Biochemistry Flashcards
What are the stop codons, what do they bind?
UAA, UAG, UGA. Bind releasing factor.
Poly-A tail added how and for what on mRNA?
AAUAAA = consensus sequence
Add poly-A tail to 3’ end after that so that the mRNA doesn’t get degraded after it exits the nucleus.
Insulin - binds what receptor, what downstream effects in the cell?
Insulin-R: tyrosine kinase receptor!
TK -> phosphorylates some substrates -> activation of protein phosphorylase
- dephos glycogen synthase - activates - glycogen synthesis
- dephos fructose 1,6 bisphosphatase - inactivates - inhibits gluconeogensis.
How can thiamine deficiency be diagnosed?
Measuring erythrocyte transketolase activity.
Thiamine involved in enzymes that help utilize glucose.
1. pyruvate dehydrogenase
2. alpha-ketogluturate dehydrogenase
3. transketolase
Which enzyme has 5’ to 3’ exonuclease activity?
DNA Poly I - removes RNA primer.
Also has same fxns as DNA Poly III - 5’ to 3’ synthesis and 3’ to 5’ exonuclease.
What are factors that utilize tyrosine kinase receptors with intrinsic enzyme activity vs. tyrosine kinase associated receptors and JAK/STAT pathway?
Tyrosine Kinase-R: Insulin, PDGF, FGF, EGF JAK/STAT: Cytokines, Growth Hormone, Prolactin, IL2
How does radiation induce cell death?
Causes dsDNA breaks!
How does hyperammonia influence metabolic intermediates in the brain?
Glutamate-Glutamine Cycle
1. Decreased Glutamate, Increased Glutamine (Glu + HN4 -> Glutamine in astrocytes). Glutamine cause astrocyte swelling and dysfunction
- Decreased alpha-ketoglutarate (alpha-keto + NH4 -> Glutamate in neurons). Depletion causes inhibition of Krebs cycle.
What biochemical processes occur in the cytoplasm?
GlycolysisFA synthesis HMP shunt (pentose phosphate shunt) Protein synthesis (RER) steroid synthesis (SER)cholesterol synthesis
What biochemical processes occur in BOTH the cytoplasm and mitochondria?
Heme synthesis
Urea cycle
Gluconeogenesis (HUGS take two)
Metabolism of what amino acids may lead to propionic acidemia?
Valine
Isoleucine
Threonine
Methionine
Deficiency of proprionyl CoA carboxylase
Gestational diabetes is caused by a decrease in what? If this is genetically predisposed, what enzyme would have decreased activity?
Glucokinase - beta cells of the pancreas -> once in glucolysis -> ATP -> close ATP sensitive K channels -> Ca let in -> release of insulin.
What are the sx of phenylketonuria?
PKU: deficiency of tyrosine hydroxylase or BH4
Sx: intellectual disability seizures (metabolites of phenylalanine) growth retardation hypopig skin (no dopa -> melanin) brain nuclei eczema musty odor
What causes accumulation of ceramide trihexoside?
Fabry’s disease: X-linked
Deficient in alpha-galactosidase. Peripheral Neuropathy Angiokeratomas Renal disease - progressive renal failure Cardio disease Hypohidrosis (dec. sweating)
What is pantothenate used for?
Oxaloacetate + Acetyl CoA -> Citrate (Citrate synthase)
Fatty Acid synthesis: Acetyl CoA carboxylase It is an essential component of coenzyme A and fatty acid synthase.
What enzyme is defective in xeroderma pigmentosum?
Endonuclease. Excise stretches of DNA which contain the pyrimidine dimers formed by UV light.
Deficiency of what vitamin causes peripheral neuropathy, sensory and motor impairments + cardiac failure, edema?
B1 = Beri Beri
Wet beri beri = nerve + heart
Dry beri beri = nerve.
What is BH4 used to synthesize? (cofactor)
Tyrosine
Dopa
Serotonin
NO
Dihydrobiopterin reductase deficiency (converts BH4 -> BH2) can result in PKU.
What vitamin can present with a long delay btwn insufficient intake and sx?
Vitamin B12 - stored in liver.
B6 is used in what reactions?
Transamination: Amino acid + alpha-keto acid; transfer of the amino group
Decarboxylation
What does arginase do?
Arginine -> Urea + Ornithine Part of Urea cycle.
Metabolism of protein, fat, carbohydrates.
4 cal = 1g of protein, carb
9 cal = 1g fat
Riboflavin is needed for what enzyme?
succinate dehydrogenase think what needs FAD!
What liver specific enzyme facilitates metabolism of TAG breakdown products?
Glycerol kinase. Q1889
What are the two causes of PKU? How do you differentiate it?
PKU:
1. dec. phenylalanine hydroxylase
- dec. BH4 cofactor - with this, tyr -> DOPA is also decreased, so even if you substitute tyr, will still have dec. dopa -> elevated prolactin.
Vitamin C deficiency causes what?
Scurvy
Cause: defective collagen synthesis.
Sx: hemorrhages, subperiosteal hemorrhages, hemarthrosis, gingival swelling, 2nday periodontal infection, anemic, impaired wound healing, weakened immune response, hyperkeratotic papular rashes,
ALL the reactions of the Urea cycle >_>
poop!
What are the function of the different apolipoproteins? Apo AI, Apo B48, Apo B100, Apo CII, Apo E
ApoE = mediates chylomicron and VLDL remnant uptake
Apo AI = activate LCAT (catalyzes esterification of cholesterol in HDL particles)
Apo CII = lipoprotein lipase cofactor (on vascular endothelial surface - degradation of TG circulating in chylomicrons and VLDLS)
Apo B48 = chylomicron secretion from intestine
Apo B100 = binds LDL-R
Deficiency of what vitamin causes pancreatic columnar -> squamous metaplasia?
Vitamin A - can be seen in CF due malabsorption of ADEK.
Activating mutations of PRPP predispose to what condition?
Gout - inc. production of purines.
What condition causes urine to turn black when allowed to stand?
Alkaptonuria: deficiency of homogentistate oxidase: can’t convert tyrosine -> fumurate.
Accumulation of homogentisic acid, which selectively binds collagen causing “ochronosis” a blue black pigmentation most evident in ears, nose, cheek.
Glycogen Storage Diseases:Von Gierke Disease Pompe CoriMcArdle
Von Gierke = Glucose 6 phosphatase - inc. glycogen in liver = hepatomegaly - can’t release glucose = hypoglycemia- inc. lactic acidosis
Pompe = Lysosomal alpha 1,4 glucosidase- nl blood sugar, but glycogen accumulates in lysosome
cardiomegaly
liver failure
Cori = debranching enzyme (alpha 1,6)
small dextrin like material acccumulates within hepatic cytosol
same sx as Von Gierke, but no lactic acidosis
McArdle = muscle glycogen phosphorylase
lots of glycogen in muscle, but can’t break it down weakness, fatigue with exercise
muscle cramps, myoglobinuria- predisposed to arrhythmias due to electrolyte abnl.
MAP-kinase pathway:
Binding of GF ligand -> auto tyrosine phosphrylation -> SOS protein -> activation of RAS with GTP -> RAF -> MAP kinase -> gene transcription
Base Excision Repair order of enzymes
Glycosylase (removes the altered base)
Endonuclease (5’ stand ends)
Lyase (3’ strand ends) DNA polymerase Ligase
Lipoic Acid is a cofactor for what 3 enzymes? What would deficiency result in?
Pyruvate Dehydrogenase -> will get lactic acidosis
Alpha Ketogluturate Dehydrogenase
Alpha Ketoacid Dehydrogenase (branched ketoacid dehydrogenase - Isoleucine, Leucine, Valine) -> leads to maple syrup disease
Fructose 2,6 Bisphosphate would decrease what?
Gluconeogenesis.
What enzyme deficiency is associated with hypoglycemia and low ketones after prolonged fasting?
Messed up beta-oxidation.Acyl CoA Decarboxylase.
Night blindness + Skin dryness + pruritis = indicative of what
Vitamin A deficiency Which can result from fat malabsorption, such as with biliary obstruction.
Palmitoylation
Increases protein hydrophobicity Anchor carboxyl tails to the plasma membrane.
Platelet aggregation associated with intracellular signaling mechanism?
Platelet Activating Factor:
Gq Phospholipase C -> IP3 -> Ca++ release from ER
Neurofibromatosis 1 inheritance, penetrance? How can NF1 arise in children with parents without the disease?
Autosomal Dominant
100% penetrance
Variable expressivity
NF1 can arise in children whose parents are unaffected if there is germline mosiacism (novel germline mutation).
What oncoprotein is involved in signal transmission from cell surface to nucleus?
Ras - GTPase”myc” = transcription factor
What percentage of energy per glucose molecule metabolized is produced in RBC vs. CNS neurons?
Anaerobic = 2 Aerobic = 385%
Wild Mushroom Toxin (Amatoxin) does what?
Inhibits RNA Polymerase II
no mRNA
Life-threatening!
G6PD is involved in what reaction of the HMP shunt?
Glucose 6 P —> 6 phosphogluconate + NADPH
What enzyme is responsible for the cataracts developed in galactosemia?
Aldose Reductase.
Galactose —> Galactitol.
How is lac operon regulated?*
No Lactose, Glucose: NO transcription
- Repressor protein binds to operator - inhibiting transcription.
- GLUCOSE causes DECREASED cAMP. CAP can’t bind upstream of promoter.
Lactose, No Glucose: Transcription.
- Lactose binds repressor - it doesn’t bind operator
- cAMP-CAP complex binds upstream of promoter - positive regulator.
Very LCFA and phytanic acid are oxidized in what part of the cell?
Peroxisome!
Condition associated with Lipoprotein lipase deficiency or altered apo CII (cofactor for LPL)?
Increased chylomicrons
Causes acute pancreatitis!!
Also HSM, eruptive/pruritic xanthomas. But NO increased risk for atherosclerosis.
Familial Hypercholesterolemia
AD = Absent or defective LDL-R
Premature CAD
Corneal arcus, Tendon Xanthoma, Xanthelasma
Familial Dysbetalipoproteinemia
ApoE - Inc chylmicron and VLDL remnants
Premature CAD and PVD
Tuboeruptive and Palmar Xanthomas.
HyperTAG
AD = hepatic overproduction of VLDL Pancreatitis!
prokaryotic 16S rRNA used for what?
16s rRNA = 30S
- Sequence complentary to Shine Dalgarno sequence on all mRNAs - help bind the mRNA
- Bind the incoming aminoacyl tRNA
Glutamate residue carboxylation of proteins synthesized in liver - need what vitamin?
Vitamin K.
What must be known for PCR reaction?
Nucleotide sequence of the primers flanking the DNA. For PCR, need:
DNA template (doesn’t have to be known)
Two primers - sequence must be known
DNA polymerase
DNA nucleotides
Steps:
- Denature
- Anneal
- Elongation
How does cortisol influence catecholamine synthesis?
In adrenal medulla, NE —– phenylethanolamine-N-methyltransferase–> Epi PMNT transcription increased by cortisol.
Venous drainage of cortex goes thru medulla, so cortisol has effect and 80% medulla secretion = Epi.
Vitamin E deficiency
Mech: Antioxidants - protect RBC and cells with high lipid content, such as neurons, from oxidative injury.
Sx: Hemolytic Anemia, Acanthocytosis. Posterior column and spinocerebellar tract demyelination (like B12) Muscle weakness
How is glycogen phosphorylase regulated?
- Glucagon (liver) and Epinephrine (muscle) - Gs -> inc. cAMP -> PKA -> +PO4 on phosphorylase kinase (activate) -> + PO4 on glycogen phosphorylase (activate)-> + PO4 on glycogen synthase (inactivate)
- Muscle - Ca++ from contraction -> allosteric regular -> increase activity of glycogen phosphorylase
Sorbital Metabolism
Glucose –aldose reductase–> Sorbital – sorbital dehydrogenase –> Fructose
Both enzymes: liver, ovaries, seminal vesicles (sperm use fructose as primary energy source)
Both enzymes, but gets overwhelmed in states of longstanding hyperglycemia (DM) : lens - leads to lens opacification, cataracts.
No sorbital dehydrogenase: schwann cells - neuropathy, retina - retinopathy, renal papilla
What are the 3 main reactions that require NADPH (and therefore G6PD)?
- Reduction of glutathione inside RBC
- FA synthesis
- Cholesterol synthesis.
What cells use bisphophoglycerate mutase?
Erythrocytes1,3 bisphosphoglycerate -> 2,3BPG sacrifice making ATP in the process. During hypoxemia and chronic anemia.
Sx of Alkaptonuria
Mech: Deficiency of homogentisate oxidase (AR) - metabolism of tyrosine to fumurate
Sx:
dark connective tissue
brown pigmented sclerae (ochronotic pigment - deposits of homogenistic acid)
urine turns black on prolonged exposure to air
debilitating arthralgias* (homogenistic acid is toxic to cartilage)
DNA synthesized in what direction
5’ -> 3’ SO READ THE DNA CORRECTLY!!!
Some sx of Ehler’s Danlos similar to what vitamin deficiency?
Sx:
- Hyperextensible skin
- Hypermobile joints
- Tendency to bleed/Easy Bruising
Different Variants: Hypermobile type (joint instability) Classical type (joint and skin) - collagen V Vascular type (vascular and organ rupture) - collagen III
Mech:
Kyphoscoliosis type
Lysyl Hydroxylase deficiency - can’t add hydroxy group to lysine and proline residues on procollagen.
Similar to Vit C deficiency (cofactor).
Insulin increases what in terms of glycolysis?
Fructose 2,6 Bisphosphate Insulin -> dephosphorate the PFK-2/FBPase complex -> more activity of PFK-2 -> fructose 6 phos to fructose 2,6 bisphosphate -> activates PFK1 -> more glycolysis!
What synthesizes apoB100 vs. apoB48?
apoB48 = synthesized by intestine = mediates chylomicron secretion (cytidine to uridine deamination reaction on the transcribed
apoB100 mRNA resulting in premature stop codon).
apoB100 = synthesized by hepatocytes
Enzyme that converts Dopamine -> NE?
Dopamine beta-hydroxylase.
Restriction Fragment Length Polymorphism (RFLP)s - most common cause of different RFLPs
Single nucleotide polymorphisms (SNP) bc restriction enzymes depend on recognition of a specific sequence of base pairs in order to cleave DNA.
nuclear protein with repeated leucine residues at every 7th position.
leucine zipper!
nucleic acid binding domain.
Others: zinc finger, helix loop helix.
PLEASE READ.
