Biochemistry Flashcards
Function of SER?
Steroid and phospholipid biosynthesis (adrenals, gonads, liver); detoxification (liver); sarcoplasmic reticulum in muscles
dTMP de-novo production
Catalyzed by thymidylate synthetase; 5,10-methyleneTHF + dUMP -> dihydrofolate + dTMP (dihydrofolate reductase)
Thalassemia intermedia
Associated with mutation 3 bases upstream from AUG in Kozak; Hypochromic, microcytic anemia
4 Types of Blots - detect what and probe?
Northern - RNA detection; ssDNA or RNA probe
Western - protein; Ab probe
Southern - DNA; ssDNA or RNA probe
Southwestern - DNA-binding protein; dsDNA
SNoW, DRoP
Which histone is not in the nucleosome core?
H1, which binds to nucleosome and linker DNA
Nucleosome characteristics?
Neg-charged DNA looped TWICE around histone OCTOMER (H2A, H2B, H3, H4)
Heterochromatin vs. euchromatin?
HeteroChromatin = Highly condensed Euchromatin = true; transcriptionally active
Three major epigenetic mechanisms
DNA methylation of CpG islands represses transcriptions; histone methylation mostly represses; histone acetylation relaxes DNA coiling and makes DNA more active
Difference between uracil and thymine?
Thymine has methyl group
AA’s necessary for purine synthesis
GAG - Glycine, Aspartate, Glutamine
Nucleoside v. nucleotide
Side = sugar + base; Tide = Sugar + base + phosphate
de novo purine synthesis how?
Ribose 5-P -> PRPP (PRPP synthase)
—> pathway (PRPP glutamyl amidotransferase = committed)
IMP —> AMP or GMP
What drugs affect purine synthesis and where?
6-MP at PRPP amidotransferase; Mycophenolate, ribavarin at IMP -> GMP (IMP dehydrogenase); drugs affecting folate
What enzyme makes deoxyribunucleotides?
Ribonucleotide reductase;
de novo pyrimidine synthesis?
Glutamine, CO2, ATP -> Carbamoyl phosphate
+ asparatet -> Orotic acid
+ PRPP -> UMP -> UDP -> dUDP -> dUMP -> dTMP
Orotic aciduria mutation?
UMP synthase (= orotate phosphoribosyl transferase + OMP decarboxylase) mutation; megaloblastic anemia, lethargy, weakness, growth retardation; treated with uridine –> salvage pathway to make UMP, which inhibits CPS-II to dec. orotic acid production
What are the two major targeted enzymes involved in the creation of dTMP?
Made from dUMP via thymidylate synthase, which requires N5N10-methylene THF, which requires Dihydrofolate reductase
What drugs target dTMP synthesis?
5-FU targets thymidylate synthase; MTX, TMP, pyrimethamine target dihydrofolate reductase
Hydroxyurea acts on what enzyme?
Ribonucleotide reductase (the enzyme that makes deoxyribonucleotides; in particular the UDP -> dUDP version)
Two major enzymes of purine salvage pathway?
HGPRT - Guanine -> GMP; Hypoxanthine -> IMP
APRT - Adenine -> AMP
Major cause of AR SCID?
Adenosine deaminase deficiency: leads to increased dATP -| ribonucleotide reductase -> prevention of DNA synthesis -> dec. lymphocyte count
Lesch Nyhan?
Absent HGPRT -> guanine and hypoxanthine all turn into xanthine -> EXCESS uric acid. HGPRT - Hyperuricemia, Gout, Pissed off, Retardation, dysTonia. Tx = allopurinol (2nd - febuxostat; both xanthine oxidase inhibitors)
Only AA’s coded by ONE codon?
AUG - methionine; UGG - tryptophan
DNA polymerases involved in prokaryotic DNA replication?
DNA pol I = degrades RNA primer (5’->3’ exonuclease) and makes DNA. DNA pol III = major 5’->3’ synthesis activity; 3’->5’ exonuclease proofreading
Transition vs. transversion mutation?
Transition = same type; Transversion = different type; What sounds weirder?
Four types of DNA repair?
Nucleotide excision, base excision, mismatch, nonhomologus end joining (dsDNA ; ataxia telangectasia)
Nucleotide excision repair?
Endonucleases release oligonucleotide-containing damaged bases; Bulky distorting lesions
Xeroderma pigmentosum - defect prevents repair of pyrimidine dimers (UV exposure - the NUCLEAR option)
Base excision repair?
Base-specific glycosylase recogs then creates AP site. 1 or more nucleotides removed by AP-endouclease (5’) and Lyase (3’); Non-bulky lesions; spontaneous/toxic deamination injury (purine->(hypo)xanthine); Quit stealing OTHER BASES
Mismatch repair?
MSH2 and MLH1 genes (MutS, MutL); Defective in HNPCC
mRNA stop codons?
U Go Away; U Are Away; U Are Gone;
UGA, UAA, UAG
RNA pols
In eukaryotes, I - rRNA, II - mRNA, III - tRNA (in ORDER); alpha-amanitin (Amanita phalloides) -| RNA pol II -> hepatotoxicity;
Prokaryotes only have one RNA pol that does it all
RNA processing
heterogeneous nuclear RNA = initial; 5’ cap (t-methylguanosine), polyadenylation (~200), splicing, then leaves nucleus as mRNA
mRNA quality control occurs where? And contains what?
Cytoplasmic P-bodies - contain exonucleases, recapping enzymes, microRNA’s
Polyadenylation signal?
AAUAAA
Intron vs. exon?
EXon = EXPRESSIVE; INtron is INTRUSIVE
Splicing works how?
snRNP’s + others bind to form spliceosome, lariat intermediate; removal. anti-snRNP’s ~ SLE
Where on tRNA is aa bound?
CCA (Can Carry Aa’s) on 3’ end
tRNA structure?
5’ to D-arm (recog by aminoacyl-tRNA synthase; contains dihydrouracil residues) to Anti-codon loop to T-arm, which has thymine, pseudouridine, cytidine sequence for tRNA-ribosome binding
Enzyme responsible for charging tRNA?
aminoacyl-tRNA synthetase (requires ATP); good proofreading
Ribosome’s sites for translation.
APE - A for incoming aminoacyl-tRNA, P for growing peptide, E for exit (holding)
ATP and GTP uses in translation?
ATP for charging; GTP for initiation and translocation
Cell cycle types (3)?
Permanent - Always in G0 and must regen from stem cells (Neurons, skeletal and cardiac m., RBCs)
Stable - Enter G1 from G0 when stimulated (hepatocytes, lymphocytes)
Labile - Never go into G0; short G1 (bone marrow, gut epithelium, skin, hair follicles, germ cells)
Function of RER?
Synthesis of secretory proteins; Called Nissl bodies in neurons
Functions of Golgi?
Distribution and modification; N-oligosaccharide mod on spargine, adds O-oligosaccharides on serine and threonine, adds mannose-6-phosphate for lysosomal trafficking
I-Cell disease
Failure of golgi to phosphoorylate mannose residues on glycoproteins that are intended for lysosomal trafficking; Instead secreted. Coarse facial features, clouded corneas, joint, high plasma levels of lysosmal enzymes
What vesicular trafficking proteins are involved in which areas?
Clathrin: trans-Golgi to lysosome; PM -> endosomes. COPI: retro golgi; Golgi -> ER. COPII: antero golgi; ER -> Golgi. Cops head backwards first!
Function of peroxisome?
Catabolizes VLCFAs, branched-chain FA’s, AA’s
Molecular motor directions?
Kinesin: Anterograde towards positive; Dynein: retrograde towards negative
What makes up microtubules?
alpha, beta tubulin; GTP
Drugs that act on MT’s
Mts Get Constructed Very Poorly: Mebedazole, Griseofulvin, Colchicine, Vincristine/Vinblastine, Paclitaxel
Cilia structure
9+2 (9 doublets, 1 doublet inside)
Primary ciliary dyskinesia (Kartagener syndrome)
Immotile cilia b/c of dyne in arm defect of dyne in; infertility, bronchiectasis, sinusitis, situs inversus
Intermediate filament immunohistochemistry
Vimentin - connective tissue; Desmin - muscle; Cytokeratin - epithelial cells; GFAP - neuroglia; neurofilaments - neurons
Drugs that act on Na-K pump?
Ouabain inhibits by binding K+ site Cardiac glycosides (digoxin) directly inhibits --> indirect inhibition of Na/Ca exchange -> inc Ca -> increased cardiac contractility
Four types of collagen
Be (So Totally) Cool, Read Books
I - Bone, Skin, Tendon, dentin, fascia, cornea, SCAR tissue
II - Cartilage, vitreous humor, nucleus puposus
III - Reticulin - skin, lungs, intestines, bone marrow, Granulation tissue, blood vessels, uterus
IV - basement membrane, basal lamina, lens
4 Major Diseases due to collagen problems?
Scurvy - Vit C required for hydroxylation; presents with bleeding gums, ecchymoses, impaired wound healing
Ehlers Danlos - vascular type (III); problems in cross-linking
Menkes - Impaired Cu absoprtion and transport (cross-linking problem b/c of lysyl oxidase);
Osteogenesis imperfecta - AD is dec prod of type I (fx, blue sclera, hearing loss, dental imperfections); triple helix bad
Alport syndrome - IV; Goodpasture syndrome - Ab against IV
Collagen synthesis
Synthesis (Gly-X-Y), Hydroxylation (scurvy), glycosylation and formation of pro collagen via H and S-S bonds to form triple helix (osteogenesis imperfecta), exocytosis, Proteolytic processing (procollagen -> insoluble tropocollagen via N- and C- peptidases), fibril assembly, cross-linking (covalent linkages lysine-hydroxylysine with Cu2+ containing lysyl oxidase) to make collagen fibrils
Marfan syndrome’s etio?
Defect in fibrillin; glycoprotein that sheathes elastin
Three main steps for PCR?
Denature, Anneal primers, Elongation
Purpose of ELISA
Used to detect presence of a specific Ag (Direct) or Antibody (indirect) in patient’s blood;
Direct Detects antiDen (b/c antibody sounds weird)
What is pleiotropy?
One gene causing multiple phenotypic effects
Locus vs. allelic heterogeneity?
Locus heterogeneity means that the same phenotype occurs with mutations at different loci. Whereas allelic heterogeneity is the same phenotype occurs with mutations at the same loci.
Heteroplasmy?
Presence of both nl and mut mtDNA. Examples of mitochondrial syndromes are Leber hereditary optic neuropathy, myoclonic epilepsy w/ ragged-red fibers, mitochondrial encephalomyopathy w/ lactic acidosis and stroke-like episodes (MELAS)
Uniparental disomy
2 copies of a chromosome from 1 parent; heterodisomy (meiosis I error); isodisomy (meiosis II or later error). Can cause what appears to be imprinting-related disease (Prader-Willi or angelman)
Hardy-Weinberg assumptions
No mutations, no natural selection, no migration, random mating
What is imprinting?
At some loci, only one allele is active while the other is inactivated/imprinted by methylation.
Prader-Willi - normally maternal imprinting; Disease occurs if PATERNAL gene problem;
AngelMan - nl paternal imprinting; disease occurs if MATERNAL gene problem
Example of X-linked dominant disease?
Hypophosphatemic rickets
What are the two parts of the pentose phosphate pathway? (And what is its function)
Irreversible oxidative pathway (G-6P ->-> Ribulose-5-phosphate); creates 2 NADPH
Reversible nonoxidative pathway (Ribulose-5-P Fructose-6-P –> Glycolysis)
Function = generate NADPH for synthetic pathways and detox + produce Ribose-5P for nucleotide synthesis
Rate limiting step of pentose phosphate pathway?
1st step done by glucose-6-phosphate dehydrogenase
G6PD Deficiency
Deficiency in rate-limiting step of pentose phosphate pathway. Decreased production of NADPH. RBC’s in particular are vulnerable to oxidative stress (e.g. fava beans, tylenol, primaquine, sulfa, dapsone, DKA). Heinz bodies (denatured hgb). Bite cells from phagocytic removal of Heinz.
Sickle cell anemia point mutation?
6th codon of Beta-globin gene: glutamic acid -> valine
What vitamin does the WHO recommend administering to those with measles?
Vitamin A
Alpha-ketoglutarate dehydrogenase complex requires what coenzymes?
Thiamine, lipoic acid, CoA, FAD, NAD+
Presentation of phenylketonuria
Scandinavian descent; Within a year - mental retardation, sz, hyperactivity, gait, postural muscle control, dec. pigmentation, “mousy” odor. There exists maternal PKU where baby is affected.
Etio of phenylketonuria
Enzyme phenylalanine hydroxylase (phenylalanine req. BH4-> tyrosine); Tyrosine req. BH4 -> DOPA -> melanine and catecholamines; Tyrosine -> Fumarate -> TCA
OR
Dihydrobuipterin reductase (BH2->BH4) deficiency
What are the substrates for gluconeogenesis?
Pyruvate from lactate, glycerol, and glycogenic amino acids
How does sucrose/sorbitol get into glycolysis?
Sucrose -> fructose -(fructokinase)> fructose 1-P -(Aldolase B)> Glyceraldehyde -(triokinase)> Glyceraldehyde 3-P
Hereditary fructose intolerance?
Aldolase B deficiency - vomiting and hypoglycemia (b/c accumulation of fructose-1-phosphate and depletion of Pi) about 20-30 minutes after fructose intake
Essential fructosuria?
Fructokinase deficiency -> secretion into urine of fructose; a benign AR disorder
Methionine metabolism?
Methionine to SAM (ATP). SAM to Homocysteine. Homocysteine to Methionine (Homocysteine methyltransferase,B12). Homocysteine to Cystathionine to Cysteine (Cystathionine synthase,B6,serine)
Role of leptin
Decreases NPY (appetite stimulant) and stimulates POMC and alpha-MSH to inhibit food intake
How is isoniazid metabolized?
Acetylation to N-acetyl-isoniazid in hepatic microsomal system –> urine. “Slow acetylators” exist -> increased risk of side effects
How do thiazolidinediones work?
Activate PPAR-gamma, nuclear receptor, that increases transcription of Adiponectin, FA transport protein, insulin receptor substrate, glut-4
ADPKD mutation?
PKD1 on chromosome 16 (85%); 16 letters in PK
Familial adenomatous polyposis gene v. HNPCC (lynch)
FAP is APC gene on chr 5 (polyp =5); HNPCC = mismatch repair genes (MSH2, MLH1)
Familial hypercholesterolemia defect?
Defective/absent LDL receptor; tendon xanthomas (Achilles)
Hereditary spherocytosis defect?
Spectrin or ankyrin -> hemolytic anemia (inc. MCHC); tx = splenectomy
HD defect
(CAG)n on chromosome 4; (The CAG is hunting 4 cylons.)
Marfan syndrome defect
Fibrillin-1.
MEN 2A/2B gene
ret
NF1 vs. NF2 chromosome
NF1=17 (von Recklinghausen); NF2 = 22
von Hippel Lindau disease chromosome
del of VHL gene on ch 3p. AD disorder w/ cereballar hemangioblastomas, clear cell renal carcinomas, pheochromocytomas
Genetics of CF
Del of Phe508 on chromosome 7 (most common lucky number?)
CFTR function
ATP-using Cl- secretion in lungs and GI and Cl- absorption in sweat glands
X-linked recessive disorders
Be Wise, Fool’s GOLD Heeds HOpe.
Bruton agammaglobulinemia, Wiskott-Aldrich, Fabry, G6PD, Ocular albinism, Lesch-Nyhan, Duchenne, Hunters syndrome, Hemophilias, Ornithine transcarbamylase deficiency
Duchenne defect and presentation
X-linked frameshift -> truncated dystrophin (DMD gene). Anchors muscle fibers (actin to transmembrane proteins); pelvic girdle weakness moves sup. pseudohypertrophy. < 5 yr onset; dilated cardiomyopathy
Becker defect
X-linked POINT mutation. onset in adolescence or early adulthood
Myotonic type 1 muscular dystrophy defect and presentation
CTG repeat expansion of DMPK gene; myotonia, m. wasting, frontal balding, cataracts, testicular astrophy, arrhythmia.
Fragile X defect and presentation
X-linked FMR1 gene w/ CGG (n=200) expansion leads to hypermethylation. Xtra large testes, LONG face with large jaw, large everted ears, autism. Short X -> Long face, large jaw, large testes, large ears.
Trinucleotide repeat expansion diseases
X-Gf’s First Aid Helped Ace My Test; C_G (Community group!) Fragile X = cGg. Friedrich ataxia = gAa. HD = cAg. Myotonic dystrophy = cTg
1st and 2nd trimester Screen for Down’s is?
1st: Increased nuchal translucency, hypo plastic nasal bone, serum PAPP-A down, free Beta-hcg up
2nd: quad screen; L alpha, Up beta, L estriol, Up inhibin
Edwards syndrome
E for election = chromosome 18. Severe ID, rocker-bottom feet, micrognathia, low-set ears. Death within 1 year. 1TM - low PAPP-A and free Beta. 2TM - L alpha, low Beta, low estriol, low A. Overriding fingers (2>3, 5>4)
Patau syndrome
P for puberty = chromsome 13. Severe ID, rocker-bottom, micropthalmia, microcephaly, celft liP/Palate, HOLOPROSencephaly, polydactyly. 1TM - Up Beta, low PAPP-A, increased nuchal translucency
Robertsonian translocation
Nonreciprocal of 13, 14, 15, 21, 22 where two q arms fuse, losing p arms. Balanced ok. Unbalanced palms.
Cri-du-chat syndrome
Microdeletion of short arm of chromosome 5. (A little high 5 for the cat.) Microcephaly, mod-sec ID, mewing, epicentral folds, VSD
Williams syndrome
Microdeletion on 7q (# Ivies - 1 = 7; Little ivy). Elfin facies, ID, hypercalcemia, good verbals, very friendly
CATCH-22
Cleft palate, Abnl facies, Thymic aplasia (T-cell def), Cardiac defects, Hypocalcemia (No C-cells!). 22q11. Abberant dvpt of branchial 3rd and 4th. diGeorge - thymic, parathyroid, . cardiac. Velocardiofacial - palate, facial, and cardiac
Fat soluble vitamins
Fat soluble - A, D, E, K. Very dependent on gut and pancreas for absorption. More likely to go toxic. KADE skywalker is fat.
Water soluble vitamins
B1,2,3,5,6,7,9,12.C. B deficiencies -> dermatitis, glossitis, diarrhea.
Excess Vit A?
Acute (n/v/vertigo), long (alopecia, HLD, HEPATO, PSEUDOTUMOR), teratogenic (microcephaly, cleft palate, cardiac)
Deficient Vit A?
Night blindness, dry, xerosis cutis, alopecia, corneal degen, immunosuppression, squamous metaplasia.
Vit A F(x)?
Antioxidant, visual pigment, DIFFerentiation, tx for measles.
Thiamine f(x)?
BIG 3 (alpha-ketoglutarate dehydrogenase, alpha-ketoacid dehydrogenase, pyruvate dehydrogenase) + transketolase (for HMP shunt)
Deficient Vit B1?
Impaired glucose breakdown -> highly aerobic tissue damage.
Wernicke-Korsakoff - confusion, opthalmoplegia, ataxia
Dry beriberi - polyneuritis, symmetrical muscle wasting
Wet beribi - dilated cardiomyopathy, edema
Measured in lab by dec. transketolase activity in RBC’s
B2 f(x)?
Riboflavin. Part of flavins FAD and FMN req. for redox reactions.
Deficient B2?
Cheilosis and corneal vascularization
B3 f(x) and name?
Niacin. Derived from tryptophan. Makes NAD+. Impairs hepatic production of VLDL -> lower LDL. (Higher HDL)
Excess B3?
Facial flushing, hyperglycemia, hyperuricemia
Deficient B3?
glossitis, PELLAGRA - diarrhea, dementia, dermatits. Etios - hartnup disease, malignant carcinoid, INH
B5 f(x) and name?
Pantothenate. CoA and FA synthase.
Only vitamins with excess problems.
Vit A, Vit B3, Vit C, Vit D
Deficient B5?
Dermatitis, enteritis, alopecia, adrenal insufficiency
B6 f(x) and name?
Pyridoxine. Pyridoxal phosphate used for transamination, decarbox, glycogen phosphorylase. Neurotransmitter synthesis.
Deficient B6?
Peripheral neuropathy, sideroblastic anemia. Cheilosis, glossitis, dermatitis. INH –> B6 deficiency symptoms b/c chemically similar to pyridoxine and competes in synthesis of neurotransmitters while also increasing urinary excretion.
B7 f(x) and name?
Biotin. Cofactor for 1C adding rxns (acetyl-Coa carboxylase, pyruvate carboxylase, propionyl carboxylase)
Deficient B7?
Abx or excessive ingestion of egg whites. Dermatitis, alopecia, enteritis.
B9 f(x) and name?
Folic acid. Converted to THF for base synthesis. Absorbed in jejunum. Leafy green veggies. Small pool in liver.
Deficient B9?
Macrocytic, megaloblastic anemia. Inhibits dTMP synthesis. Glossitis, no NEURO. Dx - inc. homocysteine and normal methylmalonic acid. Tx w/ folate and thymidine.
B12 f(x) and name?
Cobalamin. Homocysteine methyltransferase (methionine pathway) and methylmalonyl-CoA mutase co-factor. Large reserve in liver.
Deficient B12?
Macrocytic, megaloblastic anemia. Parasthesias, subacute combined degen due to abnl myelin. UMN signs (lateral corticospinal dmg). Inc homocysteine AND methylmalonic acid. Buildup of methylmalonic acid -> myelin synthesis abnormalities. Etios - vegan, malasorption, lank of intrinsic factor, absence of terminal ileum
Vit C f(x) and name?
Ascorbic acid. Antioxidant, iron absorption, hydroxylation of collagen residues, dopamine -> NE.
Excess Vit C?
N/v, d, fatigue, calcium oxalate nephrolithiasis.
Deficient Vit C?
Scurvy - collagen syntehsis defect. Swollen gums, brusing, anemia, poor wound healing, corkscrew hair
Vit D f(x) and name?
D2 - (ergocalciferol from plants). D3 (cholecalciferon from milk). 1,25 = active form. Intestinal absorption of Ca+ AND phosphate. Inc. bone mineralization.
Deficient Vit D?
Rickets - bone pains and deformity. Osteomalacia (bone pain and weakness in adults).
Excess Vit D?
Hypercalcemia, hypercalciuria, loss of appetite, stupor. Scene in sarcoidosis.
Vit E f(x) and name?
Tocopherol/tocotrienol. Antioxidant for ERYTHROCYTES and membranes.
Deficient Vit E?
Hemolytic anemia, acanthocytosis (spiked RBCs), muscle weakness, posterior column and spinocerebellar tract demyelination. (Similar to B12 def except NO megaloblastic anemia and hypersegmented neutrophils)
Vit K f(x) and name?
Cofactor for carboxylation for Glu for Klotting. (1972, Canada-Sweden).
Deficient Vit K?
Neonatal bleeding (inc. PT and aPTT). Injection (guts can’t absorb b/c sterile intestine).
Deficient zinc?
Delayed wound healing, hypogonadism, dec. adult hair, dysgeusia (Taste distortion)
Ethanol metabolism?
Alcohol dehydrogenase (cytosol); Acetalaldehyde dehydrogenase (mitochondria) producing acetate. Limiting reagent is NAD+. Zero-order. Increases NADH/NAD+ ratio in liver ---> lactic acidosis, fasting hypoglycemia, hepatosteatosis)
What drugs affect ethanol metabolism pathway?
Disulfiram -| acetylaldehyde dehydrogenase.
Fomepizole inhibits alcohol dehydrogenase. Antidote for methanol or ethylene glycol poisoning.
Kwashiokor?
Protein deficient MEAL -> Malnutrition, Edema, Anemia, Liver (large b/c of fatty change 2/2 dec. apolipoprotein to move out VLDL). Also ascites.
Marasmus?
Total calorie malnutritions -> MUSCLE wasting.
What metabolic pathways occur in the mitochondria?
FA oxidation, acetyl-CoA production, TCA, oxidative phosphorylation; Parts of heme synthesis, urea cycle, and gluconeogenesis.
What metabolic pathways occur in cytoplasm?
Glycolysis, FA synthesis, HMP shunt, protein, steroid, cholesterol synthesis. Parts of heme, urea cycle, gluconeogenesis.
Net ATP production w/ glucose?
32 w/ malate-asp shuttle (heart and liver). 30 net w/ gylcerol-3-phosphate shuttle (muscle). 2 net if anaerobic.
Enzyme responsible for first step of glycolysis?
Hexokinase (most tissues) - high affinity, basal, feedback inhibited by glucose-6-P.
Glucokinase (liver, beta cells) - faster response, insulin induced, inhibited by fructose-6-P, implicated in MODY
Key enzymatic step of glycolysis? Regulation?
Phosphofructokinase-1 (PFK-1). Fructose-6-P -> Fructose-1,6-bisP. Inhibited by ATP, citrate, phosphoenolpyruvate. Activated by AMP and fructose-2-6-BP
ATP investing steps of glycolysis?
Hexo/glucokinase. Phosphofructokinase-1.
ATP producing steps of glycolysis?
Phosphoglycerate kinase (1,3-BPG -> 3-PG) Pyruvate kinase (Phosphoenolpyruvate -> pyruvate). Inhibited by ATP, alanine. Pushed by Fructose-1,6-BP.
Glycolysis overview?
Glucose, glu-6-p, fructose-6-p,fructose-1,6-bp,G3P+DHAP,->->Phosphoenolpyruvate, pyruvate.
Glycolysis and gluconeogenesis are both regulated via this bifunctional enzyme how?
Fructose bisphosphatase-2/pFK-2. fructose-2,5-BP fructose-6-P
Fasting - inc. glucagon, inc cAMP, inc PKA, inc FBPase, inc gluconeogenesis
Fed - inc insulin, dec cAMP, dec PKA, inc PFK-2, inc glyolysis
Glycolysis is coupled to TCA how?
Pyruvate dehydrogenase complex: pyruvate + NAD+ + CoA -> acetyl-CoA + CO2 + NADH
5 cofactors: Pyrophosphate (B1), FAD (B2), NAD (B3), CoA (B5), Lipoic acid (inhibited by arsenic)
Inhibited by ATP, Acetyl-CoA, NADH
Pyruvate dehydrogenase complex deficiency?
Buildup of pyruvate shunted to lactate (LDH) and alanine (ALT). Tx = Lysine and leucine (ketogenic) to minimize lactic acidosis (shunting metabolism to fat burning)
Four ways pyruvate is metabolized
(1) Alanine aminotransferase (B6)
(2) Pyruvate carboxylase (biotin) - makes oxaloacetate for TCA cycle or gluconeogenesis
(3) Pyruvate dehydrogenase (B1-3, 4, liopic acid)
(4) Lactic acid dehydrogenase (B3) - makes lactate. RBCs, leukocytes, kidney medulla, lens, testes, and cornea
Krebs cycle overview?
Citrate Is Krebs’ Starting Substrate For Making Oxaloacetate
Citrate, Isocitrate, alpha-ketoglutarate, Succinyl-CoA, Succinate, Fumarate, Malate, Oxaloacetate
Produces 3 NADH, 1 FADH2, 2CO2, 1 GTP/CoA = 10 ATP/acetyl-CoA
Rate-limiting step of TCA cycle?
Isocitrate dehydrogenase (Isocitrate -> a-KG) Inhibited by ATP and NADH. Pushed by ADP.
Pyruvate carboxylase?
Pyruvate + CO2 -> Oxaloacetate; Used for TCA, gluconeogenesis via malate.
Deficiency - limits TCA cycle. Lactic acidosis. Mental retardation < age 5.
What is the gradient in oxidative phosphorylation?
H+ produced in inter membrane space. NADH, FADH2, H20, and ATP are in the matrix.
1 NADH -> 2.5 ATP; 1 FADH2 -> 1.5 ATP
Oxidative phosphorylation poisons?
E- transport inhibitors: rotenone (I), antimycin A (III), cyanide & CO (IV)
ATP synthase inhibitors: oligomycin
Uncoupling agent: ATP synthesis stops but electron transport continues. (2,4-dinitrophenol, ASA, thermogenin in brown fat)
Gluconeogenesis overview?
Pathway Produces Fresh Glucose. Starts after fasting 12-18h.
1. Pyruvate carboxylase (Pyruvate -> oxaloacetate; biotin, ATP); mitochondria
2. Phosphoenolpyruvate carboxykinase (Oxaloacetate -> phosphoenolpyruvate)
3. Fructose-1,6-bisphosphatase (Fructose-1,6-BP–> Fructose-6P); Inhibited by F 2,6P. Pushed by citrate.
4. Glucose-6-phosphatase (Glycose-6P->Glucose). ER
Primarily in liver, also kidney. Odd-chain FA’s can enter TCA via succinyl-CoA to become glucose but even-chains destined for acetyl-CoA.
Key enzymes in HMP shunt?
Glucose-6-P dehydrogenase (glucose-6P -> ribulose 5-P)
Phosphopentose isomerase, transketolases (Ribulose 5-P -> ribose-5-P, G3P, F6P). Req. b1.
What is the respiratory/oxidative burst?
Phagocytic NADPH oxidase complex that rapidly releases ROS to kill bacteria. Most important enzyme = NADPH oxidase (whose deficiency = chronic granulomatous disease). O2->O2–>H2O2+Cl- -(Myeloperoxidase)-> bleach
Other enzymes degrade H2O2 and require SELENIUM to do so.
What type of organisms are patients with chronic granulomatous disease susceptible to?
Catalase + specieies (e.g. Staphs, Aspergillus). B/c these organisms catalase their own H2O2 leaving phagocytes w/o any substrate for oxidative burst.
Leber’s hereditary optic neuropathy
Mitochondrial (maternal transmission) mutation of complex I often leads to optic nerve death 2/2 ischemia by early adulthood.
Arsenic poisoning symptoms
Cholera-like symptoms. tx - chelation; Arsenic inhibits lipoid acid requiring enzymes like PDH complex, aKG DH, transketolase
Conversion of NE to Epi occurs where and how?
Adrenal medulla. Phenylethanolamine-N-methyltransferase (PNMT). Controled by cortisol (increases transcription).
Synthesis of serotonin?
Tryptophan req. BH4 -(tryptophan hydroxylase)-> 5-hydroxytryptamine -> serotonin
Elastin synthesis?
Tropoelastin precursors (Gly, ala, val w/ non-hydroxylated pro and lys). After secretion, binds with fibrillin. Lysine residues bound covalently as desmosine cross-link = elastic properties. NO triple helix.
What protein regulates G1->S transition?
Rb. Active=hypophosphorylated, which binds to E2F. Hyperphosphorylated Rb (via CDK4) -> E2F transcription factor release.
Niemann-Pick disease
Spingomyelinase. Spinhingomyelin. AR. Ashkenazi, 1st yr with hepatosplenomegaly, hypotonia, ID. “FOAMY histiocytes” in liver and spleen and neuro. CHERRY-red macular spot (Tay-sachs like). Death by 3.
What monosaccharide is most rapidly metabolized?
Fructose. B/c F-1-P bypasses PFK-1 by being converted by Aldolase B (Hereditary fructose intolerance) into DHAP and Glyderaldehyde.
P50 of Hgb v. P50 of Mgb?
25 mmHg v. 1 mmHg; 1 Quarter for the hemoglobetrotters.
Galactose metabolism?
Most commonly from lactose (glucose-galactose), with lactase in GI breaking down. Galactose -(galactokinase)-> galactose-1P -(Uridyltransferase)-> Glucose-1-P
Galactokinase deficiency?
AR. Galactose in blood and urine. Galactitol accumulation (via aldose reductase) -> infantile cataracts (failure to track or develop social smile).
Classic galactosemia
AR. Absence of galactose-1-phosphate uridyltransferase. Galactitol accumulation (via aldose reductase) -> cataracts. FTT, jaundice, hepatomegaly, ID. Tx = exclude galactose and lactose. e. coli sepsis.
Sorbitol
Keeping glucose in a cell for later use into fructose via sorbitol dehydrogenase. (Glucose -aldose reductase-> sorbitol). Liver, ovaries, seminal vesicles have both. Schwann cells, retina, kidneys, lens primarily has aldose reductase, making these cells susceptible to osmotic dmg with hyperglycemia OR with high galactose lvls.
Lactase deficiency
Primary - age-dependent decline (absence of lactase-persistent allele). Secondary - loss of BRUSH BORDER. Dx - stool w/ dec. pH and breath with inc. hydrogen content with lactose tolerance test, or inc. stool osmotic gap.
What aa’s found in histones?
Positively charged (basic) Arginine and lysine.
Glucogenic aa’s v. Ketogenic aa’s?
Met, Val, His v. Leu, Lys; Ile, Phe, Thr, Trp are both.
VeHeMetly sugary. Kato went to LaLa land.
PITT - best of both worlds.
Rate limiting enzyme of urea cycle?
Carbomyl phosphate synthetase I. In mitochondria. CO2 + NH3 + 2ATP -> Carbomyl phosphate. Activated by N-acetylglutamate (formed by enzyme N-acetylglutamate synthetase from acetyl-CoA and glutamate).
Urea Cycle?
Carbomyl phosphate + ornithine -(ornithine transcarbamylase)-> citrulline + Asp + ATP -(argininosuccinate synthetase)-> argininosuccinate -(argininosuccinase)-> arginine + (fumarate) -(Arginase)-> Urea + ornithine
Point is to remove ammonia. (Urea gets N from ammonia and aspartate).
How does ammonia from muscle get to the liver?
Turned into alanine before transported to liver for transamination into pyruvate + glutamate (->-> urea)
AST and ALT do what?
ASP + alpha-ketoglutarate -> oxaloacetate + glutamine; Alanine + alpha-ketoglutarate -> pyruvate + glutamine.
Hyperammonemia
Acquired (liver disease) or secondary (urea cycle pblem) - excess free NH4, depleting alpha-ketoglutarate, which stops TCA. Tx = limit protein. Benzoate or phenylbutyrate, which bind aa to excrete. Lactulose to acidify GI and trap NH4+ for excretion. Asterixis, slurring, somnolence.
Hereditary hyperammonemias
Ornithine transcarbamylase deficiency - X-linked rec. Mitochondria. Excess carbonyl phosphate -> orotic acid. Inc. orotic acid, dec. BUN, hyperammonemia symptoms. NO megaloblastic anemia unlike orotic acuduria.
CPS-1 deficiency
Phenylalanine, Tryptophan, and Histidine make what important compounds?
Phe - Thyroxine, Melanin (tyrosinase), Dopamine (DOPA decarboxylase), NE, Epi; Try - Niacin, NAD, Serotonin, Melatonin; His - Histamine
Glycine, Glutamate, Arginine make what important compounds?
Gly - Porphyrin, heme; Glut - GABA, glutathione; Arginine - Creatine, Urea, Nitric oxide
Overview of Phenylalanine/Tyrosine catabolism?
Phe -(phenylalanine hydroxylase, BH4)-> Tyr; PKU ||Tyr -(tyr hydroxylase,BH4)-> DOPA -(DOPA decarboxylase, B6)-> dopamine-(r. VitC)-> NE -(r. SAM)-> Epi -> Metanephrine ||
Dopamine -> homovanillic acid || NE -> Normetanephrine -> vanillylmandelic acid || DOPA -(tyrosinase)-> melanin; ALBINISM |_| Tyr ->-> homogentisic acid -(Homogentisate oxidase)-> Maleylacetoacetic acid -> TCA; Alkaptonuria
Alkaptonuria
AR. Benign. Deficiency of homogentisate oxidase (tyr -> fumarate pathway). Dark CT, brown sclerae, urine turns black in air. Arthralgias (2/2 cartilage tox of homogentisic acid)
Homocystinuria
Homocysteine in urine, ID, osteo, marfinoid, kyphosis, dislocated lens, atherosclerosis -> THROMBOEMBOLISM. Etios include cystathionine synthase deficiency (Cysteine becomes essential AA), homocysteine methyltransferase deficiency, dec. pyridoxal phosphate binding to cystationine synthase. Treatment with B6 helps a lot.
Cystinuria
Defect of aa transport (COLA) in renal proximal convoluted tubule leading to hexagonal cystine (=cysteine x2) stones. AR. Dx = cyanide-nitroprusside test. Tx = urinary alkalinization and chelating.
Maple Syrup Disease
Normally branched chained aa’s (Ile, Leu, Val) converted to alpha-keto acids peripherally via alpha-ketoacid dehydrogenase (B1). Urine smells like syrup. FTT, CNS defects, ID. Tx = restrict ILV (I Love Vermont), and thiamine +keto acid supplementation
Glycogen regulation by insulin and glucagon/epi?
Glucagon and epi both eventually act on glycogen phosphorylase kinase, which phosphorylates glycogen phosphorylase. Adenylate cyclase pathway vs. Ca2+; Insulin inhibits glycogen phosphorylase via a phosphatase. And pushes glycogen synthase.
Glycogenolysis?
Glycogen phosphorylase removes branch down to 4 residues (Dextrins). 4-alpha-D-glucanotransferase moves 3 glucose-1P’s, then alpha-1,6 glucosidase cleaves last one
Cleaves off glucose-1P -(glucose-6-phosphatase)-> Glucose-6-P
Glycogenesis?
Glucose 1-P -(UDP-glucose pyrophosphorylase)-> UDP-glucose -(glycogen synthase)-> glycogen;
Links are alpha-1,4 while branches are alpha-1,6
Glycogen storage disease (four of them)
Very Poor Carbohydrate Metabolism: Von Gierke (most common), Pompe, Cori, McArdle (V)
Von Gierke disease (type I)
Glucose-6-phosphatase; Severe fasting hypoglycemia. Lactate high, glycogen high, hepatomegaly. Cells can’t remove phosphate off of glucose-6P; AR. Tx = freq. oral glucose; avoid fructose and galactose.
Pompe disease (II)
LYSOSOMAL alpha-1,4-glucosidase (small amount of glycogen degraded via this method). Cardiomyopathy. AR. LYSE his head, he’s so pompous.
Cori disease (III)
Alpha-1,6,glucosidase (last debranch). AR. Gluconeogenesis okay. Mild von Gierke.
McArdle disease (IV)
Skeletal muscle glycogen phosphorylase. AR. Increased Glycogen in MUSCLE but CAN’T break down-> cramps, MYOglobinuria with exercise, arrhythmias, weakness.
Fabry Disease
alpha-galactosidase A. Ceramide trihexoside. XR. Peripheral neuropathy, angiokeratomas, cardio/renal. AGA - American GI association, cuz Dr. Fabry was a dermatologist.
Gaucher disease
Glucocerebrosidase (B-glucosidase). Glucocerebroside. AR. Hepatosplenomegaly, pancytopenia, GAUCHER cells (lipid-laden macrophages!). Recombinant glucocerebrosidase available tx. Gaucher is a Cerebral!
Tay-Sachs disease
Hexosaminidase A. GM2 ganglioside. AR. CHERRY-Red spot on macula. No hepatosplenomegaly. A HEX on the people.
Krabbe disease
Galactocerebrosidase. Most Cerebral of the Galactosy. AR. Peripheral neuropathy, dvpt delay.
Metachromatic leukodystrophy
Arylsulfatase. Central and peripheral demyelination with ataxia, dementia. Many-colored Arya faces sulfur pits.
Hurler syndrome
alpha-L-iduronidase. AR. Heparan sulfate. Dvpt delay, gargoylism, airway, corneal. iDuron duran is a hurler.
Hunter syndrome
iduronate sulfatase. X-linked recessive. Mild hurler + aggressive. Hunter sounds more sophisticated than hurler right?
Carinitine deficiency?
Carnitine shuttle is required to move LCFA’s into mitochondria to be broken down. W/o carnitine, accumulated LCFA’s –> cardiomyopathy, myopathy, encephelopathy, fasting hypoglycemia (carnitine palmitoyltransferases I or II)
Ketogenesis
Only occurs in mitochondria of liver cells with lots of acetyl-CoA present. Acetoacetate and 3-hydroxybutyrate can be used peripherally. Acetone, cannot, and leaves via lungs (fruity odor)
Kcal per protein, carb, fat?
4,4,9. (Area code in Mexico; 449. And 9 is fat).
How much time does it take to deplete glycogen?
1 day
Starvation days 1-3:
Hepatic glycogenolysis, adipose release of FFA, muscle and liver use FFA, hepatic gluconeogenesis
Starvation >3days
Adipose stores mostly. Ketone bodies dominate brain energy source. Afterwards, vital protein degradation accelerates.
Main purpose of Chlyomicrons, VLDL, LDL, HDLs
Chylos take dietary lipid to tissues. VLDL’s deliver hepatic TG’s to peripherals. LDL delivers hepatic cholesterol to peripheral tissues (receptor-mediated endocytosis). HDL takes excess tissue cholesterol back to liver.
What enzyme removes supercoils?
Topoisomerase II
Fetal hemoglobin is made up of what subunits?
2alpha, 2GAMMA;
Different hemoglobins?
a2b2 = HbA1; a2d2 = HbA2; a2g2 = HbF
How does NE get to Epi?
NE + SAM -Phenylethanolamine-N-methyltransferase(PNMT)-> Epi + S-adenosylhomocysteine
The Five Great cofactors are needed for what 3 enzymes?
Pyruvate dehydrogenase, alpha-ketoacid dehydrogenase (Maple), alpha-ketoglutarate dehydrogenase (TCA). Thiamine, lipoic acid, CoA, FAD, NAD+
What part of ribosome binds to Shine-Dalgarno sequence of mRNA?
16S rRNA of 30S ribosomal subunit (prokaryotic); You Shine when you’re 16.
Where do all the electron acceptors come from in the Krebs?
NADH produced by isocitrate dehydrogenase, a-KG dehydrogenase, and malate dehydrogenase. FADH2 produced by succinate dehydrogenase. GTP produced by succinyl CoA synthetase.
Lead overdose?
Affinity for sulfhydryl groups leading to inhibition ALA-dehydrase and Ferrochetolase -> dec. heme synthesis. Microcytic anemia (2/2 inhibited delta-ALA dehydrates and reduced Fe into heme), Basophilic stippling (abl aggregation of ribosomes), colicky abdominal pain, constipation, BLUISH pigment at gum tooth, wrist drop/foot drop. 10ug/dL Tx = EDTA or dimercaprol
Cyanide poisoning?
Rapidly cutaneous flushing, tachypnea, HA, tachycardia, n/v, confusion. Severe lactic acidosis. Mech - binds cytochrome a-a3, stopping oxidative phosphorylation. Tx = nitrites. Induce formation of methemoglobin, which sequesters cyanide. Sodium thiosulfate can also bind.
Heme synthesis overview
Fe2+ and protoporphyrin IX -(ferrochelatase)-> Heme…requires mitochondria. Rate-limiting step is Gly + Succinyl CoA -(ALA synthase)-> aminolevulinic acid. ALA synthase is activated by alcohol, barbiturates, and hypoxia. Mostly synthesized in hepatocytes and erythrocytes, which lose their ability when they lose their mit. Lead affects ferrochelatase and ALA DEhydratase.
Poryphyria
Photosensitivity is key feature. Pink-tinted urine that darkens 2/2 porphobilinogen secretion (intermediate). Chronic porphyria due to def. of uroporphyrin decarboxylase. Acute porphyria often due to liver (excessive expression of ALA synthase.
GPCR characteristics
SEVEN transmembrane regions. Alpha-GDP -> Alpha-GTP—> alpha dissociates w/ beta+gamma -> activates adenylate cyclase or phospholipase C. Phospholipase C - produce IP3 and DAG. DAG -> PKC. IP3 -> inc. intracellular Ca -> elevated PKC.
Harnup disease -
Niacin deficiency b/c of loss of dietary tryptophan b/c of defective intestinal and renal tubular absorption. B3 is made from typtophan.
lac operon
Reg gene, promoter gene, operator gene, 3 structural genes called z, y a. Beta-galactosidase, permease, repressor protein. Lactose binds to repressor protein –> PREVENT attachment of repressor to operator. Glucose –> decreased cAMP -> decreased expression (b/c high cAMP activates CAP to bind to promoter)
Propionyl CoA
Involved with catabolism of Ile, Val, Met, Threonine (“Ill Val Met Three”) cholesterol and odd-chain FA’s. Converted to methylmalonyl CoA (propionyl CoA carboxylase, biotin, carboxylation), which is then converted to Succinyl CoA (methylmalonyl CoA isomerase, B12, isomerization)
Ricin
Potent toxin from castor oil plant that inhibits protein synthesis by cleaving rRNA component of euk. 60S
Ketones are metabolized by what tissues?
Brain, skeletal muscle, cardiac muscle, renal cortex. Cells w/o mitochondria can’t use ketone bodies. Liver cannot either b/c they lack succinyl CoA-acetoacetate coA transferase
Linkage disequilibrium
When a pair of alleles from two loci are inherited together more or less often than would be expected by random chance alone. Not necessarily physical proximity.
Role of liver in triglyceride metabolism?
TG’s are stored in adipose, metabolized to FA’s + glycerol by hormone sensitive lipase. The glycerol is transported to liver where phosphorylated by glycerol kinase. Then converted to DHAP -> glycolysis or gluconeogenesis.
Genetic heterogeneity
Mutations in different genes leading to similar phenotypes
Variable expresivity
Same genotype, different phenotypic expression. (NOT penetrance)
Marfan vs. Ehlers-Danlos syndrome
EDS - hypermobile joints, hyper elastic skin, fragile tissue susceptible to bruising. Marfan - lens dislocation, aortic aneurysms, long and tall, also hypermobile joints
Well-known promoter sequences of eukaryotic genes?
TATA box and CAAT box.
Apo B 100 vs. 48
ApoB-100 is synthesized by the liver and binds LDL receptor for LDL uptake. ApoB-48 is truncated form synthesized in the intestines and incorporated into chylomicrons (via cytidine to uridine deamination reaction on transcribed mRNA -> premature stop).
Down syndrome characteristics
ID, epicanthal, flat face, cleft palate, nuchal fold, palmar simian crease, endocardial cushion, duodenal/jejunal atresia, hypotonia, gap between 1-2nd toes
Absorption of B12?
(1) Requires salivary R protein to bind B12 and protect it from acid. It also binds B12 released from acidified food in the stomach (2) Pancreatic enzymes cleave R protein from B12, allowing it to bind to intrinsic factor (made by parietal cells) -> absorption at terminal ileum.
Familial Dyslipidemia Type I
I - hyperchylomicronemia. AR. Lipoprotein lipase deficiency or altered C-II. Pancreatitis, hepatosplenomeg, xanthomas.;
Familial Dyslipidemia Type IIa
IIa - familial hypercholesterolemia. AD. LDLR. Heteros have chol 300, homozys with 700+. Acc. atherosclerosis, tendon xanthomas, corneal arcus;
Familial Dyslipidemia Type IV
IV - hypertriglyceridemia. AD. Overproduction of VLDL. Pancreatitis.
Lipoprotein lipase
Degrades TG’s in chylo and VLDL’s
Hepatic TG lipase
Degrades TG’s into IDL
Hormone-sensitive lipase
Puts TG into adipocytes
LCAT
Esterifies cholesterol into nascent HDL to make mature?
CETP
Transfers cholesterol esters from mature HDL to other lipoproteins
Apo B-48 vs. B100
Chylomicron secretion vs extrahepatic uptake
Apo A-1
A-I - activates LCAT
Apo C-II
Lipoprotein lipase cofactor. Familial chylomicronemia syndrome (Acute pancreatitis)
ApoE 3 & 4
ApoE-3 &4 - VLDL and chylomicron remnant uptake by liver (ApoE4 associated w/ late-onset AD)
