First Aid: Biochemistry
Terms
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- Chromatin Structure
-
negatively charged DNA wrapped around a histone (H2A, H2B, H3, H4), connected by H1.
Condensed = hetero-, inactive
Less condensed = eu-, active - Nucleotides
-
Purines (A, G) large rings
Pyrimidines (C, U, T) small rings
PURe As Gold
CUT the PY (pie) - Eukaryotic DNA polymerases
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alpha - replicates lagging strand, synthesizes RNA primer
beta - repairs DNA
gamma - replicates mitochondrial DNA
delta - replicates leading strand
epsilon - repairs DNA - DNA repair process
-
endonuclease cleaves strand upstream
exonuclease clease strand downstream
DNA polymerase Beta fills gap - DNA repair defects lead to disease
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Xeroderma Pigmentosum (UV light)
Ataxia-Telangiectasia (X-rays)
Bloom's syndrome (radiation)
Fanconi's anemia (crosslinking agents) - Eukaryotic RNA polymerases
-
polymerase I - rRNA
polymerase II - mRNA, snRNPs
polymerase III - tRNA
no proofreading
alpha-amanitin inhibits poly II - Start and Stop Codons
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Start
AUG (Are U Going?)
Stop
UGA (U Go Away)
UAA (U Are Away)
UAG (U Are Gone) - Regulation of Gene Expression
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Promoter - where RNA polymerase/transcription factors bind upstream
TATA (25 bp upstream)
CAAT (70 bp upstream)
Enchancer - where transcription factors bind to increase expression - RNA processing
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1. 5' 7-methyl-guanine cap
stability, mediates translation
2. 3' Polyadenylation
stability, mediates nuclear export
3. Splicing out introns
for fun? - tRNA Structure
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75-90 nucleotides
anticodon end is opposite 3' aminoacyl
3' CCA sequence
chemically modified bases - tRNA charging
-
aminoacyl-tRNA synthetase
adds 1 aa to 3' end, using 1 ATP
proofreading capability - tRNA wobble
- allows many codons to match one tRNA with only the first two bases of it's anticodon
- PCR
-
ligate/denature DNA,
add premade specific probes
add heat-stable DNA polymerase
repeat until DNA sequence is amplified - Molecular Biology Techniques
-
Southern - DNA probe to find DNA
Northern - DNA probe to find RNA
Western - Ab probe to find protein
Southwestern - DNA probe for TFs - ELISA
-
labeled Ab/Ag to Ag/Ab in pt sample
used in HIV
Sn = Sp = ~100% - Inheritance Modes
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Auto Dom - structural genes
M/F affected equally
presents after puberty
Auto Rec - 25% offspring of carriers
enzyme deficiencies
present in childhood
X-link Rec - 50% sons of hetero mom
X-link Dom - all F kids of sick dad
M/F kids of sick mom
hypophosphatemic rickets
Mitochondrial - transmitted by mom
all kids may show dz
leber's hereditary optic neuropathy
mitchondrial myopathies - Variable expression
- nature and severity of phenotype varies from one pt to another
- Incomplete penetrance
- Not all individuals with mutant genotype show dz phenotype
- Pleiotropy
- one gene has greater than one effect on phenotype
- Imprinting
-
Differences in phenotype depend on whether the mutation is of maternal or paternal origin
Angelmans - maternal transmission
Prader-Willi - paternal transmission - Anticipation
- Severity of disease worsens or age of onset decreases in successive generations
- Loss of heterozygosity
- if a pt inherits or develops a mutation in a tumor suppressor gene, the complementary allele must be deleted/mutated before cancer develops (not true of oncogenes)
- Dominant negative mutation
- exerts a dominant effect because the body cannot produce enough of the normal gene product with only one functioning allele or presence of the altered gene product inhibits the normal product
- Linkage disequilibrium
- two alleles at linked loci occur together more often than probability would suggest.
- Hardy Weinberg population genetics
- assumes no migration, no mutation, no natural selection, no mating preferences
- Down Syndrome
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mental and growth retardation
trisomy 21
tested with karyotyping
1:800
increased risk with maternal age
decreased AFP in amniotic fluid
polyhydramnios - Fragile X
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mental retardation
characteristic facial features
large testes
X-linked
failure to express RNA binding protein - Sickle cell anemia
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recurrent painful crises
autosplenectomy -> imm def
autosomal recessive
1 missense mutation in beta globin
1:400 Af-Am - Cystic fibrosis
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recurrent pulmonary infections
exocrine pancreas insufficiency
infertility
autosomal recessive
mutated CFTR (Cl- channel)
1/2000 whites - Neurofibromatosis
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cafe-au-lait spots
neurofibromas
pheochromocytomas
autosomal dominant
signaling molec loss-of-fxn mutations - Duchenne's Muscular Dystrophy
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muscular weakness and degeneration
X-linked recessive
dystrophin gene deletion
Dx DNA test
pseudohypertrophy of calf - Osteogenesis Imperfecta
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increased bone fx
blue sclera - translucent CT over choroid
many mutations - abn collagen synth
1:10000 - Phenylketonuria
-
autosomal recessive
phenylalanine hydroxylase deficiency
tetrahydrobiopterin cofactor deficiency
tyrosine becomes essential
mental retardation
fair skin (decreased melanin)
eczema
musty body odor
decrease phenylalanine in diet
increase tyrosine in diet - Fabry's disease
-
X-linked recessive
alpha galactosidase deficiency
ceramide trihexoside accumulation
renal failure
peripheral neuropathy hands/feet
CV disease - Krabbe's disease
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Autosomal recessive
Bgalactosidase def
galactocerebroside accumulation
optic atrophy
peripheral neuropathy/spasticity
developmental delay - Gaucher's disease
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glucocerebrosidase def
glucocerebroside accumulation
hepatosplenomegaly
aseptic necrosis of femoral head
bone crises
Gaucher's cells (macrophages) - Niemann-Pick disease
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Autosomal recessive
sphingomyelinase def
sphingomyelin accum in reticuloendothelial cells/parenchyma
leading to organomegaly and progressive neurodegeneration
cherry red spot on macula
No Man PICKs his nose w/ a SPHINGer - Tay-Sachs disease
-
Autosomal recessive
Absence of hexosaminidase A
GM2 ganglioside accumulation
Askenazi Jews (carriers = 1/30)
death by age 3
cherry red spot on macula - Metachromatic Leukodystrophy
-
Autosomal recessive
arylsulfatase A deficiency
demyelination with w/ ataxia, dementia
Cerebroside sulfate in brain, liver, kidney, PNS - Hurler's syndrome
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Autosomal recessive
alpha-L-iduronidase deficiency
corneal clouding
gargoylism
developmental delay
Hurlers (shot put) do more damage than hunters (arrows) - Hunter's syndrome
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X-linked recessive
iduronate sulfatase deficiency
mild form of Hurler's (mild retardation)
with aggressive behavior
no corneal clouding - Lineweaver Burke plots
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noncompetitive inhibitors change the Vmax (the y-intercept will increase)
competitive inhibitors change the Km (the x-intercept will increase) - Sodium Potassium Pump
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BL membrane
moves 3 Na out, 2 K in, uses 1 ATP
inhibitied by oubain, digoxin - Collagen synthesis and structure
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hydoxylation of proline/lysine residues in RER requires Vit C
procollagen exocytosed into ECM
peptidases cleave terminal portion
self-assembly into collagen fibrils
crosslinked by lysyl oxydase - Ehlers-Danlos Syndrome
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faulty collagen synthesis causes:
hyperextensible skin
tendency to bleed
hypermobile joints - S-adenosyl methionine
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ATP + methionine = SAM
methyl group donor
makes phosphocreatine
regeneration with B12 - NAD+/NADPH
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NAD+ catabolic electron acceptor
NADPH anabolic electron donor
product of HMP shunt
makes superoxide
regenerates GSH
p450 - Glycolysis: irreversible reactions
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glu to G6P
G6P inhibits hexokinase
F6P to F1,6BP
ATP/citrate inhib PFK
F2,6BP/AMP upreg PFK
PEP to pyruvate
ATP/Ala inhib Pyr Kinase
F1,6BP upreg Pyr Kinase
Pyr to AcetylCoA
ATP/NADH/AcylCoA inhib Pyr DeH - Pyruvate Dehydrogenase Complex
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pyr + NAD+ + CoA ->
AcylCoA + CO2 +NADH
3 enzymes
5 cofactors:
B1 thiamine
B2 FAD
B3 NAD
B5 CoA
lipoic acid - Pyruvate Dehydrogenase Deficiency
-
buildup of pyruvate and alanine
reduced to lactate -> acidosis
seen in alcoholics in B1 deficiency
Rx: high fat/ketogenic nutrients - Cori cycle
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shuttles lactate from muscle to liver for regeneration to pyruvate
allows muscles to fxn anaerobically - TCA cycle
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12 ATP/Acyl CoA
24 ATP/glu molec
1st four enzymes are inhib by ATP/NADH
Cindy Is Kind So She's Friendly More Often - Gluconeogenesis: irreversible reactions
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Pyr to oxaloacetate
Pyr carb req ATP/AcylCoA/biotin
Oxaloacetate to PEP
PEP carbK req GTP
F1,6BP to F6P
F1,6BPase
G6P to glu
G6Pase
enzymes in liver, kidney, intestine
hypogly with G6Pase def (von Gierke's) - Glucose 6 Phosphate Dehydrogenase Deficiency
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rate limiting enzyme of HMP shunt
necessary for RBCs to produce NADPH for GSH regeneration
loss leads to hemolytic anemia
triggered w/ oxidizing agents: sulfas, primaquine, fava beans
Heinz bodies - Hb precipitates
prevalent in Af-Am
X-linked recessive - Fructose intolerance
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aldolase B deficiency
all phosphate accum in F1P
inhib glycogenolysis/gluconeogenesis
hypoglycemia, jaundice, cirrhosis
Rx: decrease fructose/sucrose - Galactose intolerance
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galactose-1P uridyltransferase def
accum of toxic metabolites
cataracts
hepatosplenomegaly
mental retardation
Rx: decrease galactose/lactose - Essential Amino Acids
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PVT TIM HALL
phe
val
trp
thr
ile
met
his
arg
leu
lys - Urea Cycle
-
C from CO2 (mitochondria)
N from NH4 (mitochondria)
N from aspartate (cytosol) - Phenylalanine derivatives
- Tyrosine, Dopa, DA, NE, Epi, Melanin, Thyroxine
- Tryptophan derivatives
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Niacin (NAD, NADP)
Serotonin
Melatonin - Histidine derivatives
- Histamine
- Glycine derivatives
- Porphyrin/Heme
- Arginine derivatives
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Creatine
Urea
Nitric Oxide - Homocytinuria
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defective cystathionine synthase or
defective methionine synthase
cysteine become essential
mental retardation
osteoporosis
lens subluxation
tall stature
kyphosis - Maple Syrup Urine Disease
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alpha ketoacid dehydrogenase def blocked degradation of branched aa (Ile, Leu, Val = I Love Vt maple syrup)
CNS defects, mental retardation, death - Adenosine Deaminase Definiciency
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SCID
Excess dATP prevents production of other deoxyribose nucleotides via ribonucleotide reductase
-> lymphopenia - Lesch-Nyhan Syndrome
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X-linked recessive
LNS (Lacks Nucleotide Salvage)
HGPRT deficiency -> dec IMP/GMP prod -> inc uric acid excr
retardation
self-mutilation
aggression
hyperuricemia, gout, choreoathetosis - Fatty Acid Metabolism
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Synthesis = cytosol
enters via citrate shuttle
degradation = mitochondria
enters via carnitine shuttle - von Gierke's disease
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Glycogen storage disease type I
glucose-6Pase deficiency
(liver becomes like muscle)
severe fasting hypoglycemia
glycogen accum in liver
Very - Pompe's disease
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Glycogen storage disease type II (trashes the pump)
lysomal alpha-1,4-glucosidase def
cardiomegaly
early death
Poor - Cori's Disease
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Glycogen storage disease type III
deficiency of debranching enzyme
alpha-1,6-glucosidase
Carbohydrate - Glycogen storage disease type V
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McArdle's disease
muscle glycogen phosphorylase def
glycogen in musc -> painful cramps,
myoglobinuria w/ strenuous exercise
Metabolism - Ketone bodies
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acetoacetate and betahydroxybutyrate
made in liver from HMG-CoA
excr in urine (test for acetoacetate)
elevated in starvation/DM ketoacidosis
fruity breath
converted to 2 AcetylCoA in brain - Insulin
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from pancreatic beta cells
inc glu uptake in musc/liver/fat
GLUT2 R in beta cells
GLUT4 in periphery
inhib glucagon from alpha cells
C-peptide cleaved -> activation - Glucagon vs. Insulin
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Glucagon phosphorylates
turns OFF glycogen synthase
turns ON glycogen phosphorylase
Insulin dephosphorylates
turns ON glycagen synthase
turns OFF glycagen phosphorylase - Cholesterol synthesis and esterification
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HMG-CoA reductase is the rate limiting enzyme in synthesis
inhib by Lovastatin
Esterification via LCAT - Chylomicrons
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dietary TGs to peripheral tissues, dietary chol to liver
travel in lymphatics to thoracic duct to blood
excess -> xanthomas
Apo B48 mediates excretion
Apo CII for lipoprotein lipase
Apo E mediates liver uptake - VLDL
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hepatic TGs to periphery
excess causes pancreatitis
apo B100 mediates secr
apo CII for lipoportein lipase
apo E mediates liver uptake - LDL
-
produced via VLDL modification
hepatic cholesterol to periphery
uptake via R-med endocytosis (Apo B100)
excess causes ATH, xanthomas
Bad for you - HDL
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periphery cholesterol to liver
repository for Apo C/E
Apo A-1 for LCAT & chol-esters
Good for you - Familial Hypercholesterolemia
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Increased Cholesterol/LDL
Auto Dom defect in LDL R
xanthomas
MI before 30y in homozygous pt - Familial Hypertriglyceridemia
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Increased TGs/VLDL
Hepatic overproduction of VLDL - Heme Synthesis
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Rate limiting step: glycine + succinyl CoA -> ALA via ALA synthase
occurs w/in mitochondria
inhibition -> porphyrias
Pb inhib other enzymes -> microcytic/hypochromic anemia and porphyria - Heme catabolism
-
scavenged from RBCs
heme -> biliverdin -> bilirubin
bilirubin excr in bile
converted to urobilinogen
excreted as urobilin in urine - Methemoglobinemia
-
Fe in ferric (oxidized) state
low O2 affinity - Hb structure/affinity
-
Cl, H, CO2, DPG, heat favor the T (taut) form over R (relaxed)
causes decreased O2 affinity - Vitamin A
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Retinol, in retinal pigment
deficiency: night blindness, dry skin - Vitamin B1
-
Thiamine, cofactor in pyruvate carboxylase
deficiency: Beriberi and Wernicke's encephalopathy - Vitamin B2
-
Riboflavin, FAD/FADH2
deficiency: corneal vascularization, cheilosis - Vitamin B3
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Niacin, NAD/NADH (from Trp)
deficiency: Pellagra
caused by carcinoid syndrome, INH, Hartnup Dz
Diarrhea, Dermatitis, Dememtia - Vitamin B5
-
Pantothenate -> Coenzyme A
FA synth, Kreb's Cycle
deficiency: Dermatitis, Enteritis, Alopecia, adrenal insufficiency - Vitamin B6
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Pyridoxine
Converted to Pyridoxal Phosphate
cofactor in transamination (ALT/AST) - Biotin
-
cofactor for carboxylation
1. pyruvate -> oxaloacetate
2. acetyl CoA -> malonyl CoA
3. proprionyl CoA -> methylmalonyl CoA - Folic Acid
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Coenzyme for 1-C transfer
methylation rxns for nitrogenous bases
most common vitamin deficiency in US: macrocytic, megaloblastic anemia - Vitamin B12
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Cobalamin
Cofactor for homocyteine methylation & methylmalyonyl handling
Stored in liver
deficiency caused by: malabsorption (sprue, enteritis, diphyllobothrium latum), pernicious anemia, ileectomy
Dx: Schilling test - Vitamin C
-
Ascorbic Acid
cofactor for hydroxylation of proline/lysine in collagen
facilitates Fe adsorption by keeping it reduced
Deficiency: scurvy = swollen gums, bruising, poor healing - Vitamin D
-
D2 absorbed from gut
D3 formed in skin
25OH D3 storage form
1,25OH D3 active form
increases Ca/PO4 absorption
deficiency: rickets, osteomalacia, hypoCa tetany
excess: hyperCa, stupor,
caused by sarcoidosis mphages producing active D3 - Vitamin E
-
antioxidant protects RBCs against hemolysis
increased fragility of RBCs - Vitamin K
-
synthesis of clotting factors II, VII, IX, X and Proteins C/S
synth'd by intestinal flora
deficiency seen in broad-spectrum ABx, warfarin use
inc PT, PTT, INR
Neonatal hemorrhage - Ethanol Metabolism
-
alcohol and acetaldehyde dehydrogenase produce NADH and acetate
excess NADH shunts pyruvate away from gluconeogenesis to lactate
leads to hypoglycemia and FA synth (fatty liver) - Kwashiorkor vs. Marasmus
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Kwashiorkor - protein deficiency with skin lesions, edema, fatty liver
Marasmus - protein malnutrition with muscle wasting