Studied by 7 people
What are primary metabolites?
they are needed for normal operation of metabolic pathways and main cellular functions
What are secondary metabolites?
organic compounds NOT needed for cell growth, development, or reproduction
What are the functions of secondary metabolites?
ward off pathogens and predators
protect against osmotic damage
treat various illnesses
What are some examples of keto-acids?
pyruvate, oxaloacetate, a-ketoglutarate
Where is pyruvate found?
cytosol
Where is Oxaloacetate found?
cytosol and mitochondria
used in gluconeogenesis and citric acid cycle
Where is a-ketoglutarate found?
mitochondria
used in citric acid cycle
What is the structure of pyruvate, oxaloacetate, and a-ketoglutarate?
What are the sources of amino acids?
digestion of protein in food
synthesis of amino acids
prides aa's needed for protein synthesis
adjust aa pools in different tissues
adjusts energy metabolism by controlling levels of central pathway metabolites
allow cells to adapt to metabolic stress
needed to synthesize neurotransmitters and nucleotides
What is the use of Amino Acids?
intracellular proteolysis:
removes misfolded proteins
removes old and damaged proteins
regulates metabolism
controls cell-cycle transitions
"What are the 9 ""nutritionally essential (not made in body) amino acids?"
Phe, Val, Trp, Thr, Ile, Met, His, Leu, Lys
PVT TIM HiLL
What are the conditionally essential amino acids?
Arg: needed for growth childhood and pregancy
Tyr: becomes essential when Phe is inadequate
Cys: becomes essential when Met is inadequate
What is most Met presented as?
S-Adenosyl-Met
T or F: Omnivores are disadvantaged when is comes to getting a varied balance of amino acids in their diet.
F: they are advanataged
What is found in the 3 areas of proteolysis (enzymatic cleavage of proteins)?
Saliva: proteases principally from bacteria and white blood cells
stomach: pepsin
intestine: neutral proteases like chymotrypsin (cleaves on the carboxyl end of aromatic residue), trypsin (cleaves on carboxyl end of lysine and arginine residues), carboxypeptidases (cleaves C-terminal AA), Elastase (cleaves elastin)
What is the path for proteolysis?
proteins --> stomach --> proteins that can't refold --> intestine --> amino acids + Di- and Tri-peptides
T or F: dietary proteins are absorbed by healthy intestines
F: must be proteolyzed to amino acids, di and tri- peptides
What begins enzymatic proteolysis?
making inactive proteases (zymogen)
- synthesized and stored in pancreas
- secreted into small intestine
- converted to active catalysts
What happens in trypsinogen activation?
Pancreas makes and stores trypsinogen in vesicles
secretory vesicles contain trypsin inhibitor (revents unwanted proteolysis of host cells)
enterokinase, an ectoprotease on intestinal mucosal wall, converts trypsinogen into trypsin
trypsin activates chymotrypsinogen
What is Pro-carboxypeptidase?
activated to carboxypeptidase
removes amino acids one-by-one from C-termini of food proteins
Where does zymogen synthesis, processing, and transport occur?
ribosomes attached to rough ER -> golgi complex
Where does zymgen vesicale targeting and release occur?
zymogen granule
T or F: Zymogen formation prevents autophage and apoptosis
T
Where is pepsinogen formed in and released by?
gastric chief cells within the stomach
What does it mean by pepsinogen activation is autocatalytic?
once a little active pepsin forms, the latter catalyzes cleavage of many pepsinogen molecules to form more catalytically active enzyme molecules
How does pepsin operate at low pH?
by using its aspartic acid carboxyl groups for catalysis (aspartic proteinase)
T or F: turnover rate depends on metabolic state.
T: greater protein degradation, when nitrogen intake is low, because cells need amino acids to make vital proteins (ex: antibodies and hormones like insulin)
What is the lysosomal/phagolysosomal pathway?
lysosome is an acidic compartment, where proteins undergo isoelectric expansion (partial unfolding
low pH makes them more susceptible to proteolysis
What is true nitrogen balance? positive? negative?
True: intake = excretion
Positive: intake > excretion
Negative: excretion > intake
What is positive nitrogen balance required for?
growth in childhood
growth in pregnancy
healing of wounds
convalescence
When does negative nitrogen balance occur?
starvation
malnutrition
disease (burns, trauma, surgery)
What is marasmus?
malnutrition associated with extensive tissue and muscle wasting, with little/no edema
protein-energy malfunction resulting from inadequate intake of proteins and calories
severe deficiency of nearly all nutrients, especially protein, carbohydrates, and lipids"
What is Kwashiorkor?
sickness last baby gets when the new baby arrives
acute childhood protein malnutrition
unlike marasmus, kwashiorker has inadequate protein intake, BUT otherwise adequate caloric intake
charactertistics: irritability (neurotransmitter deficit), enlarged liver (fatty infiltrates), edema (caused by hypoalbuminemia)"
Transaminases use ________ coenzymes
Vitamin B6
transaminases catalyze 2 half reactions
What is the mechanism of enzyme-bound reactions?
1st half-reaction: aldimine forms; converts to ketimine; hydrolyzes to ketoacid
2nd half-reaction: reverse of 1st half reaction, using R2-KA to make R2-AA
aldimine vs ketamine
What is the Keq for transamination?
Keq= 1 (same bonding in substrates and products)
-fully reversible
alanine: alpha- ketogluterate transaminase
glutamate: oxaloacetate transaminase
Which 4 amino acids CANNOT undergo transamination?
proline and hydroxyproline: don't have the needed primary amine for transamination
lysine: if transaminated, the keto acid would cyclize to form a toxic nonmetabolite
threonine: if transaminized, the keto acid would dimerize into a toxic nonmetabolite
T or F: transaminases cannot bind prolines and hydroxyprolines.
F: cannot bind lysine or threonine
What is the reaction equation foer glutamate dehydrogenase?
major route for oxidative deamination
glutamate + NAD^+ + H2O <---> a-ketoglutarate + NADH + NH3
What is the structure for a-ketoglutarate?
Where is glutamate dehydrogenase (GDH) located?
mitochondrial matrix
What are nature's batteries?
NAD+ and NADH
NADH oxidation yields enerfy needed to make 3 mol ATP from ADP and Pi through oxidative phosphorylation
What are the exceptions to the coupling of GDH with transaminases allowing for oxidative degradation of 14 other amino acids?
Pro, Hyp, Thr, Lys, His
memorize
How does GDH use NAD+ in oxidative deamination reaction?
NADH is re-oxidized to NAD+ in oxidative phosphorylation
a-KA1 enters citric acid cycle
excess NH4+ enters urea cycle.
operating in the opposite direction,
NADPH drives reductive amination to form glutamate.
GDH uses what?
NAD+and NADPH (NOT NADH and NADP+)
What happens when the mitochondria rapidly re-oxidizes NADH to NAD+?
excess NAD+
NAD+>>NADH
NADH oxidation makes ATP in Mitochondria
What happens when there is excess NADPH?
NADPH>>NADP+
NADPH is used to make fatty acids, sterols, etc.
What inhibits GDH?
high ATP, GTP, and NADH
reduces AA degradation and favors protein synthesis
What activates GDH?
high ADP, GDP, and free amino acids
a-KG stimulates citric acid cycle, fueling ATP synthesis
Glutaminase catalyzes __________?
hydrolysis of glutamine
What is the glutaminase reaction equation?
glutamine + H2O ----> glutamate + NH3
Histidinase (or Histadine ammonia lyase) catalyzes _________?
Why do we need both L- and D- Amino acid oxidases?
there are D- amino acids in damaged proteins
D- amino acids are also abundant in old and dried food
by forming ketoacids from D-AA, D- amino acid oxidase allows cells to harvest carbon skeletons as an energy source
Asparaginase catalyzes _____________?
hydrolysis of asparagine
asparagine -----> Aspartate + NH3
What are the 4 enzymes that catalyze NH3 assmilation?
Glutamate Dehydrogenase:
NADPH + NH3 + a-KG ---> Glutamate + H2O + NADP+
Glutamine Synthetase:
ATP + NH3 + Glutamate ----> Glutamine + Pi + ADP + H+
Carbamoyl-Phosphate Synthetase I:
2 ATP + NH3+ CO2 ----> H2N(C=O)-O-P+ Pi + 2ADP + H+
What is Glutamine Synthetase?
Main way to trap NH3
Gln is a major nitrogen source
Gln is a major inter-organ nitrogen shuttle, avoiding direct transfer of NH3 from distant organs to liver
What are the 2 SN2 reactions that occur in sequence for glutamine synthetase?
Glutamate ----ATP ADP---> gamma-Glutamyl-P (essential intermediate) ----> Glutamine
What drives ammonium ion deprotonation?
∆GATP-hydrolysis
pK of ammonium ion deprotonation= 9.2
∆Gdeprotonation= 10 kJ/mol
driven by ATP-dependent conformation change that moves guanidium group of a nearby arginine residue near enzyme-bound NH4+ to allow electrostatic repulsion to form NH3
What would happen if opposing enzymes were kept in the same compartment?
futile cycles would pointlessly hydrolyze ATP
Glutamine synthetase would convert glutamate to glutamine and glutaminase would convert glutamine to glutamate in a continuous cycle
What is Carbamoyl-Phosphate Synthetase- I?
main ammonia-assimilating reaction in mitochondria
highly energy-dependent reaction
1st reaction resembles glutamine synthetase reaction and second reaction is a phosphorylation reaction
Why is glutamine vital for the efficient biosynthesis of nitrogen-containing metabolites?
allows glutamine-dependent biosynthetic enzymes to generate ammonia in situ
that ammonia is then used as a nucleophile without ever touching water
What is CPS II?
glutamine dependent
uses a transfer tunnel to move unprotonated NH3 from glutamine-hydrolysis site to biosynthetic site
covalently bound glutamate acts as a ""lid"" covering the glutamine site, preventing entry of H2O or H3O+
used throughout metabolism
Which subunit in CPS-II hydrolyzes Gln to Glu + NH3?
glutamine-hydrolyzing subunit
T or F: The use of CPS-II allows are body to hydrolyze glutamine to deprotonate NH3 exactly where and when it is needed to avoid toxicity of ammonia elsewhere in out cells.
T
What are the characteristics of glutamine-dependent biosynthetic enzymes?
exhibits a low Km (high affinity) for glutamine
essential -SH group generates a gamma-glutamyl thioester that accupies active site, permitting NH3 transfer
two active sites connected by ammonia transfer tunnel that prevents protonation of NH3 even at neutral pH
What are the series of reactions that represent glutamine-dependent biosynthetic enzymes?
What is the differences between CPS I and CPS II?
What is the structure of Uric Acid? What is the structure of ammonia?
What do fish excrete?
NH3 - Ammonotelic
What do birds excrete?
Uric Acid - Uricotelic
What do mammals excrete?
Urea - Ureotelic
What is gout?
Diseased caused by creating too much uric acid
What is the principal site of NH3 detoxification?
liver
high levels of ammonia in the blood is toxic so it is transported in organic forms like alanine, glutamate, glutamine, and urea
What is the overall stoichiometry for urea synthesis?
T or F: Urea cycle is an energy-independent pathway which liberates considerable acid to help control body pH.
F: Urea cycle is energy-dependent
What is the reaction equation for ornithine transcarbamoylase? Reaction mechanism for argininosuccinate synthase?
Reaction: Aspartate + Gln + ATP <---> Asparagine + Glu + AMP
One site hydrolyzes Gln to generate nascent NH3
NH3 travels through aprotic tunnel
Other site already made B-Aspartyl-AMP intermediate
NH3 attacks B-Aspartyl-AMP to make asparagine + AMP
What is the structure for ornithine, citrulline, and arginino-succinate?
What is the reaction equation for argininosuccinate lyase?
Reaction equation for arginase?
What is the Urea Cycle?
How does a high-protein diet induce urea cycle enzymes?
certain amino acids stimulate glucagon release (casein or milk protein is rich in certain AAs)
glucagon stimulates biosynthesis of urea cycle enzymes
reduces ammonia load and increases pyruvate, OAA, and aKG for glucogenesis.
How do arginine and glutamate regulate the urea cycle?
CPS-I is the 1st commited step of the Urea Cycle
CPS-I is allosterically activated by N-acetylglutamate.
When amino acid catabolism increases, glutamate levels rise and so does N-acetyl-glutamate.
What is the reaction equation for NAGS (N-Acetyl-Glutamate Synthase)?
Glutamate + Acetyl CoA <---> N-Acetyl-Glutamate + CoA
How are glutamine and arginine related to amino acid content and NAG?
Glu and Arg are indicators of high amino acid content
Glu is substrate for NAG synthase
Arg activates NAGS allosterically
NAG synthase deficiency results in hyperammonemia
How does the liver acinus avery ammonia toxicity?
liver acinus is an ammonia trap
endothelial lining within the liver is fenestrated (full of openings, exposing hepatocytes to blood)
hepatocytes are in direct contact with blood components which permits rapid metabolite exchange between liver and blood
What does the liver acinus do?
prevents ammonia re-entry into circulation through differential utilization of ammonia
Cells in the first segment of the acinar space contain ____________?
glutaminase and urea cycle enzymes
CPS-I has low affinity for NH3
Urea cycle removes bulk of NH3
Low affinity, High Capacity
After the blood goes through the first segment of the acinar space, blood passes through ____________, which are rich in ______________.
perivenous scavenger cells; glutamine synthetase
GS gas 40x higher affinity for NH3
GS mops up NH3 that gets past the first segment
Supplies glutamine to many organs
High affinity, Low capacity
How is Arginine synthesized?
What is creatinine?
break-down product of creatine-P in our muscles
produced at a fairly constant uncatalyzed rate
yield depends on muscle mass; higher in men
clearance rate tells us how well kidney is working
glutamate synthesis
transamination → reductive amination →hydrolysis
how is glutamine made?
What enzyme exclusively makes glutamine?
Glutamine synthetase (located in cytosol)
aspartate synthesis
transamintion → hydrolysis
What is the reaction for Asparagine synthesis? Explain the reaction.
Reaction: Aspartate + Gln + ATP <---> Asparagine + Glu + AMP
One site hydrolyzes Gln to generate nascent NH3
NH3 travels through aprotic tunnel
Other site already made B-Aspartyl-AMP intermediate
NH3 attacks B-Aspartyl-AMP to make asparagine + AMP
Note
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