biochem - protein metabolism Flashcards
primary site of amino acid metabolism
LIVER
what happens to components of amino acid
- amino groups -> excreted as urea
- carbon skeletons -> metabolic fates (acetyl coa, pyruvate, krebs cycle intermediates
what is cystinuria
- failure in reabsorption and uptake of cystine, ornithine, arginine, lysine (COAL)
- cause cystine kidney stones
what is hartnup’s disease (neuropsychiatric symptoms)
- failure in the reabsorption and uptake of trp, phe and other neutral amino acids
- cerebellar ataxia (lack of coordination of involuntary
movement) - pellagra-like symptoms eg. skin lesions, dermatitis (nicotinic acid/nicotinamide deficiency)
what is nitrogen balance
- intake of N = output of N
+ve N balance:
- intake of N > output of N (eg growth, pregnancy)
-ve N balance
- intake of N < output of N
amino acid with the highest concentration in blood
- glutamine
what happens to excess amino acids
- deamination (removal of N group) to form KETOACIDS
via:
- oxidative deamination **(most common)
- transamination
- non-oxidative deamination
why is L-glutamate dehydrogenase (enzyme in oxidative deamination) so special
- can utilise both NAD+ and NADP+ as oxidizing agents (forms NADH, NADPH) -> used in energy pdn (NADH) or biomolecule synthesis (NADPH)
- reaction is reversible
what is transamination
- conversion of an amino acid to ketoacid, while another ketoacid accepts the amino group to form an amino acid
what is required for PLP (pyridoxal phosphate) cofactor synthesis
- Vit B6
what is the purpose of transamination
- (transdeamination) releasing ammonia in the form of NH4+ from OTHER amino acids (other than glutamate) through transamination with glutamate -> then oxidative deamination of glutamate
- synthesis of non-essential amino acids (through conversion between diff types of amino acids)
what is an indication of necrosis in muscles/ liver/ brain
- raised blood serum ALT, AST
ALT - alanine aminotransferase (used in alanine-glutamate transamination)
AST - asparatate aminotransferase (used in aspartate-glutamate transamination)
structure of an aminotransferase
- PLP bonded to enzyme (usually an amino acid, eg Lys)
- bond is known as a SCHIFF BASE/ aldimine linkage
mechanism of PLP dependent transamination
- transamination
- tautomerization
- hydrolysis
*forms ketoacid from amino acid
steps are repeated but in reverse for 4. 5. 6.
*forms amino acid from ketoacid
describe the phenomenon of ion trapping (NH4+)
- pertains to NH4+
- under physiological pH of 7.4 (pKa NH4+ = 9) -> majority of NH3 exists as NH4+ (associated form) -> cannot exit cell membrane and cannot be excreted
how is ion trapping overcome
glutamine can be transported out of cell (glutamine = glutamate + NH4+ = a-KG + 2NH4+)
- NH4+ converted to glutamate (involves glutamate dehydrogenase, a-KG, NADPH)
- glutamate converted to glutamine (involves glutamine synthetase) -> transported out of cell to kidney
- glutamine converted back to glutamate to release NH4+ outside of cell (involves glutaminase) -> excreted
- glutamate converted back to aKG to release NH4+ (involves glutamate dehydrogenase) -> excreted
**one glutamine releases 2 NH4+ molecules
why is ammonia toxic to humans
- presence of glutamate dehydrogenase -> high NH3 concentration forces backward reaction (conversion of aKG -> L-glutamate)
- backward reaction depletes NADH/ NADPH -> inability to generate energy -> TOXICITY
regulation of urea cycle (4)
- compartmentalization (mitchondria vs cytosol)
- transcriptional & translational control of enzymes
- feed forward activation (activation by reactants)
- allosteric regulation
what is the rate limiting enzyme in urea cycle
- CP synthetase 1 (CPS1)
what is CPS1 allosterically activated by
N-acetylglutamate
how is N-acetylglutamate activated
- formed from glutamate via addition of arginine -> high [Arg] -> increased activation of N-acetylglutamate -> activation of CPS1
why is urea excreted instead of ammonia
- urea is more soluble -> less water wasted to excreted same amount of water
enzyme defect in urea cycle - inherited disease
- Carbamoyl phosphate synthetase I -> Hyperammonemia Type I
- Ornithine transcarbamoylase -> Hyperammonemia Type II
- Argininosuccinate synthetase -> Citrullinemia
- Argininosuccinate lyase
(Argininosuccinase) -> Argininosuccinic aciduria
(Argininosuccinic acidemia) - Arginase -> Argininemia
*any urea enzyme defect causes HYPERAMMONEMIA
effect of hyperammonemia
hepatic coma, nausea, seizures, ataxia
how to treat hyperammonemia
give glucose and arginine
- arginine -> required for urea formation from NH4+ -> reduce blood [NH4+]
- glucose -> metabolism of glucose provides reducing equivalents → allow GDH to remove ammonia + glucose is metabolized to aspartate → feeds into urea cycle for activation
fate of NH3
- Assimilation (Incorporation into organic compounds)
a) by glutamine synthetase
b) by glutamate dehydrogenase
c) by carbamoyl phosphate synthetase - Excretion
a) as ammonium ions
b) as urea
c) as creatinine
d) as uric acid
ketogenic vs glucogenic amino acids
ketogenic: aa has potential to form ketone bodies under starvation
glucogenic: aa has potential to form glucose under starvation
what fuel does brain use
- glucose
- ketone body (if no glucose)
why are ketogenic aa not considered glucogenic even though they enter TCA and can eventually form glucose
- enters TCA as acetyl-coA (2C) -> 2 decarboxylation steps of TCA removes the acetyl-coA C -> C from aa is lost -> not counted as glucogenic
aa that are both ketogenic and glucogenic
phenylalanine, tryptophan, leucine, isoleucine, valine
*can form both acetoacetate (ketone body) and TCA metabolites
what happens in leucine/ isoleucine turnover disorders (ie metabolism disorder)
- maple syrup urine disease -> DARKENING of urine
how is NH3 in muscles primarily removed (2)
- glucose-alanine cycle (using alanine as carrier of NH3) -> closed cycle between liver and muscle
- through amination of aKG to glutamine -> transport to liver (less common, alanine preferred)
how is NH3 in muscles produced (2)
- breakdown of amino acids
- substrate level phosphorylation (from ADP)
how does substrate level phosphorylation produce NH3
- 2 ADP used to generate ATP and AMP (consequence of generating energy)
- AMP needs to be deaminated to form IMP
essential vs non essential amino acids
essential
- needed in the diet to ensure positive nitrogen balance
- body CANNOT synthesize from simple precursors
- body CANNOT synthesize enough for its own bodily
needs
non-essetial
- not needed in diet
- body CAN synthesize from precursor
- body CAN synthesize enough for own needs
glutamate metabolisms that can occur (4)
- synthesis of non essential aa (aspartate, alanine, glutamine, ornithine, proline)
- synthesis of aKG
- synthesis of glutathione
- synthesis of GABA
glutamine metabolisms that can occur (4)
- synthesis from glutamate + catabolism to glutamate
- transamidation
- synthesis of purines/ pyrimidines
- nucleotide metabolism (forming CTP and GMP)
metabolism of aspartate & asparagine
- synthesis of aspartate from oxaloacetate (by transamination)
- synthesis of asparagine from aspartate
- synthesis of aspartate from asparagine
- synthesis of purines/ pyrimidines from aspartate
how is tyrosine formed from phenylalanine
- phenylalanine hydroyxylase + cofactor tetrahydrobiopterin
how is tetrahydrobiopterin regnerated
- by enzyme dihydropteridine reductase, with one NADPH molecule
phenylketonuria pathogenesis and presentation
- deficiency of enzyme in phenylalanine metabolism -> cause metabolic block and phenylalanine is shunted to other pathways
presentation
- high amounts of PHENYLPYRUVATE, phenyllactate & phenylacetate in urine (normal: trace amounts)
- symptoms of mental retardation due to phenylpyruvate buildup
enzyme defects in phenylketonuria (3)
- phenylalanine hydroxylase (classical)
- dihydropteridine reductase OR biopterin synthesis (non-classical, related to terahydrobiopterin generation)
enzyme defect in tyrosinemia type 1 (1)
- fumarylacetoacetate hydrolase
how to treat phenylketonuria in newborns
- supply tyrosine and reduce phenylalanine from diet
OR - introduce smart living microbes into GI -> convert excess phenylalanine to tyrosine
what enzyme defect causes albinism
- tyrosinase (Cu-dependent Tyr hydroxylase) -> prevents formation of melanin from tyrosine
treatment of parkinson’s disease
- administer DOPA (needed by CNS cells to transmit info via dopamine)
- administer DOPA analogs (cannot cross BBB; carbidopa, methyldopahydrazine) -> inhibits dopamine carboxylase around the body except brain -> reduce systemic side effects of dopamine administration
how to synthesize a primary amine from an amino acid
- decarboxylation using an enzyme decarboxylase
types of physiologically important amines and their synthesis routes
- histamine (from histidine)
- GABA (from glutamate)
- serotonin (from 5-hydroxytryptophan)
- dopamine (from DOPA)
- tyramine (from tyrosine)
what are some examples of polyamines
- putrescine, spermidine, spermine
functions of polyamines
- polycationic -> can interact with nucleic acids (polyanions) by binding to phosphate groups -> DNA stabilization & packaging
- cell growth and proliferation
is methionine needed for polyamines synthesis
yes. need methionine to form S-adenosylmethionine
how does creatine act as a storage of energy
- creatine can be converted to creatine phosphate by creatine kinase in muscles
- energy needs: creatine kinase can dephosphorylate creatine phosphate anytime to produce ATP
*most abundant source of ATP in muscles is creatine phosphate
what happens to creatine phosphate that is stored and not used
- broken up over time -> to form creatinine which is excreted
nitrogen substances excreted by body
- urea: 30g
- creatinine: 1-1.8g
- NH4+: 0.7g
- uric acid: 0.5-1g
components of a nucleotide (3)
- inorganic phosphate (Pi or HPO32-)
- 5-carbon sugar (D-ribose or 2-deoxy-D-ribose)
- nitrogenous base (purine or pyrimidine)
how does caffeine keep us awake
- caffeine are purine derivatives
- binds and inhibits phosphodiesterase -> prevents breakdown of cyclic AMP -> cyclic AMP keeps us awake
what are the components of nucleosides (2)
- nitrogenous base (purine/ pyrimidine)
- sugar ring
*diff btwn nucleoside & nucleotide is phosphate group
*nucleosides are more soluble than its free nucleotide
two important nucleotides to know
- SAM (S-adenosylmethionine) -> METHYL donor
- PAPS (3’-phosphoadenosine 5’-phosphosulphate) -> SULFUR donor
steps in the biosynthesis of purine nucleotides
- converting ribose-5-phosphate to PRPP (ATP dependent)
- de novo pathway
- formation of AMP and GMP from IMP
- formation of purine ribonucleoside triphosphate
how is the conversion of ribose-5-phosphate to PRPP regulated
- regulation of PRPP synthetase (activated by Pi, inhibited by purine ribonucleotides)
what is the de novo pathway in purine nucleotide synthesis
- pathway that converts PRPP to IMP
how is the de novo pathway in purine nucleotide synthesis regulated
- glutamine-PRPP amidotransferase upregulated by PRPP, inhibited by AMP, GMP
how is the synthesis of AMP/ GMP from IMP regulated
- end product inhibition
function of purine salvage pathways
- recover catabolised free nitrogenous bases and incorporate them into purine synthesis by binding to PRPP
bases involved in purine salvage pathways
catalysed by HGPRT
- hypoxanthine + PRPP -> IMP
- guanine + PRPP -> GMP
catalysed by APRT
- adenine + PRPP-> AMP
how is pyrimidine nucleotide synthesis regulated
- CPS II inhibited by end product UTP
- OMPDC (orotidine 5-monophosphate decarboxylase) inhibited by end product UMP
bases involved in pyrimidine salvage reactions
catalysed by ribose 1-phosphate
- uracil, cytosine -> uridine, cytidine
catalysed by deoxyribose 1-phosphate
- thymine -> thymidine
in biosynthesis of deoxyribonucleotides from ribonucleotides, when does reduction occur
- at NUCLEOTIDE level; ie ribonucleotide -> deoxyribonucleotide (NOT sugar level; ie ribose -x-> deoxyribose)
- nucleotide is at the DIPHOSPHATE level (ie NDP -> dNDP)
*reaction is mediated by ribonucleotide reductase
conditions required for proper functioning of ribonucleotide reductase (3)
- Fe-dependent
- requires NADPH as the reducing agent
- contains thioredoxin as mediator protein (NADPH reduces thioredoxin reductase -> reduce thioredoxin -> reduce ribonucleotide reductase -> reduce NDP)
what are the 3 main sites of ribonucleotide reductase
- catalytic site -> site of NDP catalysis to dNDP
- activity site -> site where ribonucleotide reductase can be activated/ inactivated; determined by ATP/ dATP
- specificity site -> determines type of NDP that will be reduced at catalytic site (diff NDPs exist -> ADP, CDP, UDP, GDP)
purpose of 1:1:1:1 ratio of deoxyribonucleotide pdn by ribonucleotide reductase
- equal amount of each building block -> prevents mutations
what is the FINAL END PRODUCT of all purine catabolism (AMP, IMP, XMP, GMP)
- URIC ACID
what is the FINAL END PRODUCT of all pyrimidine catabolism (CMP, UMP)
- malonyl-CoA
*can be fed back into metabolic pathways like lipid synthesis -> NOT AN EXCRETORY PRODUCT
diseases related to purine metabolism (4)
- lesch-nyhan syndrome
- gout
- von Gierke’s glycogen storage disease
- SCID
Lesch-Nyhan syndrome pathogenesis
- sex linked congenital; more common in MALES
- severe HGPRT deficiency -> accumulation of PRPP -> excess de novo pathway activation -> increase purine nucleotide synthesis & breakdown -> increase URIC ACID
presentation:
- neurological abnormality
what is gout
- disease characterized by painful arthritic joint inflammation (acute arthritis) due to urea crystal precipitation (can also ppt in kidneys as stones)
- caused by high uric levels in blood
pathogenesis
- impaired uric acid excretion
- excessive uric acid production (1. HGPRT deficiency in Lesch-Nyhan syndrome; 2. glucose-6-phosphatase deficiency in von Gierke’s glycogen storage disease causing G6P increase -> ribose-5-P increase -> PRPP increase)
- overactivity of PRPP synthetase
treatment of gout
- colchicine -> anti-inflammatory
OR - allopurinol -> hypoxanthine analogue & inhibitor of xanthine oxidase + inhibits PRPP amidotransferase activity
what is SCID (severe combined immunodeficiency disease)
- inherited disorder, fatal in infancy due to lack of immune response to infection
- T and B lymphocytes cannot proliferate
- 30% SCID patients associated with adenosine deaminase (ADA) deficiency
SCID pathogenesis
- ADA involved in deamination of adenosine & deoxyadenosine -> ADA deficiency causes metabolic block -> increase adenosine & deoxyadenosine -> diverted to form more dATP
- dATP accumulation inhibits NDP reductase at activity site -> prevent synthesis of dNTPs -> T & B cells cannot proliferate
diseases related to pyrimidine metabolism
- orotic aciduria
orotic aciduria pathogenesis and presentation
- inherited disorder
type 1 orotic aciduria
- deficiency in OPRT & OMP decarboxylase
- excretion of large amounts of orotic acid in urine
type 2 orotic aciduria
- deficiency in OMP decarboxylase
presentation
- retarded growth, severe anemia
how to treat orotic aciduria
- supply uridine or cytidine
- use salvage enzyme to bypass pyrimidine de novo pathway
