USMLE World biochemistry Flashcards

DNA
Terms Definitions
Uncouplers
2,4-dinitrophenol, aspirin and salicylates, UCP (thermogenin) of brown adipose tissue.
neurofilaments
intermediate filaments of neurons
What gluconeogenic mitochondrial enzyme requires biotin?
Pyruvate carboxylase
pyrimidine components
aspartate and carbamoyl phosphate
ApoC-II
Activates lipoprotein lipase. Donated to chylomicrons and VLDL by HDL
Farnesyl ppi
Cholesterol synthesis intermediate important for synthesis of CoQ, dolichol ppi for N-linked glycosylation and prenylation
Kwashiorkor
Protein malnutrition --> edema, anemia, fatty liver
What water-soluble-vitamin deficiency is associated with poor wound healing, easy bruising, bleeding gums, anemia, and painful glossitis?
Vitamin C
Are the following conditions associated with a negative or positive nitrogen balance?
• Growth
Positive
What cytoplasmic pathway produces NADPH and is a source of ribose 5-phosphate?
HMP shunt
What enzyme catalyzes the rate-limiting step in pyrimidine synthesis?
Aspartate transcarbamylase
Lesch Nyhan
Deficiency of HGPRT (hypoxanthine guanine phosphoribosyl pirophosphate transferase) which converts guanine to GMP and hypoxanthine to IMP. Hyperuricemia, retardation, self-mutilation, aggression, gout, choreoathetosis.
Acute intermitent porphyria
Abdominal pain, neurologi manifestations, no photosensitivity, coluria, increased ALA and PB
What effect do noncompetitive inhibitors have on Vmax?
Decrease Vmax
SR-B1 receptors
Transfers HDL cholesterol into steroidgenic tissues ( ovaries, testes, adrenal, hepatocytes)
What cytoplasmic organelle carries the enzymes for elongation and desaturation of fatty acyl CoA?
SER
What presents with intracranial hypertension, skin changes and hepatosplenomegaly?
Vitamin A overuse
What X-linked recessive disorder is characterized by hyperuricemia, spastic cerebral palsy, mental retardation, and self-mutilation?
Lesch-Nyhan syndrome
What blotting technique uses the following for analysis?• DNA
Southern blot
What pattern of inheritance does G-6-PD deficiency follow?
X-linked recessive
Name the type of mutation:• New codon specifies for a stop codon
Nonsense
black urine and black spots in sclera
alkaptonuria
Glutamine synthetase
Captures excess nitrogen by aminating glutamate to glutamine. Located in most tissues.
non-clathrin-coated vesicles
for proteins destined for the membrane
AA used as site for N-linked glycosylation
Asparagine
What is the precursor of all sphingolipids?
Ceramide
What pyrimidine base is found
• In both DNA and RNA?
Cytosine
Name the lipoprotein based on the following characteristics.
• apo E
IDL
What toxin ADP-ribosylates via Gs protein to increase cAMP?
Cholera toxin
What causes an increase in bone mineralization and Ca2+ along with PO4- absorption from the GI tract and kidney tubules?
Vitamin D
What pathway uses HMG CoA synthetase in the cytoplasm?
Cholesterol biosynthesis
Name the RNA subtype based on the following:• Found only in the nucleus of eukaryotic cells and are precursors of mRNA
hnRNA
What topoisomerase makes ssDNA cuts, requires no ATP, relaxes supercoils, and acts as the swivel in front of the replication fork?
Topoisomerase I (Relaxase)
infant with failure to thrive and big tummy, brittle hair and skin depigmentation
Kwashiorkor
Order of oxidative phosphorylation intermediate synthesis
Citrate, isocitrate, a-ketoglutarate, succinyl CoA, succinate, fumarate, malate, OAA
Mep-1
trans factor binds HMRE in response to heavy metals
Vitamin B3
Niacin. Precursor to NAD and NADPH used by dehydrogenases.
What effect does increasing the enzyme concentration have on Vmax?
Increase Vmax
glycolipids of the cell membrane
cerebrosides, gangliosides (contains sialic acid), neutral glycolipids
Substrates for gluconeogenesis
Lactate --> pyruvate
Alanine + ALT --> pyruvate
Glycerol 3P from triacylglycerol
Source of ATP for gluconeogenesis
From β-oxidation (gluconeogenesis depends on β-oxidation)
Pyruvate dehydrogenase
Converts pyruvate to acetyl-CoA in the mitochondria for citric acid cycle and fatty acid synthesis. Requires NAD, FAD, CoA and thiamine. Negative feedback by acetyl-CoA.
What enzyme of the purine salvage pathway is deficient in the following?
• SCID
Adenosine deaminase
What is the major ketone body produced during alcoholic ketoacidosis?
β-Hydroxybutyrate
What complex of the ETC contains Cu2+?
Complex 4
Name the eukaryotic RNA polymerase based on the following:
• Synthesizes 28S, 18S and 5.8S rRNAs
RNA polymerase I
Name the phase of the eukaryotic cell cycle:• Period of DNA replication (preparing for mitosis)
S phase
What enzyme of the TCA cycle catalyzes the substrate level phosphorylation?
Succinyl CoA synthetase
alcoholic develop rash diarrhea and altered mental status
pellagra, vit b3 deficiency
fatty acyl CoA dehydrogenase
Enzyme of B-oxidation in mitochondrial matrix. Oxidizes activated fatty acids to acetyl CoA producing FADH2 (for CoQ) and NADH (for NADH DH). Also called LCAD and MCAD. Inhibited by Ackee fruit.
proximal promoter region
upstream from the core promoter; CCAAT box and GC-rich sequence
Myopathic CAT deficiency
No FA for B-oxidation. Muscle aches and weakness, rhabdomyolisis, myoglobinuria, elvated muscle TG
What is Vmax?
The maximum rate possible to achieve with a given amount of enzyme
What are palindromes?
Sequences of 4-8 bases that are inverted repeats and are recognized by restriction endonucleases. Example: GAATTC
Biochemical defect in Menkes disease
Deficient cross-linking of collagen secondary to functional copper deficiency: depigmented hair, arterial tortuosity, osteoporosis, anemia
Mention 3 specific transcription factors
steroid receptors, CREB protein PPARs
What are sources of cyanide?
Burning polyurethane. Byproduct of nitroprusside (thiosulfate can be used to destroy cyanide).
What component of the ETC is inhibited by the following?
• Barbiturates
Complex I
Regarding the Lac operon, for what do the following genes code?
• Y gene
Galactoside permease
Name the phase of the eukaryotic cell cycle:
• Period of DNA replication (preparing for mitosis)
S phase
Name the type of mutation:
• Unequal crossover in meiosis with loss of protein function
Large segment deletions
What type of bilirubin is found in neonatal jaundice?
Indirect or unconjugated
What is the term for production of a DNA copy from an RNA molecule?
Reverse transcription
Biochemical defect in Ehlers-Danlos
Mutations in collagen genes and lysine hydroxylase gene: hyperextensible fragile skin, hypermobile joints, dislocations
In which condition is glycogen synthesis active in spite of high levels of glucagon and epinephrine?
Von Gierke disease. Profound hypoglycemia, so glucagon is high but glucose-6P stimulates glycogenesis.
Rate-limiting enzyme in cholesterol synthesis
HMG-CoA reductase converts HMG-CoA to to mevalonate. Insulin activates it by dephosphorylation, gene expression repressed by cholesterol, competitively inhibted by statins
Metabolic processes in the cytoplasm
Glycolysis, fatty acid synthesis, HMP shunt, protein synthesis (RER), steroid synthesis (SER)
Mechanism of action: 1,25 DHCC
Binds its zinc finger intracellular receptor in intestinal cells, which binds response elements in enhancer regions to induce synthesis of calcium binding proteins
Cofactors required by dehydrogenases
FAD, NAD, thiamine, CoA, lipoic acid. Deficiencies of these results in lactic acidosis (piruvate DH) and maple syrup urine (branched-chain ketoacid DH)
What form of bilirubin can cross the blood-brain barrier?
Unconjugated free bilirubin
From where is the energy for gluconeogenesis derived?
β-Oxidation of fatty acids
What enzyme catalyzes the covalent bonding of the AA's carboxyl group to the 3' end of tRNA?
Aminoacyl-tRNA synthetase, which uses 2 ATPs for this reaction.
True or false? Methylation of bacterial DNA prevents restriction endonuclease from cutting its own chromosomes.
True. Restriction endonucleases cut only unmethylated DNA.
As what AAs do muscles send nitrogen to the liver?
Alanine and glutamine
What enzyme has a 5' to 3' synthesis of the Okazaki fragments, 3' exonuclease activity, and 5' exonuclease activity?
DNA polymerase I
Which way will the O2 dissociation curve shift with the addition of 2, 3-bisphosphoglycerate (2, 3-BPG) to adult hemoglobin (Hgb)?
Shifts it to the right
Pathophysiology of cataracts in galactosemia
Galactose is converted to galactiol by aldose reductase in the lens. In diabetes glucose is also converted to sorbitol by the same enzyme.
leucine zipper proteins
alpha helix in which every 7th AA is leucine allows dimerization; CREB, Fos, Jun
What three organs participate in production of vitamin D?
1. Skin
2. Liver
3. Kidney
What two sugars can be used to produce cerebrosides?
Glucose and galactose
What vitamin is necessary for epithelial health?
Vitamin A is responsible for vision and epithelial health.
Does a saturated fatty acid have double bonds?
No, unsaturated fatty acids have double bonds.
chest pain and xanthomas in Achilles tendon
LDL receptor defect in familial hypercholesterolemia
Define : Reverse transcriptase and AZT
It's an RNA dependant DNA polymerase. AZT might be used as a substrate and gets inserted at the 3' end, terminating replication
What does glucose do to lactose operon in prokaryotes?
Increases intracellular cAMP, which inactivates CAP (activator protein), which decreases transcription of operon.
What is the binding site for RNA polymerase?
The promoter indicates where transcription will begin.
What fructose metabolism enzyme is deficient in patients with vomiting, apathy, diarrhea, jaundice, proximal renal tubular acidosis, hypoglycemia, and hyperuricemia?
Aldolase B deficiencies are treated by eliminating fructose from the diet.
What DNA excision and repair enzyme is deficient in patients with xeroderma pigmentosum?
Excision endonuclease, which removes thiamine dimers from DNA
How many NADPHs are used per addition of acetyl CoA into a fatty acid chain?
2 NADPHs per acetyl CoA
What is the term for the pH at which the structure carries no charge?
pI (isoelectric point)
How many acetyl CoAs per glucose enter into the TCA cycle?
2 acetyl CoA per glucose, producing 12 ATPs per acetyl CoA, resulting in a total of 24 ATPs produced from glucose (via acetyl CoA) enter the TCA cycle
What are the 4 structures formed during protein folding?
1. Primary structure: sequence of AA; 2. Secondary: stable a-helix and b-pleaded sheets; 3. Tertiary: interaction between secondary structures and final protein structure; 4. Cuaternary: multiple subunit interaction
What is the term for the number of trinucleotide repeats increasing with successive generations and correlating with increased severity of disease?
Anticipation, associated with fragile X syndrome; Huntington's disease is also associated with a decrease in onset of age.
How many high-energy bonds does the cycle of elongation cost?
Four high energy bonds, two from ATP in AA activation and two from GTP
What is the sigma factor; what is the rho factor
required for prokaryote initiation and termination of transcription
What are the three posttranscriptional modifications?
1. 7-methyl guanine cap on the 5' end
2. Addition of the poly(A) tail to the 3' end
3. Removal of introns
Why and when does brain switch to ketogenolysis?
After one week of fasting acetyl CoA production from ketogenolysis inhibits pyruvate DH
Where on the codon and anticodon does the wobble hypothesis take place?
3'end of the codon (third position) on mRNA and 5' end of the anticodon (first position) on tRNA.
What is the product of eukaryotic RNA polymerase I, II and III
RNA pol I: 28s, 18s, 5.8s rRNA; RNA pol II: hnRNA/mRNA, snRNA; RNA pol III: tRNA, 5s rRNA
What is the term for a unit of DNA that encodes a particular protein or RNA molecule?
A gene (a rather simple definition but accurate)
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