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full term neonate of uneventful delivery becomes mentally retarded, hyperactive and develops musty odor. diagnosis?
executive consumes 8 martinis quickly after dinner and becomes hypoglycemic. mxn?
NADH increase -> prevents gluconeogenesis by shunting pyruvate and oxaloacetate to lactate and malate
2yr old girl has increased abdominal girth, failure to thrive, skin and hair depigmentation. diagnosis?
kWASHiorkor (needs to WASH skin and hair due to discoloration)
alcoholic develops rash, diarrhea, altered mental status. vitamin deficiency?
vitamin B3 (pellagra)
most common cause of idiopathic hyperbilirubinemia in young adults?
Gilbert's disease
51yr old man has black spots in sclera and his urine turns black when peeing. diagnosis?
young adult complains of severe chest pain and has xanthomas of Achilles tendon. disease and defect?
Familial hypercholesterolemia; LDL receptor
inactive DNA (heteros are inactive in New Haven)
charge on histones? which one links nucleosomes?
+ charge on histones (DNA is negatively charged) H1 links
how are nucleotides linked?
3' to 5' phosphodiesterase bond
transition mutation? transversion mutation?
transition: purine to purine or pyrimidine to pyrimidine transversion: purine to pyrimidine or vice versa
nonsense mutation? missense?
NonSense: New Stop codon missense: aa is changed (conservative - similar aa structure)
how does DNA replication begin? (prokaryote)
primase makes RNA primer and DNA polymerase III elongates on the 3' end
what degrades the RNA primer? what seals DNA strands together? (prokaryote) (this is replication)
DNA polymerase I (5'to3' exonuclease) DNA ligase
how does DNA polymerase III work? (prokaryote)
5' to 3' synthesis and proofreads 3' to 5'
how many origins of replication do eukaryotes have in DNA? where does it begin?
many origins consensus sequence of AT base pairs
how are eukaryotic polymerases named?
alpha beta gamma...etc.
what enzymes are involved in single strand DNA repair?
1. glycosylase recognizes error and removes damaged base 2. endonuclease makes break several bases to the 5' side 3. exonuclease removes short stretch 4. DNA polymerase fills gap 5. DNA ligase seals
Xeroderma pigmentosum
skin sensitivity to UV light; associated with dry skin and melanoma and other cancers; can't repaire thymidine dimers formed from UV light autosomal recessive DNA repair defect
x-ray damage to DNA DNA repair defect
Bloom's syndrome
radiation damage to DNA DNA repair defect
Fanconi's anemia
damage from cross-linking agents DNA repair defect
in what direction are DNA, RNA and protein synthesis conducted? in what direction are proteins linked?
5' to 3' N to C (proteins are NiCe)
on what nucleotide is the energy source during nucleic acid synthesis?
5' end of incoming nucleotide
what are the 3 types of RNA and special characteristics?
rRNA -> most abundant (Rampant) mRNA -> largest (Massive) tRNA -> smallest (Tiny)
in eukaryotes, what RNA polymerases make what RNA types?
rRNA -> RNA polymerase I mRNA -> RNA polymerase II tRNA -> RNA polymerase III "RMT" sounds like "123"
what RNA polymerase opens DNA at promotor site (AT rich sequence like TATA or CAAT)? what can inhibit the RNA polymerase? remember: eukaryotes have the numbered RNA polymerases!!
RNA polymerase II "cuts DNA in 2" inhibited by alpha-amantin
are there special RNA polymerase types in prokaryotes?
what are the start codons in eukaryotes and prokaryotes and what do they code for?
AUG (rarely GUG) is the initiation codon eukaryotes: methionine (may be removed before translation is done) prokaryotes: formyl-methionine (f-met)
what is the gene promotor? what happens if the promotor has a mutation?
site where RNA polymerase and other transcription factors bind to DNA upstream from the gene mutation: dramatic decrease in gene expression
what's a gene enhancer?
stretch of DNA that alters gene expression by binding transcription factors; may be close to or far from or even within (in an intron) the gene being regulated
what are exons?
exons EXit the nucleus and are EXpressed by the cell
what are snRNP's?
small nuclear ribonucleoprotein particles; they facilitate splicing by binding to primary RNA transcripts and forming spliceosomes
where does RNA processing occur in eukaryotes?
in the nucleus; only processed RNA can leave the nucleus
what RNA processing occurs in the nucleus?
1. capping on 5' end (7-methyl-G) 2. polyadenylation on 3' end (~200 A's) 3. splicing out introns
what is the initial RNA transcript called? after processing?
heterogeneous nuclear RNA (hnRNA) mRNA
what does tRNA have at the 3' end?
a CCA sequence and it covalently binds the appropriate amino acid
what is aminoacyl-tRNA synthetase?
charges correct amino acid on the appropriate tRNA
where does the energy come from for forming peptide bonds between aa's?
from the aa-tRNA bond on the 3' end of the tRNA
what are the 3 ribosomal sites in protein synthesis?
EPA E: uncharged tRNA (Exit) P: tRNA with growing Peptide A: incoming tRNA to be Added
what is the energy source for tRNA gripping and translocation?
what is PCR used for?
synthesis many copies of a desired DNA fragment
what are the steps of PCR (polymerase chain reaction)?
1. denature DNA by heating to make 2 strands 2. DNA primers anneal to specific sequence on each strand during cooling 3. heat-stable DNA polymerase replicates DNA sequence following each primer repeat several times for amplification!
what are the targets of Southern blot, Northern blot and Western blot?
SNoW DRoP Southern: DNA Northern: RNA Western: protein
what is the technique in Southern and Northern blots?
Southern: DNA is electrophoresed on gel and then transferred to filter; filter soaked in denaturant and then labeled DNA probe is added to filter to visualize on film Northern: same thing, but radioactive DNA binds to the RNA
how does Western blot work?
protein is electrophoresed then transferred to filter; labeled antibody is used to bind relevant protein
what is the ELISA technique?
Enzyme-Linked Immunosorbent Assay; a rapid immunologic technique where the target is either a pt's antibody or a suspected antigen; in the reaction, a positive result yields an intense color change in the test sensitivity and specificity are close to 100%
transmitted only through mom. all offspring of affected mom can show disease. inheritance?
mitochondrial inheritance
transmitted through both parents. ALL female offspring of affected dad are diseased. inheritance?
X-linked dominant
no male to male transmission. sons of heterozygous moms have 50% chance of being affected. inheritance?
X-linked recessive
25% of offspring from 2 carrier parents affected. often seen in only one generation and often enzyme deficiency. inheritance?
autosomal recessive
often pleiotropic and presents clinically often after puberty. inheritance?
autosomal dominant
what's more severe, AR or AD inherited diseases?
variable expression
nature and severity of phenotype varies among individuals
incomplete penetrance
not everyone with mutant genotype shows the mutant phenotype
1 gene has more than 1 effect on phenotype
differences in phenotype depend on mutation is of maternal or paternal origin
severity of disease worsens or age of onset is earlier in succeeding generations
loss of heterozygosity. what is it and in what gene types is it a problem?
pt inherits or develops mutation in a tumor suppressor gene, but the other allele must be damaged to develop cancer. oncogenes only need one allele to be damaged
dominant negative mutation
heterozygote produces non-functional altered protein that also prevents normal gene from functioning
linkage disequilibrium
tendency for alleles at 2 linked loci to occur together more often than predicted by chance in the population
cells in the body have different genetic makeup
what is assumed in Hardy Weinberg equilibrium?
1. no mutation at locus 2. no selection for that genotype 3. random mating 4. no migration in or out of population
what is the Hardy Weinberg equation and what do the variables mean?
p^2 + 2pq + q^2 = 1 p,q are 2 alleles 2pq = heterozygote prevalence p + q = 1
what 2 lysosomal diseases are X-recessive inheritance?
Fabry's disease and Hunter's syndrome
Fabry's disease. findings and deficiency?
peripheral neuropathy of hands/feet, angiokeratomas, CV and renal disease alpha-galactosidase A
Gaucher's disease. findings and deficiency?
hepatosplenomegaly, asceptic necrosis of femur, bone crises, Gaucher's cells (macrophages) beta-glucocerebrosidase
Niemann-Pick disease. findings and deficiency?
progressive neurodegeneration, hepatosplenomegaly, cherry red spot on macula sphingomyelinase
Tay-Sachs disease. findings and deficiency?
progressive neurodegeneration, developmental delay, cherry-red spot, lysozymes with onion skin hexosaminidase A
Krabbe's disease. findings and deficiency?
peripheral neuropathy, developmental delay, optic atrophy beta-galactosidase
Metachromatic leukodystrophy. findings and deficiency?
central and peripheral demyelination with ataxia and dementia arylsulfatase A
Hurler's syndrome. findings and deficiency?
developmental delay, gargoylism, airway obstruction, corneal clouding, hepatosplenomegaly alpha-L-iduronidase
Hunter's syndrome. findings and deficiency?
mild Hurler's plus aggressive behavior and no corneal clouding iduronate sulfatase
Hunter's syndrome. biochem?
iduronate sulfatase (low) heparan sulfate, dermatan sulfate (high)
Hurler's syndrome. biochem?
alpha-L-iduronidase (low) heparan sulfate, dermatan sulfate (high)
metachromatic leukodystrophy. biochem?
arylsulfatase A (low) cerebroside sulfate (high)
Krabbe's disease. biochem?
beta-galactosidase (low) galactocerebroside (high)
Tay Sachs disease. biochem?
hexosaminidase A (low) GM2 ganglioside (high)
Niemann Pick disease. biochem?
sphingolyelinase (low) sphingomyelin (high)
Gaucher's disease. biochem?
beta-glucocerebrosidase (low) glucocerebroside (high)
Fabry's disease. biochem?
alpha-galactosidase A (low) ceramide trihexoside (high)
enzyme kinetics: what is Km? how is it related to enzyme affinity?
Km = [S] at 1/2 Vmax low Km means high affinity
how do competitive and non-competitive inhibitors compare?
competitive: bind to active sites like substrates, high substrate conc. will overcome inhibitor, Vmax unchanged and Km goes up non-competitive: bind to enzyme but not necessarily to active site, inhibition is NOT overcome by more substrate, Vmax is lower and Km is unchanged
enzyme kinetics: graph of (1/V) vs. (1/[S]), what are the X and Y intercepts?
X intercept = 1/(-Km) Y intercept = 1/Vmax
most cells are in what phase? rapidly dividing cells have a shorter XX phase.
Go G1
what are plasma membranes made of? what is cholesterol for?
cholesterol (~50%), phospholipids (~50%), sphingolipids, glycolipids, proteins cholesterol is for membrane stability
what are the uses of phosphatidylcholine (lecithin)?
component of... RBC membrane, myelin, bile, surfactant used in esterification of cholesterol
what does ouabain do?
inhibits Na/K ATPase by binding to K+ site
what does the beta1 receptor do?
+ HR, + contractility, + renin release, + lipolysis, + aqueous humor production
what does the H1 receptor do?
+ nasal and bronchial mucus production, contraction of bronchioles, pruritis and pain
what receptors act on Gq -> phospholipase C -> IP3 ?
a1, H1, M1, V1, M3
what receptors act on Gi which inhibit adenylyl cyclase?
a2, M2, D2
what receptors act on Gs to stimulate cAMP production?
B1, B2, D1, H2, V2
what is collagen?
most abundant protein in human body; organizes and strengthens extracellular matrix
what is most abundant collagen type? where is it located?
type I (90%) ("one is bONE") bone, tendon, skin, dentin, fascia, cornea, late wound repair
type II collagen
two is "carTWOlage" cartilage (incl hyaline), vitreous body, nucleus pulposus
type III
aka. reticulin (reTHREEculin) skin, blood vessels, uterus, fetal tissue, granulation tissue
type IV
"four is under the FLOOR" basement membrane or basal lamina
type X
epiphyseal plate of bone
what vitamin is required for hydroxylation step in ER for collagen production?
vitamin C
what are the 2 key ingredients in collagen synthesis?
lysyl and prolyl residues
Ehler Danlos syndrome
faulty collagen synthesis causing: 1. hyperextendible skin 2. easy bruising and bleeding 3. hypermobile joints 4. associated with berry aneuryisms
what collagen disease might be confused with child abuse?
osteogenesis imperfecta
what are signs of osteogenesis imperfecta?
1. multiple fractures (brittle bone disease) during birth 2. blue sclerae 3. hearing loss (abnormal middle ear bones) 4. dental imperfections
malate shuttle produces X ATPs. G3P shuttle produces Y ATPs.
X = 38 Y = 36
what is S-adenosyl-methionine (SAM) used for?
transfer methyl units SAM the methyl donor man
what vitamin is necessary for methionine synthesis?
vitamin B12
how is GABA made and what vitamin is necessary?
glutamate decarboxylase need B6
what are 3 uses for NADPH?
1. anabolic processes 2. respiratory burst 3. p450 cytochrome system
how is NADPH made?
HMP shunt and the malate dehydrogenase reaction
what is the rate-limiting step in glycolysis? is it reversible?
phosphofructokinase irreversible
what are the 3 irreversible enzymes in glycolysis?
1. hexokinase/glucokinase 2. phosphofructokinase 3. pyruvate kinase
the 3 irreversible enzymes in glycolysis are... 1. hexokinase 2. phosphofructokinase 3. pyruvate kinase what reactions do they control?
1. D-glucose -> glucose-6-phosphate 2. fructose-6-P -> fructose-1,6-BP 3. phosphoenolpyruvate -> pyruvate
what enzyme catalyzes the conversion of pyruvate to acetyl-CoA? is it reversible?
pyruvate dehydrogenase NO
where do you find glucokinase? what does it do?
in the liver phosphorylates glucose-6-phosphate to sequester in the liver
how many ATPs are needed to make glucose from pyruvate?
6 ATP equivalents
what electron acceptors are made using niacin and riboflavin?
NAD+ and FAD+
what is NADPH used for?
provides reducing equivalents for fatty acid synthesis and allows for reduction of glutathione
why is vitamin B12 important?
1. helps form methionine by tranferring methyl group from tetrahydrofolate to homocysteine
TCA intermediates are used to make what in the fasting state? fed state?
glucose during fasting fatty acids during fed state
what are the cofactors for the pyruvate dehydrogenase complex?
same as those for alpha-ketoglutarate dehydrogenase: 1. thiamine 2. pantothenate 3. niacin 4. riboflavin 5. lipoic acid
where is pyruvate dehydrogenase located?
in the mitochondrial matrix
what are the 2 important products of the pentose phosphate pathway?
NADPH and ribulose 5-phosphate
what is ribulose 5-phosphate used for?
provides ribose 5-phosphate for nucleotide biosynthesis
how are ketone bodies formed during fasting?
triacylglycerol from adipose tissue splits into fatty acids and glycerol and ends up in the liver the liver converts fatty acids to acetyl CoA and then to ketone bodies
what happens to glycerol during fasting? where does the glycerol come from?
glycerol is used to form glucose to deliver to brain and RBCs glycerol comes from splitting triacylglycerol into fatty acids and glycerol
how can alcohol cause hypoglycemia?
alcohol metabolism leads to high NADH levels, which inhibit gluconeogenesis
how can alcohol cause lactic acidosis?
high NADH levels promote pyruvate to lactate conversion
what is the big picture problem in glycogen storage diseases?
glycogen accumulates in the liver or muscle or both due to enzyme deficiencies
in general, what are mucopolysaccharidoses and gangliosidoses?
these are also known as lysosomal storage diseases, they occur in deficiency of lysosomal enzymes prevent full degradation of carbohydrate portions of proteoglycans and sphingolipids tissues are engorged with residual bodies
in what part of the cell does the HMP shunt (pentose phosphate pathway) occur? in what tissues does it predominate?
in the cytoplasm tissues needing fatty acid and steroid synthesis (mammary glands, liver, adrenal glands)
what is glucose-6-phosphate dehydrogenase?
rate-limiting enzyme in HMP shunt (pentose phospate pathway)
protein malnutrition resulting in skin lesions, edema, liver malfunction (fatty change). small child with large belly. NO wasting.
Kwashiorkor MEAL Malabsorption Edema Anemia Liver (fatty)
what malnutrition disease can occur in the developed world due to trauma or after a serious surgery?
protein-calorie malnutrition resulting in tissue wasting.
swollen gums, bruising, anemia, poor wound healing. disease?
scurvy due to vitamin C deficiency
what vitamin is needed to keep Fe++ reduced for absorption, and needed for hydroxylation of proline and lysine in collagen synthesis?
vitamin C
what is the storage form of vitamin D?
25-OH D3
function of vitamin D?
increase intestinal absorption of Ca++ and phosphate
what vitamin deficiency causes rickets, osteomalacia, hypocalcemic tetany?
vitamin D
what does vitamin E deficiency cause?
increased fragility of Erythrocytes
neonatal hemorrhage with increased PT and aPTT is due to what vitamin deficiency?
vitamin K
what are the 2 steps in ethanol catabolism? what is limiting reagent?
ethanol --[alc. dehydrogenase]-> acetaldehyde --[acetald. dehyrogenase]-> acetate NAD+ is limiting reagent and 1 NADH is produced at each step
what enzyme does disulfiram (antabuse) block? what substrate is increased?
acetaldehyde dehydrogenase
how does liver fatty change occur in alcoholics?
chronic increase in NADH/NAD+ ratio shunts liver from glycolysis to fatty acid synthesis
what 2 metabolic steps are preferred when NADH/NAD+ increases in liver from alcohol?
pyruvate -[NADH]-> lactate OAA -[NADH]-> malate
what vitamin is found only in animal products?
vitamin B12
what inflammatory bowel disease can cause vitamin B12 deficiency? what test is used to detect B12 deficiency?
Crohn's Schilling test
vitamin B12 is a cofactor for what 2 reactions? problems in these reactions can lead to what?
homocysteine --> methionine methylmalonyl CoA --> methylmalonic acid
B complex deficiencies can lead to what clinical problems?
dermatitis, glossitis and diarrhea
night blindness, dry skin, impaired immune response. vitamin deficiency?
vitamin A (aka. retinol) think "retin-A"
what vitamin is a constituent of retinal pigments?
vitamin A
which vitamin is a cofactor for oxidative decarboxylation of alpha-keto acids (pyruvate, alpha-ketoglutarate)?
vitamin B1
what is cheilosis? cause?
scaling and fissures at the angles of the lips; due to riboflavin deficiency (B2)
what vitamin deficiency causes cheilosis, corneal vascularization and angular stomatitis?
vitamin B2 (riboflavin)
what is stomatitis?
sores on the lining of the mouth
what is the function of vitamin B2?
cofactor for oxidation and reduction (FADH2)
what is vitamin B3 used for? what molecule is it derived from?
cofactor in reduction and oxidation (NAD+, NADP+) made from tryptophan
what vitamin deficiency causes dermatitis, enteritis, alopecia, adrenal insufficiency?
vitamin B5 (pantothenate) think: PENTothenate = 5
what vitamin is a constituent of CoA, part of fatty acid synthase?
vitamin B5 (pantothenate)
INH and oral contraceptives can induce deficiency of this vitamin.
vitamin B6 (pyridoxine)
what vitamin is a cofactor in transamination (ALT, AST), decarboxylation and trans-sulfuration?
vitamin B6 (pyridoxine)
what vitamin deficiency is caused by antibiotic use and ingestion of raw eggs?
what vitamin is a cofactor for the following carboxylations? pyruvate -> OAA acetyl-CoA -> malonyl-CoA propionyl-CoA -> methylmalonyl-CoA
what's the most common vitamin deficiency in the US? in what foods is this vitamin found?
folate in FOLiage
what vitamin is important for the synthesis of nitrogenous bases in DNA and RNA?
what vitamin is a coenzyme for 1-carbon transfers and methylation reactions?
what is the folate precursor in bacteria?
sulfa and dapsone are analogs of what molecule?
PABA, the folate precursor in bacteria
what's the major regulatory enzyme in the citric acid cycle? what inhibits the enzyme?
citrate synthetase ATP and long-chain acyl-CoA
what substrates build up in deficiency of pyruvate dehydrogenase? what are clinical findings?
pyruvate and alanine neurologic defects
what aa serves as a carrier of amino groups from muscle to liver?
what enzyme triggers the interconversion (both ways) of lactate and pyruvate?
lactate dehydrogenase
what is the purpose of the Cori cycle?
transfer excess reducing equivalents from RBCs and muscle to liver, allowing muscle to function anaerobically
what molecule is transferred to the liver in the Cori cycle?
what enzyme irreversibly converts pyruvate to acetyl-CoA?
pyruvate dehydrogenase: pyruvate + (NAD+) + CoA -> acetyl-CoA + CO2 + NADH
what 3 molecules trigger the conversion of pyruvate to acetyl-CoA?
lots of exercise leads to 1. high NAD+ levels 2. high ADP 3. high Ca+
what are the 4 irreversible enzymes in gluconeogenesis? in what tissues are they found?
Pathway Produces Fresh Glucose Pyruvate decarboxylase PEP carboxykinase Fructose 1,6 bisphosphate Glucose-6-phosphatase liver, kidney, intestinal epithelium (muscle can't participate in gluconeogenesis)
pyruvate carboxylase. pathway? reaction? location in cell?
gluconeogenesis pyruvate -> oxaloacetate mitochondria
PEP carboxykinase. pathway? reaction? location in cell?
gluconeogenesis OAA -> phosphoenolpyruvate cytosol
fructose 1,6 bisphosphatase. pathway? reaction? location in cell?
gluconeogenesis fructose 1,6 bisphosphate -> fructose 6 P cytosol
glucose 6 phosphatase. pathway? reaction? location in cell?
gluconeogenesis glucose 6 P -> glucose cytosol
severe fasting hypoglycemia, LOTS of glycogen in the liver. disease?
type I glycogen storage disease von Gierke's disease glucose-6-phosphate deficiency
what are the 4 key glycogen storage diseases?
Very Poor Carbohydrate Metabolism Von Gierke's Pompe's Cori's McArdle's
what glycogen storage disease leads to cardiomegaly, systemic findings and early death?
type II: Pompe's disease lysosomal alpha-1,4-glucosidase deficiency
what glycogen storage disease is due to deficiency of debranching enzyme alpha-1,6-glucosidase?
type III: Cori's disease
lots of glycogen in muscle, painful cramps, myoglobinuria with strenuous exercise. disease?
type V: McArdle's disease skeletal muscle phosphorylase deficiency
how does the brain use ketone bodies?
makes 2 molecules of acetyl-CoA
what ketone body is not detected in urine tests?
what are the precursor molecules for ketone bodies in the liver? where are ketone bodies used?
fatty acids and amino acids brain and muscle
what are the 2 ketone bodies made in the liver?
acetoacetate and beta-hydroxybutyrate
what does HMG-CoA reductase do?
rate limiting step in cholesterol synthesis converts: HMG-CoA -> mevalonate
how do glucagon and insulin work?
PHasting -> PHosphorylate glucagon phosphorylates: turn glycogen synthetase OFF and phosphorylase ON insulin DE-phosphorylates: turn glycogen synthetase ON an phosphorylase OFF
what organs DON'T need insulin to transport glucose into cells?
BRICKL Brain RBCs Intestine Cornea Kidney Liver
what 2 tissue types really need insulin for glucose uptake?
adipose and skeletal muscle
what does insulin do to glucagon release?
blocks release at alpha cells of pancreas
what type of glucose receptors are found in muscle and fat?
GLUT4 at the 4 extremities!
what are 5 anabolic effects of insulin?
1. +glucose transport 2. +glycogen synthesis and storage 3. +triglyceride synthesis and storage 4. +sodium retention in kidneys 5. +protein synthesis in muscles

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