid
Cysteine is also used in the synthesis of
coenzyme A from pantothenic acid
Cysteine

173. The mercaptoethanolamine portion of
coenzyme A is derived from cysteine
Cysteine is also a constituent of glutathione

175. Gamma-aminobutyric acid acts as a neuro-
transmitter in brain as does glutamate itself
Glutamate is also used to form glutathione

176. The most important compounds formed
from arginine are creatine and nitric
oxide
Nitric oxide acts as a local hormone,
as a neurotransmitter and as a free
radical
Arginine

178. The local hormone, histamine is formed
by decarboxylation of histidine
The reaction is catalysed by histidine
decarboxylase
Histidine

180. A number of specialized compounds are
formed from tyrosine
All these compounds can also be formed
form phenylalanine after its hydroxylation
to tyrosine
Tyrosine

181. Specialized products formed from
tyrosine or phenylalanine are:
Epinephrine
Norepinephrine
Tri-iodothyronine (T3)
Thyroxine (T4)
Melanin

182. Epinephrine and norepinephrine are
known as catecholamines
Phenylalanine/tyrosine is first converted
into dihydroxyphenylalanine (DOPA)
DOPA is decarboxylated to dopamine, a
neurotransmitter

184. Dopamine is hydroxylated to norepinephrine
Epinephrine is formed by methylation of
norepinephrine

186. T3 and T4 are formed from tyrosyl residues
of thyroglobulin
Some tyrosyl residues are converted into
mono-iodo-tyrosyl (MIT) residues
Some are converted into di-iodo-tyrosyl
(DIT) residues

187. One MIT and one DIT can form tri-iodo-
thyronine (T3)
Two DIT residues can form tetra-iodo-
thyronine (T4)

189. Melanin, the black pigment present in skin,
hair and iris, is formed from tyrosine
The exact structure of melanin is not known
These two are formed from tyrosine
It is believed to be a polymer of 5,6-
dihydroxyindole and indole-5,6-quinone

191. The hormones, serotonin and melatonin, are
synthesized from tryptophan
Serotonin is an intermediate in the synthesis
of melatonin
Tryptophan

194. Nicotinic acid (niacin) can also be
synthesized from tryptophan
3-Hydroxyanthranilic acid formed during
catabolism of tryptophan can be converted
into nicotinic acid