4/8 biochem review Flashcards
Amino acids necessary for purine synthesis:
She’s not PUR(e)ine if she GAGs.
- Glycine
- Aspartate
- Glutamine
- carbamoyl phosphate synthetase 1 = which reaction?
- carbamoyl phosphate synthetase 2 = which reaction?
CPS1 = urea cycle CPS2 = pyrimidine synthesis
mycophenolate
- mech:
- same mech as which other drug?
- inhibit IMP dehydrogenase.
- ribavirin.
ribavirin
- mech:
- same mech as which other drug?
- inhibit IMP dehydrogenase.
- mycophenolate.
hydroxyurea
-mech:
-inhibits ribonucleotide reductase, inc. HbF.
Azathioprine & 6-MP
-mech:
-inhibit PRPP amidotransferase (de novo purine synth).
PRPP amidotransferase
- what does it do?
- what inhibits it?
- PRPP => IMP (purine synth).
- inhibited by IMP, AMP, GMP, azathioprine, 6-MP.
*inhibited by purines bc thats what it makes.
IMP dehydrogenase
- whats it do?
- what inhibits it?
- IMP => GMP (purine synth).
- mycophenolate, ribavirin.
Orotic aciduria
- which step in which pathway is messed up?
- Tx:
- pyrimidine synth: orotic acid => UMP.
- uridine monophosphate (basically just give UMP so you skip the step w/the faulty enzyme).
Which bases does xanthine oxidase convert to xanthine and then uric acid?
Guanine & hypoxanthine.
HGPRT
- this enzyme converts what to what?
- its products have neg. feedback on what enzyme?
Guanine & hypoxanthine = bases.
-HGPRT adds a ribose & phosphate to these bases and makes nucleotide monophosphates = GMP & IMP.
-GMP & IMP (& AMP) have (-) feedback on amidotransferase of purine synthesis. You’re salvaging purines so no need to make more.
Adenosine deaminase deficiency
- adenosine deaminase catalyzes which reaction?
- what builds up in this enzyme deficiency?
- build up of this inhibits what enzyme?
- Adenosine => inosine.
- Excess ATP and dATP imbalances nucleotide pool via feedback inhibition of ribonucleotide reductase, prevents DNA synthesis and thus dec. lymphocyte count.
Genetic code:
-which AAs are only coded by one codon?
-methionine and tryptophan encoded by only 1 codon (AUG and UGG, respectively).
Genetic code is universal except where?
human mitochondria.
Prok. vs Eukaryote.
-which one has multiple origins of replication?
-eukaryote.
DNA Pol
-builds in what direction?
5’ => 3’
-you add things to the 3’ hydroxyl group.
Which prok. DNA Pol has 5’ to 3’ exnuclease?
-what does it use it for?
DNA Pol I
-excise RNA primers.
Telomerase
-An ____ dependent _____ polymerase.
RNA dep. DNA polymerase.
*so its a reverse transcriptase.
Purine => purine or pyr => pyr mutation: called what?
transition
purine => pyrimidine or pyr => pur mutation: called what?
transversion
Ataxia telangiectasia
- whats dysfunctional here?
- what are these pts vulnerable to?
Nonhomologous end joining: method for fixing ds breaks.
*ionizing radiation causes ds breaks.
Incoming nucleotide for DNA synth: how many phosphates does it have?
3
mRNA read in what direction?
5’ to 3’
Protein synthesis in what direction?
N-terminus to C-terminus.
Why is template DNA strand laid out in a 3’ to 5’ direction?
You synthesize 5’ to 3’ so polymerase reads 3’ to 5’.
Sense strand
- coding/non-coding strand?
- template/new strand?
sense = coding = new.
tRNA
- what is at the 3’ end?
- function of 3’ end?
- in relation to 3’ end, where is anti-codon?
- CCA at 3′ end along with a high % of modified bases.
- The amino acid is covalently bound to the 3 ′ end of the tRNA. “CCA Can Carry Amino acids”.
- Anticodon end is opposite 3′ aminoacyl end.
tRNA
-T-arm: whats its special base? whats its function?
- T-arm: pseudouridine, necessary for tRNA-ribosome binding.
- D-arm: contains dihydrouracil residues necessary for tRNA recognition by the correct aminoacyl-tRNA synthetase.
Mischarged tRNA
-does it read the wrong codon? or does it charge w/wrong AA?
-A mischarged tRNA reads usual codon but inserts
wrong amino acid.
Ribosomal subunits
- euk:
- prok:
- Eukaryotes: 40S + 60S = 80S (Even).
- PrOkaryotes: 30S + 50S = 70S (Odd).
I-cell disease
- whats the problem here?
- Sxs:
- inherited lysosomal storage disorder.
- failure of the Golgi to phosphorylate mannose residues on glycoproteins. proteins are secreted extracellularly rather than delivered to lysosomes.
- Results in coarse facial features, clouded corneas, restricted joint movement, and high plasma levels of lysosomal enzymes. Often fatal in childhood.
Peroxisome
-catabolizes what?
Very-long-chain FAS, branched-chain FAs, and AAs.
nucleus pulposus
-what type of collagen?
type 2.
Alport syndrome
-defective type __ collagen.
type 4.
Collagen
-disulfide bond formation & triple helix formation happens in which compartment of the cell?
RER
Osteogenesis imperfecta
-most common form has what inheritance pattern?
auto dom.
Skin elasticity: marfans or Ehlers danlos?
Ehlers Danlos
Agarose gel electrophoresis:
-separates by ____.
Size separation of PCR products (smaller molecules travel further).
Indirect ELISA
-testing for a specific _____ in pts blood.
Ab
*just like indirect Coombs was an Ab screen.
Direct ELISA
-testing for a specific _____ in pts blood.
Antigen.
Karyotype
-what phase are chromosomes in?
metaphase
Locus heterogeneity
-define:
Mutations at different loci can produce a similar
phenotype (ie. Albinism).
Allelic heterogeneity
-define:
Different mutations in the same locus produce the same phenotype (ie. beta-thal).
Heteroplasmy
-define:
Presence of both normal and mutated mtDNA, resulting in variable expression in mitochondrial inherited disease.
-so if you see a disease that is maternally inherited and she has 2 kids with varying degrees of the disease phenotype, think heteroplasmy.
Uniparental disomy:
-heterodisomy: explain what it is and if its a meiosis 1 or 2 problem.
-heterodisomy: you get one parents homologous
chromosomes. Called hetero bc your mom gives you
her homologous chroms, one from her mother and one
from her father. Homologous chromosomes separate
at end of meiosis 1.
-sister chromatids separate at end of meiosis 2.
What gets separated at end of meiosis 1?
homologous chromosomes
What gets separated at end of meiosis 2?
sister chromatids
X-linked dominant disorder
-name one:
Hypophosphatemic rickets—aka vitamin D–resistant rickets.
-Inherited disorder resulting in phosphate wasting at proximal tubule. Results in rickets-like presentation.
Auto Dom Disorders:
-mnemonic:
Very Powerful DOMINANT (5)Humans FAP
- VHL disease/Von-willebrand disease
- Pseudo-hypoparathyroidism
- Dystrophia Myotonica (myotonic dystrophy)
- Osteogenesis imperfecta/Osler-Weber Rendu
- Marfan
- Intermittent porphyria (acute)
- Neurofibromatosis
- Achondroplasia/ADPKD
- Noonan syndrome
- Tuberous sclerosis
- Hypercholesterolemia
- Huntingtons Disease
- HCM
- Hereditary spherocytosis
- HNPCC
- FAP
ADPKD
- PKD1 which chrom?
- PKD2 which chrom?
- PKD1 = chrom 16.
- 16 letters in “polycystic kidney”.
- PKD2 = chrom 4.
Marfans
-which direction does the lens usually sublux?
Typically upward and temporally.
ret gene
-associated w/which diseases?
MEN 2A & 2B.
Cystic fibrosis
- inheritance pattern:
- which chrom?
- most common mutation?
- Auto recessive.
- chrom 7.
- commonly a deletion of Phe508.
Cystic fibrosis
-where will the protein be retained?
RER
Cystic fibrosis
-Tx:
- N-acetylcysteine to loosen mucus plugs (cleaves disulfide bonds within mucus glycoproteins).
- dornase alfa (DNAse) to clear leukocytic debris.
X-linked recessive disorders
-mnemonic:
A = Alport syndrome B = Brutons Agammaglobinemia C = CGD D = Duchenne MD (& Becker) E = Ehlers Danlos F = Fragile-X syndrome/ Fabry disease G = G6PD deficiency H = Hemophilia A & B/Hunter Syndrome. ... Oh = Ocular albinism/OTC def. Wait = Wiskott Aldrich Lester is Here = Lesch Nyhan.
Duchenne MD
-common cause of death?
Dilated cardiomyopathy is common cause of death.
myotonia = abnormally slow relaxation of muscle.
-classic case here is someone that has a hard time
letting go of a doorknob.
-which disease could it be?
Myotonic MD
-or ion channel myopathies (less common).
Fragile X syndrome
-mnemonic:
Can Grow Gonads (CGG repeat).
X chrom = woman, so fragile X = not a lot of woman in you so everything is manly and BIG, like big jaw, big nuts, and big mitral valve (which then can prolapse).
Downs syndrome
- 95% of cases due to what problem?
- does this problem happen in meiosis 1 or 2?
-95% of cases due to meiotic nondisjunction of
homologous chromosomes.
-homologous chroms separate in meiosis 1.
Autosomal trisomies: shared features
- PAPP-A level?
- intellectual problems?
- PAPP-A is dec. in all 3 trisomies.
- all 3 have intellectual disability.
Down Syndrome
- 1st trimester: b-HCG level?
- 2nd trimester: AFP, b-HCG levels?
- inc b-HCG
- inc b-HCG, dec AFP.
Down Syndrome
-2nd trimester: estriol & inhibin levels?
- dec estriol.
- inc inhibin A.
Edwards syndrome
- 1st trimester: b-HCG level?
- 2nd trimester: AFP, b-HCG levels?
- mnemonic:
Everything is decreased in Edwards:
- b-HCG, AFP, estriol, inhibin A.
- inhibin A can be normal.
*John Edwards is DOWN bc he lost election.
Patau Syndrome
-b-HCG level?
dec. b-HCG.
* opposite Down syndrome.
Robertsonian translocation
- which chromosomes undergo this?
- mechanism?
- what type of chromosomes are these?
- acrocentric.
- 13, 14, 15, 21, and 22.
- Occurs when the long arms of 2 acrocentric chromosomes (chromosomes with centromeres near their ends) fuse at the centromere and the 2 short arms are lost.
Williams syndrome
- which chrom?
- mnemonic?
Bill Clinton (william) is extremely friendly and talkative. -he served two terms (8 years) but almot got impeached so lets go w/7. Its a q7 deletion.
Williams syndrome
-Sxs:
-“elfin” facies, intellectual disability, hypercalcemia (sensitivity to vitamin D), well-developed verbal skills, extreme friendliness with strangers, cardiovascular problems.
mineral oil intake can cause:
fat-soluble vitamin deficiencies.
B6
-aka?
Pyridoxine: PLP
B5
-aka?
Pantothenic acid: CoA
B9
-aka?
Folate
B-complex deficiencies often result in what 3 common Sxs?
dermatitis, glossitis, and diarrhea.
Thiamine
-cofactor for which enzymes?
- Pyruvate DH
- α-ketoglutarate DH
- Transketolase (HMP shunt)
- Branched-chain ketoacid dehydrogenase
How to remember beri-beri is B1 def?
-mnemonic:
Spell beriberi as Ber1Ber1 to remember vitamin B1.
Most common cause of B1 (thiamine) def?
alcoholism = most common cause of B1 def. by
interfereing w/absorption of thiamine in gut
Wernicke-Korsakoff syndrome
- lack of which vitamin?
- damage to what parts of brain?
- thiamine
- medial dorsal nucleus of thalamus, mammillary bodies.
Dry beriberi Sxs:
Wet beriberi Sxs:
- Dry beriberi—polyneuritis, symmetrical muscle wasting.
- Wet beriberi—high-output cardiac failure (dilated cardiomyopathy), edema.
Mechanism behind wet beriberi?
Thiamine def = not enough ATP.
-not enough ATP for smooth muscle cells of the peripheral resistance arterioles => dec. resistance. This will lead to high output cardiac failure bc the heart needs to pump more and the heart is ATP def. as well (bc of low thiamine).
Name a TCA enzyme that uses B2 (FAD) as cofactor.
Succinate DH.
B2 def:
-Sxs:
Cheilosis (inflammation of lips, scaling and fissures at the corners of the mouth), Corneal vascularization.
Niacin (B3)
- derived from what AA?
- needs which other vitamins to be synthesized?
- tryptophan.
- B2 & B6.
Carcinoid syndrome can lead to which vitamin deficiency?
-how?
Niacin deficiency.
- wasting lots of serotonin.
- tryptophan used to make serotonin, so you get tryptophan deficiency.
- tryptophan (& B2 + B6) needed to make niacin (B3).
Niacin def
-Sxs?
Symptoms of pellagra:
-Diarrhea, Dementia (also hallucinations), Dermatitis (e.g., Casal necklace or hyperpigmentation of sun-exposed
limbs)
Isoniazid can cause which vitamin deficiencies?
B6 and also B3 bc B6 needed to make B3.
Niacin excess
-Sxs:
Facial flushing (induced by prostaglandin, not histamine), hyperglycemia, hyperuricemia.
B6 (pyridoxine)
-uses?
-Cofactor for: transamination (e.g., ALT and AST),
decarboxylation reactions, glycogen phosphorylase.
-Synthesis of cystathionine, heme, niacin, histamine, and neurotransmitters including serotonin, epinephrine, norepinephrine, dopamine, and GABA.
Liver uses transaminases to detox ammonia, so anything that causes inc. action of the transaminases will dec. B6 levels (they are cofactors for these enzymes so they get used up).
No surprise that isoniazid is also hepatotoxic.
-it causes you to run out of B6, so your transaminases wont work in your liver, so you cant detox toxic substances like ammonia, so that causes liver damage.
When you’re taking levodopa, stay away from which vitamin supplement?
- do not take B6 supps while taking levodopa! It
inc. peripheral metabolism of levodopa!
B6 deficiency inducible by?
isoniazid, OCPs.
B6 deficiency
-Sxs:
-Convulsions, hyperirritability, peripheral neuropathy, sideroblastic anemias due to impaired hemoglobin synthesis and iron excess.
Biotin (B7)
-cofactor for which enzymes?
Carboyxlation enzymes
-Pyruvate carboxylase: pyruvate => OAA
- Acetyl-CoA carboxylase: acetyl-CoA => malonyl-CoA
- Propionyl-CoA carboxylase: propionyl-CoA => methylmalonyl-CoA
Carboxylase enzymes need what cofactors?
-mnemonic:
Carboxylase enzymes = ABC
A = ATP
B = biotin
C = CO2
Most common vitamin deficiency in the United States. Seen in alcoholism and pregnancy.
Folate deficiency
-B9.
B12 (cobalamin)
-cofactor for which enzymes?
Homocysteine methyltransferase & methylmalonyl-CoA mutase.
B12 def
-can lead to what neuro problem?
subacute combined degeneration:
-degeneration of dorsal columns, lateral corticospinal tracts, and spinocerebellar tracts due to abnormal myelin.
How does B12 deficiency lead to a megaloblastic anemia?
-if it doesn’t strip methyl off methylated THF, then you can’t use THF and you get an indirect megaloblastic anemia. Thymidilate synthase needs active THF.
Two common reasons you would have decreased production of intrinsic factor:
pernicious anemia, gastric bypass surgery.
Diphyllobothrium latum
-eats up which vitamin?
B12
Vitamin C: cofactor for which enzyme?
dopamine b-hydroxylase, which converts dopamine to NE.
Vitamin C tox can cause tox of what other vitamin/mineral?
Iron
-vit C facilitates iron absorption by reducing it to
Fe2+ state.
Active form of vitamin D =
calcitriol
Which layer of skin is D3 (cholecalciferol) produced in?
stratum basale
Pigmented skin: does that inc or dec amount of vitamin D you make?
decrease
Vitamin E def
-Sxs:
- Hemolytic anemia, acanthocytosis, muscle weakness, posterior column and spinocerebellar tract demyelination.
- same neuro problems as B12 def.
What does gamma-carboxylation do to coag factors?
These coag factors already have one negative charge. One you gamma carboxylate them, they have 2 negative charges. This is now perfect for binding Ca2+.
gamma-carboxylation
-cofactor?
vitamin K
-warfarin = vitamin k antagonist.
Warfarin
-functions:
- vitamin K antagonist (for gamma carboxylase enzyme).
- inhibits epoxide reductase.
How long does it take for warfarin effect to kick in?
- warfarin takes 2-3 days to work b/c its working on the next generation of coag. factors. The ones that are already made are working just fine.
- Only works in vivo since it messes up w/coag factor synthesis in the liver.
How would warfarin lead to thrombosis?
Warfarin can cause transient protein C deficiency, leading to thrombosis.
dysgeusia, anosmia, hypogonadism
-deficiency of what?
zinc.
Alcohol dehydrogenase
-0 or 1st order kinetics?
0 order.
Acetyl-Coa production
-where in the cell does this happen?
mitochondria.
FA synthesis
-where in the cell does this happen?
cytosol.
HMP shunt
-where in the cell does this happen?
cytosol.
Which pathways take place in mito & cyto?
-mnemonic?
Heme synthesis, Urea cycle, Gluconeogenesis.
*HUGs take two (i.e., both).
Adds inorganic phosphate onto substrate without using ATP.
-whats the enzyme family?
phosphorylase
Rate-limiting enzyme: Glycolysis
Phosphofructokinase-1 (PFK-1)
Rate-limiting enzyme: Gluconeogenesis
Fructose-1,6-bisphosphatase
Rate-limiting enzyme: TCA cycle
Isocitrate dehydrogenase
Rate-limiting enzyme: De novo pyrimidine synthesis
CPS 2
Rate-limiting enzyme: Urea cycle
CPS 1
Rate-limiting enzyme: Fatty acid synthesis
Acetyl-CoA carboxylase (ACC)
Rate-limiting enzyme: Fatty acid oxidation
Carnitine acyltransferase I
Rate-limiting enzyme: Ketogenesis
HMG-CoA synthase
Obligate activator of pyruvate carboxylase (gluconeo)?
- acetyl coa
- unless your liver is burning fat, it wont have enough energy to produce sugar.
- Acetyl-Coa will turn ON pyruvate carboxylase and also turns OFF PDH (neg. feedback).
What enzyme does G6PD catalyze?
Glucose-6-phosphate => 6-phosphogluconolactone
Acetyl-Coa used for FA synthesis
-where does it come from?
Acetyl Coa from PDH is NOT the acetyl coa used in FA synthesis b/c this one is in the mitochondria. Once citrate spills out of mito and into cytoplasm, it is converted to OAA and acetyl coa, and its this acetyl coa that is used
in FA synthesis!
Pyruvate Carboxylase
- 1st step of what?
- where is this enzyme?
- cofactors:
1st step of gluconeo
- mitochondrial enzyme.
- biotin (B7), ATP, and CO2.
Why would you get hypoglycemia if FA beta-oxidation didnt work?
FA beta-oxidation creates acetyl-coa, which activates gluconeogenesis (pyruvate carboxylase): so if beta-oxidation of FAs doesn’t work, you will see hypoglycemia.
PEP-carboxykinase
- 2nd step in which pathway?
- Turned on by what?
- location?
- Turned on by glucagon & cortisol on the genetic level.
- cytoplasm.
Both pyruvate carboxylase & PEP carboxykinase uses energy (ATP & GTP), so gluconeo = requires energy.
-where is the energy coming from?
The ATP used for this is from FA oxidation. So FA oxidation can not provide any carbons for gluconeo, but it does provide the ATP needed in gluconeo!
*also activated pyruvate carboxylase (1st step of gluconeo) via acetyl-coa.
fructose-1,6-bisphosphatase is opposing PFK-1
- which one = glycolysis?
- which one = gluconeo?
- fructose-1,6-bisphosphatase = gluconeo
- PFK-1 = glycolysis
Glucagon activates PEP-carboxykinase (gluconeo).
-how does metformin help diabetics?
Metformin inhibits gluconeogenesis: Diabetes pts have lots of glucagon which want to turn on gluconeo and pump more glucose into their blood (which is already hyperglycemic).
Glucokinase
- present in which tissues?
- Km?
- capacity?
- is it induced by insulin?
Liver, b cells of pancreas -high Km. -high capacity. -yes, induced by insulin. *when we eat carbs, all the excess carbs are funneled to our liver due to the GLUT2 transporter. Glucokinase traps all those excess carbs in hepatocytes by phosphorylating them.
Glucokinase
-Feedback-inhibited by glucose-6-P?
No.
-that would defeat the purpose of using the liver to store excess glucose 6 phosphate.
PFK-1 is rate-limiting step of glycolysis
- inhibitors?
- inducers?
- inhibitors= ATP, citrate.
- inducers = AMP, fructose-2,6-BP.
- NADH and ATP inhibit isocitrate DH of TCA cycle. This causes build up of citrate which spills into cytoplasm and then inhibits glycolysis via PFK-1 inhibition.
- keep in mind all these inhibitors of PFK-1 will be over run in the liver due to F-2,6-BP (insulin promotes its prod.)
highest energy molecule of glycolysis:
PEP
Pyruvate Kinase
- inhibitors?
- inducers?
- inhibit: ATP, alanine.
- induce: F-1,6-BP
-PFK-2 only found in what tissue?
LIVER.
- PFK-2 converts F6P -> F2,6BP.
- F2,6BP overrides any inhibition of PFK-1. So high ATP and high citrate will no longer inhibit PFK-1 activity, and glycolysis can continue past F-6-P.
- This will drive pyruvate & acetyl-coa prod. and subsequent fatty acid production. Remember PFK-2 is only found in the LIVER.
PFK-2 regulation
-when is it active?
PFK-2 is highly regulated, you only want it on after
you have a high carb meal.
-Insulin activated PFK-2.
-glucagon turns PFK-2 off.
-You dont want to be making fatty acids when you’re fasting. You want to have gluconeogeneis.
*when PFK-2 is active so is PFK-1. They work together.
PFK-2
-is it active when its phosphorylated or de-phosphorylated?
Activated when its dephosphorylated.
-Fasting state:glucagon => inc. PKA => inc. FBPase-2, dec. PFK-2, less glycolysis, more gluconeogenesis.
-Fed state: insulin dec. PKA activity so there is more PFK-2 action so liver can make fructose-2,6-BP and continue glycolysis even when there is high citrate & high ATP around (which inhibits PFK-1, the rate limiting step of glycolysis).
PDH
- where is it found?
- active in fed or fasting state?
mitochondria
-active in fed state (only in fed state do you burn glucose, in fasting state you send glucose to blood stream).
PDH = Tender Loving Care For Nancy enzyme
-what is that a mnemonic for?
Tender Loving Care For Nancy T=thiamine L=lipoic acid C=Coenzyme A F=FAD N=NAD
PDH
-inhibited by?
- acetyl coa = neg. feedback on PDH.
- acetyl coa = activates pyruvate carboxylase (gluconeo).
*high energy = stop TCA and glycolysis = shunt
toward glycogen and FA synthesis = in liver.
PDH
-activated by:
- Activated by exercise, which:
inc. NAD+ /NADH ratio
inc. ADP
inc. Ca2+
Arsenic poisoning:
- Sxs:
- Tx:
- inhibits lipoic acid.
- Findings: vomiting, rice-water stools, garlic/metallic breath.
- Tx: Penicillamine, Dimercaprol, succimer.
Thiamine def. pt gets just glucose IV - how does he die?
If you give JUST glucose, you can kill the pt via lactic
acidosis! This is b/c you dont have enough thiamine
so PDH doesn’t work and the glucose gets shunted
to fermentation which produced lactic acid!
*pyruvate accumulates in mitochondria, spills out
into cytoplasm where lactate dehydrogenase is.
How severe is pompe disease?
Very severe, there is early death.
Why would hydrochlorothiazide use cause lithium toxicity to pt on lithium?
any hyponatremic state can induce lithium toxicity to pts that are taking lithium.