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Biochemistry

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1. What is the RDE of the urea cycle
BOne
Malabsorption (sprue - enteritis) lack of intrinsic factor from pernicious anemia - gastric bypass surgery or absence of terminal ileum as in Crohns
3 NADH - 1 FADH2 - 2 CO2 - 1 GTP = 12 ATP (x2 per glucose)
Carbomoyl phosphate synthetase I

2. What does primase do
Uses ATP to add high energy phophate group onto substrate
Makes RNA primer on which DNA poly III can initiate replication
1 gene had >1 effect on an individuals phenotype - PKU causes many seemingly unrelated symptoms ranging from mental retardation to hair/skin changes
Aldolase B - AR - fructose 1P accumulates causing a dec in availabel phosphate which inhibts glycogenolysis and gluconeogenesis leading to hypoglycemia - cirrhosis - jaundice and vomiting

3. Which direction does dynein go
Cystine kidney stones - cystine staghorn calculi - cystine is made of two cysteines connected by disulfide bond
Specific glycosylases - AP endonuclease
Post to neg
25OHD3

4. In what cell is collagen synthesis initiated
ATP hyrdolysis couple to energetically unfavorable rxns
Pantothenate - essential component of CoA - a cofactor for acyl transfers and fatty acid synthase
Chronic granulomatous disease - no respiatory burst - no formatino of ROS
Fibroblast

5. What do B- complex vitamin deficiencies often result in
NADH - NADPH - FADH2
Base + ribose
Neither of 2 alleles is dominant - blood groups
Dermatitis - glossitis - and diarrhea

6. Acetyl - CoA carboxylase catalyzes what rxn
Fasting
Epithelial cells
Acetyl - CoA to malonyl - CoA (2C to 3C)
Phosphofructokinase 1

7. What happens on the oxidative arm of the HMP shunt and What is the key enzyme
D2 = ergocalciferol - ingested from plants D3 = cholecalciferol - ingested from milk - formed in sun exposed skin
Regulatory proteins that control cell cycle events; phase specific; activate CDKs
Microtuble polymerization defect causing a dec in phagocytosis results in recurrent pyogenic infections - partial albinism - and peripheral neuropathy
Glucose 6P to CO2 - 2NADPH - ribulose 5P - G6PD - rate limiting step

8. what findings are associated with marfans
Core proteins
Cyclin dependent kinases;constitutive and inactive
Macrocytic - megaloblastic anemia - no neurologic sx - most common vit def in the US - seen in EtOH and pregs
Tall with long extremeties - pectus excavatum - hyperextensive joints - arachnodactyly

9. What is the result of vit B5 def
Convulsions - hyperirritability - peripheral neuropathy - deficiency inducible by INH and oral contraceptives - sideroblastic anemais
Gaucher's - beta glucocerebrosidase - glucocerebrosie - AR
Q -
Dopa decarboxylase

10. How do tetracyclines work
Attachment of ubiquitin to defective proteins tag them for breakdown
Bind 30s subunit preventing attachment of aminoacyl - tRNA
Phosphenolpyruvate to pyruvate catalyzed by pyruvate kinase
Fed

11. What shape does the RNA generate during splicing and why?
Lariat shape in order and remove intron precisely and join 2 exons
Pyroxidine - converted to pyroxidine phosphate a cofactor used in transamination - decarboxylation - glycogen phosphorylase - cystathionine synthesis and heme synthesis - required for synthesis of niacin and tryptophan
Regulatory proteins that control cell cycle events; phase specific; activate CDKs
Inc insulin - dec cAMP - dec PKA

12. How do stable (quiescent) cells grow and regenerate and What are examples
Enter G1 from G0 when stimulated - hepatocytes and lymphocytes
Defect in fibrillin
UGA - UAA and UAG
Malapsorption syndromes like sprue or CF or mineral oil intake

13. What is chediak higashi
Glucose - 2Pi - 2ADP - 2NAD+
Initiate chains
Evident in first few days of life - can present last onest - excess carbamoyl phosphate converted to orotic acid - orotic acid in blood and urine - dec BUN and symptoms of hyerpammonemia
Microtuble polymerization defect causing a dec in phagocytosis results in recurrent pyogenic infections - partial albinism - and peripheral neuropathy

14. What does PURe As Gold and CUT The Py stand for
Makes RNA primer on which DNA poly III can initiate replication
Sucrose = glucose + fructose - lactose = glucose + galactose
Purines= A - G pyrimidine = C - T (U)
Wrinkles and acne

15. What co - factors are required for the pyruvated dehydrogenase complex
Tall with long extremeties - pectus excavatum - hyperextensive joints - arachnodactyly
N to C
Inc intestinal absorption fo calcium and phosphate - inc bone resorption
Pyrophosphate (B1 - thiamine - TPP) FAD (B2 - riboflavin) - NAD (B3 - niacin) - CoA (B5 pantothenate) - lipoic acid

16. What is the fxn of vit K
VMA
Limit protein diet - benzoate or phenylbutarate (both bind amino acids leading to excretion) can decrease ammonia levels
Meiotic nondisjunction of homologous chromosomes (associated with advanced maternal age) leading to trisomy 21
Gamma carboxylation of glutamic acid residues on various proteins concerned with blood clotting - synthesized in intestinal flora

17. In eukaryotes - What does RNA poly III make
Catabolic processes to carry reducing equivalents away as NADH
40 - 60 - 80
TRNA
Binds to LDL receptor - mediates VLDL secretion

18. In which single strand DNA repair mechanism do specific endonucleases release the oligonucTIDE containing bases and DNA poly and ligase fill and reseal - and what disease occures when this is mutated
Degredation of dietary TG in small intestine
2pq
Pyroxidine - converted to pyroxidine phosphate a cofactor used in transamination - decarboxylation - glycogen phosphorylase - cystathionine synthesis and heme synthesis - required for synthesis of niacin and tryptophan
Nucleotide excision repair - xeroderma pigmentosum; unable to repair thymidine dimers caused by UV light

19. Why can't even chain fatty acids produce new glucose
Cleft palate - cardiac abnl - pregs test
Heme synthesis - urea cycle and gluconeogenesis - HUGs take two
They yield only acetyl - CoA equivalents
Proline and lysine - vit C

20. How do permanent cells grow and regenerate and What are examples of permanent cells
Marasmus - muscle wasting
Binds to LDL receptor - mediates VLDL secretion
Remain in G0 - regenerate from stem cells - neurons - skeletal/cardiac muscle - RBCs
Pseudomonas and s aureus

21. Which step in the de novo purine and pyrimidine synthesis pathway requires aspartate - glycine - glutamine and THF
Catabolic processes to carry reducing equivalents away as NADH
Comlex II
Ribose 5- P to PRPP
CTG

22. What two rxns in in glycolysis require ATP
Cri du chat
EtOH dehydrogenase and acetaldehyde dehydrogenase
Glucose to G-6P - hexokinase and fructose -6P to fructose 1 -6 BP phosphofructokinase -1
Essential fructosuria - fructokinase AR

23. peripheral neuropathy - developmental delay - optic atrophy - glopoid cells
Von gierkes - glucose 6 phosphatase
UGA - UAA and UAG
Krabbes - galactocerebrosidase - galactocerebroside - AR
AMP - fructose 2 -6 BP

24. What converts NE to epi
Phenylethamolamine N methyl transferase
PMNs
Proline and glycine (non glycosylated forms)
Immotile cilia due to dynein arm defect - male and femail infertile - bronchiectasis - recurrent sinusitis - associated with situs inversus

25. What is the name is fxn of vit B3
Niacin - constituent of NAD and NADP - derived from tryptophan
Base + ribose + phosphate (3' -5') phosphodiester bond
Phenylalanine
Trisomy 13 - severe mental retardation - rocker bottom feet - micophthlamia - microcephaly - cleft lip/palate - holoprosencephaly - polydactyly - congenital heart disease - death usually within the first year

26. What enzyme converts phenylalanine to tyrosin
RER - translation of alpha chains - usually Gly-X-Y polypeptide (preprocollagen)
Phenylalanine hydroxylase
Stored and undergoes glycogenolysis to maintain blood sugar at appropriate levels
Scrutinizes - hydrolyzes the bond

27. caf
Miscarriage - stillbirth - chromosomal imbalance (down - patau)
SAM
Pyruvate to oxaloacetate (3C to 4C)
Neurofibromatosis type 1 (von Recklinghausens disease)

28. What is the composition of urea and where do each part derive from
Transmitted only through mother - all offspring of affected females may show signs of disease
NH2-(C=O) - NH2 one NH2 from ammonia the C=O from CO2 - and the other NH2 from aspartate
Glutamine PRPP amidotransferase
Severity of disease worsens or age of onset of disease is earlier in succeeding generations - huntingtons

29. How does cytosine become uracil
Deamination
Genetic code is conserved throughout evolution - except for mito - archaebacteria - mycoplasma - and some yeast
Stop codon is recognized by release factor - and completed protein is released from ribosome
Binds to LDL receptor - mediates VLDL secretion

30. What does glycosylation of pro alpha chian yield and What is the structure
Hypercalciuria - loss of appetite - stupor - seen in sarcoidosis from activation fo vit D by epithelioid macrophage
CGG
Procollagen - triple helix of 3 alpha collagen chains
Mebendazole/thiabendazole

31. What are the findings with homocystinuria and What amino acid is needs to be supplemented
Homocystein in ruine - mental retardation - osteoporosis - tall stature - kyphosis - lens subluxation and atherosclerosis leading to stroke and MI - cysteine
Changed AA (convservative - new AA is similar in chemical structure)
IDL
Prokaryotic only - degrades RNA primer and fills in the gap with DNA

32. Which tumor suppresors inhibit G1 to S progression - where mutations result in unrestrained growth
Fatty acid oxidation - acetyl - Coa production - TCA cycle - OXPHOS
Rb and p53
Ca/calmodulin in muscle to coordinate with muscle activity
Enter G1 from G0 when stimulated - hepatocytes and lymphocytes

33. What is the defect in I- hyperchylomicronemia
LPL def - or altered apoCII - elevated TG and cholesterol - causes pancreatitis - hepatosplenomegaly and eruptive/pruritic xannthomas - no risk of atherosclerosis
Active secretion in lungs and GI - reabsorbs in skin
Liver and beta cells of pancreas - low affinity - high Km - high capacity - high Vmax - induced by insulin
Progressive hreditary nephritis and deafness - associated with occular disturbances - due to abnl type IV collagen - usually x- linked recessive

34. What kind of branches do glycogen branches have
Orotic acid to UMP
40 - 60 - 80
Alpha 1 -6 and alpha 1 -4
Aminoacyl - tRNA binds A site - ribosomal rRNA catalyzes peptide bond formation - transfers growing peptide to AA in A site - ribosome advances 3 nucTIDE toward 3' end of RNA - moving peptidyl RNA to P side

35. What is imprinting and give an example

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36. What amino acid makes up most of the octamer
Many generations - both male and female affected - often pleiotropic - can present clinically after puberty
Lysine and arginine
Malonyl coa (+ biotin= palmitiate - 1 16C fatty acid)
Sever atherosclerotic disease early in life - and tendon xanthomas on the achilles - MI may develop before 20

37. What is the RER called in neurons and What is made there
Binds to LDL receptor - mediates VLDL secretion
Von hippel lindau - 3
Nissl body - enzyme and NTs
ATP and methionine

38. colon becomes covered witih adenomatous polyps after puberty - progresses to colon cancer unless resected
Coenzyme A - lipoamide
Pyruvate carboxylase - PEP carboxykinase - fructose 1 -6 biphosphatase - glucose 6 phosphatase
FAP
Von hippel lindau - 3

39. delivers hepatic TGs to peripheral tissue - secreted by liver
Hunters - iduronate sulfatase - heparan sulfate/dermatan sulfate - XR
VLDL
Loss of brush border enzyme causing bloating - cramps - osmotic diarrhea
Transmitted only through mother - all offspring of affected females may show signs of disease

40. How many rings do purines have
Cartilage - hyaline - vitreous body - nucleus pulposus
2 rings
Stop codon is recognized by release factor - and completed protein is released from ribosome
SAM

41. How many ATP are created by aerobic metobolism of glucose in muslce via what shuttle
AD absent of dec LDL receptors causes accelerated atherosclerosis - achilles xanthomas and corneal arcus - increase LDL and elecated cholesterol
Adenosine to inosine
30 - glycerol -3- phosphate shuttle
Cobalamin - cofactor of homocysteine and methyltransferase - methylmalonyl CoA mutase

42. What enzymes metabolize fatty acids and amino acids
2 rings
1 gene had >1 effect on an individuals phenotype - PKU causes many seemingly unrelated symptoms ranging from mental retardation to hair/skin changes
Acetoacetate and beta hydroxybutyrate
Phosphofructokinase 1

43. What is the active form of vit D
Deamination
Hunters - iduronate sulfatase - heparan sulfate/dermatan sulfate - XR
Eu - methionine - pro - formyl - methionine
1 -25 OH2 D3 = calcitriol

44. What can vit B3 be used to treat
Hyperlipidemia
Inhibit DNA gyrase specific for prokaryotic topoisomerase
Asp and Glu
High output cardiac failure - dilated cardiomyopathy - edema

45. The golgi apparatus fxns as a distribution center between what organelles in the cell and What does it process
For proteins and lipids from ER to plasma membrane - lysosomes and secretory vesicles
Asp and Glu
Thiamine - in thiamine pyrophosphate a cofactor for pyruvate dehydrogenase (glycolysis) - alpha ketoglutarate dehydrogenase (TCA cycle) - transketolase (HMP shunt) - and branched - chain AA dehydrogenase
5' to 3'

46. What enzyme adds Cl - to the H202 to makes bleach
Cleft palate - cardiac abnl - pregs test
Locus heterogeneity - ocular albinism is x- linked recessive
Myeloperoxidase
Acetyl - CoA

47. What order kinetics does EtOH dehydrogenase have
Liver and leafy veggies
Retardation - self mutilation - aggression - hyperuricemia - gout - choreoathetosis
Zero
Neural tube

48. What does a phosphorylase do
Phosphorylation excess glucose to sequester it - liver becomes blood glucose buffer
Adds an inorganic phosphate onto substrate without using ATP
Chylomicrons
CGG

49. What substance inside the cells replenishes NADPH
FISH
Facial flushing
Protective against malaria
G6PD

50. What does the addition of mannose -6 phosphate do
Myeloperoxidase
PCR - denaturation - annealing - elongation
DsRNA promotes degradation of target mRNA knocking down gene expression
Targets the proteins for lysosome

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Biochemistry

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