Amino Acid Metabolism
生化教研室：牛永东
生物化学的学习方法
特点一：与数理化不同，尚未进入
定量科学的阶段，还处在定性科学阶段。因此
不可能通过公式或定理推出一个准确的结论；
特点二： 是没有绝对，几乎所有的
结论都可以被一些例外打破（生物多样性）。
一般性结论：生物化学的学习应以
概念为主---以记忆为主，在记忆的基础上加
以理解。
【目的与要求】
• 掌握脱氨基作用、氨的来源、去路，氨的转运……
• 掌握尿素合成的部位和全过程
• 掌握一碳单位的概念、来源、载体和功能
• 需要掌握的概念：
必需氨基酸、蛋白质的互补作用、氨基酸库、
联合脱氨基作用.……
Metabolism
• consists of both catabolic and anabolic processes
• Catabolism comprises all processes, in which complex
molecules are broken down to simple ones
• Anabolism means any constructive metabolic process by
which organisms convert substances into other
components required for the organism's chemical
architecture
Introduction
• Amino acids (AAs) are the building blocks of proteins (precursors
for proteins) (物质代谢)
• Energy metabolites (17.9KJ/g Pr)：When degraded, amino acids
produce glucose/carbohydrates and ketone bodies（能量代谢）
• Precursors for many other biological N-containing compounds ，
Involved as direct neurotransmitters or as precursors to
neurotransmitters, eg. （信息分子代谢）
- Tyrosine gives DOPA and dopamine
- Precursors to peptide hormones and thyroid hormone
- Precursors to histamine, NAD and other compounds of
biological importance
some major biological functions
• Detoxification of drugs, chemicals and metabolic by-products
* Excess dietary AAs are neither stored nor excreted. Rather, they
are converted to common metabolic intermediates
outline
1. The nutrition of protein
2. The digestion、absorption and putrefaction of
protein
3. The general metabolism of AA
4. Metabolism of ammonia
5. Single AA metabolism
Section 1 The nutrition of protein
• Nitrogen balance
• The requirements
• Classification of amino acids
Nitrogen balance
• Zero or total nitrogen balance:
the intake = the excretion (adult)
Amount of nitrogen intake is equal to the amount of nitrogen excreted
is zero or total nitrogen balance
• Positive nitrogen balance:
the intake > the excretion
during pregnancy, infancy, childhood and recovery from severe illness or
surgery
• Negative nitrogen balance:
the intake < the excretion
following severe trauma, surgery or infections. Prolonged periods of
negative balance are dangerous and fatal if the loss of body protein
reaches about one-third of the total body protein
The requirements
• The requirements of protein for the health: the
minimal requirement of protein is 30~50 gram for the
adult
• Advice: 80 gram/day (中国营养学会)
???
Classification of amino acids
• non-essential amino acids
- can be synthesized by an organism
- usually are prepared from precursors in 1-2 steps
• Essential amino acids ***
- cannot be made endogenously
- must be supplied in diet
eg. Leu, Phe…..
Nonessential
Alanine
Asparagine
Aspartate
Cysteine
Glutamate
Glutamine
Glycine
Proline
Serine
Tyrosine
Essential
Arginine*
Histidine *
Valine
Lysine
Isoleucine
Leucine
Phenylalanine
Methionine
Threonine
Tyrptophan
借
来
一
两
本
淡
色
书
*The amino acids Arg, His are considered “conditionally essential” for
reasons not directly related to lack of synthesis and they are essential for
growth only
nutritional value
•
Legumes(豆类) poor in Trp, but rich in Lys;
Cereals (谷类) poor in Lys, but rich in Trp
•
Mutual complementation of amino acids
•
Protein deficiency-kwashiorkor, generalized edema and liver
enlargement, abdomen bulged
•
Suggestion: the combined-action of protein in diet
Section 2
The digestion、absorption and
putrefaction of protein
Digestive Tract of protein
• Proteins are generally too large to be absorbed by
the intestine and therefore must be hydrolyzed to
the amino acids
• The proteolytic enzymes responsible for hydrolysis
are produced by three different organs: the stomach、
pancreas and small intestine (the major organ)
Stomach
•
HCl (parietal cells ) and Pepsinogen (chief cells )
•
The pH of gastric juice is around 1.0. Food is retained in the
stomach for 2-4 hrs
•
HCl kills microorganisms, denatures proteins, and provides an
acid environment for the action of pepsin
•
Autocatalysis: pepsinogen is converted to active
pepsin(Pepsin A) by HCl
•
Pepsin coagulates milk in presence of Ca2+ ions
Pancreas and small intestine
• Endopeptidase (pancreas)
Trypsin: carbonyl of arg and lys
Chymotrypsin: carbonyl of Trp, Tyr, Phe, Met, Leu
Elastase: carbonyl of Ala, Gly, Ser
Exopeptidase (pancreas)
Carboxypeptidase A:amine side of Ala, Ile, Leu, Val
Carboxypeptidase B: amine side of Arg, lys
• Aminopeptidase (small intestine):
cleaves N-terminal residue of oligopeptidaes
Dipeptidase (small intestine)
endopeptidase
carboxypepidase
O
O
O
H2N CH C NH CH- - -NH CH C NH CH- - -NH CH C NH CH COOH
R1
R2
R3
aminopeptidase
Amino acids +
1/3
R4
R5
R6
dipeptidase
O
H2N CH C NH CH COOH
R'
R"
Amino acids
95%
absorption
• There is little absorption from the stomach apart from short- and
medium- chain fatty acids and ethanol
• Under normal circumstances, the dietary proteins are almost
completely digested to their constituent amino acids, and these
end products of protein digestion are rapidly absorbed from the
intestine into the portal blood
•
Amino acids are transported through the brush border by
the carrier protein and it is an active transport
1.
The classification of carrier protein:
aciditic; basic; neutral and gly-carrier
2. -glutamyl cycle (-谷氨酰基循环)
3. The bi-and tri- peptidase carrier system in the intestinal
mucosa cell
The mechanism of AA’s absorption
K+-ATPase
K+
Na+
Na+
Amino acids
outer
Member
innner
Carrier protein
ATP
ADP+Pi
K+
Na+
intestine
Na+
Amino acids
COOH
CHNH 2
-glutamyl| cycle|
|
|
|
|
|
|
COOH|
|
H2N CH
-GGT
|
|
R
|
|
AA
|
|
membrane
|
|
|
|
| GSH
|
-Gln
CH 2
COOH
CH 2
C
HN CH
R
O
COOH
H2N CH
-gltamyl
R
cyclotransferase
Cys-Gly
peptidase
ATP
Cys
GCS synthetase
Gly
Glu
ADP+Pi
ATP
ADP+Pi
GSH
synthetase
5oxoprolinase
-glutamylcysteine
ATP
ADP+Pi
Putrefaction
• Putrefaction: the process of decay of un-digestive and unabsorbed protein and the products by bacterial, fungal in the
intestine
5％
1.Amines(胺):
R
CH
COOH
–CO2
NH2
AA
RCH2NH2
Amines
False neurotransmitter are similar with neurotransmitter
2. Ammonia(氨)-1:
A. some amino acids are degraded by the in the intestine
bacteria
R
CH
NH2
AA
COOH
intestine
bacteria
R
CH 2 COOH
+ NH3
diffuse blood
Ammonia
2. Ammonia(氨)-2:
B. urea from the blood to the intestine with resultant increased
diffusion of NH3 into the intestinal
NH2
urea
Urea enzyme
C=O
CO2 +2NH3
NH2
diffuse blood
Enter instein
Urea in blood
ammonia
3. The other toxic material:
phenol, indole, sulfureted hydrogen……
Section 4
The general metabolism of AA
• Protein and amino acid turnover
• Degradation of Amino Acids （Fate of amino
group）
• The metabolism of α-ketoacid
Protein and amino acid turnover
1-2%
Protein
degradation
Body protein
Reutilization for
new protein synthesis
Amino acids
75-80%
Protein turnover
T1/2 ?
(half time)
introduction
1. Proteins constantly being synthesized and degraded - need
constant supply of amino acids
- need to degrade to protect from abnormal proteins
- regulate cellular processes
2. Degraded by ubiquitin label
- Ubiquitin binds lysine side chain
- Targets for hydrolysis by proteosomes in cytosol and
nucleus
- ATP required
3. Degraded by the protease and the peptidase in the Lysosome
- non- ATP required
- the hydrolysis-selective are bad
The ubiquitin degradation pathway
ATP AMP+PPi
E1-S-
（ubiquitin）
E3
E2-SH
E2-SE1-SH
E1-SH
E2-SH
E1：activiting enzyme E2：carrier protein
E3：ligase
ubiquitinational protein
19S regulate substrate
ATP
ATP
20S Proteasome
阿龙-西查诺瓦
26S Proteasome
Diet protein
Nonprotein nitrogen
derivatives
Amino acid pool
Tissue protein
transamination
Carbohydrate
(glucose)
Ketone dodies
Acetyl-CoA
Amino nitrogen in glutamate
Citric
deamination
Acid
NH3
Urea
Cycle
CO2
Overview of the protein metabolism
Degradation of Amino Acids
- Reactions in amino acid metabolism
Amino acid
COO
Carboxylic group
+
H3N
Amino group
a
H
R group
introduction
• Free amino acids are metabolized in identical ways,
regardless of whether they are released from dietary
or intracellular proteins
• The metabolism of the resulting amino group and
nitrogen excretion are a central part of nitrogen
metabolism
FATE OF AMINO GROUP
DEAMINATION
A. Transamination
B. Oxidative deamination
C. purine nucleotide cycle
A. Transamination
• Transamination by Aminotransferase (transaminase)
• always involve PLP coenzyme (pyridoxal phosphate)
• reaction goes via a Schiff’s base intermediate
• all transaminase reactions are reversible
Aminotransferases
• Aminotransferases can have specificity for the alpha-keto acid
or the amino acid
• Aminotransferases exist for all amino acids except proline and
lysine
• The most common compounds involved as a donor/acceptor pair
in transamination reactions are glutamate and a-ketoglutarate,
which participate in reactions with many different
aminotransferases
to an alpha-keto acid  alpha-amino acid
Transamination
aminotransferases
Glu+pyruvate
(丙酮酸）
Glu+Oxaloacetate
（草酰乙酸）
glutamate-pyruvate aminotransferase
GPT, ALT
（α-酮戊二酸）
Glutamic oxaloacetictransaminase
GOT, AST
-Ketoglutarate+Ala
-Ketoglutarate+Asp
*** ALT and AST are components of a "liver function
test". Levels increase with damage to liver (cirrhosis,
hepatitis) or muscle (trauma)
The mechanism of transamination
CH 2OPO 3H2
H
HOOC
C
R1
H
NH2
+
O C
N
OH CH3
AA
PLP
Schiff’s base
–H2O
+H2O
Molecule rearrange
Schiff’s base isomer
CH 2OPO 3H2
+H2O
–H2O
H2N CH2
N
+
OH CH3
PMP(磷酸吡哆胺)
HOOC C O
R1
-ketoacid
Transamination
• Interconversion of amino acids
• Collection of N as glu
• Provision of C-skeletons for catabolism
B. Oxidative Deamination
• L-glutamate dehydrogenase (in mitochondria)
Glu + NAD+ (or NADP+) + H2O  NH4+ + aketoglutarate + NAD(P)H +H+
Requires NAD+ or NADP + as a cofactor
Plays a central role in AA metabolism ?
urea cycle
?
It is inhibited by GTP and ATP, and activated by GDP and
ADP
Combined Deamination
?
Combined deamination ＝
Transamination + Oxidative Deamination
The major pathway ！！！
NH3
AA
Asp
IMP
-Keto
glutarate
H2O
aminotransferases AST
C. purine nucleotide cycle
-Keto
acid
Oxaloacetate
malate
fumarate
AMP
The metabolism of α-ketoacid
• Biosynthesis of nonessential amino acids
TCA cycle member + amino acid α-keto acid +
nonessential amino acid
• A source of energy (10%) ( CO2+H2O )
• Glucogenesis and ketogenesis
* Classification of amino acids
* glucogenic amino acid : are converted into either pyruvate or one
of the citric acid cycle intermediates
(a-ketoglutarate, succinyl CoA, fumarate or malate)
* ketogenic amino acid: will be deaminated via Acetylc-CoA and
thus can be made into a ketone body. such as: Leucine and
lysine
* glucogenic and ketogenic amino acid: isoleucine, phenylalanine,
tryptophan and tyrosine, threonine
Ammonia is toxic, so cells need to get rid
of it…..
***
Sources
1. amino acids degradation
RCCO2H2NH2
MAO
RCHO+NH3
Monoamine oxidase
2. glutamine (glutaminase, kidney)
3. catabolism from bacteria in intestine (two)
4. purine and pyrimidine catabolism
Metabolism of ammonia
• Fix ammonia onto glutamate to form glutamine and
use as a transport mechanism
• Transport ammonia by alanine-glucose cycle and Gln
regeneration
• Excrete nitrogenous waste through urea cycle
Transport of ammonia
• alaninie - glucose cycle *
• regenerate Gln
Alanine-Glucose cycle
In the liver alanine
transaminase tranfers
the ammonia to α-KG
and regenerates pyruvate.
The pyruvate can then be
diverted into
gluconeogenesis. This
process is refered to as
the glucose-alanine cycle
Gln regeneration
**** Urea synthesis
• Synthesis in liver (Mitochondria and cytosol)
• Excretion via kidney
• To convert ammonia to urea for final excretion
The urea cycle：1932 by Hans Krebs and Kurt
Henseleit as the first metabolic cycle elucidated
arginase
Ornithine cycle
Krebs-henseleit cycle
1
Mitochondria
OCT
（瓜氨酸）
3
cytosol
4
2
（鸟氨酸）
5
UREA CYCLE (liver)
1. Overall Reaction:
NH3 + HCO3– + aspartate + 3 ATP + H2O  urea +
fumarate + 2 ADP + 2 Pi + AMP + ppi
2. Requires 5 enzymes:
2 from mitochondria and 3 from cytosol
Regulation of urea cycle
1.Mitochondrial carbamoyl phosphate synthetase I
(CPS I)
CPS I catalyzes the first committed step of the urea cycle
CPS I is also an allosteric enzyme sensitive to activation
by N-acetylglutamate（AGA） which is derived from
glutamate and acetyl-CoA
Increased rate of AA degradation requires higher rate of urea
synthesis

AA degradation  ↑glutamate concentration → ↑synthesis
of N-acetylglutamate  ↑CPS I activity  ↑urea cycle
efficiency
2. All other urea cycle enzymes are controlled by the
concentrations of their substrates
Deficiency in an E  ↑(substrate) ↑rate of the
deficient E
3. The intake of the protein in food
the intake ↑ ↑urea synthesis
Hyper-ammonemia
and the toxic of the ammonia
• Hyperammononemia: ammonia intoxication - tremors,
slurring of speech, and blurring of vision, coma/death
• Cause by cirrhosis of the liver or genetic deficiencies
Section 5
Single AA metabolism
• Decarboxylation
some neurotransmitters’ precursors for the
decarboxylation of AAs production– bioactive
amines
-aminobutyric acid (GABA)
Glutamine can be decarboxylated in a similar PLPdependent fashion, outputting -aminobutyric acid
(neurotransmitter, GABA)
COOH
COOH
(CH 2) 2
CHNH 2
COOH
L-Glu
L-Glu decarboxylase
– CO2
(CH 2)2
CH 2NH 2
GABA
Taurine
L-cysteine can be decarboxylated and converted into
outputted the taurine
CH2SH
CHNH 2
COOH
L-Cys
CH2SO 3H
3（O）
CHNH 2
COOH
Decarboxylase
-CO2
CH2SO 3H
CHNH 2
taurine
H
N
CH2 C COOH
NH
NH2
L-Histidine
Histamine
Histidine can also be
decarboxylated in a similar
PLP-dependent fashion,
outputting the Histamine
CH2CH2NH 2
N
NH
Histamine
5-hydroxytryptophan （5-HT）
NH2
CH 2
CH COOH
Tryptophan
N
H
Hydroxylase
decarboxylase
– CO2
HO
CH 2 CH 2NH 2
N
H
5-HT
Polyaminies: (putrescine,spermidine,spermine)
CO2 is then cleaved off in a PLP-dependent
decarboxylation, resulting in the polyaminies (such as:
SAM, spermidine, spermine)
*****
One carbon unit metabolism
• One carbon unit: some AA may turn into the group including one
carbon in the AA metabolism
Such as:
methl
-CH3
甲基
methylene
-CH2
亚甲基/甲烯基
methenyl
-CH=
次甲基/甲炔基
formyl
-CHO
甲酰基
formimino
-CH=NH
亚氨甲基
But without CO2
One carbon unit metabolism
• Folic acid / folate is an essential vitamin, and as such it
cannot be synthesized within the human body
• Folate itself is not an active cofactor; its doubly-reduced form,
is tetrahydrofolate (THF)
• Tetrahydrofolate (THF) : the carrier of one carbon
accepts one carbon groups from amino acids
Folate is reduced first by dihydrofolate reductase (DHFR) into
dihydrofolate (DHF), oxidizing an NADPH in the process.
DHFR, again oxidizing an NADPH+H+/NADP+, can also reduce
DHF into THF
(Folate)
R
10
O
CH3
5N
HN
10 N
R
O
CH 2
5N
HN
H2N
HN
N
N
H
（ N5-CH3-FH4）
H2N
N
N
H
（N5，N10-CH2-FH4）
THF – biosynthetic pathways
• There are three important biosynthetic precursors synthesized
from THF：
N ,N 甲烯四氢叶酸
N5,N10-methylene-THF
N5-methyl-THF
N10-formyl-THF
• N5,N10-methylene-THF acts in a central processing role in the
synthesis of all of these enzymes: in order to synthesize either of
the other two, one must first produce N5,N10-methylene-THF
5
10
Serine
Histidine
biosynthesis
methionine
N5-methyl-THF
NAD+
THF
Serine
Hydroxymethyl
Transferase
NADH
N5,N10-methylene-THF
N5,N10甲烯四氢叶酸
biosynthesis
thymidylate
NADP+
Glycine
NADPH
NAD+
THF
Glycine
cataboase
NADH
CO2+ NH3
N5,N10-methenyl-THF
N5,N10甲炔四氢叶酸
H2O
N10-formyl-THF
Tryptophan
biosynthesis
purines
• Sulfanilamide (磺胺) is a compound that the human body
can create. It is a close analog to PABA, and it has the
effect of stopping folate synthesis in bacteria. There are a
wide variety of “sulfa drugs ” (磺胺类药) based on PABA
analogs such as sulfanilamide
• Trimethoprim (TMP) and pyrimethamin(百炎净), on the
other hand, are DHFR inhibitors. Because bacterial DHFR
is structurally simpler than human DHFR, these two drugs
have a more drastic effect on bacteria than they do on us
Metabolism of sulfur-containing amino acids
S-CH 3
(CH 2 ) 2
CH-NH 2
CH 2 SH
CH 2—S——S— CH 2
CHNH 2
CHNH
COOH
COOH
2
CHNH
COOH
COOH
Met
cysteine
cystine
2
Methionine Catabolism
• The principal fates of methionine are incorporation into
polypeptide chains(protein synthesis), and use in the production
of a-ketbutyrate and cysteine via S-adenosyl methionine (SAM)
S-adenosyl methionine (SAM)
• is a powerful methylating agent (in the methylating gene regulation of
DNA and RNA, It is constantly regenerated in a cyclical) with uses in
many biochemical pathways
COOH
• formed from ATP and Met
H C-NH 2
S-CH3
(CH2)2
O
HO
+
CH-NH
P
O
O
P
(CH 2)2
O
O
P
+
R
O
S
O
OH
OH
Adesine transferase
OH
CH2
O
R
CH3
2
COOH
Met
OH
ATP
OH
– PPi +Pi
OH OH
SAM
S-adenosylmethionine (SAM)
• methyl group is donated to form several products
norepinephrine --> epinephrine
gamma-butyric acid --> carnitine
guanidinoacetate --> creatine
(胍乙酸)
COOH
Met cycle
S-CH3
(CH 2)2
+
(CH2)2
Met
PPi +Pi
FH4
OH OH
COOH
FH4 is produced!!!
H C-NH
N5-CH3-FH4
COOH
A
H2 O
RH
2
(CH 2 ) 2
S
H C-NH 2
R-CH3
R
CH 2
O
(CH 2)2
HS SAH
R
CH3
COOH ATP
methyltransferase
CH2
O
S
CH-NH2
N5-CH3-FH4
SAM
H C-NH 2
SAHH
同型半胱氨酸
S-腺苷同型半胱氨酸
OH OH
NADH
N5,N10 -methylene- FH4
Carbon donors (serine, glycine) combine
with THF
NAD+
FH4
N5-CH3-FH4
同型半胱氨酸
homocysteine
Only one!
vitamin B12
methionine
adenosine
ATP
FH4 and Met cycle
all 3 phosphate
groups are lost!
H2O
s-adenosylhomocysteine
PPi + Pi
s-adenosylmethionine
S-腺苷同型半胱氨酸
methyl group donated to biological substrate,
e.g. norepinephrine
Regulation of the Met metabolism
• If methionine and cysteine are present in adequate quantities,
SAM accumulates and is a positive effector on cystathionine
synthase(胱硫醚合成酶), encouraging the production of cysteine
and a-ketobutyrate
• If methionine is scarce, SAM will form only in small quantities,
thus limiting cystathionine synthase activity. Under these
conditions accumulated homocysteine is remethylated to
methionine, using N5-methyl THF and other compounds as
methyl donors
(胍乙酸)
Creatine metabolism
H2O
Metabolism of Cystine and Cysteine
CH2SH
2 CHNH 2
COOH
cysteine
– 2H
+ 2H
CH2—S——S— CH2
CHNH 2
CHNH 2
COOH
COOH
cystine
Cysteine Catabolism
• The pathway is catalyzed by a liver desulfurase and produces
pyruvate and hydrogen sulfide (H2S)
• The enzyme sulfite oxidase uses O2 and H2O to convert HSO3to sulfate (SO4-) , and H2O2. The resultant sulfate is used as a
precursor for the formation of 3'-phosphoadenosine-5'phosphosulfate, PAPS
Metabolism of aromatic amino acid
COOH
COOH
CHNH 2
CHNH 2
CH 2
CH 2
OH
Phenylalanine
Tyrosine
tryptophan
Phenylalanine metabolism
Phenylalanine
hydroxylase
THF
NADP+
phenylalanine
DHF
NADPH+H+
tyrosine
Tyr metabolism
1. Catecholamine/melanin
NH3+
|
- CH2 - CH - COOPhe
Hydroxylase
Tyr
HO -
Tyr Catabolism
Homogentisate
尿黑酸
HO -
NH3+
|
- CH2 - CH - COO-
Tyr
aminotransferase
HO -
- OH
CH2 - COO-
O
||
- CH2 - C - COO-
对
羟
基
丙
酮
酸
HO -
- OH
CH2 - COO-OOC
trans
-OOC
Homogentisate
尿黑酸
- CH = CH - C - CH2 - C - CH2 - COO||
||
cis
O
O
- CH = CH - C - CH2 - C - CH2 - COO||
||
O
O
乙酰乙酸
O
fumarate
acetoacetate
H
||
-OOC - C = C - COO+
H3C - C - CH2 - COO延胡索酸 H
Phenylalanine Hydroxylase & PKU
• Phenylketonuria (PKU) = lack of phenylalanine
hydroxylase
- can’t hydroxylate phenylalanine to tyrosine
[Phe] = 0.1 mM normally
 1.2 mM in PKU
1 in 20,000 homozygous
1 in 150 heterozygous
IQ study:
53  93
• People with phenylketonuria must avoid excess
phenylalanine, but both tyrosine and phenylalanine
are essential amino acids, so they shouldn’t exclude it
completely or brain disorders with result
The Metabolism of
Branched Chain Amino Acids
• Branched-chain amino acids (BCAAs):
isoleucine, leucine and valine
• The catabolism of all three BCAAs initiates in muscle
and yields NADH and FADH2 which can be utilized
for ATP generation
Isoleucine / Leucine / Valine
-ketoglutarate
transamination
A metabolic
block here causes
maple syrup
urine disease
glutamate
-keto acid
NAD+, CoASH
-keto acid dehydrogenase
gluconeogenesis
NADH, CO2
-keto-S-CoA
(if Leu or Lys, only
this path can be used)
Succinyl-CoA
Proprionyl-CoA
丙酰CoA
ketogenesis
• Most nitrogen metabolism pathways are very complex
require many steps
require input of ATP and NADPH
are regulated by feedback inhibition mechanisms
(allosteric)