Unit 3 Flashcards
Describe how proteins are broken down to AAs in the gut and tissues
- proteins are broken down by peptidases that are activated in the gut into AAs –> absorbed –> enter circulation
- two pathways for breakdown: ubiquination and lysosomes
Describe the flow of nitrogen from an AA to urea
- AA donates an NH2 to an alpha-ketoglutarate (by AT) to make L-glutamate + keto acid
- released as NH3 from glutamate, which regenerates the alpha-ketoglutarate
- urea cycle occurs in liver
- glutamate, NH3, and aspartate enter urea cycle
- NH3 from transamination –> carbamoyl phosphate by carbamoyl phosphate synthase 1 (RLS)
- nitrogen in carbamoyl phosphate enters urea cycle, combines with NH3 from aspartate to make urea
- urea is peed out
- AA+alpha-kg –> glutamate + alpha-keto acid –> NH3 –> urea cycle –> urea
List soem of the special issues assoc w sulfur containing, gluconeogenic, ketogenic, branched chain, and aromatic AAs
1) sulfur containing:
- cysteine and methionine
- disulfide bridges
- S-adenosylmethionine is important energy source for wound healing, vascular disease, and B12
- glutathione containse cysteine and is protective agaisnt ROS
2) branched chain:
- require special enzymes for breakdown
- def can lead to MSUD
3) aromatic:
- precursors for 5HT, niacin, dopamine, NE, epi, tetrahydrobiopterin, and thyroid hormone
Ways to categorize AAs
1) chemical properties:
- acidic/basic
- polora/non-polar
2) synthesis ability of body:
- essential: body can’t make
- non-essential: body can make
- conditionally essential: limited capacity for body to make
3) chem constituents:
- sulfur containing
- nitrogen side chain
- branched chain
- aromatic
4) energy needs:
- glucogenic: for gluconeogenesis
- ketogenic: make acetylCoA –> make ATP through TCAC or make ketones
Pathways for protein degradation
1) ubiquination in proteasomes
2) lysosomes
Pathways for protein degradation
1) ubiquination in proteasomes
2) lysosomes
Transamination
- for gluconeo, NH2 of AA needs to be removed
- for carbon skeleton to AA, need to add NH2
- bidirectional
- in liver
- AA donates NH2 to alpha-ketoglutarate –> L glutamate and alpha-keto acid (catalyzed by aminotransferase) –> NH3 released and alpha-ketoglutarate made again
Urea cycle
- NH3 from transamination converted to carbamoyl phosphate from carbamoyl phosphate synthase 1 (RLS)
- CP enters urea cycle and combines with NH3 from aspartate –> make urea which is peed out as urea nitrogen
- urine nitrogen as urea measures AA catabolism
- glutamine accepts N from other AAs –> brings to liver and kidney and donates to glutamate –> alpha-ketoglutarate (catalyze by glutamate dehydrogenase) (RLS)
Recognize the 20 AAs and list examples of post-translational mods
- each AA has their own tRNA
- examples:
1) collagen: triple helix with hydroxyproline and hydroxylysine - Hyp –> H-bonding in collagen to inc strength; prolyl hydroxylase converts Pro to Hyp
- Hyl –> crosslinks; lysyl hydroxylase coverts Lys to Hyl
- PH and LH rely on vitC
2) g-Carboxyglutamate (Gla): target proteins to membranes via Ca chelation
- G-glytamyl carboxylase converts Glu to Gla and required vitK
Describe scurvy
- vitamin C deficiency –> reduced collagen strength because of failure of post-trans mods of Hyp and Hyl
Describe cellular aspects of protein degradation and proteases involved in protein degradation
1) ubiquitin-proteasome:
- ATP-dep
- crosslink protein to ubiquitin –> sequestered to proteasome that has proteolytic activity
2) lysosome:
- ATP-indep
- engulf EC proteins
- broken down by acid hydrolysis
- proteases are in proenzyme form usually
1) pepsinongen –> pepsin by HCl to cleave proteins
2) enteropeptidase cleaves trypsinogen to trypsin
3) trypsinogen cleaved to trypsin –> cleaves all other zymogens in SI (chymotrypsinogen, procarboxypeptidase)
Describe transamination and list liver damage markers
- aminotransferase transfers amino groups
- converts alpha-keto acid to corresponding AA and also does reverse
- Keq is about 1
- reversible
- 100s of ATs for 20 AAs
- ATs move N to Asp and NH3 for urea cycle
- alanine aminotransferase (ALT) and aspartate aminotransferase (AST)
- PLP (pyridoxal phosphate) is a derivated of vitB6: used by ATs to hold/transfer amino groups
Describe the control points for the urea cycle
- carbamoyl phosphate synthase1 (CPS1)
- N-acetyl glutamate (formed by N-acetylglutamate synthase act by arginine) act CPS1
List the means of NH3 transport in the blood
- cannot be transported in blood, so rely on urea
- glutamine holds 2 NH3 groups
- GDH is a control pt for protein metabolism to remove N or add to AAs
- glutamine synthase converts glutamate to glutamine for transport to liver and entry into urea cycl
- in muscle, use alanine instead of glutamine for transport in alanine-glucose cycle
- in muscle, pyruvate –> alanine by transamination and in liver, alanine –> pyruvate by transamination and use it for gluconeo
Explain the difference between ketogenic and glucogenic AAs
- depends on outcome of keto acid
- glucogenic: makes pyruvate or TCAC intermediates (OAA from aspartate transam)
- ketogenic: no net prod of glucose (lysine and leucine breakdown gives acetylCoA)
Describe urea cycle disorders, hyperammonemia, MSUD
Hyperammonemia:
- elevated NH3 in blood due to UC enzyme defects –> inhibition of TCAC
- encephalopathy, coma, death
- asterixis
- limit protein intake
- give lactulose and trap NH4
MSUD:
- inc BCAAs (leucine, valine, isoleucine)
- BCAA –> deaminated to alpha-keto acid –> decarboxylated to succinlCoA or acetylCoA
Describe thyroid chemistry and understand how thyroxin is produced
- tyrosine makes T4 which is converted to T3
- TSH stimulated iodide uptake and stim release of T4 and T3
- thyroid peroxidase: oxidizes iodide to I2
- thyroglobulin: contains Tyr residues iodinated to form T4 and T3
- Thyroxin binding globulin: transport T4 and T3
- T4 (deiodinase) –> T3, which is a more active form of thyroxin with one less iodine
- T4 and T3 transported from thyroid through blood via TBG
Describe heme metabolism and porphyrias
- porphyrins are cyclic molecules of 4 pyroles made in liver
- pyrole –> bilirubin –> porphyrin
- bind Fe2+
- porphyrin synthesis:
1) gly + succinylCoA –> gamma-aminolevulinic (ALA) acid (by gamma-aminolevulinate synthase)
2) 2xALA –> porphobilinogen (by gamma-aminolevulinate dehydratase)
3) porphobilinogen ———> protoporphyrin 4 (by 4 enzymes)
4) protoporphyrin 9 –> heme (by ferrochelatase) - lead inhibits gamma-aminolevulinate dehydratase and ferrochelatase
- degradation: heme –> biliverdin (green) –> bilirubin (red orange) –> bilirubin diglucuronide –> urobilinogen –> stercobilin (brown)
- bilirubin is transported bia albumin to the liver where it is conjugated with glucuronic acid –> bilirbuin diglucuronide (conjugated bilirubin)
- in intestine, bilirbuin diglucuronide is oxidized to stercobilin
Urea cycle components
1) ornitihine –> citrulline:
- by carbamoyl phosphate synthetase 1
2) cirtulline + aspartate –> arginosuccinate
- by argininosuccinate synthase
3) argininosuccinate –> arginate
- by argininosuccinate lyase
4) arginine –> ornithine + urea
- by arginase
Carbamoyl phosphate synthetase 1
- found in mito
- bicarb + NH3 –> carbamoyl phosphate
- this rxn uses 2 ATPs
- N-acetylglutamate allosterically activates CPS1
- arginine activates N-acetylglutamate synthase which converts acetylCoA+glutamate –> N-acetylglutamate
Carbamoyl phosphate synthetase 1
- found in mito
- bicarb + NH3 –> carbamoyl phosphate
- this rxn uses 2 ATPs
- N-acetylglutamate allosterically activates CPS1
- arginine activates N-acetylglutamate synthase which converts acetylCoA+glutamate –> N-acetylglutamate
Maple Syrup Urine Disease
- when BCaKADHC is deficient –> build up of alpha-keto acids in urine
What are the 2 entry points of N into the urea cycle?
1) NH3 from glutamate by GDH –> free NH3 and an alpha-ketoglutarate; NH3 combines with CO2 to make carbamoyl phosphate
2) OAA converted to aspartate via transam and enters after citrulline
What is the key RLS of entry of N into the urea cycle and its allosteric activation?
Glutamate –> alpha-ketoglutarate + NH3 (by GDH)
- act by ADP and GDP
- inh by ATP and GTP
List the sulfur containing AAs
Methionine:
- essential AA
Cysteine:
- unessential AA
- ## sulfur plays important role in disulfide bonds for membrane receptors
Describe the biological utility of Cys in regard to its ox state (alone or within GSH)
- forms disulfides with other cys
- GSH is a tripeptide that controls redox potential vis GSH –> GSSG where cysteine is important
- the oxidized form makes disulfide bonds for structural integrity of proteins
- reduced form occurs when bonds are broken
Describe Met, its relation to SAM and the energy provided in SAM
- Met + ATP by SAM synthase –> SAM
- met produces S-adenosylmethionine (SAM) which is high energy storage unit in the form of a methyl group
- SAM produced in first step of methionine degradation –> converted to S-adenosylhomocysteine (SAH)
- SAM is involved in methylation, epigenetics, etc.
- SAM turns NE into epi and methylates cystein residues
Describe where vitamins are used in Cys, Met metabolism: Folate, B6, B12
- B12 and THF in converting homocysteine to Met
- B6 in converting homocystein + serine –> cystathionine –> cysteine
List biologically important molecules derived from Trp metabolism
- glucogenic and ketogenic
- makes serotonin (NTs), melatonin (hormone), niacin (vitamin)
Describe diseases related to Pre, Tyr metabolism: Phenylketonuria (PKU), tyrosinemia, parkinson’s, and the use of MAOis
a
Hyperhomocysteinemia
- inc homocysteine levels –> lots of problems including CV disease
- due to dec folate, B6, B12
- Cys is essential
- treat with folate, B6, B12
Homocystinuria
- defect in cystathionine-b-synthase (CBS)
- cannot convert homocysteine to cystathionine (and eventually cysteine)
- mental retardation, osteoporosis, and vascular disease
- cysteine is essential
- treat with vitB6 to force CBS to work
Cysteinuria
- kidney stones
- due to defect in transporter of cysteine (and ornithine, lysine, and arginine) –> crystallization in urea
- treat with acetazolamide which makes cysteine more soluble
Cysteinuria
- kidney stones
- due to defect in transporter of cysteine (and ornithine, lysine, and arginine) –> crystallization in urea
- treat with acetazolamide which makes cysteine more soluble
Cofactors for transferring carbons
- SAM
- THF from bacteria and folate
GSH as a redox buffer
- GSH is very soluble
- thiol acts as redox buffer to maintain proteins in reduced forms and regulate activity
- cofactor for several enzymes
- reduce H2O2 to H2O and general protection against ROS
Trp metabolism
- Trp metabolized to pyruvate or acetylCoA
- first hydroxylated by tryptophan hydroxylase using BH4 as a cofactor
- Trp used to make 5HT, melatonin, and niacin
Phenylketonuria
- defect in phenylalanine hydroxylase –> build up of byproducts (phenyllactate, phenylacetate, phenylpyruvate)
- smell bad with phenylacetate
Tyrosinemias
- defects in tyrosine degrad
- 3 types
- hydroxylation of tyrosine to catecholamines is ok, but decarboxylating aromatic AA is defective
Tyroseinemias
- defects in tyrosine degrad
- 3 types
GSH as a reducing agent and SH buffer
- GSH is a product of PPP/HMS
- allows formation, breakage, and reformation of disulfide bonds for correct protein folding
- GSH is more soluble than cys
THF
- made during regen of Met from homocysteine
- from vitB9
- needed for synthesis of AAs and nucleic acids
- SAM only donates methyl groups, but THF can donate CH2, CH=NH, and CH=O as well
Conversion of Met to homocystein back to met
met –> SAM (by SAM synthetase) –> SAH (by methyltransferases) –> homocysteine (by adoHcy hydrolase) –> methionine (by methionine synthase + B12+THF)
ID the sources of atoms in purine and pyrimidine bases, the key cofactors, and the sources of energy involved in de novo synth
Source of atoms:
- purines: AAs - Glu, Gly, Asp; THF, CO2
- pyrimidines: AAs - Glu, Asp; CO2
Cofactors:
- purines: THF, ATP, CO2, AAs
- pyrimidines: ATP, CO2, PPRP
Energy source:
- purines: AMP and GMP (to make these requires GTP and ATP respectively)
- pyrimidines: UDP and CTP (both require ATP)
List the key differences between the synth of purine and pyrimidine nucleotides
1) source of base:
- purines build base on sugar
- pyrimidines make base separately then add base to sugar
2) source of atoms:
- purines: Glu, Gly, Asp; THF, CO2
- pyrimidines: Glu, Asp, CO2
3) intermediates:
- purines: IMP –> GMP or AMP
- pyrimidines: UMP –> UDP –> UTP –> CTP
Name the key regulated steps and feedback loops within the de novo purine and pyrimidine synth and degrad pathways
Purine - regulated steps:
1) ribose 5’ phosphate –> PRPP
- catalyzed by PRPP synthase
- ribose 5’ phosphate from HMP
- act by Pi, inh by AMP, GMP, IMP
2) PRPP+glutamine –> 5 phosphoribosylamine
- catalyzed by glutamine phosphoribosyl pyrophosphate amidotransferase (GPPAT)
- IMP, GMP, AMP inh early enzymes
- act by PRPP
Pyrimidine - regulated steps:
1) 2ATP+CO2+glutamine –> carbamoyl phosphate
- catalyzed by CPS2
- act by PRPP and ATP
- inact by UTP, UDP
2) feedback:
- UMP –> UDP –> UTP –> CTP
- UTP inact CPS2
ID the enzyme that reduces ribose to deoxyribose, describe the regulation of this enzyme, and name its substrates
- ribonucleotide reductase
- substrates are diphosphates ADP, GDP, CDP, UDP
- UDP –> dUDP –> dephos to dUMP –> dTMP by thymidylate synthase –> dTDP and dTTP by kinases; uses THF as cofactor
- regulation: dATP turns off, ATP turns on
- can specify which dNTP needs to be made
Describe how 5-fluorouracil and similar drugs inhibit nucleotide synth
- 5-fluorouracil: pyrimidine analog that inh thymidylate synthase –> dec dTMP –> failure of cells to divide; anti cancer
- methotrexate: folic acid analog –> inh dihydrofolate reductase –> dec dTMP and protein synth
- 6-mercaptopurine: purine analog, inh AMP synth, block de novo purine synth
- AZT: inhibit viral polymerase
- acyclovir: target viral DNA polymerase and reverse transcriptase
Why is purine and pyrimidine synth important?
1) make DNA and RNA
2) make ATP and GTP
3) make CoA, FAD NAD, NADP
4) make cAMP, cGMP
5) make UDP-glucose for glycogen synth and CDP-diacylglycerol for glycerophospholipid synth
Purine nucleotide synthesis
- start with ribose sugar and then build base on sugar
- *key regulated step: at start when PRPP (which contains ribose) and glutamine are used by glutamine phosphoribosyl pyrophosphaye amidotransferase to add N to PRPP
- second regulated step: conversion of ribose 5’-phosphate to PRPP
- adds AAs and CO2 to growing base and also THF and ATP are important
- first base produced is inosine monophosphate (IMP) –> used to make GMP and AMP
Pyrimidine nucleotide synthesis
- base is not made on ribose sugar; made separately and then added to sugar
- first step is catalyzed by carbamoyl phosphate synthetase 2
- CPS2 is act by PRPP and inh by UTP
- first molecule made is UMP then converted to UTP then converted to CTP by CTP synthase
Pyrimidine nucleotide synthesis
a
Changes in phosphorylation states and conversion of rNDPs to dNDPs
- use kinases to convert NMP to NDP to NTP by taking phosphate from ATP
- ribonucleotide reductase converts ribose to deoxyribose by operating on the NDPs
- RR act by ATP and inact when dATP builds up
- also sensitive to specific dNTPs
Changes in phosphorylation states and conversion of rNDPs to dNDPs
-
De novo synth of dTTP and dCTP
UMP –> UDP –> dUDP –> dUMP –> dTMP –> dTDP –> dTTP
also
UMP –> UDP –> UTP –> CTP –> CDP –> dCDP –> dCMP –> dUMP –> dTMP –> dTDP – dTTP
for dCTP:
UMP –> UDP –> UTP –> CTP –> CDP –> dCDP –> dCTP
Nucleotide degradation
- consume a lot of nucleotides than we need so need to degrade and excrete
- for purines: first remove base from sugar to have adenosine or guanine –> bases are further broken down to uric acid which is peed out –> problems can lead to diseases like gout and SCID
- for pyrimidines: first remove base ring from sugar –> base ring is opened up (no uric acid) –> breakdown base ring to succinylCoA, malonylCoA, and acetylCoA –> water soluble so no problems like in purine degradation
Salvage pathways
- reuse partially degraded nucleotides to make nucleotides
- takes free bases and attaches them to ribose sugar in the form of PRPP
SCID
- sever combine immunodeficiency syndrome
- mutation in gene encoding adenosine deaminase –> defect in purine degrad –> buildup of dATP –> inh ribonucleotide reductase –> prevent dNTP production –> affects rapidly proliferating cells most (lymphocytes, epithelial cells, mucous cells)
- treat with gene therapy
- occurs in kids
Gout
- build up of uric acid in blood –> deposition of monosodium urate crystals in joints
- usually due to underexcretion of uric acid
- less common is overprod of purines
- RFs: age, meat, seafood
- see negatively birefringent yellow crystals under parallel light
- result of purine degrad
Lesch-Nyhan syndrome
- deficiency in one of the primary enzymes in purine salvage pathway (HGPRT) –> inc rates of de novo synth of purines and inc PRPP because defect in salvage pathway –> inc degradation –> see gout symptoms, self-mutilating behavior, and other mental probs
- X-linked rec
Lesch-Nyhan syndrome
- deficiency in one of the primary enzymes in purine salvage pathway (HGPRT) –> inc rates of de novo synth of purines –> see gout symptoms, self-mutilating behavior, and other mental probs
Drugs for nucleotide synth and degrad
1) methotrexate and 5-florouracil:
2) 6-mercaptopurine:-
3) azidothymine (AZT):
4) cytosine arabinoside (araC)
5) acyclovir (ACV)
6) acivicin
methotrexate and 5-florouracil
- targets thymidylate synthase/folate metabolism cycle
- anti cancer
6-mercaptopurine
- inh AMP synth
- anti cancer
azidothymine (AZT)
- inh viral polymerase
- anti HIV
cytosine arabinoside (araC)
- targets DNA polymerase
- anti leukemia
acyclovir (ACV)
- targets viral DNA polymerase and reverse transcriptase
- anti HSV
acivicin
- Gln analog
- inh nucleotide synth, mostly GMP
- anti cancer
PKU
- def of phenylalanine hydroxylase –> build up of phenylalanine –> irreversible intellectual disability
- AR inheritance
- 6Ms: microcephaly, (epilepsy), mentally retarded, mischievous, musty body odor, dec myelin formation, dec monoamines
- diagnosis: newborn screening (BIA, flurometric, MS) for inc phenylalanine >120 and normal BH4
- management: low protein diet and restrict phe, BH4 supplement; supplement with LNAA transporters; prevent in pregnant women
- symptoms: microcephaly, epilepsy, intellectual disability, behavior problems, musty body odor, eczema
- dec melanin, dec catecholamine synth
Maple Syrup Urine Disease
- maple syrup odor in cerumen/urine after birth
- inc BCAAs due to def degradation (def BCKAD)
- ketonuria
- irritability, lethargy, neuro problems
- poor feeding in 2-3days
- diagnosis: clinical features, dec BCKAD, inc BCAAs and alpha-keto acids, genetic testing
- management: dietary restriction of BCAAs, give sufficient calories, insulin, AAs for protein synth, thiamine supplement
- AR inheritance
Tyrosinemia type 1
- young infants
- liver problems in 1st year, renal problems, growth failure, rickets
- neuro probs, neuropathy, abd pain, resp failure
- treat with nitisinone and low tyrosine diet, dec intake of phe and tyr, liver transplant for children
- due to def of FAH
- see inc succinylacetone in blood and urine
- inc tyr, met, phe in plasma
- inc tyr metabolites and gamma-ALA
- genetic testing for FAH mutations
Classical homocystinuria
- caused by defect in CBS
- see intellectual disability, myopia, skeletal abnormalities, thromboembolism
- marfanoid habitus
- prone to bone problems
- diagnosis: inc plasma homocystine, total homocystine, homocystein-cysteine mixed disulfide, and met
- inc urine homocystine
- dec CBS activity
- genetic testing for CBS mutations
- management: dec met, inc cysteine, inc B12 and folate, give B6 if responsive
- control homocysteine concentrations and prevent thrombosis
Urea Cycle Disorders
- defect in enzymes lead to accumulation of NH3 in first few days of life
- rapidly develop cerebral edema, lethargy, anorexia, seizures, etc.
- diagnosis: plasma NH3 >150 with normal anion gap and normal glucose –> UCD
- measure orotic acid for specific UCDs
- can be def in CPS2, ASS, ASL, NAGS, OTC, or ARG
- AR inheritance (OTC is X-linked)
- treatment: dialysis and hemofiltration to dec Nh3, IV arginine hydrochloride and N scavenger drugs for alternative N excretion; restrict protein
- if not treated –> cerebral edema, lethargy, anorexia, hyper/hypoventilation –> resp alkalosis, hypothermia, seizures, coma
- initial signs: failure to feed, loss of thermoregulation, low temp, somnolence
CPS1 deficiency
- most severe of UCDs
- hyperammonemia in newborn period