Biochem Review Flashcards
What is the rate-limiting enzyme in purine synthesis? Pyrimidine synthesis?
purine - glutamine PRPP amidotransferase
pyrimidine - CPS-2
What are the sources of carbon in the synthesis of purines? In pyrimidine synthesis?
purines - CO2, glycine, THF (nitrogen source = aspartate and glutamine)
pyrimidines - aspartate and CO2 (nitrogens = glutamine)
Which medication inhibits ribonucleotide reductase?
hydroxyurea
Which medication inhibits dihydrofolate reductase?
methotrexate, trimethoprim
Which medication inhibits thymidylate synthase?
5-FU
Which medication inhibits inosine monophosphate dehydrogenase?
mycophenolate
Which medication inhibits PRPP amidotransferase?
6-MP
What accounts for the positive charge of histones? What accounts for the negative charge of DNA?
Lysine and arginine on histones
phosphate groups on DNA
How many adenosine residues are found in a molecule of DNA if one strand contains A=2000, G=500, C=1500, T=1000?
3000 - 2000 A plus the 1000 from the other strand
A boy with self-mutilating behavior, intellectual disability, and gout
Lesch-Nyhan
Orotic acid in the urine elevated serum ammonia
ornithine-transcarbamoylase deficiency
Orotic acid in the urine + normal serum ammonia
oratic aciduria
Megaloblastic anemia that does not improve with folate and B12
oratic aciduria
Lesch Nyhan syndrome
defective purine savage due to absent HGPRT (which converts hypoxanthine to IMP and guanine to GMP)
X-linked recessive
Sx = intellectual disability, self-mutilation, aggression, hyperuricemia (orange sand crystals in diaper), gout, dystonia
Tx = allopurinol, febuxostat
oratic aciduria
inability to convert orotic acid to UMP because of defect in UMP synthase
Autosomal recessive
megaloblastic anemia refractory to folate and B12; no hyperammonemia (vs ornithine transcarbamylase deficiency)
Tx = uridine monophosphate to bypass mutated enzyme
What strand of DNA nucleotides opposes this DNA strand: 5’-ATTGCGTA-3’?
5’-TACGCAAT-3’ (DNA is always written 5’->3’
How does UV radiation damage DNA?
pyrimidine dimers on same strand of DNA (usually thymine-thymine, but can be cytosine-cytosine also)
Which eukaryotic DNA polymerase replicates the lagging strand?
DNA polymerase alpha for the first 20 bases then DNA polymerase delta
Which eukaryotic DNA polymerase synthesizes RNA primer?
DNA polymerase alpha
Which eukaryotic DNA polymerase repairs DNA?
DNA polymerase beta
Which eukaryotic DNA polymerase replicates mitochondrial DNA?
DNA polymerase gamma
Which eukaryotic DNA polymerase replicates the leading strand of DNA?
DNA polymerase alpha for the first 20 bases, then DNA polymerase epsilon
Nucleotide excision repair
DNA polymerase and ligase fill and reseal the gap, respectively; repairs bulky helix distorting lesions
What disorder results from a problem in nucleotide excision repair?
xeroderma pigmentosum (very susceptible to damage from the sun)
Base excision repair
base-specific glycosylase removes altered base and creates AP site; AP endonuclease cleaves 5’ end; lyase cleaves the 3’ end; DNA polymerase beta fills the gap and DNA ligase seals it
Mismatch repair
mismatched nucleotides are removed, and the gap is filled and resealed
What disorder results from a defect in mismatch repair processes?
Lynch syndrome (hereditary nonpolyposis colorectal cancer)
Nonhomologous end joining
brings together two ends of DNA fragments to repair double-stranded breaks
What disorders result from defects in nonhomologous end joining?
ataxia telangiectasia
breast/ovarian cancers with BRCA1 mutation
Fanconi anemia
What is Bloom syndrome?
mutation of helices; affects both DNA replication and repair
Patients are hypersensitive to sunlight, have increased susceptibility to leukemias and lymphomas, immunodeficiency, infertility, and facial anomalies
What is a silent mutation?
nucleotide substation but codes for the same amino acid
What is a missense mutation? What is an example of this?
nucleotide substitution resulting in changed amino acid
Ex = sickle cell disease (substation of glutamic acid with valine)
What is a nonsense mutation?
nucleotide substation resulting in early stop codon (UAG, UAA, UGA); usually results in a nonfunctional protein
What is a frameshift mutation? What is an example of this?
deletion or insertion of a number of nucleotides not divisible by 3, resulting in misreading of all nucleotides downstream
Ex = Duchenne muscular dystrophy, Tay-Sachs disease
What does helicase do?
unwinds template DNA at the replication fork
What do single-stranding binding proteins do?
prevents strands from reannealing
What does DNA topoisomerase do? What are the auto-Abs to it?
removes supercoils
Auto Abs = anti-Scl-70 Abs found in diffuse scleroderma
What are the drugs that inhibit eukaryotic DNA topoisomerase? Prokaryotic?
eukaryotic - etoposide/teniposide
prokaryotic - fluoroquinolones (also inhibit topoisomerase IV)
What elongates the lagging strand in prokaryotes?
DNA polymerase III
What elongates the leading strand in prokaryotes?
DNA polymerase III
What does DNA polymerase I do in prokaryotes?
degrades RNA primer; replaces it with DNA
What does DNA ligase do?
Joins Okazaki fragments
What amino acid is encoded by the most common start codon?
methionine
What is the difference between an intron and an extron?
introns get spliced out of the mRNA by the spliceosome
externs go into the mature mRNA to be expressed
Production of what enzyme is regulated by the lac operon?
beta-galactosidase
What two proteins regulate the lac operon?
CAP and lac repressor
What two substrate conditions must be met for the lac genes to be transcribed?
- presence of lactose in excess (moves repressor)
2. no glucose (CAP presence)
What are the different eukaryotic RNA polymerases?
RNA pol I -> rRNA
RNA pol II -> mRNA
RNA pol III -> tRNA
What is the difference between CPS1 and CPS2 enzymes? (location, pathway, nitrogen source)
location - CPS1 - mitochondria; CPS2 - cytosol
pathway - CPS1 - urea cycle; CPS2 - pyrimidine synthesis
nitrogen source - CPS1 - ammonia; CPS2 - glutamine
What is the first enzyme in the glycolysis pathway that catalyzes glucose/fructose -> what?
hexokinase or glucokinase catalyzes glucose/fructose -> glucose-6-phosphate
What enzyme catalyzes fructose-6-phosphate to fructose-1,6-bisphosphate in glycolysis?
phosphofructokinase-1
What stimulates phosphofructose-1?
AMP and fructose-2,6-bisphosphate
What inhibits phosphofructose-1?
ATP and citrate
What enzyme catalyzes the conversion of phosphoenolpyruvate to pyruvate in glycolysis?
pyruvate kinase
What stimulates the enzyme pyruvate kinase?
fructose-1,6-bisphosphate
What inhibits the enzyme pyruvate kinase?
ATP, alanine
What is the rate-limiting enzyme in glycolysis?
phosphofructokinase-1
What is the most commonly deficient enzyme in glycolytic enzyme deficiency? What are the symptoms?
most common cause: pyruvate kinase deficiency
presentation: hemolytic anemia because RBC cannot make ATP without glycolysis; glycolysis is their sole source of ATP
A muscle biopsy on a patient of yours reveals elevated glycogen levels, elevated fructose-6-phosphate, and decreased pyruvate. What enzyme deficiency do you suspect most?
phosphofructokinase-1
What reaction does PFK-2 catalyze, and when is it active?
PFK2 catalyzes fructose-6-phosphate -> fructose-2,6-bisphosphate; active when insulin is present (fed state)
What reaction does FBPase-2 catalyze, and when is it active?
FBPase-2 catalyzes fructose-2,6-bisphosphate -> fructose-6-phosphate; active when glucagon in present (fasting) -> when you’re fasting, you don’t want to breakdown glucose; you want ht liver to make glucose, so you go through gluconeogenesis
What are the irreversible enzymes involved in glycolysis?
- hexokinase/glucokinase
- PFK-1
- pyruvate kinase
What are the irreversible enzymes involved in gluconeogenesis?
- pyruvate carboxylase
- PEP carboxykinase
- fructose-1,6-bisphosphatase
- glucose-6-phosphatase
What enzyme catalyzes the rate-limiting step in gluconeogenesis?
fructose-1,6-bisphosphatase
Order the following molecules by how much energy they contain that can be made available to fuel endergonic reactions: pyruvate, adenosine monophosphate, glucose, adenosine, adenosine triphosphate
glucose, pyruvate, ATP, AMP, adenosine