Biochem Flashcards
Phase during which DNA and histones are synthesized
S phase
Amino acids necessary for purine synthesis
Glycine, aspartate, glutamine (also folate)
Cytosine –> Uracil –> Thymine
Deamination –> Methylation
Bond with 3 H bonds
G-C
End of incoming nucleotide with triphosphate, attacking_____
5’ attacking 3’ OH
Nucleotides with two rings
Purines (AG)
CPS II
Initiates de novo pyrimidine pathway, part of CAD
CAD
CPS II, aspartate transcarbamoylase, dihydroorotase
CPSI vs CPS II (location, pathways, source of nitrogen, regulation)
1: Mitochondria, urea cycle, ammonia, activated by N-acetylgluatmate; 2: cytoplasm, pyrimidine synthesis, inhibited by UTP and activated by ATP
Leflunomide MOA
inhibitis dihydroorotate dehyndrogenase (carbamoyl phosphate + aspartate –> orotic acid), part of de novo pyrimidine pathway
Methotrexate and the drugs that act like it MOA
Methotrexate (human), TMP (bacteria), pyrimethamine (protozoa) – inhibit dihydrofolate reductase –> less dTMP, part of de novo pyrimidine pathway
Orotic aciduria
Defect in pyrimidine synthesis, UMPS deficiency (orotic acid –> UMP), megaloblastic anemia refractory to B9/B12, normal BUN/ammonia
Hydroxyurea MOA
Inhibits purine AND pyrimidine synthesis via ribonucleotide reductase (reduces 2’ carbon of ribose to make DP–>dDP)
5-FU MOA
Inhibits pyrimidine synthesis by forming 5-f-dUMP –> inhibits thymidylate synthase
6-MP/Azathiprine MOA
Disrupts de novo purine synthesis (PRPP——–>IMP)
Mycophenolate and ribavirin MOA
Inhibit inosine monophosphate dehydrogenase –> less GMP
Amino acids necessary for pyrimidine base production
Aspartate
HGPRT Function
Purine salvage, guanine/hypoxanthine –> GMP, IMP
HGPRT deficiency
Lesch Nyhan – Excess uric acid and de novo purine synthesis, x-linked recessive, sx: intellectual disability, self-mutilation/agression, hyperuricemia (orange “sand” MSU crystals in diaper), gout, dystonia; tx: allopurinol (febuxostat)
ADA fxn and deficiency disorder
Fxn: Degrades adenosine –> inosine; Disorder: SCID, –> leads to accumulation of dATP which inhibits ribonucleotide reductase, buildup of dNTPs –> toxic to lymphs, autosomal recessive
Amino acids with only one codon
Methionine and tryptophan (AUG, UGG)
of origins of replication
Bacteria: 1, humans: multiple
TATA box fxn
Origin of replication/promoters
Helicase mutation
Bloom syndrome – autosomal recessive, short stature, predisposition to cancer/genomic instability
Irenotecan/topotecan MOA
Inhibit topoisomerase I
Etoposide/teniposide MOA
Inhibit topoisomerase II
Fluoroquinolones MOA
Inhibit prokaryotic topoisomerase II (DNA gyrase) and topoisomerase IV
DNA Polymerase III (E/P, synthesis/prooreading)
P only, 5’–>3’ synthesis and 3’–>5’ exonuclease proofreading
DNA Polymerase I (E/P, synthesis/proofreading)
P only, degrades RNA primer to replace with DNA –> 5’–>3’ exonuclease (backwards from normal)
Telomerase is a ________
RNA dependent DNA polymerase (avoid loss genetic material with replication)
Transition
Purine to purine mutation or pyrimidine to pyrimidine
Transversion
Purine to pyrimidine or vice versa mutation
Missense
Nucleotide substitution –> changed amino acid (e.g. glutamic acid –> valine in sickle cell(
Nonsense
Nucleotide substitution –> early stop codon (UAG, UAA, UGA) –> nonfxnal protein
Examples of frameshift mutation diseases
DMD, Tay-Sachs
Splice site mutation
Retain intron in mRNA–> impaired/altered protein fxn (as in some cancers, dementia, epilepsy, beta-thal)
Base excision repair
Base specific glycosylase removes base –> apurinic/apyrimidinic site –> endonuclease removes backbone at 5’ end, lyase at 3’ end –> DNA polymerase beta fixes; throughout cell cycle; fixes spontaneous/toxic deamination
Nucleotide excision repair
Endonuclease cuts chunk of DNA out –> DNA polymerase and ligase fix hole, only during G1; for bulky-helix distorting lesions (e.g. pyrimidine dimers from sunlight – this is defective in xeroderma pigementosum –> BCC and other skin CA)
Mismatch repair
Newly synthesized strand mismatches removed in G2, defective in Lynch syndrome (defective 3’–>5’ endonuclease activity)
Start codon E/P
AUG (methonine for E, fMet for P –> neutrophil chemotaxis)
Stop codons
UGA, UAA, UAG
RNA polymerase I
Makes rRNA
RNA polymerase II
Makes mRNA –> inhibited by a-amanitin in amanita phalloides –> severe hepatotoxicity
RNA polymerase III
tRNA, 5’ rRNA
Drugs that inhibit RNA polymerases
E/P – actinomycin D, P only – rifampin
Nuclear processing of RNA
- 5’ capping (7-methylguanosine), 2. PolyA of 3’ end, 3. Splicing of introns
Fxn of SnRNPs
Splicing of pre-mRNA
Abs to SnRNPs
Anti-smith – SLE
Anti-U1 RNP ab
Mixed connective tissue disease
miRNA fxn
Post-transcriptional gene expression regulation (target 3’ UTR of mRNAs for degradation or repression) –> can cause malignancies
Where does amino acid bind on tRNA?
CCA 3’ end opposite to anticodon (acceptor stem)
T-arm of RNA
TYC – ribothymidine, pseudouricine, cytidine –> tRNA ribosome binding (tethers)
D arm of RNA
has D (dihydrouridine) residues for tRNA recognition by correct aminoacyl tRNA synthetase (detects)
What initiates protein synthesis?
GTP hydrolysis
MYC fxn
GF –> TKr –> MYC formed –> MYC-MAX heterodimers –> bind DNA –> modulate genes promoting cell division; downregulated by MAX homodimers or MAD-MAX heterodimers; MYC accumulation where nutrient deprived or DNA damage –> apopotosis
Cell Cyle G0/G1
RB is not heavily phosphorylated – holds onto E2F
Cell Cycle G1
Cyclin D synthesized –> CDK/cD complexes –> hypophos of Rb and formation of cE –> CDK/cE complexes (cE COMPLEXES – loss of dependency on growth factor – restriction point) –> hyperphos of Rb –> E2F dissociation –> transcription of E2F genes essential for S phase (e.g. cA)
Cell Cycle S
Nuclear DNA replication; cA synthesis –> CDK/cA complexes –> activate DNA polymerase
Cell Cycle G2
Prep for cell division (syntehsize microtubules/new membranes, etc.); synthesis of cB –> CDK/cB complexes
Cell Cycle M
cB/CDK –> nuclear localization –> starts mitosis; at completion, phosphate removed from Rb
G1/S Checkpoint
DNA damage –> p53 activation –> up-regs CDKN1A gene –> increased p21 which inhibits CDKs and stimulates DNA repair; if repair successful –> p-52 induces self-degradation –> resume cell cycle; if repair unsuccessful –> p-53 induces pro-apoptotic genes (BAX) and represses pro-proliferative/anti-apoptotic genes (e.g. cyclins and BCL2) –> apoptosis
G2/M Checkpoints
Check for DNA damage before separation and after replication; damage –> cell cycle arrest via p53 and non-p53
Free ribosomes
Synthesize cytosolic and organellar proteins
RER
Synthesize secretory proteins (and add N-linked oligosaccharides)
Golgi additions and modifications
Modifies N-oligos on asparagine; adds O-oligos to serine and threonine, adds M6P for lysosomal trafficking
I-Cell disease
Deficient N-acetylglucoaminyl-`-phophotransferase –> goligi doesn’t phosphorylate mannose to traffic to lysosome –> proteins secreted into ECM –> coarse facial features, clouded corneas, restricted joint movement (like hurlers but worse) –> fatal in childhood
COPI
cis-golgi –> RER
COPII
RER –> cis-golgi
Clathrin
Plasma membrane –>endosome or trans-golgi –> lysosomes
Peroxisome
breakes down very long chain fatty acids, branched chain fatty acids, amino acids, and ethanol
Zellweger syndrome
Hypotonia, seizures, hepatomegaly, early death (peroxisomal disease)
Refsum disease
Scaly skin, ataxia, cataracts/night blindness, shortening of 4th tow, epiphyseal dysplasia (peroxisomal disease)
Vimentin
Mesenchymal tissue IF –> mesenchymal tumors (sarcoma) and endometrial carcinoma, renal cell carcinoma, meningioma
Desmin
Muscle tissue IF –> muscle tumors (e.g. rhabdomyosarcoma)
Cytokeratin
Epithelial cell IF –> epithelial tumors (e.g. SCC)
GFAP
Neuroglia IF –> Astrocytoma, glioblastoma
Neurofilaments
Neuron IF –> neuronal tumors (e.g. neuroblastoma)
Dynein
Retrograde transport (DIES away from synapse), +–>- NEGATIVE NUCLEUS
Kinesin
Anterograde transport (KINETIC towards synapse) - –> + POSITIVE PERIPHERY
Drugs that act on microtubules
Mebendazole (antihelminth), griseofulvin (antifungal), colchicine (antigout), vincristine/vinblastine (anticancer), paclitaxel (anticancer)
Kartagener syndrome
Primary ciliary dyskinesia – immotile cilia due to dynein arm defect; sx: decreased male/female fertility (immotile sperm, dysfxnal fallopian tube cilia), increased risk ectopic pregnancy, bronchiectasis, recurrent sinusitis, chronic ear infxns, conductive hearing loss, situs inversus
Ouabain
Inhibits Na/K ATPase by binding K+ site
Digoxin
Directly inhibits Na/K ATPase –> indirectly inhibits Na/Ca exhchange –> increased intracellular Ca –> increased contractility
Type I Collagen – location and disorder
bONE, skin, tendon, dentin, fascia, cornea, wound repair; osteogenesis imperfecta type I
Type II Collagen
Cartilage (hyaline), vitreous body, nucleus pulposus
Type III collagen – location and disorder
Aka reticulin – skin, blood vessels, uterus, fetal tissue, granulation tissue; vascular type III ehlers danlos
Type IV Collagen – location and disorder
Basement membrane, basal lamina, lens; defective in Alport, autoab target in Goodpasture
Collagen synthesis
Translation preprocollagen (Gly-XY – proline/lysine) –> hydroxylation of proline/lysine using vitamin C –> glycosylation of hydroxylated lysine and formation of procollagen via hydrogen/disulfide bonds (triple helix of collagen alpha chains) –> exocytosed into EXM –> cleavage of disulfide rich terminal regions into insoluble tropocollagen –> crosslinking via Cu containing lysl oxidase –> fibrils –> combine to make fibers
Osteogenesis imperfecta genes
COL1A1 and COL1A2, usually autosomal domninant
Osteogenesis imperfecta sx
Blue sclerae (translucent connective tissue), tooth abnormalities – wear easily because little dentin, multiple fractures w/ little trauma, hearing loss (abnormal ossicles) BITE
Ehlers Danlos (w/ types)
AD Faulty collagen synthesis –> easy bruising, hypermobile joints; joint dislocation, aortic aneurysms, organ rupture
Hypermobility – most common,
Classical (joint and skin) – defect in typeV collagen (COL5A1, COL5A2)
Vascular (vascular and organ rupture) – deficient type III collagen
Menckes disease
XLr – impaired copper absorption/transport – defective Menkes protein (ATP7A) –> less lysyl oxidase cross linking –> brittle kinky hair, growth retardation, hypotonia
Marfans
AD disorder, FBN1 gene mutation on chr 15 –> defective fibrillin scaffolding for elastin; sx: tall w/ long extremities, pectus carinatum/excavatum, hypermobile joints, arachnodactyly, cystic medial necrosis of aorta–> dissetive aortic aneurysms and aortic incompetence, floppy mitral valve, subluxation of lenses up and out
Southern Blot
DNA
Northern blot
RNA (mRNA – gene expression)
Western Blot
Protein
Southwestern blot
DNA binding proteins (e.g. transciption factors) using oligonucleotide probes
Flow cytometry
Detection of size, granularity, protein expression (immunophenotype)
Microarray
Can detect single nucleotide polymorphisms and copy number variations
ELISA
Detection of antigen or ab in sample (verify with western blot)
Karyotyping
Diagnose chromosomal imbalances (autosomal trisomies, sex chromosome disorders)
FISH
Detects microdeletion (no fluoresence), translocation (signal corresponds to that of another chromosome), duplication (extra signal relative to homologous chromosome)
Alpha 1 antitrypsin def
SERPINA1 on chr14, normal is PiMM, abnormal is PiZZ; codominant
McCune Albright – cause, sx and what makes it livable
Caused by mutation in G-protein signalling; sx: unilateral cafe au lait spots, polyostotic fibrous dyplasia, at least one endocrinopathy; livable because of mosaicism (otherwise lethal)
Locus heterogeneity
Mutations at DIFFERENT LOCI produce similar phenotype
Alleleic heterogeneity
DIFFERENT MUTATION at SAME LOCUS produce same phenotype
Heterodisomy error
Meiosis I – heteozygous from one parent
Isodisomy error
Meiosis II or post-zygotic chromosomal duplication– homozygous from one parent
Hardy-Weinberg equations
- p^2+2pq+q^2 = 1
- p+q=1
p^2: freq. of homozygosity for allele A
2pq: frew of heterozygosity (carrier freq. if autosomal recessive)
q^2: freq. of homozygosity for allele a
Hardy Weinberg for X-linked recessive
Females: q^2, males: q
Hardy Weinberg assumptions
- No mutation occurring at the locus
2 Natural selection is not occuring - Completely random mating
- No net migration
Prader Willi
Chr 15 PATERNAL deletion/mutation (maternally imprinted) or maternal uniparental disomy; sx: hyperphagia, obesity, intellectual disability, hypergonadism, hypotonia
Angelman syndrome
Chr 15 MATERNAL deletion/mutation (paternally imprinted) or paternal uniparental disomy; sx: inappropriate laughter, seizures, ataxia, severe intellectual diability
Autosomal dominant
structural genes, pleiotropic, variably expressive
Autosomal recessive
Enzyme deficiencies, more severe
Hypophosphatemic rickets
(Vit D resistant rickets), X-linked dominant, increased phosphate wasting at PCT –> rickets-like presentation;
X linked dominant
Hypophosphatemic rickets, Alport, fragile X
Mitochondrial inheritance often variable in expression because of ______________
Heteroplasmy
Cystic fibrosis genetics
AR, CFTR on chr 7 (most commonly deletion of Phe508)
CFTR gene product
ATP-gated Cl- channel that secretees Cl- in lungs and GI tract and reabsorbs in sweat gland – mutation –> protein stuck in RER, so less H2O and Cl secretino and increased intracell Cl –> increased Na reabosrption and increased H2O reabsorption –> abnormally thick mucus in lungs/GI tact and more neg. transepithelial potential difference
CF presentation electrolytes
Decreased Cl in sweat, contraction alkalosis, hypokalemia due to ECF H2O and Na losses and concomitant renal K/H wasting
Newborn screen for CF
Increased immunoreactive trypsinogen
Complications of CF
Pulm infxns, pancreatic insufficiency –> malabsorption/steatorrhea/fat-soluble vit def, billiary cirrhosis, liver disease, meconium ilius in newborn; infertility in men (absence of vas deferens) and subfertility in women (mucous thick in cervix), nasal polyps, nail clubbing
Cause of DMD
X linked, framshift or nonsense –> truncated/absent dystrophin –> myofiber damage
Most common cause of death in DMD
Dilated cardiomyopathy
Pathognomonic for DMD
Calf pseudohypertrophy and Gower’s sign (using hands to walk up their legs to stand)
Fxn of dystrophin
Anchor muscle fibers in skeletal and cardiac muscle – connects intracellular actin to transmembrane dystroglycan on the extracellular matrix
Labs in DMD
Increased CK and aldolase
Becker MD
Non-frameshift mutation in dystrophin – less severe than duchenne
Myotonic type 1 MD Genetics and presentation
AD, CTG trinucleotide repeat expansion in DMPK –> abnormal myotonin protein kinase –> myotonia, muscle wasting, cataracts, testicular atrophy, frontal balding, arrhythmia
Fragile X genetics and presentation
X-Dom, trinucleotide CGG repeat in FMR1 gene –> hypermethylation–> decreased expression; inherited intellectual disability/autism, post-pubertal macroorchidism, long face and large jaw, large everted ears, mitral valve prolapse (x-tra large)
Trinucleotide repeat diseases
Huntingtons (CAG), myotonic dystrophy (CTG), fragile x (CGG), Friedreich ataxia (GAA)
Common unbalanced Robertsonian translocation –> DS
14 and 21
First trimester DS
Increased nuchal translucency, hypoplastic nasal bone, decreased serum PAPP-A, increased free b-hCG
Second trimester DS
Decreased AFP, increased bhCG, decreased estriol, increased inhibin A
Edwards Syndrome genetics and sx
Trisomy 18, prominent occiput, rocker-bottom feed, intellectual dis, clenched fists w/ overlapping fingers, low set ears, micrognathia, congenital HD, death by 1yr
Edwards syndrome quad screen
Decreased AFP, bhCG, estriol, and normal inhibin A
Patau syndrome genetics and sx
Trisomy 13, severe intellectual dis, micropthalmia, microcephaly, cleft lip/palate, holoprosencephaly, polydactyly, cutis aplasia, congenital HD, death by 1 yr
Patau 1st tri screen
Decreased free bhCG and PAPP-A
Chr 3 disorders (2)
VHL, renal cell carcinoma
Chr4 disorders (3)
ADPKD (PKD2), achondroplasia, Huntington
Chr5 disorders (2)
Cri-du-chat, FAP
Chr 6 disorder
Hemochromatosis
Chr 7 disorders (2)
Williams syndrome, CF
Chr 9 disorder
Freidrich ataxia
Chr 11 disorders (4)
Wilms tumor, beta-globin gene defects (e.g. sickle cell, beta thalassemia), MEN1
Chr13 disorders (4)
Patau syndrome, Wilson disease, retinoblastoma (RB1), BRCA2
Chr 15 disorders (3)
Angelman, Prader-Willi, Marfan
Chr16 disorders (2)
ADPKD (PKD1), alpha globin defects (a-thalassemia)
Chr 17 disorders (3)
NF-1 (von Recklinghausen), BRCA1, p53
Chr 18 disorder
Edwards
Chr 21 disorder
DS
Chr 22 disorders (2)
NF-2, DiGeorge (22q11)
X Chr disorders (3)
Fragile X, X-linked agammaglobulinemia, Kline felter (XXY)
Common robertsonian translocation chromosomes
Long arms fuse and short arms lost– 13, 14, 15, 21, 22
Cri-du-chat genetics and sx
Microdeletion of short arm of chr 5; microcephaly, mod to severe intellectual dis, high pitched crying/meowing, epicanthal folds, VSD
Williams syndrome genetics and sx
Microdeletion of long arm of chr 7 (includes elastin gene); sx: elfin facies, intellectual dis, hypercalcemia (increased sens to vit D), well-developed verbal skills, extreme friendliness w/ strangers, cardio probs
22q11 deletion syndromes and sx
DiGeorge: thymic, parathyroid, cardiac defects
Velocardiofacial: palate, facial, cardiac defects
Due to aberrant dev of 3/4 branchial pouches
Vit B1 – fxn and def
Thiamine – TPP; cofactor for dehydrogenase enzymes (pyruvate DH linking glycolysis and TCA, akg DH in TCA cycle, transketolase in HMP shunt, branched-chain ketoacid DH); def: impaired glucose breakdown –> ATP depletion made worse by glc infusion – brain/heart affected first (WK syndrome, dry beriberi, wet beriberi) – diagnosed by increased RBC transketolase activity following admin of B1
Vit B2 – fxn and def
Riboflavin – FAD, FMN; cofactors in redox rxn (e.g. succinate DH in TCA) –> 2 ATP; def: cheliosis and corneal vascularization
Vit B3 – fxn and def
Niacin – NAD/NADP; redox rxns, derived from tryptophan w/ B2/B6; def: glossitis, pellagra –> DIARRHEA, DEMENTIA, DERMATITIS)
Vit B5 – fxn and def
Pantothenic acid – CoA; CoA is cofactor for acyl transfers and fatty acid synthase; def: dermatitis, enteritis, alopecia, adrenal insufficiency
Vit B6 – fxn and def
Pyridoxine – PLP; cofactor in transamination, decarboxylation, glycogen phosphorylase, used in synthesis of cystathionine, heme, niacin, histamine, neurotransmitters (5HT, epi, NE, dop, GABA); def: convulsions, hyperirritability, peripheral neuropathy, sideroblastic anemias (impaired hemoglobin synth and iron excess)
Vit B7 – fxn and def
Biotin; cofactor for carboxylation enxymes –
- pyruvate –pyruvate carboxylase–> oxaloacetate
- acetyl-CoA–acetylCoA carboxylase–>malonyl-CoA
- propionyl-CoA–propionyl-CoA carboxylase–>methylmalonyl CoA; def: dermatitis, alopecia, enteritis (caused by abx or excessive egg white ingestion – avidin)
Vit B9 – fxn and def
Folate; converted to THF for 1-C transfer rxns – e.g in synth of DNA and RNA; absorbed in jejunum and small pool in liver; def: macrocytic megaloblastic anemia, hypersegmented PMNs, glossitis, NTD in pregnancy
Vit B12 – fxn and def sx/causes
Cobalamin; cofactor for methonine synthase (CH3 group transfer) and methylmalonyl-CoA mutase – DNA synthesis; def: caused by malabsorption, lack of IF (e.g. pernicious anemia, gastric bypass), absence of terminal ileum, insufficient intake (e.g. veganism) – macrocytic megaloblastic anemia, hypersegmented PMNs, paresthesia and subacute combined degeneration (degen of dorsal columns, lateral corticospinal and spinocerebellar tracts) due to abnormal myelin –> can lead to irreversible nerve damage
Vit C – fxn and def
Ascorbic acid; antioxidant and facilitates iron absorption/collagen hydroxylation, also necessary for dopamine b-hydroxylase (dop–>NE); def: scurvy –> swollen gums, bruising, petechiae, hemarthrosis, anemia, poor wound healing, perifollicular and subperiosteal hemorrhages, corkscrew hair, decreased immune respon – due to collagen synth defect (less osteoid seam because cannot make collagen)
Vit A – fxn and def
Retinol; Dx of epithelial cells into specialized tissue (prevents squamous metaplasia); used to tx measles and APL; def: night blindness, xerosis cutis, keratomalacia, Bitot spots on conjunctiva, immunosuppression
Vit A excess
Acute: NV, vertigo, blurred vision
Chronic: alopecia, dry skin, hepatic tox, enlargement arthralgias, pseudotumor cerebri
Teratogen: cleft palate, cardiac abnormalities
W-K syndrome
Low B1; Confusion, opthalmoplegia, ataxia + confabulation, personality change, memory loss – damage to medial dorsal nuc thalamus and mammillary bodies
Dry beriberi
Low B1; Polyneuritis symmetrical muscle wasting
Wet beriberi
Low B1; high-output cardiac failure (dilated cardiomyopathy), edema
Hartnup disease
AR, deficiency of neutral amino acid transporters in PCT and enterocytes – e.g. tryptophan –> neutral aminoaciduria and less absorption –> less tryptophan for conversion to niacin –> pellagra-like; tx: high-protein diet and nicotinic acid
Vit B3 excess
Facial flushing (induced by prostaglandins – can be reduced by taking aspirin), hyperglycemia, hyperuricemia
Vit B9 def labs
Increased homocysteine, normal MMA
Vit B12 def labs
Increased homocysteine, increased MMA and 2o folate def
Vit C excess
NVD, fatigue, calcium oxalate stones, increase risk of iron tox in those susceptible
Vit D – fxn and def
Calcitriol; increases absorption of Ca and phos – increases bone mineralization at low lvls but increases bone resorption at higher lvls; rickets in kids (genu varum), osteomalacia in adults (bone pain, muscle weakness)
Vit D excess
Hypercalcemia, hypercalciuria, loss of appetite, stupor – seen in granulomatous disease (e.g. sarcoidosis) –> increased activation of vit D by epithelioid macs
Vit E – fxn and def
tocopherol/tocotrienol; antoxidant – protects RBCs and membranes from free radicals; def: hemolytic anemia, acanthocytosis, muscle weakness, posterior column and spinocerebellar tract demyelination
Vit K – fxn and def
phytomenadione, phylloquinone, phytonadione; fxn: activated by epoxide reductase –> reduced form cofactor for gamm carboxylation of glutamic acid on factors 2, 7, 9, 10 prot C/S; synth by intestinal flora (may be low in newborns/after abx–>hemorrhage)
Zinc – fxn and def
Zinc fingers (transcription factor motif); def: delayed wound healing, hypogonadism, decreased adult hair, dysgeusia (sense of taste), anosmia, acrodermatitis enteropathica
Kwashiorkor
Low protein diet –> edema (low oncotic pressure from less liver apoproteins), anemia, fatty liver, skin lesions
Marasmus
Calorie deficient –> muscle wasting
Fomepizole MOA and use
Inhibits alcohol DH; antidote for methanol or ethylene glycol poisoning
Disulfram MOA and use
Inhibits ALDH; used in alcoholism
Alcohol dehydrogenase – first or zero order kinetics?
Zero – same amount eliminated independent of conc.
Alcohol’s effect on NADH and consequences
Increases NADH/NAD:
- pyruvate–>lactate (lactic acidosis)
- Oxaloacetate–>malate (prevents gluconeogenesis –> fasting hypoglycemia)
- Dihydroxyacetone phosphate –> g3p (combines with fatty acids to make trigs –> hepatosteatosis)
- Disfavors TCA production of NADH –> increased use of acetyl-CoA for ketogenesis and lipogenesis (ketoacidosis and hepatosteatosis)
Mitochondrial metabolism
Fatty acid oxidation, acetyl CoA prodxn, TCA cycle, oxidative phosphorylation, ketogenesis
Cytoplasmic metaobolism
Glycolysis, HMP shunt, synthesis of steroids, proteins, FAs, cholesterol, and nucleotides
Mitochondrial AND cytoplasmic metabolism
Heme synth, urea cycle, gluconeogenesis
NAD is used in _____ Processes
Catabolic to make NADH
NADPH is used in ______ processes
Anabolic as a supply of reducing equivalents (product of HMP shunt)
NADPH processes (4)
- anabolic processes
- respiratory burst
- cyt p450 system
- glutahione reductase
Hexokinase vs. glucokinase: Location Km Vmax Insulin induction Feedback inhibition by G6P
Hexokinase:
Most tissues except liver and pancreatic beta cells
Lower Km(higher affinity) –> at lower conc, sequestered into tissue
LowerVmax (less capacity)
Feedback inhibited by G6P (1 rxn in glycolysis)
Glucokinase: Liver and beta cells of pancreas Higher Km (lower affinity) --> at higher conc taken into liver for rxns Higher Vmax (more capacity) Induced by insulin
When is pyruvate DH active and purpose?
Fed state (increased NAD/NADH ratio, increased ADP, increased Ca), link glycolysis and TCA
Pyruvate DH cofactors
(B1235, Lipoic acid) Thiamine, lipoic acid, CoA, FAD, NAD (same as akg DH)
Arsenic poisoning MOA and sx
Inhibits kipoic acid, sx: vomitting, rice water tools, garlic breath, QT prolongation
PDH Complex def
X linked, buildup of pyruvate shunted to lactate (LDH) –> neuro defects, lactic acidosis, increased serum alanine in infancy; tx: increase intake ketogenic nutrients (high fat, high lysine/leucine)
High LDH activity cells
RBC, WBC, kidney medulla, lens, testes, cornea
Fates of pyruvate
- Via ALT to alanine to liver
- Via pyruvate carboxylase to oxaloacetate for gluconeogen or TCA
- Via pyruvate DH for TCA
- Via LDH to lactate (end anaerobic glycolysis)
TCA/Krebs mnemonic
Citrate Is Kreb’s Starting Substrate For Making Oxaloacetate
ETC Inhibitors
1: RotenONE
3: AnTHREE(ti)mycin A
4: CO/CN
RAC
ATP synthase inhibitor
Oligomycin
Uncoupling agents
2,4 Dinitrophenol, aspirin, thermogenin in brown fat
Odd or even chain FA can enter gluconeogenesis
Odd
Can cause hemolytic anemia in G6PD deficiency
Fava beans, sulfonamides, primaquine, anti tuberculosis drugs, infxn
Genetics of G6PD def
African american prevalence, XLr
Cell presentation in G6PD def
Heinz bodies (precipitated hemoglobin) and bite cells (phagocytosis of Heinz bodies)
Essential fructosuria – enzyme, genetics, sx
Defect in fructokinase, Ar, fructose in blood/urine (assymptomatic)
Fructose intolerance – enzyme, genetics, sx
Aldolase B, Ar, F1P accumulation –> less phosphate –> inhibits glycogenolysis and gluconeogenesis; sx after consuming fruit/juice/honey, reducing sugar in urine; sx: hypoglycemia, jaundice, cirrhosis, vomitting – tx by reducing fructose and sucrose in diet
Galactokinase def – enzyme, accumulation, genetics, sx
Galactokinase def (Gal–>G1P), accumulate galicitol, Ar; sx: galactose in blood and urine, infantile cataracts (failure to track objects/develop social smile) – less severe than classic galactosemia
Classic galactosemia – enzyme, genetics, sx, tx
Galactose-1-phosphate uridyltransferase def (Gal1P–>Glu1P); Ar; sx upon feeding: failure to thrive, jaundice, hepatomegaly, infantile cataracts, intellectual disability, E coli sepsis predisposition; tx: exclude galactose and lactose
Tissues that trap glucose via aldose reductase
Lens, retina, kidneys, schwann cells (think diabetic cataracts, retinopathy, nephropathy, peripheral neuropathy)
Lab findings in lactase def
Decrease stool pH, increase breath H content; normal mucosa if heriditary
Essential amino acids
Glucogenic: methionine, histidine, valine
Glucogenic/ketogenic: isoleucine, pheylalanine, threonine, tryptophan
Ketogenic: leucine, lysine
Acidic amino acids
Aspartic acid and glutamic acid (negative charge at body pH)
Basic amino acids
Histidine, lysine, arginine (no charge at body pH)
When are arg and his required?
Growth – in histones to bind negative DNA
Rate limiting in urea cycle & reg
CPSI (upregulated by NAG)
Rate limiting in glycolysis & reg
PFK1 (upregulated by AMP, insulin, F26BP, glucose)
Rate limiting in HMP shunt & reg
G6PD (upregulated by NADP, downregulated by goal – NADPH)
Rate limiting in TCA cycle & reg
Isocitrate DH (upregulated by ADP, downregulated by ATP/NADH – goal)
Rate limiting in gluconeogenesis & reg
F16BPtase (upregulated by ATP, glucagon, citrate, pyruvate)
Rate limiting in glycogenesis & reg
Glycogen synthase (up regulated by G6P, insulin, cortisol)
Rate limiting in glycogeneolysis & reg
Glycogen phosphorylase (upregulated by epinephrine and glucagon)
Rate limiting in de novo pyrimidine synth & reg
CPS II (upregulated by ATP, PRPP; down reg by UTP)
Rate limiting in de novo purine synth & reg
PRPP Amidotransferase (down regulated by AMP, IMP, GMP)
Rate limiting in fatty acid synth & reg
ACC (upregulated by insulin, citrate; down regulated by glucagon and palmitoyl CoA)
Rate limiting in fatty acid ox and reg
Carnitine acyltransferase I (down reg by malonyl CoA)
Rate limiting in ketogenesis
HMG-CoA synthase
Rate limiting in cholesterol synth & reg
HMG CoA reductase (upregulated by insulin, thyroxine, down regulated by glucagone and cholesterol)
Tx of hyperammonemia
- Limit protein in diet
- Lactulose (acidifies GI tract to trap NH4 to excrete)
- Antibiotics to decrease ammonigenic bacteria (rifaximin)
- Benzoate, phenylacetate, or phenylbutyrate – react to bind glycine/glutamine to renally excrete
OTC def genetics, sx, labs
Xr, sx: first few days of life –> excess carbamoyl phosphate goes to pyrimidine synthesis to make orotic acid –> incrased orotic acid in blood/urine, low BUN, symptoms of hyperammonemia (tremor, somnolence, vomiting, cerebral edema), NO megaloblastic anemia (present in orotic aciduria – UMPS defect)
PKU – gen, def, cause, sx, tx
Ar, low phenyalanine hydroxylase or BH4 (cofactor) –> cannot synth tyrosine; sx: intellecutal disabililty, growth retardation, seizures, fair skin (upstream of tyrosine–>DOPA–>melanin), eczema, musty body odorl txL less phenylalanine and more tyrosine, BH4 supplement
MSUD – gen, def, accumulation, sx, tx
Ar, low branched chaiin a-ketoacid dehydrogenase (B1) that breaks down isoleucine, leucine, valine –> increased a-ketoacids in blood (esp. leucine); sx: vomiting, poor feeding, urine smells like syrup/burnt surgar –> severe CNS defects, intellectual disability, death; tx: restrict ILV and supplement B1
Alkaptonuria – gen, def, accumulation, sx
Ar, Def of homogentisate oxidase (degrades tyrosine–> fumarate), accumulate homogentisic acid; sx: bluish CT, cartilage, sclerae, urine turns black on prolonged exposure to air, arthralgias
Homocystinuria causes/tx; sx
All Ar
1. Cystathionine synthase def (tx by less methionine, more cysteine, B6, B12, folate)
2. Decreased affinity cystathione synth for B6 (tx increase B6 and cysteine in diet)
3. Methionine synthase def (tx increase methionine in diet)
Sx: osteoporosis, marfaoid, ocular changes (down and in), cardiovascular thrombosis/atherosclerosis –> stroke/MI, kyphosis, intellectual dis
Cystinuria gen, defect, sx, tx
Ar, defet in PCT/intesting amino acid transporter –> no reabsorption of cystine, ornithine, lysine, arginine; sx: cystine stones, urinary cyanide nitroprusside to diagnose; tx: alkalinize urine (potassium citrate, acetazolamide) and chelating agents (penicillamine), hydration
Type I glycogen storage disease – name, def, sx, tx
Von Gierke
Def: G6Ptase – impaired gluconeogenesis and glycogenolysis
Sx: severe fasting hypoglycemia, increased glycogen in liver, increased blood lactate, increased trigs, gout, hepatomegaly
Tx: oral glucose/cornstarch, avoid fructose/galactose
Type II glycogen storage disease – name, def, sx
Pompe disease
Def: lysosomal acid 1,4 glucosidase w/ alpha 1,6 glucosidase activity (acid maltase – basically debranching enzyme in a lysosome)
Sx: CARDIOMEGALY, hypertrophic cardiomyopathy, hypotonia, exercise intolerance, early death
Type III glycogen storage disease – name, def, sx
Cori disease
Def: debranching enzyme
Sx: mild von Gierke (fasting hypoglycemia, hepatomegaly, increased trigs and uric acid) because gluconeogenesis intact – accumulate limit dextrin-like structures in cytosol
Type V glycogen storage disease – name, def, sx
McArdle Disease
Def: skeletal muscle glycogen phosphorylase –> cannot breakdown glycogen in muscle
Sx: Muscle cramps, myoglobinuria and hypoglycemia (red urine) w/ exercise, arrhythmia from electrolyte abnormalities, second wind from increased musclar blood flow
Her’s disease
Hepatic mcardles – glycogen phosphorylase def –> hepatomegaly and fasting hypoglycemia
Anderson disease
Lack of branching enzyme –> one long glycogen chain –> cirrhosis –> fatal
Tay-Sachs – gen, def, accumulation, sx
Gen: Ar Def: Hexosaminidase A Accum: GM2 Ganglioside Sx: progressive neurodegen, developmental delay, cherry red spot on macula, lysocomes w/ onion skin, NO hepatosplenomegaly "There'S SIX SMALL JEWS in a GANG"
Fabry Disease – gen, def, accumulation, sx
Gen: Xr Def: alpha-galactosidase A Accum: Ceramide trihexoside Sx: episodic peripheral neuropathy, angiokeratomas, hypohidrosis, progressive renal failure and heart disease "I FABRicated A-GALA-Xy in CERAMIcs"
Metachromatic leukodystrophy – gen, def, accumulation, sx
Gen: Ar
Def: Arylsulfatase A
Accum: Cerebroside sulfate
Sx: central and peripheral demyelination with ataxia, dementia
SULF
Krabbe Disease – gen, def, accumulation, sx
Gen: Ar
Def: Galactocerebrosidase
Accum: Galactocerebroside psychosine
Sx: Peripheral neuropathy, destructin of oligodendrocytes, developmental delay, optic atrophy, globoid cells
“This KRABBE, BRO, is OUT of this WORLD”
Gaucher disease – gen, def, accumulation, sx
Gen: Ar
Def: Glucocerebrosidease
Accum: Glucocerebroside
Sx: Hepatosplenomegaly, pancytopenia, osteoporosis, avascular necrosis of femur, bone crises, Gaucher cells (lipid laden macs that look like crumpled tissue paper)
“CRYING oh my GAUCH, he was such a SWEET BRO”
Niemann-Pick – gen, def, accumulation, sx
Gen: Ar
Def: Shyingomyelinase
Accum: Sphingomyelin
Sx: progressive neurodegeneration, hepatosplenomegaly, foam cells (lipid-laden macs), cherry spot on macula
“NO MAN PICKs his nose with BIG SPHINGER”
Hurler syndrome – gen, def, accumulation, sx
Gen: Ar
Def: a-L-iduronidase
Accum: Heparan sulfate, dermatan sulfate
Sx: Developmental delay, gargoylism, airway obstruction, corneal clouding, hepatosplenomegaly
Hunter syndrome – gen, def, accumulation, sx
Gen: Xr
Def: Iduronate sulfatase
Accum: Heparan sulfate, dermatan sulfate
Sx: Mild hurler+aggression, no clouding
“X marks the HUNTERs spot” – has to SEE to aim
Pancreatic lipase fxn
Degrades dietary trigs in small int
LPL fxn
Decrads trigs circulating in chylomicrons and VLDLs, on vascular endothelial surface
Hepatic trig lipase
Degrades trigs remaining in IDL
Hormone sensitive lipase
Degrades trigs stored in adipocytes
LCAT fxn
Catalyzes esterification of plasma cholesterol (Makes HDL mature)
CETP
Mediates transfer of cholesterol esters to other lipoprotein particles (From mature HDL)
Apo E – fxn, on ____
Mediates remenant uptake, chylomicrons, remnants, VLDL, IDL, HDL
Apo AI – fxn, on ____
Activates LCAT; chylomicrons and HDL
Apo CII – fxn, on ____
LPL cofator, catalyzes cleavage; chylomicrons, VLDL, HDL
Apo B48 – fxn, on ____
Mediates chylomicron secretion into lymphatics; chylomicrons and remnants
Apo B100 – fxn, on ____
Binds LDL receptor; VLDL, IDL, LDL
Which lipoproteins carry momst cholesterol and their fxns?
LDL – cholesterol to tissues
HDL – cholestreol from periphery to liver
HDL is a repository for which apolipoproteins
C and E – for chylomicron and VLDL metabolism
Abetalipoproteinemia – gen, def/absence, sx, tx
Ar, chylomicrons VLDL LDL absent and def in ApoB48 and B100; sx: severe fat malabsorption, steatorrhea, failure to thrive, retinitis pigmentosa, spinocerebellar degeneration 2o to vit E def, progressive ataxia, acnthocytosis; tx: restriction of LCFA and large doses of vit E
Hyperchylomicronemia – gen, def/absence, blood level increases, sx
Ar; LPL or apoCII def; increased chylomicrons, TG, cholesterol; sx: pancreatitis, hepatosplenomegaly, eruptive/pruritic xanthomas and creamy layer in supernatant
Familial hypercholesterolemia – gen, def/absence, blood level increases, sx
AD; absent/defective LDL receptors;IIa –> increased LDL, cholesterol, IIb–> increased LDL, chol, VLDL; sx: heterozygotes have chol around 300, homozygotes have chol >700 –> accelerated atherosclerosis (MI before 20), tendon xanthomas, corneal arcus
Dysbetalipoproteinemia – gen, def/absence, blood level increases, sx
Ar; defective apoE, increased chylomicrons and VLDL; sx: premature atherosclerosis, tuberoeruptive xanthomas, xanthoma striatum palmare
Hypertriglyceridemia – gen, def/absence, blood level increases, sx
AD; hepatic overprodxn of VLDL; increased VLDL and trigs; hypertrig over 1000 –> acute pancreatitis
