biochem - protein metabolism Flashcards
(82 cards)
1
Q
primary site of amino acid metabolism
A
LIVER
2
Q
what happens to components of amino acid
A
- amino groups -> excreted as urea
- carbon skeletons -> metabolic fates (acetyl coa, pyruvate, krebs cycle intermediates
3
Q
what is cystinuria
A
- failure in reabsorption and uptake of cystine, ornithine, arginine, lysine (COAL)
- cause cystine kidney stones
4
Q
what is hartnup’s disease (neuropsychiatric symptoms)
A
- 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)
5
Q
what is nitrogen balance
A
- 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
6
Q
amino acid with the highest concentration in blood
A
- glutamine
7
Q
what happens to excess amino acids
A
- deamination (removal of N group) to form KETOACIDS
via:
- oxidative deamination **(most common)
- transamination
- non-oxidative deamination
8
Q
why is L-glutamate dehydrogenase (enzyme in oxidative deamination) so special
A
- can utilise both NAD+ and NADP+ as oxidizing agents (forms NADH, NADPH) -> used in energy pdn (NADH) or biomolecule synthesis (NADPH)
- reaction is reversible
9
Q
what is transamination
A
- conversion of an amino acid to ketoacid, while another ketoacid accepts the amino group to form an amino acid
10
Q
what is required for PLP (pyridoxal phosphate) cofactor synthesis
A
- Vit B6
11
Q
what is the purpose of transamination
A
- (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)
12
Q
what is an indication of necrosis in muscles/ liver/ brain
A
- raised blood serum ALT, AST
ALT - alanine aminotransferase (used in alanine-glutamate transamination)
AST - asparatate aminotransferase (used in aspartate-glutamate transamination)
13
Q
structure of an aminotransferase
A
- PLP bonded to enzyme (usually an amino acid, eg Lys)
- bond is known as a SCHIFF BASE/ aldimine linkage
14
Q
mechanism of PLP dependent transamination
A
- transamination
- tautomerization
- hydrolysis
*forms ketoacid from amino acid
steps are repeated but in reverse for 4. 5. 6.
*forms amino acid from ketoacid
15
Q
describe the phenomenon of ion trapping (NH4+)
A
- 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
16
Q
how is ion trapping overcome
A
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
17
Q
why is ammonia toxic to humans
A
- 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
18
Q
regulation of urea cycle (4)
A
- compartmentalization (mitchondria vs cytosol)
- transcriptional & translational control of enzymes
- feed forward activation (activation by reactants)
- allosteric regulation
19
Q
what is the rate limiting enzyme in urea cycle
A
- CP synthetase 1 (CPS1)
20
Q
what is CPS1 allosterically activated by
A
N-acetylglutamate
21
Q
how is N-acetylglutamate activated
A
- formed from glutamate via addition of arginine -> high [Arg] -> increased activation of N-acetylglutamate -> activation of CPS1
22
Q
why is urea excreted instead of ammonia
A
- urea is more soluble -> less water wasted to excreted same amount of water
23
Q
enzyme defect in urea cycle - inherited disease
A
- 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
24
Q
effect of hyperammonemia
A
hepatic coma, nausea, seizures, ataxia
25
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
26
fate of NH3
1. Assimilation (Incorporation into organic compounds)
a) by glutamine synthetase
b) by glutamate dehydrogenase
c) by carbamoyl phosphate synthetase
2. Excretion
a) as ammonium ions
b) as urea
c) as creatinine
d) as uric acid
27
ketogenic vs glucogenic amino acids
ketogenic: aa has potential to form ketone bodies under starvation
glucogenic: aa has potential to form glucose under starvation
28
what fuel does brain use
1. glucose
2. ketone body (if no glucose)
29
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
30
aa that are both ketogenic and glucogenic
phenylalanine, tryptophan, leucine, isoleucine, valine
*can form both acetoacetate (ketone body) and TCA metabolites
31
what happens in leucine/ isoleucine turnover disorders (ie metabolism disorder)
- maple syrup urine disease -> DARKENING of urine
32
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)
33
how is NH3 in muscles produced (2)
- breakdown of amino acids
- substrate level phosphorylation (from ADP)
34
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
35
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
36
glutamate metabolisms that can occur (4)
1. synthesis of non essential aa (aspartate, alanine, glutamine, ornithine, proline)
2. synthesis of aKG
3. synthesis of glutathione
4. synthesis of GABA
37
glutamine metabolisms that can occur (4)
1. synthesis from glutamate + catabolism to glutamate
2. transamidation
3. synthesis of purines/ pyrimidines
4. nucleotide metabolism (forming CTP and GMP)
38
metabolism of aspartate & asparagine
1. synthesis of aspartate from oxaloacetate (by transamination)
2. synthesis of asparagine from aspartate
3. synthesis of aspartate from asparagine
4. synthesis of purines/ pyrimidines from aspartate
39
how is tyrosine formed from phenylalanine
- phenylalanine hydroyxylase + cofactor tetrahydrobiopterin
40
how is tetrahydrobiopterin regnerated
- by enzyme dihydropteridine reductase, with one NADPH molecule
41
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
42
enzyme defects in phenylketonuria (3)
- phenylalanine hydroxylase (classical)
- dihydropteridine reductase OR biopterin synthesis (non-classical, related to terahydrobiopterin generation)
43
enzyme defect in tyrosinemia type 1 (1)
- fumarylacetoacetate hydrolase
44
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
45
what enzyme defect causes albinism
- tyrosinase (Cu-dependent Tyr hydroxylase) -> prevents formation of melanin from tyrosine
46
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
47
how to synthesize a primary amine from an amino acid
- decarboxylation using an enzyme decarboxylase
48
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)
49
what are some examples of polyamines
- putrescine, spermidine, spermine
50
functions of polyamines
- polycationic -> can interact with nucleic acids (polyanions) by binding to phosphate groups -> DNA stabilization & packaging
- cell growth and proliferation
51
is methionine needed for polyamines synthesis
yes. need methionine to form S-adenosylmethionine
52
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
53
what happens to creatine phosphate that is stored and not used
- broken up over time -> to form creatinine which is excreted
54
nitrogen substances excreted by body
- urea: 30g
- creatinine: 1-1.8g
- NH4+: 0.7g
- uric acid: 0.5-1g
55
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)
56
how does caffeine keep us awake
- caffeine are purine derivatives
- binds and inhibits phosphodiesterase -> prevents breakdown of cyclic AMP -> cyclic AMP keeps us awake
57
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
58
two important nucleotides to know
- SAM (S-adenosylmethionine) -> METHYL donor
- PAPS (3'-phosphoadenosine 5'-phosphosulphate) -> SULFUR donor
59
steps in the biosynthesis of purine nucleotides
1. converting ribose-5-phosphate to PRPP (ATP dependent)
2. de novo pathway
3. formation of AMP and GMP from IMP
4. formation of purine ribonucleoside triphosphate
60
how is the conversion of ribose-5-phosphate to PRPP regulated
- regulation of PRPP synthetase (activated by Pi, inhibited by purine ribonucleotides)
61
what is the de novo pathway in purine nucleotide synthesis
- pathway that converts PRPP to IMP
62
how is the de novo pathway in purine nucleotide synthesis regulated
- glutamine-PRPP amidotransferase upregulated by PRPP, inhibited by AMP, GMP
63
how is the synthesis of AMP/ GMP from IMP regulated
- end product inhibition
64
function of purine salvage pathways
- recover catabolised free nitrogenous bases and incorporate them into purine synthesis by binding to PRPP
65
bases involved in purine salvage pathways
catalysed by HGPRT
- hypoxanthine + PRPP -> IMP
- guanine + PRPP -> GMP
catalysed by APRT
- adenine + PRPP-> AMP
66
how is pyrimidine nucleotide synthesis regulated
- CPS II inhibited by end product UTP
- OMPDC (orotidine 5-monophosphate decarboxylase) inhibited by end product UMP
67
bases involved in pyrimidine salvage reactions
catalysed by ribose 1-phosphate
- uracil, cytosine -> uridine, cytidine
catalysed by deoxyribose 1-phosphate
- thymine -> thymidine
68
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
69
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)
70
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)
71
purpose of 1:1:1:1 ratio of deoxyribonucleotide pdn by ribonucleotide reductase
- equal amount of each building block -> prevents mutations
72
what is the FINAL END PRODUCT of all purine catabolism (AMP, IMP, XMP, GMP)
- URIC ACID
73
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
74
diseases related to purine metabolism (4)
- lesch-nyhan syndrome
- gout
- von Gierke's glycogen storage disease
- SCID
75
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
76
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
77
treatment of gout
- colchicine -> anti-inflammatory
OR
- allopurinol -> hypoxanthine analogue & inhibitor of xanthine oxidase + inhibits PRPP amidotransferase activity
78
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
79
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
80
diseases related to pyrimidine metabolism
- orotic aciduria
81
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
82
how to treat orotic aciduria
- supply uridine or cytidine
- use salvage enzyme to bypass pyrimidine de novo pathway
