4L4-6 Nitrogen Catabolism, Reactions, and Excretion

alanine

-CH3;

A = first in alphabet of the As;

np, Hphobic, aliphatic

glutamate

-CH2CH2CO(O-);

E= gluEtamate ,Glu;

negative charged second carbonyl

glutamine

-CH2CH2C(=O)NH2;

Q = Qtamine, amide of glutamate

Gln = Glu but with an n;

polar, uncharged, Hphilic

aspartate

-CH3CO(O-);

D = asparDate, you ASk for a Date;

negative charged second carbonyl

pyruvate

structure

aKG

structure

oxoaloactetate

structure

amino acid sources

intracellular proteolysis

dietary proteins

de novo synthesis

intracellular proteolysis

• removes misfolded and damaged proteins

• supplies essential amino acids when diet insufficient

de novo synthesis

• nonessential for protein synthesis

• amino acid pools in tissues

• energy metabolism by controlling metabolites for central pathways

• needed for NuTides, hemes, hormones, NeuroTs

essential amino acids

valine, leucine, isoleucine, tryptophan, phenylalanine, lysine, histidine, methionine, threonine

***MILK TV FHW

valine

-CH(CH3)2;

np, Hphobic, aliphatic

leucine

CH2CH(CH3)2;

L = alphabetically first of the Ls

leuc = 4C;

np, Hphobic, aliphatic

isoleucine

CH(CH3)(CH2CH3);

I = only I

leuc = 4C, iso = split;

np, Hphobic, aliphatic

tryptophan

-CH2 cyclo =C-N-C=Ph;

W = twyptophan, W before Y in alphabet,

polar, uncharged, Hphobic

phenylalanine

-CH2Ph;

F = fenyl;

polar, uncharged, Hphobic

lysine

-4CH2 NH3+;

K = next to L, Leuc = lys = 4, 4CH2;

positive charge, Hphilic

histidine

-CH2(NHCH=NCH=C) loop;

positive charge, Hphilic, ionizable side chain with neutral pKa

methionine

-CH2CH2SCH3;

Me = CH3, Thio = S;

np, Hphobic, aliphatic

threonine

CH-(OH)(CH3);

T = alphabetically first T, THREE (CH3) O (OH);

polar, uncharged, Hphilic

conditionally essential amino acids

we make it but occasionally need more

• arg cys gln gly pro tyr

• R Q G P Y C (real quick go produce your conditionals)

aa catabolism overview

sources proteolysis, digestion, or de novo synthesis

amino and carbon are separated

• carbon > aKA > CAC

• NH3 > biosynthesis / Urea cycle

• combine with the asp-arg-succ shunt of CAC

ketogenic v glucogenic

ketone bodies v glucose

IC protein turnover

constant flux of synthesis / degradation

regulated by proteostasis

three machines: lysosome, ubiquitin proteasome, autophagic pathway

ubiquitination

adding ubiquitin to a protein to target it for proteolysis via proteosome

done by ubiquitin ligases, *1= Initiate, 2 = conJugate, 3 ligate

1. E1 initiates by grab Ub, pass to E2

2. E2 conjugates

3. E3 ligase, adds Ub tag

E1 E2 E3 ubiqiutin

1 = initiates,

2 = conJUgates

3 = ligases

***1 = i. two = ju

overall digestion process

first catalyzed by sol enzumes in stomach and SI

digestive enzymes in salivary, stomach, and pancreas

pancreatic enzymes and bile acids help intraluminal digestion

gastrin

secreted as dietary proteins enter stomach by gastric mucosa

stimulate HCl release by parietal cells

chief cells secrete pepsinogen

parietal cells

secrete HCl bc gastrin signalled

chief cells

secrete pepsinogen, inactive form of pepsin, low pH

autocatalytic cleavage

converts pepsinogen to pepsin for peptide breakdown

pepsin

cleaves polypeptides at low pH

cleaves phenyl alanine leucine or glutamic acid

secretin

secreted in low pH in intestine,

stimulates pancreas to secrete bicarbonate to neutralize HCl to 7

zymogens

inactive enzymes, cleaved to turn into active proteases

released by pancreas at pH 7

dietary protein degradation overview

1. chewing, amylase and lipase in saliva break carbs and lipids

2. proteins enter stomach, protonated by acidity,

3. gastric mucosa releases gastrin,

4. gastrin lowers pH with parietal cells’ HCl, also chief cells’ pepsinogen,

5. pepsinogen activated to pepsin at low pH,

6. pepsin cleaves aromatic polypeptide chains,

7. in intestine, secretin tells pancreas to release HCO3 to neutralize pH,

8. pancreas releases zymogens at ph 7, they turn into active proteases

   1. trypsinogen + enteropeptidase > pi > alpha trypsin

   2. chymotrypsinogen > chymotrypsin

   3. procarboxypeptidase > carboxypeptidase

   4. proelastase > elastase

pepsin activation

pepsinogen made and released in stomach

autocatalytic activation, acid catalyzed, low pH

helps activate itself to pepsin

activated by removing masking sequence

____is removed to turn pepsinogen into active pepsin

masking sequence

____ zymogen turns into _____ peptidase

trypsinogen > trypsin

chymotrypsinogen > chymotrypsin

proelastase > elastase

procarboxypeptide > carboxypeptidase

chymotrypsin cleaves at

carboxy side of aromatic residues

trypsin cleaves_____; activates ___

carboxy of lysine and arginine residues;

chymotrypsinogen to alpha

carboxypeptidase cleaves

one residue off carboxy end

proteolysis stomach overview

stomach makes HCl and pepsinogen

pepsinogen +HCl > pepsin;

protein + HCl > denatured protein

pepsin + denatured protein > polypeptides

proteolysis pancreas overview

trypsinogen > trypsin

chymotrypsinogen > chymotrypsin

proelastase > elastase

procarboxypeptidase > carboxypeptidase

zymogen + polypeptide > smaller polypeptide / olygopeptides

proteolysis intestine overview

carboxypeptidase and aminopeptidase turn olygopeptides > amino acids and dipeptides

dipeptidases turn dipeptides > amino acids

zymogens

inactive proteases made and stored in pancreas

secreted into small intestine via vesicles and converted to catalysts

_____inogen is transported in vesicles which also contain ____

trypsinogen, a trypsin inhibitor to prevent unwanted proteolysis

chymotrypsinogen

processed through sequential proteolytic cleavage

first to pi, second to alpha which is way more active

enteropeptidase

converts trypsinogen to trypsin

microvilli

increase SA and facilitate intestinal mucosa to absorb amino acids

form brush border cells

aa transporters

mediated by Na/K ATPase,

specificity for amino acids,

secondary active / facilitative transporters

from intestinal cells, enter blood, taken to liver

aa oxidation

deamination, not needed for synthesis or needed for energy (bad)

unless reused, amino groups channeled into single excretory end product (pee)

dietary requirements

0.8g protein per kg of body weight.

RDA = amount to achieve zero nitrogen balance

nitrogen balance

consumption = excretion, no net change

positive could be in children / pregnancy

negative is in starvation or trauma

kwashiorkor / marasmus

childhood malnutrition, large belly, edema

lose skin, underweight, inadequate intake of proteins

essential amino acid

cannot be synthesized

proteasome

Large protein complex that degrades ubiquitinated proteins in a regulated way (selective degradation in cytosol/nucleus).

pepsinogen

Inactive zymogen secreted by the stomach that is converted to pepsin by low pH.

trypsinogen

Inactive zymogen from the pancreas; ****activated by enteropeptidase.

keto acid

Carbon skeleton of an amino acid after deamination—can be used for energy, gluconeogenesis, or fat synthesis.

most ingested proteins turn into

free amino acids in the liver

transamination

removal of nitrogen / amino group, deamination

almost always begins with transfer to aKG to yield glutamic acid

for all amino acids except for proline, lysine, and threonine

amino acids that don’t participate in transamination

proline, lysine, threonine

**Please, lets transmainate

aKG in transamination yields

glutamic acid

almost all amino acids use ___ to deaminate

aKG

amino acid + alpha keto acid =

new alpha keto acid + new amino acid

a-Amino group transfer uses enzyme ____ and ___, which carries ____

aminotransferase / transaminase, PLP, CO2

important aminotransferases / transaminases

AST = aspartate; aKg > L-glutamate; high in liver heart and muscle, indicator of muscle damage in high quantities

ALT = alanine > pyruvate; can release into blood in high concentrations. signifies excess liver usage, meaning damage

PLP

pyridoxal phosphate, prosthetic group

in all of pathways for amino degradation, protects release of amino group

PDP: C=O > NH3

Vitamin B6,

*looks like if a P and an L had a baby

PLP enzyme overview

AA1 + KA2 > KA1 + AA2

1. internal (enzyme bound) aldimine > external (amino acid bound) aldimine

2. DP and rearranges, quinonoid formation

3. rearrangement to help resonance

4. hydrolysis to aKA and PMP

PLP starts ___ linked to residue on enzyme, this is an ____ aldimine

covalently;

internal

after amino acid approaches enzyme, PLP forms an ___ because amino acid ____s it

external aldimine;

activates

external aldimine becomes a ____ because of ____

quinonoid intermediate;

deprotonation

quininoid intermediate becomes ____ by ___

PDP + aKA;

rearrangement and hydrolysis

alanine aKG transaminase steps

1. alanine + PLP + H2O > PMP + pyruvate

2. PMP + aKG > G + PLP

*same as PLP but uses aKG specifically

aminotransferase reactions make what byproduct

aKA, often pyruvate

proline and hydroxyproline exceptions

secondary amines cannot react, only primary amino groups

lysine and threonine exceptions

lysine releases a toxic aKA metabolite (cyclic)

threonine releases a toxic aKA metabolite (dimerize)

glutamate dehydrogenase GDH

oxidative deamination; L-glutamate > aKG, helps renew ala-aKG transaminase

produces NADH and NH4+ ammonia

in mitoC matrix of liver

reversible, has intermediate

glutamate acts as a gate between

AAs and NH4+

coupling transamination and deamination

trans = aKG > glutamate

de = glutamate > aKG

in liver

GDH regulation

*high energy inhibits anabolic (protein synthesis, reduction), low energy activates deam (catabolic, oxidation)

inhibit protein synthesis = ATP, GTP, NADH

activate deamination = GDP, ADP, FAAs

glutaminase

deamination mitoC enzyme, glutamine > glutamate

other route for deamination

produces energy and ammonia

asparaginase

asparagine > aspartate + NH3

other route for deamination

amino acid oxidases

L and D, stereospecific, FMN or FAD involved as cofactor in redox rxn

H2O2 is a byproduct, which is highly regulatde

***other deamination

transdeamination involves ___ being transferred to ____ by ______, followed by release of ____ from ____ by _____

aA groups; glutamate; transaminations; NH4+; glutamate; L-GDH

ureotelic

pee out ammonia

urea cycle begins in ___ but has steps in ___

liver mitoC; cytoS

glutamase GMAse

glutamase + glutamine from extrahepatic tissue > glutamate + NH4+

glutamate dehydrogenase GMDHase

GMDHase + Glutamate > NH4 + aKG

CPS1 CPSI

carbamoyl phosphate synthetase I

CPS1 + NH4+ + HCO3- + 2ATP > carbamoyl P

in mitoC activates urea cycle,

urea structure

NH2-C=O-NH2

carbamoyl phosphate (step 0 urea cycle)

enters urea cycle mostly in liver

activates ornithine trans carbomylase OTCM

NH4+ + CPS1 > CP

step 1 urea cycle

OCMP + ornithine + CMP > citrulline

**structures

step 2 urea cycle

1. citrulline facilitated diffusion into cytoS

2. ArgSStase + Citu + ATP > int + Asp > ArgS + AMP

**structures

step 3 urea cycle

ArgSSase + ArgS > F (> malate > CAC) + Arg

step 4 urea cycle

Arginase + Arg + H2O > Ornithine

transported back via diffusion

urea cycle review

CO2 from CAC + ATP from OP + AA transported and aminated > glutamate,

glutamine > glutamate through GDH,

NH4+ + CO2 > CMP,

1. CMP + Ornithine + ATP > citrulline

2. citrulline + Asp > ArgS

3. ArgS > Arg + F

4. Arg > ornithine

*OCAsAO sounds like acacia

links between paths

urea cycle needs 3 ATP,

asp-arg shuttle of CAC works with urea cycle to make ArgS

regulation of urea cycle

at enzyme synthesis;

high protein diet; ala, gly, met, cys help glucagon, which stimulates biosynthesis

AA catabolism reduces NH4 load, increases OA and aKG for gluconeogenesis

glu and arg help synthesis of NAG

CPS1 is first committed step and highly regulated, allosteric activate N-Aglutamate

NAG n-acetyl glutamate

glutamate + NAGS + Arg > NAG + CoASH