Biochem First Aid
Quiz yourself by thinking what should be in
each of the black spaces below before clicking
on it to display the answer.
Help!
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| DNA exists in the condensed, _________ form in order to fit into the nucleus. | chromatin
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| ____________ charged DNA loops twice around positively charged histone octamer to form nucleosome “beads on a string.” | negatively
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| Histones are rich in the amino acids ________ and _________ | lysine
arginine
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| In mitosis, DNA condenses to form chromosomes. DNA and histone synthesis occur during _ phase. | S
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| heterorchromatin: Transcriptionally ________, sterically inaccessible. (Increase/decrease) methylation, (increase/decrease) acetylation. | inactive
increase
decrease
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| Euchromatin: Less condensed, appears lighter on EM (labeled E in A ). Transcriptionally _______, sterically accessible. | active
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| base + (deoxy)ribose (Sugar) | nucleoside
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| base + (deoxy)ribose + phosphate; linked by 3′-5′ phosphodiester bond. | nucleotide
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| Deamination of ________ makes uracil. | cytosine
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| Amino acids necessary for purine (3) synthesis: | glycine, aspartate, glutamine
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| ___________ inhibits thymidylate synthase (decreases dUMP --> dTMP) | 5-florouracil (5-FU)
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| inhibit dihydrofolate reductase (decrease deoxythymidine monophosphate [dTMP]) in humans, bacteria, and protozoa, respectively | methotrexate,
trimethoprim
pyrimethamine
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| Defective purine salvage due to absent HGPRT, which converts hypoxanthine to IMP and guanine to GMP. Results in excess uric acid production and de novo purine synthesis. X-linked recessive. | Lesch-Nyhan syndrome
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| Findings: intellectual disability, self-mutilation, aggression, hyperuricemia (orange “sand” [sodium urate crystals] in diaper), gout, dystonia. | Lesch-Nyhan syndrome
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| Starting 2 molecules for pyrmidine synthesis | Glutamine + CO2
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| One of the major causes of autosomal recessive SCID. | Adenosine deaminase
deficiency
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| definition explains Most amino acids are coded by multiple codons. Codons that differ in 3rd, “________” position may code for the same tRNA/amino acid. Specific base pairing is usually only required in the first 2 nucleotide positions of mRNA codon. | wobble
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| Genetic code is conserved throughout evolution. Exception in humans: _______________. | mitochondria
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| DNA replication is ______________, involves both continuous and discontinuous (Okazaki fragment) synthesis, and occurs in the 5′ --> 3′ direction. | semi-conservative
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| function of helicase | Unwinds DNA template at replication fork.
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| Single-stranded binding proteins function: | Prevent strands from reannealing.
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| ____________ inhibit prokaryotic topoisomerase II (DNA gyrase) and topoisomerase IV. | Fluoroquinolones
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| Transition mutation | purine to purine (eg, A to G) or pyrimidine to pyrimidine (eg, C to T).
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| Transversion mutation | purine to pyrimidine (eg, A to T) or pyrimidine to purine (eg, C to G).
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| type of mutation: Nucleotide substitution but codes for same (synonymous) amino acid; often base change in 3rd position of codon (tRNA wobble). | silent
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| type of mutation: Nucleotide substitution resulting in changed amino acid (called conservative if new amino acid is similar in chemical structure). | missence
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| type of mutation: Nucleotide substitution resulting in early stop codon (UAG, UAA, UGA). Usually results in nonfunctional protein. | nonsense
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| Type of mutation: Deletion or insertion of a number of nucleotides not divisible by 3, resulting in misreading of all nucleotides downstream. Protein may be shorter or longer, and its function may be disrupted or altered. | Frameshift
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| Duchenne muscular dystrophy, Tay-Sachs disease are caused by a _______________ mutation | Frameshift
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| Lac operon: (low/high) glucose: increased adenylate cyclase activity leads to increased generation of cAMP from ATP leads to activation of catabolite activator protein (CAP) and increases transcription. | low
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| Lac operon: High lactose --> unbinds repressor protein from repressor/operator site leads to (increase or decrease) transcription. | increase
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| Defective in xeroderma pigmentosum, which prevents repair of _________ __________ that are formed as a result of ultraviolet light exposure. | pyrimidine dimers
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| Specific endonucleases release the oligonucleotides containing damaged bases; DNA polymerase and ligase fill and reseal the gap, respectively. Repairs bulky helix-distorting lesions. Occurs in __ phase of cell cycle. | G1 (Nucleotide excision
repair)
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| Newly synthesized strand is recognized, mismatched nucleotides are removed, and the gap is filled and resealed. Occurs predominantly in ___ phase of cell cycle. | G2 (Mismatch repair)
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| Promoter mutation commonly results in dramatic __________ in level of gene transcription | decrease
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| α-amanitin, found in Amanita phalloides (death cap mushrooms), __________ RNA polymerase II. Causes severe hepatotoxicity if ingested | inhibits
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| Site of synthesis of secretory (exported) proteins and of N-linked oligosaccharide addition to many proteins. | Rough endoplasmic
reticulum
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| Site of steroid synthesis and detoxification of drugs and poisons. Lacks surface ribosomes. ex.Liver hepatocytes and steroid hormone– producing cells of the adrenal cortex and gonads | Smooth endoplasmic
reticulum
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| inherited lysosomal storage disorder; defect in N-acetylglucosaminyl-1-phosphotransferase failure of the Golgi to phosphorylate mannose residues (ie, mannose-6-phosphate) on glycoproteins | i-cell
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| Membrane-enclosed organelle involved in catabolism of very-long-chain fatty acids (through β-oxidation), branched-chain fatty acids, amino acids, and ethanol. | Peroxisome
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| Barrel-shaped protein complex that degrades damaged or ubiquitin-tagged proteins. | Proteasome
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| Defects in the ubiquitin-proteasome system have been implicated in some cases of _____________ ____________ | Parkinson disease.
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| Peroxisomal disorders commonly lead to neurologic diseases due to deficits in synthesis of plasmalogens, important phospholipids in myelin. Name 2 | Zellweger
syndrome (hypotonia, seizures, hepatomegaly, early death) and Refsum disease (scaly skin, ataxia,
cataracts/night blindness, shortening of 4th toe, epiphyseal dysplasi
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| Most common collagen (90%)—Bone (made by osteoblasts), Skin, Tendon, dentin, fascia, cornea, late wound repair. | type 1
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| Cartilage (including hyaline), vitreous body, nucleus pulposus. | Type II: cartwolage.
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| Hydroxylation—hydroxylation of specific proline and lysine residues. Requires vitamin _, defiency leads to ________ | C, Scurvy
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| XR connective tissue disease caused by impaired Cu absorption and transport due to defective _____ protein (ATP7A). decreases activity of lysyl oxidase. Results in brittle, “kinky” hair, growth retardation, and hypotonia. (disease same as protien) | Menkes disease
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| Lac operon: Low glucose Lactose available | Lac genes strongly expressed
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| Lac operon: High glucose Lactose unavailable | Lac genes not expressed
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| Lac operon: Low glucose Lactose unavailable | Lac genes not expressed
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| Lac operon: High glucose Lactose available | Very low (basal) expression
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| Promoter mutation commonly results in dramatic ____________ in level of gene transcription. | Decrease
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| _____________ deficiency results in excess elastase activity, which can cause emphysema. Wrinkles of aging are due to collagen and elastin production. | α1-Antitrypsin
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| Marfan syndrome—autosomal ___________ connective tissue disorder affecting skeleton, heart, and eyes. FBN1 gene mutation on chromosome 15 results in defective fibrillin, a glycoprotein that forms a sheath around elastin. | dominant
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| disease: tall w/ long extremities; pectus carinatum or pectus excavatum; hypermobile joints; long, tapering fingers & toes (arachnodactyly);and dissecting aortic aneurysms; floppy mitral valve. Subluxation of lenses, | Marfan syndrome
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| acronym for remembering differents in blot: SNoW DRoP | Southern = DNA
Northern = RNA
Western = Protein
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| Thousands of nucleic acid sequences are arranged in grids on glass or silicon. DNA or RNA probes are hybridized to the chip, and a scanner detects the relative amounts of complementary binding. | Microarrays
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| A process in which metaphase chromosomes are stained, ordered, and numbered according to morphology, size, arm-length ratio, and banding pattern | Karyotyping
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| Can be performed on a sample of blood, bone marrow, amniotic fluid, or placental tissue. Used to diagnose chromosomal imbalances (eg, autosomal trisomies, sex chromosome disorders). | Karyotyping
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| dsRNA is synthesized that is complementary to the mRNA sequence of interest. When transfected into human cells, dsRNA separates and promotes degradation of target mRNA, “knocking down” gene expression. | RNA interference
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| Both alleles contribute to the phenotype of the heterozygote. eg.Blood groups A, B, AB; α1-antitrypsin deficiency. | Codominance
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| Patients with the same genotype have varying phenotypes. eg.2 patients with neurofibromatosis type 1 (NF1) may have varying disease severity. | Variable expressivity
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| Not all individuals with a mutant genotype show the mutant phenotype. eg.BRCA1 gene mutations do not always result in breast or ovarian cancer. | Incomplete
penetrance
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| One gene contributes to multiple phenotypic effects. eg.Untreated phenylketonuria (PKU) manifests with light skin, intellectual disability, and musty body odor. | Pleiotropy
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| Increased severity or earlier onset of disease in succeeding generations. eg. Trinucleotide repeat diseases (eg, Huntington disease). | Anticipation
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| If a patient inherits or develops a mutation in a tumor suppressor gene, the complementary allele must be deleted/mutated before cancer develops. This is not true of oncogenes. | Loss of heterozygosity
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| Mutations at different loci can produce a similar phenotype. eg. Albinism. | Locus heterogeneity
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| Different mutations in the same locus produce the same phenotype. eg. β-thalassemia. | Allelic heterogeneity
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| Presence of both normal and mutated mtDNA, resulting in variable expression in mitochondrially inherited disease. | Heteroplasmy
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| Hardy-Weinberg law assumptions include: (4) | No mutation occurring at the locus
Natural selection is not occurring
Completely random mating
No net migration
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| At some loci, only one allele is active; the other is inactive (imprinted/inactivated by methylation). With one allele inactivated, deletion of the active allele --> disease. | Imprinting
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| Sons of heterozygous mothers have a 50% chance of being affected. No male-to-male transmission. Skips generations. | X-linked recessive
note bono: Commonly more severe in males. Females
usually must be homozygous to be affected.
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| Transmitted through both parents. Mothers transmit to 50% of daughters and sons; fathers transmit to all daughters but no sons. | X-linked dominant
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| Robertsonian translocation: Chromosomal translocation that commonly involves chromosome pairs __,__,__,__,__, | 13, 14, 15, 21, and 22
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| Congenital microdeletion of short arm of chromosome __ (46,XX or XY, 5p−). Findings: microcephaly, moderate to severe intellectual disability, high-pitched crying/ meowing, epicanthal folds, cardiac abnormalities (VSD). | 5
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| Congenital microdeletion of long arm of ch.7 deleted region includes elastin gene). Findings: distinctive “elfin” facies, intellectual disability, hypercalcemia, well-developed verbal skills, extreme friendliness with strangers, cardiovascular problems. | wilson's disease
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| rare disorders; often present with myopathy, lactic acidosis, and CNS disease, eg, MELAS syndrome 2° to failure in oxidative phosphorylation. Muscle biopsy often shows “ragged red fibers” (due to accumulation of diseased mitochondria | Mitochondrial myopathies
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| Autosomal recessive; defect in CFTR gene on chromosome 7; commonly a deletion of Phe508. Most common lethal genetic disease in Caucasian population. | Cystic fibrosis
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| X-linked dominant inheritance. Trinucleotide repeat in FMR1 gene hypermethylation | Fragile X syndrome
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| Most common cause of inherited intellectual disability and autism and 2nd most common cause of genetically associated mental deficiency (Down syndrome#1). Post-pubertal macroorchidism (big testes), long face w/ a large jaw, large everted ears, autis | Vitamin A (retinol) deficiency
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| Acute toxicity—nausea, vomiting, vertigo, and blurred vision. Chronic toxicity—alopecia, dry skin (eg, scaliness), hepatic toxicity and enlargement, arthralgias, and pseudotumor cerebri. | Vitamin A (retinol) excess
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| vitamin co-factor -Pyruvate dehydrogenase (links glycolysis to TCA cycle) -α-ketoglutarate dehydrogenase (TCA cycle) -Transketolase (HMP shunt) -Branched-chain ketoacid dehydrogenase | Vitamin B1 (thiamine)
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| _________________ syndrome—confusion, ophthalmoplegia, ataxia (classic triad) + confabulation, personality change, memory loss (permanent). Damage to medial dorsal nucleus of thalamus, mammillary bodies. | Wernicke-Korsakoff
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| vitamin deficiency: Impaired glucose breakdown ATP depletion worsened by glucose infusion; highly aerobic tissues (eg, brain, heart) are affected first. In alcoholic or malnourished patients, | Vitamin B1 (thiamine)
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| vitamin def: Cheilosis (inflammation of lips, scaling and fissures at the corners of the mouth), Corneal vascularization. | Vitamin B2 (riboflavin) (The 2 C’s of B2).
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| Constituent of NAD+, NADP+ (used in redox reactions). Derived from tryptophan. Synthesis requires vitamins B2 and B6. Used to treat dyslipidemia; lowers levels of VLDL and raises levels of HDL. | Vitamin B3 (niacin)
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| Symptoms of________ : Diarrhea, Dementia (also hallucinations) , Dermatitis (C3/C4 dermatome circumferential “broad collar” rash [Casal necklace], hyperpigmentation of sunexposed limbs A ). | pellagra (The 3 D’s of B3.)
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| Essential component of coenzyme A (CoA, a (vitamin) cofactor for acyl transfers) and fatty acid synthase. | Vitamin B5 (pantothenic acid)
(B5 is “pento”thenic acid)
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| Converted to tetrahydrofolic acid (THF), a coenzyme for 1-carbon transfer/methylation reactions. Important for the synthesis of nitrogenous bases in DNA and RNA. | Vitamin B9 (folate)
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| vit. def: Macrocytic, megaloblastic anemia; hypersegmented polymorphonuclear cells (PMNs); glossitis; no neurologic symptoms (as opposed to vitamin B12 deficiency) | Vitamin B9 (folate)
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| Cofactor for methionine synthase (transfers CH3 groups as methylcobalamin) and methylmalonyl-CoA mutase. Important for DNA synthesis. | Vitamin B12 (cobalamin)
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| Antioxidant; also facilitates iron absorption by reducing it to Fe2+ state. Necessary for hydroxylation of proline and lysine in collagen synthesis. Necessary for dopamine β-hydroxylase, which converts dopamine to NE. | Vitamin C (ascorbic acid)
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| ________ - swollen gums, bruising, petechiae, hemarthrosis, anemia, poor wound healing, perifollicular and subperiosteal hemorrhages, “corkscrew” hair. Weakened immune response | Scurvy (vit. C deficiency)
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| Vit excess: Nausea, vomiting, diarrhea, fatigue, calcium oxalate nephrolithiasis. Can risk of iron toxicity in predisposed individuals (eg, those with transfusions, hereditary hemochromatosis). | Vitamin C (ascorbic acid)
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| vitamin D_ = ergocalciferol—ingested from plants. | 2
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| vitamin D__ = cholecalciferol—consumed in milk, formed in sun-exposed skin (stratum basale). | 3
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| what is '1,25-(OH)2 D3 (calcitriol)' | activie form of vit. D
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| vit def: Rickets in children, osteomalacia in adults (bone pain and muscle weakness), hypocalcemic tetany. Breastfed infants should receive oral vitamin __. Exacerbated by low sun exposure, pigmented skin, prematurity. | Vitamin D
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| Antioxidant (protects RBCs and membranes from free radical damage). High-dose supplementation may alter metabolism of vitamin K --> enhanced anticoagulant effects of warfarin. | Vitamin E (tocopherol/tocotrienol)
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| vit def: Hemolytic anemia, acanthocytosis, muscle weakness, posterior column and spinocerebellar tract demyelination. | Vitamin E (tocopherol/tocotrienol)
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| Activated by epoxide reductase to the reduced form, which is a cofactor for the γ-carboxylation of glutamic acid residues on various proteins required for blood clotting. Synthesized by intestinal flora. | Vitamin K (phytomenadione, phylloquinone, phytonadione)
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| Necessary for the maturation of clotting factors II, VII, IX, X, and proteins C and S. Warfarin inhibits vitamin __–dependent synthesis of these factors and proteins. | K, K is for Koagulation. Necessary for the
maturation of clotting factors II, VII, IX,
X
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| Mineral essential for the activity of 100+ enzymes. Important in the formation of ____ fingers (transcription factor motif). | zinc
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| Delayed wound healing, hypogonadism, adult hair (axillary, facial, pubic), dysgeusia, anosmia, acrodermatitis enteropathica A . May predispose to alcoholic cirrhosis. | zinc DEFICIENCY
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| __________—inhibits alcohol dehydrogenase and is an antidote For Overdoses of Methanol or Ethylene glycol. | FOMEpizole
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| __________—inhibits acetaldehyde dehydrogenase (acetaldehyde accumulates, contributing to hangover symptoms), discouraging drinking. | Disulfiram
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| ____ NADH/NAD+ causes: Pyruvate--> lactate (lactic acidosis) Oxaloacetate--> malate (prevents gluconeogenesis-->fasting hypoglycemia) DHAP-->glycerol- 3-phosphate (combines with fatty acids to make triglycerides--> hepatosteatosis | high
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| ________ metabolism: Fatty acid oxidation (β-oxidation), acetyl- CoA production, TCA cycle, oxidative phosphorylation, ketogenesis. | Mitochondria
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| ________ metabolism :Glycolysis, HMP shunt, and synthesis of steroids (SER), proteins (ribosomes, RER), fatty acids, cholesterol, and nucleotides. | cytooplasm
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| type of enzyme: Catalyzes transfer of a phosphate group from a high-energy molecule (usually ATP) to a substrate (eg, phosphofructokinase). | Kinase
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| type of enzyme: Adds inorganic phosphate onto substrate without using ATP | phosphorylase
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| type of enzyme: Removes phosphate group from substrate | Phosphatase
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| type of enzyme: Catalyzes oxidation-reduction reactions | Dehydrogenase
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| type of enzyme: Adds hydroxyl group | Hydroxylase
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| type of enzyme: Transfers CO2 groups with the help of biotin | Carboxylase
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| type of enzyme: Relocates a functional group within a molecule | Mutase, (eg, vitamin B12–dependent methylmalonyl-CoA
mutase)
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| type of enzyme:Combines 2 molecules into 1 (condensation reaction) either using an energy source or not. | Synthase/synthetase
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| NADPH is a product of the ____________ and used for: (4) | HMP shunt.
Anabolic processes
Respiratory burst
Cytochrome P-450 system
Glutathione reductase
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| Location of Hexokinase and is it induced by insulin? | Most tissues, except liver
and pancreatic β cells and no
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| Causes a buildup of pyruvate that gets shunted to lactate (via LDH) and alanine (via ALT). X-linked. Neurologic defects, lactic acidosis, increased serum alanine starting in infancy. | Pyruvate
dehydrogenase
complex deficiency
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| 2,4-Dinitrophenol (used illicitly for weight loss), aspirin (fevers often occur after aspirin overdose), thermogenin in brown fat. these can cause what? | Uncoupling agents
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| ATP synthase inhibitor | Oligomycin. Directly inhibit mitochondrial ATP synthase,
causing an proton gradient. No ATP is
produced because electron transport stops.
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| Essential fructosuria | Involves a defect in fructokinase. Autosomal recessive. A benign, asymptomatic condition, since
fructose is not trapped in cells.
Symptoms: fructose appears in blood and urine.
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| Hereditary deficiency of aldolase B. Autosomal recessive. Fructose-1-phosphate accumulates, causing a in available phosphate, which results in inhibition of glycogenolysis and gluconeogenesis. | Fructose intolerance
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| Hereditary deficiency of galactokinase. Galactitol accumulates if galactose is present in diet. Relatively mild condition. Autosomal recessive. Symptoms: galactose appears in blood (galactosemia) and urine (galactosuria); | Galactokinase
deficiency
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| Galactokinase deficiency |
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| absence of galactose-1-phosphate uridyltransferase. Autosomal recessive. Damage is caused by accumulation of toxic substances (including galactitol, which accumulates in the lens of the eye). | Classic galactosemia
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| DEFICIENT ENZYME : Glucose-6-phosphatase | Von Gierke disease
(type I)
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| DEFICIENT ENZYME: Lysosomal acid α-1,4- glucosidase with α-1,6- glucosidase activity (acid maltase) | Pompe disease
(type II) (PomPe trashes the PumP (1,4)
(heart, liver, and muscle)
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| DEFICIENT ENZYME; Debranching enzyme (α-1,6-glucosidase) | Cori disease
(type III) (Gluconeogenesis is intact)
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| DEFICIENT ENZYME; Skeletal muscle glycogen phosphorylase (Myophosphorylase) | McArdle disease
(type V)
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| Disease and Enzyme: Early: Triad of episodic peripheral neuropathy, angiokeratomas B , hypohidrosis. Late: progressive renal failure, cardiovascular disease. | Fabry disease, α-galactosidase A
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| Disease and Enzyme: Progressive neurodegeneration, developmental delay, “cherry-red” spot on macula A , lysosomes with onion skin, no hepatosplenomegaly (vs Niemann-Pick). | Tay-Sachs disease, HeXosaminidase A
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| Disease and Enzyme; Peripheral neuropathy, destruction of oligodendrocytes, developmental delay, optic atrophy, globoid cells. | Krabbe disease, Galactocerebrosidase
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| Disease and Enzyme: Most common. Hepatosplenomegaly, pancytopenia, osteoporosis, avascular necrosis of femur, bone crises, Gaucher cells C (lipid-laden macrophages resembling crumpled tissue paper). | Gaucher disease, Glucocerebrosidase
(β-glucosidase); treat
with recombinant
glucocerebrosidase
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| Disease and Enzyme: Progressive neurodegenera tion, hepatosplenomegaly, foam cells (lipid-laden macrophages) D, “cherry-red” spot on macula A . | Niemann-Pick disease, Sphingomyelinase
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