Subject: Biochemistry
PROTEIN METABOLISM
PROTEIN METABOLISM
 Cont ains Nitrogen
 Amino Acids – assembled as precursors of
polypeptides & other compounds
- Broken down to recover metabolic energy
 Do not store excess Amino Acids, it’s just going to be
excreted or cataboliz ed
o Excess dietary Amino Acids are converted to
common met abolites (precursors of glucose, fatty
acids, ketone bodies) = metabolic fuels
 Mammals synthesize some AA, obtain the rest from
diet
 Protein Turnover – balance between
breakdown/degradation and synthesis of protein
o everyday, 1-2% of total body protein = 200-300g of
protein is degraded & resynthesized
o Degraded amino acids --> recycled
o 75-80%: reutilized for new protein synthesis
o 20-25%: nitrogen converted to urea – final end
product of protein metabolism in body
o Amt. of urea excreted in body is directly
proportional to amount of protein eaten
 High prot ein diet = inc. urea excretion
Vol. = up
Specific gravity = up
High solid content
 Low prot ein diet = dec. urea excretion
Vol. = down
Specific gravity = down
Low solid content
PROTEIN DEGRADATION
 Diff. ways of degrading protein
 Half-life (t1/2) – susceptibility of protein to degradation
o Time required to reduce protein’s concent ration to
50% of initial value
o Gaano kabilis ma-degrade ang prot ein
o Short half-life: fast degradation
 <30-min – 150 min/1 ½ hr
 PEST Sequence: short half-life
 (P) Proline
 (E) Glutamate
 (S) Serine
 (T) Threonine
 Target for rapid degradation
Biochemistry / Protein Metabolism
Date: Jan. 14&21, 2012
Lectur er: Dra. Santos
Transcriber: Arvin Uy & Trisha Uy
o >100hrs/6-7days: long half-life
 Aldolase – glycolysis
Cleave fructose 1,6 bisphosphate to
glyceraldehyde 3-phosphat e and
dihydroxyacetone phosphat e
Cleavage enzyme
 Lactate dehydrogenase
Converts Pyruvate to lactic acid
Anaerobic glycolysis
 Cytochrome
ETC
o Most rapidly degraded enzymes: occupy important
metabolic control points
 More import ant function of enzyme = shorter
half-life = rapid degradation
 Rate-limiting/committed/control enzymes
o Stable enzymes: nearly constant catalytic activities
 Ordinary reactions = longer half-life
 Rate of protein degradation is affected by nutritional
and hormonal state
o Adequate: not going to lose prot ein
 Maintenance of blood Glucose
st
 1 day fasting – glycogenolysis
nd
 2 day – fat deposits: break down: FFA &
glycerol -> gluc ose -> gluconeogenesis
 Muscle proteases -> AA -> glucose
o Nutritionally deprived: cells increase rate of protein
degradation to provide nutrients
PATHWAYS FOR PROTEIN DEGRADATION
1. Lysosomal Degradation
 Lysosomes – part of cell with Hydrolytic enzymes
 Enzymes in lysosomes are responsible for degradation
of protein
 Proteins with sequence Pentapeptide KFE RQ
o Lys-Phe-Glu-Arg-Gln (lysine, phenylalanine,
glutamat e, arginine, glutamine)
o Or a closely relat ed sequence
o Selective pathway
o Activated only after prolonged fast
 ATP-independent
 Contains 50 hydroly tic enzymes, including proteases
 Degrade via endocytosis
 Well-nourished cells: degradation is non-selectiv e
 Starving cell: degradation will deplete essential enzymes &
regulatory proteins
Page 1
 Subject: Biochemistry

PROTEIN METABOLISM Date: Jan. 14&21, 2012

Lectur er: Dra. Santos
Transcriber: Arvin Uy & Trisha Uy

2. Ubiquitin o Cleave peptide bonds if carbonyl grp

st
 N-terminal (amino terminal) – 1 AA in chain is Lysine or Arginine
o Aspartate, Arginine Elastase
o Rapid degradation o Cleaves elastin
 If not, slower degradation o Cleaves Carboxyl group with small
 Methionine, Serine = no degradation side chain AA (Alanine, Glecine,
 ATP-requiring Serine)
 Independent of lysosomes Chymotrypsin
 Degrades by covalently linking proteins to ubiquitin
Pepsin
 Exopeptidases: cleave one amino acid at a
AMINO ACID POOL
time from the end of the chain
 Collection of Amino Acids in body
Carboxypeptidas e
 2 sources of AA in body
Aminopeptidase
o Exogenous: diet
o Intestinal epithelial cells: produces enzymes:
 RDA for prot ein = 1g/kg of IBW
 Cleave oligopeptides -> AA
o Endogenous: within body
 Aminopeptidase: located on brush border
 From degradation of tissues during protein
 Peptidase: located within cells
turnover
 Non-essential AA ; synthesized in the liver
ABSORPTION OF AMINO ACIDS
 Use of AA - Synthesis of body proteins
 AA are absorbed thru intestinal epithelial cells and
 Hemoglobin, Collages, Keratin & other
enter the blood
structural proteins, Enzymes
 3 ways of absorption
 Excess AA: use to synthesize Essential non-
1. Secondary active Na-dependent transport
protein nitrogenous substances o In luminal membrane of intestinal cell brush border
Not proteins, but need AA for synthesis o Driven by low intracellular Na concentration
Purines: needs Aspartic acid, Glutamine, o Pumps Na out of the cell by Na-K-ATPase pump
o AA is transported out of cell by facilitated transporters
Glycine
2. Facilitated diffusion
Pyrimidines
3. Gamma-Glutamyl cycle/Meister’ s Cycle:
Porphyrin: Glycine
o Trans port of AA in cells of intestines and kidneys
Creatine- Tripeptide: glycine, Arginine,
o gamma glutamyl transpeptidase: Membrane-
Methionine
bound enzyme
Glutathione-tripeptide: Glutamic acid,
 Internalize AA that will absorbed
Cysteine, Glycine
o AA goes in membrane: immediately combine with
reduced Glutathione (GSH)
PROTEIN DIGESTION
o Combines at N-terminal side
 Any AA not used will be catabolized
o Peptide bond will be cut
 NO enzyme in mouth
o Regeneration of Glut athione: needs 3 mol A TP
 Digestion starts in stomach
 Proline – not abs orbed in Meister’s Cycle
o Pepsin – proteins -> hydrolyze -> smaller
polypeptides CENTRAL ROLE OF LIVER AA METABOLISM
 Complete digestion: Small intestine
 Liver – major organ on catabolism of AA
o Pancreatic proteases: cleave polypeptides to
o Nutrients are metabolize in liver
oligopeptides and AA
 All AA are metabolized in liver, except Branched-chain
 Endopeptidases: cleave peptide bonds at
AA (Val, Leu, Ile): metabolize in brain, muscles
various points within protein chain
 Protein Synthesis
Trypsin: most specific

Biochemistry / Protein Metabolism Page 2

 Subject: Biochemistry

PROTEIN METABOLISM Date: Jan. 14&21, 2012

Lectur er: Dra. Santos
Transcriber: Arvin Uy & Trisha Uy

 Synthesis of Essential non-protein nitrogenous AMINO ACID CATABOLISM

substances  AA that is not used
 Cent ral supplier of AA to other organs 1. One-carbon transfer – remove R group
 Catabolism of AA
 Synthesis of non-essential AA
 Not used- catabolism

Essential AA Non-e ssential AA

Indispensible Dispensible
AA that body cannot Synthesized in the body
synthesize/made
Must provide in diet Not needed to provide in
diet 2. Decarboxylation – release CO2
 Diff. : presence in diet - amine formation
 Nothing to do with function of AA - examples:
 Cannot synthesize Protein when one AA is lacking,
- histamine – from histidine
needs all AA
- serotonin/5-hydroxytryptamine – from tryptophan
- neurotransmitter
 10 Essential AA
- vasoconstrictor
Tryptophan Phenylalanine
- catecholamines (dopamine, norepinephrine,
Valine Histidine
epinephrine) – from Tyrosine and P henylalanine
Threonine Isoleucine
Methionine Leucine - Epinephrine: inc. blood sugar level
Arginine Lysine  Gluconeogenesis &glycogenolysis
 Complete protein
o Protein of high biological value
o All 10 essential AA is present in a protein
o Can sustain life by itself
o Ex.: milk, meat, eggs
 Incomplete protein
o One or more AA is lacking
o Cannot sustain life by itself
o Ex:cereals, fruits, vegetables 3. Oxygenation – add O2
o Corn: has protein Zein – lacks Tryptophan - Ex. Phe + O2 = Tyrosine
o Limiting AA: AA that is lacking

 3 enzymes needed for synthesis of non-e ssential AA

 Glutamate DH
o Synthesis of Glutamic acid
 Glutamine synthetase
o Synthesis of Glutamine
 Aminotransferase/Transaminase s
o Enzymes needed for transamination
o To synthesize other AAs

Biochemistry / Protein Metabolism Page 3

 Subject: Biochemistry

PROTEIN METABOLISM Date: Jan. 14&21, 2012

Lectur er: Dra. Santos
Transcriber: Arvin Uy & Trisha Uy

4. Removal of alpha-amino group b. Non-oxidative deamination

a. Oxidative deamination - Same equation sa oxidative deamination
Equation: AA – amino grp.  a-keto acid + NH3 - Diff. in enzymes used
(ammonia) 1. Amino Acid dehy drase
- Releases ammonia - Acts of Hydroxy amino acids (Serine, Threonine,
Tyrosine)
- coenzyme : pyridoxal phosphate (Vit. B6) (active
enzyme in protein metab)
- Vit.B6 – amino acid metabolism vitamin
= requirement directly proportional to
protein intake
2. Amino Acid desulfhydrase
- Each AA has its own keto acid - Acts on sulfur-containing amino acids (cysteine,
- Alanine – pyruvate homocysteine, methionine)
- Aspartic Acid – Oxaloacetate - coenzyme : pyridoxal phosphate
- Glutamic acid – alpha-ketoglutarate
- Glycine – glyoxalic acid c. Transamination
 3 most important Keto-acids - Trans fer amino group, amino acid -> keto-acid
1. Pyruvate  Acetyl CoA  Krebs Cycle
2. Oxaloacetat e  Krebs Cycle
3. Alpha-ketoglutarate  intermediat e of Krebs Cycle
[most important pat hway for production of energy]

3 enzymes:
1. Glutamat e dehydrogenase – most active - Keto-acid accepts amino group
- Present in almost all parts of body - 1. amino acid - amino group = keto acid
- Requires NAD as coenzyme - 2. keto acid acceptor + ammonia = amino acid
- Glutamic acid <–> alpha-ket oglutarate alanine (amino acid) + a-ketoglutarate (k eto-acid
- Glutamic acid: most active amino acid acceptor) = pyruvate + glutamic acid
metabolic ally - enzyme: aminot rans ferase/transaminase
- Alpha-ketoglutarate: most active amino-group - can synthesize other AA
acceptor - keto-acid accept or:
2. L- amino acid oxidase a-ketoglutarate
- Acts of other amino acids - amino acid:
- Ex: L-Aspartic oxidase, L-Alanine Oxidase glutamic acid
- CC: Zellweger Syndrome – deficient enzyme
activity
o Cerebrohepatorenal Syndrome (CHRS )
o Affects: Brain, Liver, Kidney
o Liver and kidney failure
3. D-amino acid oxidase
- Not working in the human body, no D-AA, only L-
AA
- Only 2 D-Amino Acids: D-Aspartate, D-Serine
- Acts on bacteria

Biochemistry / Protein Metabolism Page 4

 Subject: Biochemistry

PROTEIN METABOLISM Date: Jan. 14&21, 2012

Lectur er: Dra. Santos
Transcriber: Arvin Uy & Trisha Uy

- transfer of amino group is not direct 3. Asparagine formation

- pyridoxal-5’-phosphate: Carrier of amino group - Same as Glutamine formation
from AA to keto acid - Change Glutamic acid to Aspartic acid
- derivative of vit. B6 4. Urea formation
- coenzyme of transamination - Major way which liver detoxify ammonia
- NO ammonia is released - Most active
- Incorporated to keto-acid - All AA are metabolized in liver, except Branched-
- Non-toxic chain AA (Val, Leu, Ile)
- AA do not undergo transamination: Lysine,
Threonine, Proline, Hydroxyproline UREA CYCLE / KREB’S-HENSELEIT CYCLE
 Utilizes both cytosol & mitochondria
 Ammonia accumulates = Ammonia intoxication  Gluconeogenesis - Also uses both cytosol and m itochondria
o Manifestations: o Uses both Glycolysis (cytosol) and Kreb’s Cycle
 Initial: Headache, nausea & vomiting (m itochondria) in reverse
 Blurring of vision o Product is glucose
 Slurring of speec h  Convert AA  glucose : enter Kreb’s Cycle, reverse
 Convulsive seizures  Ex. Glutamic acid  glucose: goes in Kreb’s
 Unconscious (mitochondria) through a-ketoglutarate Succinyl CoA
 Comatose  Succinate  Fumarate  malate  (cytosol) 
 Deat h oxaloacet ate  phosphoenol pyruvate [glycolysis] 
o = severe liver dse.- liver does not function to glucose
detoxify ammonia  STEPS (refer to pg. 81 of manual):
 Easily give ammonia int oxication  coma [MITOCHONDRI A]
o Liver – major organ of body that detoxifies 1) 2 mol ATP + CO2 + NH3 + H2O Carbamoyl
ammonia Phosphate
o ~3 mos. Enzyme: Carbamoyl Phosphat e Synthetase I (CPS I)
Two types of CPS:
WAYS OF DETOXIFYING AMMONIA CPS I CPS II
1. Reverse glutamate dehydrogenase reaction Use/Biosynthe si s Urea cycle Pyrimidine
Alpha-ketoglutarate + NH3  Glutamic Acid Location mitochondria Cytosol
- Lower ammonia level Nitrogen donor ammonia Glutamine
- Use ammonia to convert a-ketoglutarate  Acti vator N-AGA none
(N-acetyl
glutamic acid
glutamic acid)
2. Glutamine formation
- Major way which brain detoxifies ammonia 2) Carbamoyl phosphate + Ornithine  Citrulline
- Brain is sensitive to ammonia Enzyme: Ornithine transcarbamoylase
- Glutamic acid + NH3  glut amine [CYTOS OL]
- Enzyme: glutamine synthet ase 3) Citrulline + Aspartic Acid  Arginosuccinate
- Glutamine: brought to kidneys Enzyme: Argininosuccinate synthetase
o Glutamine  glutamic acid +NH3 - Citrulline reacts with another ammonia through
o Reverse reaction Aspartic Acid
o Enzyme: glutaminas e(breakdown) -
nd
2 ammonia enters as Aspartic Acid
o NH3  directly excreted to urine 4) Argininosuccinate  Arginine + Fumarate
 Glutamine: Most common source of ammonia Enzyme: argininosuccinase
excreted to urine - Fumarate  Krebs Cycle

Biochemistry / Protein Metabolism Page 5

 Subject: Biochemistry

PROTEIN METABOLISM Date: Jan. 14&21, 2012

Lectur er: Dra. Santos
Transcriber: Arvin Uy & Trisha Uy

5) Arginine  Urea + Ornithine  No A TP Produced

Enzyme: Arginase o Endergonic pathway: utilizes ATP
- Arginine is cleaved to form Urea and ornit hine  4 mol ATP used per turn
st
- Urea excreted through urine o 1 reaction: 2 ATP
rd
- Ornithine – goes back to mitochondria (step 2) o 3 reaction: 1 A TP
 Arginine = semi-essential AA  ATP  AMP + PPi
o Considered non-essential and essential  PPi: pyrophosphate  use 1mol A TP  2Pi
o Can be synthesized in the body (urea cycle)  Rate-limiting steps (3):
o But needs to be provided in diet o Cont rol points – part of pat hway that you can
o Arginine produced cannot be used for prot ein stimulate or inhibit
synthesis o 1st step
nd
o Arginine immediately converted to urea & ornithine o 2 step – most rate-limiting
 Kreb’ s Bicycle  Uses Carbamoyl phosphat e (step 1) and
o Fumarate from urea cycle goes to Krebs cycle ornithine (step 5)
th
o Krebs cycle linked to urea cycle through Fumarat e o 5 step
(step 4)  Triple H (HHH) syndrome - mutation of Ornithine
o Two pathways linked toget her by Fumarate transporter gene
o Ornithine can only enter mitochondria through
ornithine transport protein
Urea Fumarate Krebs o Ornithine in cytosol cannot re-enter mitochondria
st
Cycle Cycle o Urea cycle stops after 1 reaction
nd
o 2 reaction does not proceed
o Hyperammonemia
 Urea – end product of protein metabolism in body  Inc. level of ammonia
o Excreted in urine  No conversion of ammonia to urea
 2 ammonia are detoxified o Hyperornithinemia
o 2 ammonia enters cycle  Inc. level of ornit hine in blood
st
 1 reaction  Not used, cannot re-enter mitochondria
rd
 3 reaction through Aspartic acid o Homocitrullinuria
o 2 ammonia excreted through urea  Citrulline excreted in urine

INBORN ERRORS OF METABOLISM:

UREA CYCLE
 Enzyme deficient = urea cycle stops
o Accumulation of ammonia, not converted to urea
o Hyperammonemia  Ammonia intoxication
 Baby is born wit h a defect in enzyme
INBORN ERROR ENZYME DEFECT
Aspartic acid urea Hyperammonemia Type I Carbamoyl Phosphate
Synthetase
Hyperammonemia Type II Ornithine
transcarbamoylase
Citrullinemia Argininosuccinate
synthetase
Argininosuccinate Aciduria Argininosuccinase
Arginemia Arginase

Biochemistry / Protein Metabolism Page 6

 Subject: Biochemistry

PROTEIN METABOLISM Date: Jan. 14&21, 2012

Lectur er: Dra. Santos
Transcriber: Arvin Uy & Trisha Uy

 Manifestations:  Not use a-ketoglutarate

o Hyperammonemia  Adequate amt. of a-ketoglutarate in Krebs
o Ammonia int oxication
 severe liver disease E XTRA:
o Easily give ammonia int oxication  coma  Mnemonics: 10 Essential Amino Acids
o liver cannot detoxify ammonia
The Ten Acid Pornstars Liked Very Hot Ladies In Mini-
o ammonia accumulate  goes out to systemic
skirts
circulation  brain (sensitive of ammonia)
(go back to pg. 5, ways of detoxifying ammonia #2) Threonine, Tryptophan, Arginine , Phenylalanine, Lysine,
o glutamic acid event ually runs out Valine, Histidine, Leucine, Isoleucine, Methionine
o brain will try to produce Glutamic acid
 source: a-ket oglutarate – from Krebs OR
 enzyme: a-ketoglutarate DH
o Krebs cycle will be depleted of a-ketoglutarate
o Krebs cycle stops, no ATP production = coma These Ten Valuable Amino Acids Have Long Preserved
Life In Man
TREATMENT OF AMMONIA INTOXICATION Threonine, Tryptophan, Valine, Arginine, Histidine, Lysine,
 limit protein intake
Phenylalanine, Leucine, Isoleucine, Methionine
o Ammonia comes from protein
o Low amount, high quality (complete protein)
 Admini stration of Lactulose/Levulose
o Prevent absorption of Ammonia from GIT END OF P ART 1
o Excreted in stool ^_^
 Oral Administration of Antibiotics
sencya na kung mahaba. Pero itro lahat yung sinabi ni dra. Santos. Kung
o Normal bacterial flora – harmless hindi nyu maintindihan dito tignan nyo na lang sa manual baka may
 Produces ammonia through bacterial diagram dun.
fermentation
 Adds ammonia May part 2 pa. walang susuko! Kaya natin to! Gogogo! 
 Kill harmless bacteria
o Neomycin – cheapest antibiotic
 Remove excess Ammonia, give compounds that
bind to AA
o 1 AA = 1 ammonia attached (amino group)
o Excreted to urine
o Example:
o Benzoic Acid
 Binds with Glycine  excrete as Hippuric Acid
o Phenylacetat e
 Binds with Glutamine  excret e as
Phenylacetylglut amine
 Replace depleted/missing Enzyme , alternate subs.
o Treat the cause
o Depletion of a-ketoglutarate
 A-ketoglutarate: Corrosive when injected
 Give Glutamic Acid

Biochemistry / Protein Metabolism Page 7