Biochem - WLB Flashcards
What is the rate-limiting enzyme in purine synthesis?
Glutamine PRPP Amidotransferase
What is the rate-limiting enzyme in pyrimidine synthesis?
Carbamoyl phosphate synthetase II (CPS-2)
What are the sources of carbon in the synthesis of purines?
CO2 + Glycine + THF
What are the sources of carbon in the synthesis of pyrimidines?
CO2 + Aspartate
Which medication inhibits ribonucleotide reductase?
Hydroxyurea
Which medication inhibits dihydrofolate reductase?
Trimethoprim (in prokaryotes) and Methotrexate (in eukaryotes)
Which medication inhibits thymidylate synthase?
5-Fluorouracil
Which medication inhibits inosine monophosphate dehydrogenase?
Mycophenolate
Which medication inhibits PRPP amidotransferase?
6-Mercaptopurine
What accounts for the positive charge of histones?
Lysine + Arginine
What accounts for the negative charge of DNA?
Phosphate groups
How many adenine residues are found in a molecule of DNA if ONE strand contains A=2000, G=500, C=1500, and T=1000?
3,000 adenine residues
remember DNA is a double helix: one strand has 2000 and the complementary strand has 1000 which are paired to thymine
What strand of DNA nucleotides opposes this DNA strand: 5’-ATTGCGTA-3’?
5’-TACGCAAT-3’
How does UV radiation damage DNA?
makes pyrimidine dimers on same strand
Which eukaryotic DNA polymerase replicates the lagging strand?
DNA polymerase Alpha
Which eukaryotic DNA polymerase synthesizes RNA primers?
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?
DNA polymerase Delta
Which structural motifs allow proteins to bind to DNA?
Helix-loop-helix
Helix-turn-helix
Zinc finger
Leucine zipper protein
What amino acid is encoded by the most common start codon?
Methionine (AUG)
What is the difference between an intron and an exon?
Intron => non-coding region, gets spliced out and stays in the nucleus
Exon => coding region, gets transcribed
Production of what enzyme is regulated by the lac operon?
Beta-galactosidase
What two proteins regulate the lac operon?
CAP (catabolite activating protein) and lac repressor
What two substrate conditions must be met for the lac genes to be transcribed?
Absent/no glucose, excess lactose
What enzyme matches amino acids to tRNA?
Aminoacyl-tRNA synthetase
What antibiotics are inhibitors of prokaryotic protein synthesis at the 30S ribosome?
Aminoglycosides (e.g. Gentamicin, Streptomycin, Neomycin)
Tetracyclines
What antibiotics are inhibitors of prokaryotic protein synthesis at the 50S ribosomal subunit?
Clindamycin
Chloramphenicol
Macrolides (e.g. Erythromycin, Azithromycin, Clarithromycin)
Linezolid
Streptogramins (e.g. Quinupristin/Dalfopristin)
What are the Hardy-Weinberg equations for population genetics?
p + q = 1
p^2 + 2pq + q^2 = 1
What mode of inheritance is often due mutations in one gene and due to defects in structural genes?
Autosomal dominant
What mode of inheritance is often due to enzyme deficiencies and is usually only seen in one generation?
Autosomal recessive
What mode of inheritance skips generations and has no male-to-male transmission?
X-linked recessive
What mode of inheritance results in transmission of disease from affected father to all daughters but no sons?
X-linked dominant
What mode of inheritance is transmitted only through the mother?
Mitochondrial inheritance
What is the differences between Southern blot, Northern blot, and Western blot?
Southern: DNA sample, DNA probe
Northern: RNA sample, DNA probe
Western: protein sample, Antibody probe
What type of test uses a known antigen to discern the presence of an antibody?
Indirect ELISA
What type of test is performed in order to diagnose chromosomal imbalances?
Karyotyping
What are the different eukaryotic RNA polymerases? What do they each make?
RNA polymerase I => makes rRNA (most numerous, synthesized in the nucleolus)
RNA polymerase II => makes mRNA (largest RNA, synthesized in the nucleoplasm)
RNA polymerase III => makes tRNA (tiny RNA, synthesized in the nucleoplasm)
What is the characteristic DNA sequence of the promoter region? What does a mutation in the sequence cause?
Promoter region: (-25)TATA box, (-75)CAAT box, (-10)Pribnow/TATAAT box
Mutation => decreased gene transcription
Which enzyme is responsible for tRNA charging?
Aminoacyl-tRNA Synthetase
Which enzyme catalyzes peptide bond formation?
Peptidyltransferase
What are the different prokaryotic RNA polymerases
only 1 prokaryotic RNA polymerase (multi-subunit complex)
What enzyme is deficient in Lesch-Nyhan Syndrome? What is the treatment?
Enzyme deficient => HGPRT
Tx: Allopurinol
What are the mRNA stop codons?
UAG, UAA, UGA
What are the differences between carbamoyl phosphate synthetase (CPS) I and CPS II?
CPS I: mitochondria, urea cycle, ammonia is nitrogen source
CPS II: cytosol, pyrimidine synthesis, glutamin is nitrogen source
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
How does a low insulin/high glucagon state inhibit glycolysis and lead to conversion of energy?
Low insulin/high glucagon => more active protein kinase A => active FBP-2 => less fructose-2,6-bisP => less active PFK-1 => less glycolysis
High insulin/low glucagon => less active protein kinase A => active PFK-2 => more fructose-2,6-bisP => active PFK-1 => more glycolysis
What enzymes convert glucose to glucose-6-phosphate?
Hexokinase (most tissues)
Glucokinase (liver and beta-cells in pancreas)
What is the clinical consequence of a glycolytic enzyme deficiency?
Hemolytic anemia (no ATP in RBCs)
What enzymes are responsible for increasing and decreasing the intracellular levels of fructose-2,6-bisphosphate?
Increasing => PFK-2 (more activation of PFK-1 => glycolysis)
Decreasing => FBP-2 (less activation of PFK-1 => gluconeogenesis)
What is the rate-limiting enzyme in the glycolytic pathway?
PFK-1
What is the formula for Gibbs free energy?
ΔG = ΔH - TΔS
What irreversible enzymes are involved in gluconeogenesis?
- Pyruvate carboxylase (requires Biotin)
- PEP-CK
- Fructose-1,6-bisphosphatase (rate-limiting step)
- Glucose-6-phosphatase
What enzyme catalyzes the rate-limiting step in gluconeogenesis?
fructose-1,6-bisphosphatase
What is the rate-limiting enzyme for glycogen synthesis?
Glycogen synthase
What is the rate-limiting enzyme for glycogenolysis?
Glycogen phosphorylase
Which enzyme converts glucose-6-phosphate to glucose?
Glucose-6-phosphatase
Which glycogen storage disease is characterized by a deficiency in glycogen phosphorylase?
McArdle disease (Type V)
Which glycogen storage disease is characterized by a deficiency in glucose-6-phosphatase?
VonGierke Disease (Type I)
Which glycogen storage disease is characterized by lactic acidosis, hyperlipidemia, and hyperuricemia (gout)?
VonGierke Disease (Type I)
Which glycogen storage disease is characterized by a deficiency in alpha-1,6-glucosidase?
Cori disease (Type III)
alpha-1,6-glucosidase = debranching enzyme
Which glycogen storage disease is characterized by a deficiency in alpha-1,4-glucosidase?
Pompe disease (Type II)
Which glycogen storage disease is characterized by cardiomegaly?
Pompe disease (Type II) - Infant type
Which glycogen storage disease is characterized by diaphragm weakness leading to respiratory failure?
Pompe disease (Type II) - Adult type
Which glycogen storage disease is characterized by increased glycogen in the liver and severe fasting hypoglycemia?
VonGierke Disease (Type I)
Which glycogen storage disease is characterized by hepatomegaly, hypoglycemia, and hyperlipidemia (with normal kidneys, lactate, and uric acid)?
Cori disease (Type III)
Which glycogen storage disease is characterized by painful muscle cramps and myoglobinuria with strenuous exercise?
McArdle Disease (Type V)
Which glycogen storage disease is characterized by severe hepatosplenomegaly and enlarged kidneys?
VonGierke Disease (Type I)
What vitamin deficiency results from Hartnup disease?
Niacin (Vitamin B3)
Why are alanine and glutamine found in such high concentrations in the blood?
they are the two major carriers of nitrogen from tissues
What enzymes catalyze transamination reactions?
Aminotransferases/Transaminases
transfer amino group from an amino acid to alpha-ketoglutarate => forms glutamate
What are the two most important transaminases? What reactions do they catalyze?
Alanine Transaminase (ALT): carries amino groups from the muscle to the liver (pyruvate + glutamate => alanine + alpha-KG)
Aspartate Transaminase (AST): (oxaloacetate + glutamate => aspartate + alpha-KG)
What cofactor is required by all transaminases?
Pyridoxal phosphate (a derivative of vitamin B6)
What are the four possible products of pyruvate?
Alanine (ALT)
Oxaloacetate
Lactate
Acetyl-CoA
What are the two main nitrogen transporters in the blood?
Glutamine and alanine
What are the major regulatory enzymes of the citric acid (TCA) cycle?
Citrate synthase
Isocitrate dehydrogenase (RLS)
alpha-Ketoglutarate dehydrogenase
What substances are known to inhibit the complexes of the electron transport chain?
Complex I - Rotenone, Amytal, MPP
Complex III - Antimycin A
Complex IV - Cyanide, CO, H2S, Azide (N3-)
Complex V/ATPase - Oligomycin
What substances can increase the permeability of the inner mitochondrial membrane, thereby decreasing ATP synthesis but increasing heat generation?
2,4-Dinitrophenol
Aspirin (high dose)
Thermogenin
In patients with G6PD deficiency, ingestion of what substances can induce oxidative damage to RBCs?
“Spleen Purges Nasty Inclusions From Damaged Cells”
Sulfonamides
Primaquine
Nitrofurantoin
Isoniazid
Fava beans
Dapsone
Chloroquine
What is the rate-limiting step of the pentose phosphate pathway?
Glucose-6-phosphate dehydrogenase (G6PD)
Which tissues of the body use the pentose phosphate pathway?
RBCs, Liver, adrenal cortex, mammary glands (during lactation)
How does a deficiency of the enzyme that is the rate limiter for the HMP shunt can result in hemolytic anemia?
RBCs are more susceptible to oxidative damage => RBC lysis => hemolytic anemia
What are the symptoms of classic galactosemia?
FTT, intellectual disability, hepatomegaly, jaundice, infantile cataracts
What disorder is caused by a deficiency in Galactokinase?
Galactokinase Deficiency
What disorder is caused by a deficiency in Aldolase B?
Fructose Intolerance
What disorder is caused by a deficiency in Lactase?
Lactose intolerance
What disorder is caused by a deficiency in Galactose-1-phosphate uridyltransferase?
Classic Galactosemia
What disorder is caused by a deficiency in Fructokinase?
Essential Fructosuria
What fuels are produced and used in the post-absorptive period?
Produced: Glucose (from hepatic glycogenolysis/gluconeogenesis), Fatty Acids (from adipose tissue)
Used: muscles, brain, and other tissues use predominantly glucose
When does gluconeogenesis begin in the post-absorptive period? When does it become fully active?
Begins 4-6 hours after the last meal
Fully active when glycogen stores are depleted (10-18 hours after last meal)
How does the pattern of fuel production and usage change in early starvation (24 hours after the last meal)?
Produced: Glucose, Fatty acids
Used: Brain uses predominantly glucose. Muscles and other tissues use some glucose, but predominantly fatty acids.
In intermediate starvation (48 hours after the last meal), how does the pattern of fuel production and utilization change?
Produced: Glucose, MORE fatty acids, Ketone Bodies
Used: Brain uses predominantly glucose, but also some ketone bodies. Muscles and other tissues use predominantly fatty acids, but also some ketone bodies.
What metabolic scenario favors the synthesis of ketone bodies?
When production of acetyl-CoA from Beta-oxidation of fatty acids exceeds the oxidative capacity of the TCA cycle.
True or False? Ketone bodies can be used by all body tissues including the brain.
FALSE - RBCs can only use glucose!
What is the pattern of fuel production and utilization in prolonged starvation (5 days after last meal)?
Produced: Glucose, Fatty acids, Ketone bodies
Used: Brain uses predominantly ketone bodies. Muscles and other tissues use predominantly fatty acids, but also some ketone bodies.
What is the primary energy source in a patient that has not eaten in two days?
Fatty acids
What is the rate-limiting enzyme in ketone body synthesis?
HMG-CoA synthase
A stressed physician comes home from work, consumes seven or eight shots of tequila in rapid succession before dinner, and becomes hypoglycemic. Why did she become hypoglycemic?
Ethanol metabolism => increased NADH => pyruvate and oxaloacetate => lactate and malate (respectively) => NO enzymes for gluconeogenesis!
What are some of the hallmark features of kwashiorkor?
“FLAMES”
Fatty Liver
Anemia
Malnutrition (no proteins)
Edema
Skin lesions/hypopigmentation
What deficiency causes familial hypercholesterolemia?
LDL receptors (lipoprotein lipase/Apo C-II)
Which apolipoprotein activates LCAT?
Apo A-1
Which apolipoprotein mediates chylomicron secretion?
Apo B-48
Which apolipoprotein mediates VLDL secretion?
Apo B-100
Which apolipoprotein is a cofactor for lipoprotein lipase?
Apo C-II
Which apolipoprotein mediates the uptake of remnant particles?
Apo E
What is the rate-limiting step for fatty acid synthesis?
Acetyl-CoA carboxylase
What is the rate-limiting step for beta-oxidation of fatty acids?
Carnitine acyltransferase-1
What is the rate-limiting step for ketone body synthesis?
HMG CoA synthase
What is the rate-limiting step for cholesterol synthesis?
HMG CoA reductase
What are the essential amino acids?
“PVT TIM HaLL”
PVT: Phenylalanine, Valine, Threonine
TIM: Tryptophan, Isoleucine, Methionine
HaLL: Histidine, Leucine, Lysine
What is the amino acid precursor to Histamine?
Histidine
What is the amino acid precursor to Porphyrin and heme?
Glycine
What is the amino acid precursor to Nitric Oxide?
Arginine
What is the amino acid precursor to GABA?
Glutamate
What is the amino acid precursor to SAM (s-adenosyl-methionine)?
Methionine
What is the amino acid precursor to Creatinine?
Arginine
A full-term neonate feeds poorly, is hyperactive and has a musty odor. What is the diagnosis?
PKU
decreased/deficient phenylalanine hydroxylase
A patient with PKU should have a diet low in phenylalanine. What other dietary modifications should a patient with PKU make?
Increase tyrosine and tetrahydrobiopterin in the diet
A middle-aged man has dark spots on his sclera and has noted that his urine turns black when left sitting for a period of time. What is the diagnosis?
Alkaptonuria
What is the underlying cause of maple syrup urine disease?
decreased branched-chain alpha-ketoacid dehydrogenase complex
