Unit 4 Study Guide

Module 14: Protein Digestion and the Urea Cycle

A. Protein Digestion
The process of protein digestion involves a series of proteases (from exocrine pancreas as zymogens
must be activated) that digest polypeptide strands into smaller pieces by cleaving peptide bonds between
specific amino acid residues. The single amino acids are transported into the epithelial cells by both
active and passive transport.
Protein digestion begins in the stomach with HCl and pepsin and get broken down into
peptidesin the small intestine the pancreas releases bicarbonate and zymogens to cleave the
peptides into di/tripeptides + amino acidssecondary and facilitated transport move the products
through the intestinal epithelium amino acids go into bloodstream
Zymogens must become activated and selectively cleave polypeptide bonds (proteolytic process):
amino peptidase: cleave btw N-terminal and Phe/Tyr/Glu/Asp
pepsinogen pepsin [HCl]: cleave btw Phe/Tyr/Glu/Asp and Arg/Lys
Trypsinogen trypsin [enteropeptidase]: cleave btw Arg/Lys and Phe/Tyr/Trp/Leu
Chymotrypsinogen chymotrypsin [trypsin]: cleave btw Phe/Tyr/Trp/Leu and Ala/Gly/Ser
Proelastase elastase [trypsin]: cleave btw Ala/Gly/Ser and anything
Procarboxypeptodase carboxypeptidase [trypsin]: cleave at C-terminal
Intestinal lumen: amino acids enter the brush border by Na+ secondary transport due to a
lowered Na+ concentration gradient made by Na/K ATPase transporter shuttling Na+ out. Amino
acids enter the blood by facilitated transporter that is amino acid specific
A type transporter: Na+ dependent and specific to small/polar-neutral AA
L type transporter: not Na+ dependent and specific to branched and aromatic AA
Glutamyl cycle: the synthesis of Glutathione/y-Glutamyl transpeptidase conjugates a free AA
(doesnt play big role in uptake but does facilitate synthesis of GTH) y-glutamylamino acid--[5oxoprolinase]--> 5-oxoproline + free amino acid (exits)--[ATP]-->glutamate--[ATP+cystein]--> yglutamylcystein--[ATP+glycine]-->Glutathione
contribution of proteins in the cell
dietary proteins (digested, in blood)
degradation of proteins (AA pool, broken down into C (energy) and N (urea cycle) or get
recycled back into proteins
B. Protein Turnover
Turnover is constant in the cell; proteins can be targeted for degradation by covalent modification
(ubiquitination). AA from the diet or protein degradation are either recycled for protein synthesis or
deaminated (transaminases) & C backbone to be used in GNG or for energy.
Protein recycling:
Lysosomal Degradation
under low energy: activation of AMPK-->P-TSC1/TSC2 (activates it)-->activates Rheb
[GTP-->GDP-->inactive]-->inactivates mTOR-->activates autophagy (lysosomal
degradation)
under high energy: activation of Akt by insulin-->P(different area)-TSC1/TSC2
inactivated-->inactivates Rheb[-->active]-->activated mTOR-->inactivates
autophagyprotein synthesis occurs
Protein Ubiquitination
ubiquitin: small protein (76AA)/can be added to amino group on lysine residues of
proteins the cell wants to degrade/ubiquitin target activates ubiquitination cascade (highly
conserved)

involves proteosome complex (20S subunit and 19S regulatory particle)

pest domains: target proteins for ubiquitination (contain specific AA--proline,
glutamine, serine, threonine)
intracellular proteins have rapid turnover (i.e, secondary messengers)
20S proteosome (proteolytic residues) + 19S regulatory particle--[ATP]-->Active
proteosome complex (26S)-->reqs ATP for proteolysis *20S can have up to 2
19S attached
Proteases involved in protein turnover/degredation (see table 37.2)
Diseases in CH 37 (see table 37.3)
Fate of AA in the body: Proteins-->AA-->N-->aspartate or free ammonia-->urea cycle-->urea
AA-->C-->storage (glucose/TG) or energy (TCA)
NH4+ NH3 + H+ Free ammonia found in kidney for disposal of protons/protonated
form is most common [Pka=9.3]
C. Urea Cycle
Urea Cycle (in liver): aa catabolism produces ammonia (toxic) in the cell that must be transported to the
liver (as alanine or glutamine) and used to synthesize urea as a means of disposing of the nitrogen. This
cycle is critical as ammonia is toxic to the body.
Transamination Rxns: removal of ammonia from AA/readily reversible used in synthesis and
degradation/ reqs PLP (pyroxidial phosphate) Amino acid1 gives NH3 to Keto-acid2 keto-acid1
and Amino acid2-NH3
ie: aspartate give NH3 to a-ketoglutarate--[PLP]-->oxaloacetate and glutamate(NH3)
Free ammonia can come from:
Glutamate--[NAD+/NADP+;GDH]-->a-ketoglutarate
this direction if urea cycle highly active (deamination)/opposite direction for AA
synthesis (transamination: reqs PLP)
Glutamine--[glutaminase]-->glutamate
Asparagine--[asparaginase]-->aspartate
Serine--[PLP]-->pyruvate
} AA can be directly deaminated
Threonine--[PLP]-->a-ketobutyrate
Histidine-->urocanate
bacterial rxns btw AA and urea in gut (sig contribution)
[MUSCLE/BRAIN] aspartate--[purine nucleotide cycle]-->fumerate
Shuttles getting non-toxic forms of ammonia to liver:
Glucose-Alanine cycle: MUSCLE AA + a-KG--[transaminate]-->glutamate +pyruvate -[aminate]-->alanine-->LIVER alanine--broken down C(-->glucose>>muscle) + N(->urea-->urine)
Glutamine shuttle: MUSCLE/TISSUES a-KG--[NH4+/NADPH/GDH-->glutamate-[NH4+/ATP]-->glutamine-->LIVER glutamine--[glutaminase]-->NH4+ + glutamate--[GDH]->a-KG + NH4+-->[2NH4+]-->urea-->urine
Urea Cycle: can be activated by either Fed/Fast state; gets rid of excess AA in the body
Fed State: removal of excess AA (Gut Liver (Glycogen/TG/Urea cycle) Cells
(proteins))
Fasting State: deamination used as a substrate for GNG (primary substrate is alanine)
(muscle (glutamine/alanine) gut (alanine) kidney (NH4+-->urine) liver (ketone
bodies/glucose/urea)
reliant on AA pool; high protein synthesis=low urea cycle
UREA CYCLE

mitochondria: CO2+H2O-->bicarbonate [+NH4+]--[2ATP/carbomyl phosphate synthase 1

(CPS1)* primary regulatory enzyme]-->carbomyl phosphate/orthinine--[ornithine
transcarbamolyase]-->citruline
cytosol: citruline + aspartate --[ATP/arginosuccinate synthase]-->arginosuccinate-[arginosuccinate lyase]--> fumerate(-->GNG) + arginine --[arginase]-->urea + ornithine[->mitochondria]
Krebs Bicycle: TCA and urea cycle relationship
TCA: arginosuccinatefumarate malate oxaloacetate--[glutamate]--> aspartate
arginosuccinate
Urea cycle: arginosuccinate-->arginine-->ornithine [+ urea]--[carbomyl phosphate]->citruline-->arginosuccinate
primary regulation of urea cycle: glutamate + acetyl CoA --[(+)arginine synth in urea cycle]-->NAcetylglutamate --(+)-->CPS1 [CO2+NH4+-->carbomyl phosphate
GNG/Urea cycle relationship: in liver see slide
Disorders in Urea Cycle: disfunction in ornithine trancarbomylase=high levels of carbomyl
phosphate/ornithine and orotic acid present/ in some disorders arginine becomes an essential AA
because the urea cycle is not producing it
sodium benzoate and sodium phenylacetate are alternative means of conjugating
ammonia in the body-->urea cycle

Module 15: Fasted State and Metabolic Acidosis

A. Integration of protein catabolism with other metabolic pathways:
Integrate AA catabolism into the previous pathways and underscore the importance of N balance within
body. Looking at tissue specific roles for AA.
Amino Acid Pool: amino acids can come from dietary protein digestion or endogenous protein
degradation. The pool can fluctuate throughout the day as needs and ingestion changes. This
pool can be used for:
synthesis of new proteins
for use in N-containing compounds (purines, pyrimadines, heme, NT, etc)
AA can be broken down into C (GNG, lipid synthesis, energy) and N (urea, NH4+->kidney)
catabolism of AA is the same whether its from the diet or blood
interorgan exchange of AA: see slide
kidney: glutamine facilitates 2 primary rxns (see slide)/can undergo GNG under starvation
but body isnt reliant on this process
oxidation of glutamine: provides substrate for energy and ammonium for
buffering (NH3 freely diffuses where it + H+-->NH4+ cant diffuse back->excreted into urine/H+ can cross using Na+ transport)
Skeletal muscle AA catabolism BCAA--[BCAA transferase]-->-->-->glutamine (circulation)
see slide [expressed in all tissues except liver]
generating nontoxic carriers of ammonia in the body: BCAA (isoleucine/leucine/valine),
FA, Glucose-->Alanine/glutamine-->circulation see slide
alanine-glucose cycle: LIVER alanine--[alanine amino transferase] pyruvate
+NH3 (urea) glucose MUSCLE pyruvate +NH3 (from BCAA)->alanine-->BLOOD-->LIVER
postprandial state (lumen of gut--glutamate/glutamine/aspartate) vs
postabsorptive state (blood--glutamine/BCAA/ketone bodies) see slide
shuttling AA into the brain (glutamine needed for synthesis of NT) see slide

Nitrogen balance: anabolism/catabolism of proteins about equal w/ turnover

too much N: synthesis>degradation=+ balance (during growth, pregnancy, repair)
too little N: synthesis<degradation=- balance (during injury, starvation, waste
diseases)
otherwise, neutral
immune response and negative N balance: bacterial products+immune
cascade (macrophage)-->cytokines release TNF, IL-1, IL-6 (reqs AA)->liver (GNG--reqs AA), etc see slide
add immune response to starvation negative N balance
ie: child after a meal has positive N balance (no GNG, no FA [o])

B. Comparison of the Fed/Fast state.

Revisit the metabolic pathways that are activated during the fed/fasting states. Allosteric activators,
inhibitors, and covalent modification of regulatory enzymes in the pathways of GNG, glycolysis, FA
synthesis, B-oxidation, and lipolysis. The preferential fuel for each tissue types (muscle, liver, brain,
adipose) are discussed.
Fed state pathways: glycogenesis/TAG synthesis/Urea sythesis (remains constant)
insulin signaling: binds to tyrosine kinase-->receptor autophosphorylates recruits IRS->binds Grb to phosphotyrosine residues on SH2 domain/IRS binds PLC and PI3 kinase->downstream signaling
initial response of insulin sensitive tissues: insulin binds receptor-->activates
translocation of glucose transporter to plasma membrane (GLUT4 insulin
sensitive--prevalent on skeletal muscle and adipose)
GLUT transporters:
GLUT1: RBC, brain/insulin insensitive
GLUT2: Liver/insulin insensitive
GLUT4: Adipose, muscle/insulin sensitive
1. glycogenesis: see slide
glycogenesis regulation:
in presence of glucagon: (+) protein kinase A-->P-glycogen synthase (-)
iin presence of insulin: (+) protein phosphatase-->deP-glycogen synthase (+)->UDP glucose-->glycogen
2. TAG synthesis in liver and adipose: see slide
FA synthesis regulation:
in low energy levels: (+) AMP-activated protein kinase-->P-Acetyl CoA
carboxylase (-)
palmitoyl CoA(-) Acetyl CoA carboxylase (negative feedback)
in presence of insulin: (+) phosphatase-->deP-Acetyl CoA carboxylase (+)
(regulatory enzyme for FA synthesis [Acetyl CoA-->malonyl CoA])
citrate--> (+) Acetyl CoA carboxylase
conversion of palmitate-->VLDL: see slide
Fasting state pathways: Glycogenolysis/gluconeogenesis/lipolysis/B-oxidation/muscle
catabolism/urea synthesis (very high due to deamination of AA for GNG)/ketone body synthesis.
In fasted state liver/muscle/adipose use FA to spare the glucose for RBC/brain
1. Glycogenolysis: glucagon binds to GPCR(+) adenylate cyclase-->cAMP (2nd
mess.) (+) protein kinase A-->P-glycogen synthase (-)/P-phosphorylase kinase (+)-->Pglycogen phosphorylase a (+)-->(+) glycogen-->glucose-1-phosphate-->glucose 6-phosphate-[glucose-6-phosphatase]-->blood glucose

2. Gluconeogenesis: alternative enzymes to those in glycolysis (going around them)-caMP/glucagon--> (+) P-pyruvate kinase (-) -->pyruvate--[pyruvate carboxylase*]-->OAO--[PEP
carboxylase]-->PEP-->glyceraldehyde 3-P-->Fructose-1,6-BP--[F-1,6-BPtase]-->fructose-6-P->glucose 6-P--[glucose 6-Ptase]-->GLUCOSE
*allosterically activated by Acetyl CoA
3. Lipolysis: glucagon(+) cAMPhormone sensitive lipase (-)--[(+) protein kinase A]-->Phormone sensitive lipase (+)--[hydrolyze]-->TG-->3FA (energy for liver/muscle or [o]-->acetyl
CoA) + glycerol (substrate for GNG)
effects of GC (cortisol on tissues): (+) release of FA and glycerol from
adipose/(+) AA catabolism and release (alanine and glutamine) from
muscle/glycerol and AA-->liver=GC (+) glucose and glycogen/epinephrine (+)
release of glucose into blood
Starvation state pathways: lipolysis (fuel for B-oxidation)/B-oxidation/ketone body synthesis (byproduct of B-oxidation in the liver for the brain)
C. Comparison of hyperglycemia (DKA) and hypoglycemia (MCAD).
This will integrate and reinforce the metabolic pathways by looking at an example of a patient with DKA
due to lack of insulin and one with MCAD due to deficiency of B-oxidation.
1. Diabetic Ketoacidosis: high blood glucose/havent been eating/fruity breath/low pH/high blood urine
N/high urine glucose and ketones
ration of insulin/glucagon: no insulin so <1
pathways activated: glycogenolysis/B-[o]/gluconeogenesis/lipolysis/urea cycle
no insulin: (-) GLUT 4 in adipose and muscle-->no glucose-->increase GNG in
liver/increase in KB (fruity breath--acidosis)/increase in AA catabolism in muscle->increase urea
administering insulin will help: increase GLUT 4 translocation to the plasma
membrane/dephosphorylate glycogen synthase (+) glycogen synthase/and increase activity of
pyruvate kinase (glycolysis)
bicarbonate buffering: helps regulate the disturbances in pH balance caused by increase in KB->increase in acetoacetate pH 3.6/B-hydroxybutyrate pH 4.4-->lowers physiological pH (7.4)
[decrease=acidosis, increase=alkalosis]
buffers help resist change in pH when there is metabolic disturbance (can either
contribute or remove H+ from system)
CO2 used to help regulate this (respiratory compensation)
as CO2 increase-->pH decrease (increase in H+)
as CO2 decrease-->pH increase (decrease in H+)
CO2+H2O--[carbonic anhydrase]-->Carbonic Acid--[dissociate]-->bicarbonate (HCO3- +
H+)
in case of diabetes, pH is decreased=increased H+=so equation will shift the the
left to help compensate
2. MCAD Medium Chain AcylCoA-dehydrogenase deficiency: low blood glucose/quiet/lethargic/glutaric,
ethylmalonic, and dicarboxylic acids in urine/infusion of dextrose and glucose supplementation/didnt eat
before bed
ratio of insulin/glucose <1
pathways activated: glycogenolysis/B-[o]/gluconeogenesis/lipolysis/urea cycle
B-oxidation spiral : AcylCoA dehydrogenase deficeincy-->no medium chain oxidation->once the LCFA are oxidized to MCFA they accumulate-->decrease in FADH2 and
NADH and Acetyl CoA
omega oxidation of MCFA is also not working-->MCFA go to urine

because B-[o] is not functioning properly, the muscles and are

relying heavily on glucose and it becomes strainned (decreases)
without Acetyl CoA pyruvate carboxylase isnt activated and
pyruvate does not get converted to OAO-->hypoglycemia

Module 16: Additional Hormones that Impact Metabolism

A. Metabolic Balance
Insulin and glucagon are the primary regulatory hormones involved in metabolic balance. Cortisol and EN
have also been discussed.
1. Insulin: secreted from B-cell in pancreas
glycogen synthesis
glycolysis
FA synthesis (TAG storage)
growth
suppresses glucagon release from a-cells
2. Glucagon: secreted from a and L-cells in pancreas
glycogenolysis
gluconeogenesis
lipolysis-->B-[o]-->acetyl CoA-->ketogenesis
stimulates release of insulin (so pathway can maintain blood glucose)
o not present in case of diabetic ketoacidosis
B. Additional counterregulatory hormones
In addition to insulin and glucagon there are many other hormones that affect metabolic balance such as
somatostatin, growth hormone, catecholamines, glucocorticoids (cortisol), and thyroid hormone.
1. Somatostatin (inhibitor): peptide with membrane receptor/inhibits release of other
hormones
secreted as pro-molecule (peptide that needs to be cleaved of active peptide like insulin and
glucagon)
o hypothalamus
o D cells of pancreatic islets
o CNS
o gastric/intestinal mucosa
secreted in response to
o glucose, arginine, and leucine
o stimulated by: glucagon, VIP, and CCK
physiological actions of somatostatin: signals via GCPR(+) inhibitor G protein (+) adenylate
cylase decrease cAMP (+) phosphatases/ MAPK/Ca2+ and (-) GH/TSH/insulin/glucagon
secretion/decreases gastric emptying by impacting secretion of gastric enzymes and pancreatic
enzymes
regulatory network of hormonal signalling
o glucagon (+) release of somatostatin and insulin
o insulin (-) release of glucagon
o somatostatin (-) release of insulin and glucagon

2. Growth hormone: peptide with membrane receptor/released from anterior

pituitary/water soluble/short life (20-50min)/single polypeptide chain with 2 disulfide
bonds/subject to negative feedback
growth hormone system/IGF balance: sleep rhythm/stress/exercise/low blood glucose/high blood
AA(+) hypothalamus release of somatostatin (-) and GHRH(+)GHRH (+) anterior pituitary
release of GH-->Jak-Stat receptor on liver plasma membrane-->cAMP--> (+) release IGF-1->negative feedback (-) on release of GHRH, somatostatin, and GH
factors affecting growth hormone secretion:

physiologic: (+) low blood glucose after meal, high blood AA, exercise, sleep/(-)high
blood glucose after a meal, high blood FA
o pharmacological: (+) estrogens, dopamine agonists/(-) somatostatin, progesterone,
dopamine antagonists, GF, and IGF-1
o pathological: (+) starvation, anorexia, acromegaly, hypoglycemia/(-) obesity,
hyperthyroidism
physiological effects of GH: increases energy
o Adipose: increased lipolysis (increased sensitivity to epinephrine)/decreased fat storage
o skeletal muscle: FFA taken up from lipolysis and [o] by muscle/generates ATP/increases
AA transport-->protein synthesis
o liver: increases GNG/decrease glucose uptake/increased glycogen synthesis
(storage)/increased ketogenesis from Acetyl CoA from FFA [o]/stimulates IGF release->bone growth
IGF similar to insulin: growth, Jak-Stat receptors/endogenous tyrosine kinase activity
excessive release of GH: giantism (acromegaly) is the result of excess GH secretion/begins in
young children and adolescents/usually result of tumor of somatotrophs (releases GH) *rare*
3. Catecholamines (EN): amine with membrane receptor/stress induced--fight or
flight/consists of EN and NEN (NT increase systemic blood pressure-->rapidly deliver
fuels)/released from adrenal medulla in response to stress (exercise, pain, hypoglycemia, hypoxia
(no O2))/they target a- and B-adrenergic receptors/major role is to rapidly mobilize fuel (increase
lipolysis and glycogenolysis)/counteracts insulin
epinephrine binds an a-agonist receptor-->binds GPCR(+) phospholipase C to cleave PIP
DAG (-->(+) protein kinase C(-) glycogen synthase) and IP3 (-->(+) Ca2+-->(+) calmodulin(+)
phosphorylase kinaseP glycogen phosphorylase a (active))-->-->glycogenolysis
4. Glucocorticoids (cortisol): steroid with intracellular receptor/transcription factor/long
term survival/synthesized from cholesterol (rate lmt step: cholesterol-->pregnenolone)
synthesis and secretion controlled by neuroendocrine signaling-->received by hypothalamus(+)
monoamines (acetylcholine/seratonin)-->targets paraventricular hormone-->(+) CRH (cortisol
releasing hormone)-->pituitary release of ACTH-->target adrenal gland(+) cortisol
release/negative feedback on CRH and ACTH)
impact of cortisol on tissues:
o adipose: increased lipolysis/decrease glucose utilization
o muscle: increased protein degradation/decreased protein synthesis/decreased glucose
utilization
o liver: increased GNG (precursors from muscle and adipose and PEPCK)/increase
glycogen storage (so EN can release blood glucose rapidly)
transcriptional regulation by steroid hormone receptor: see slide
defects example: cortisol levels increased but ACTH is reduced, location of defectprimary
defect (tumor in adrenal gland)
o primary defect: defect at level of adrenal gland
o secondary defect: defect at level of pituitary
cushings disease: increase in cortisol (defect of adrenal gland)/weight gain (increased glycogen
storage)/fatigue (decreased glucose utilization)
5. Thyroid hormone: peptide with intracellular receptor/transcription factor/skeleton of
tyrosine residues/T4-->4 iodines ( life 7 days) & T3-->3 iodines ( life 1-3 days)/thyroid is
bound and only free fraction of hormone has biologic activity which can diffuse through plasma
membrane and interact with intracellular receptors/initailly bound to thyroglobulin and
degradation of this protein releases free thyroid
thyroid globular binding protein: reservoir for thyroid and can rapidly release free hormone
depending on need
synthesis of thyroid in thyroid follicular cell: iodine in the blood gets pumped into cell by Na+-I
symporter by concentration gradient-->I gets [o] into iodimium ion (I+) while tyrosine gets
synthesized in cell and released into colloid space through exocytosis-->I+ reacts with tyrosine->iodotyrosine then gets coupled-->thyroxine (T4/T3) which can be stored within colloid space until
needed-->secretes more T4 than T3

o monoiodotyrosine+diiodotyrosine=T3
o 2 diiodotyrosine=T4
Review: hypothalamus secretes TRH(+) anterior pituitary to release TSH(+) GPCR on
thyroid-->synthesis of T4/T3-->peripheral cells nucleus transcription factors to illicit gene
expression -->T3 (primary negative feedback) feedback inhibits TSH and TRH
o TSh from pituitary releases circadian pattern surging in the late afternoon and peaking
before sleep
physiological effects of thyroid hormone
o liver: increases glycolysis/cholesterol synthesis/conversion of cholesterol to bile
salts/increased TAG synthesis/increased hepatic glucose secretion (by increased
sensitivity to EN)
o adipose (bipolar impact): increased lipolysis (by increased sensitivity to EN)/increased
lipogenesis (when insulin and glucose are high)
o muscle: increased glucose uptake/stimulates protein synthesis/glycogenolysis (by
increased sensitivity to EN)
o pancreas: increases sensitivity of B-cells to release insulin
interactions of thyroids: similar to steroids/binds intracellular or nuclear receptor
o thyroid receptor: resides in the nucleus bound to DNA in absence of thyroid (represses
expression)/when thryroid (T3/T4) binds the TR bound to RXR there is a conformational
change that activates the histone acetylation domain on the co-activator complex(+)
basal transcription
TR can dimerize with different target receptors:
homodimer with TR
heterodimer with RXR
vs Cortisol receptor: in cytosol and reqs cortisol for translocation to the nucleus
defects in thyroid hormone: graves disease--hyperthyroidism
o significant weight loss and heat sensitivity
the increase in thryroid-->increase in NE and cAMP-->increase in FA [o] and
thermogenin activity=sensitivity to heat
o increased T3/T4, and decreased TSH
inappropriate release of T3/T4 from thyroid=increases in both and negative
feedback from T3 on TRH/TSH-->decreased levels