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425 Cards in this Set
- Front
- Back
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What are fast growing cells in the body that synthesize collagen fibers, elastic fibers, adhesion proteins, and complex polysaccharides?
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Fibroblasts
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What type of helix does collagen form?
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Triple Left handed helix, with repeated AA sequence Glycine-X-Y, where X is often proline and Y is hydroxypoline.
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What amino acid allows for tight contact between polypeptide chains in collagen?
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Glycine
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What intracellular processes occur in the building of collagen?
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1) Cleavage of signal peptide
2) Hydroxylation 3) Glycosylation 4) Formation of disulfide bonds 5) Formation of triple helix |
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What Vitamin is required for hydroxylation of collagen? What disease occurs when these Vitamin is deficient?
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Vitamin C, Scurvy
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What enzyme requires copper to function? What disease is associated with deficiency in copper?
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Lysyl oxidase, Menke disease
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How many distinct types of collagen are there?
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25 types of collagen encoded by 100 genes, different from elastic fibers, which have only 1 genetic type
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What is the major protein responsible for the elastic property of tissues?
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Elastin
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What protein is required for elastin subunits to assemble between microfibrils?
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Fibulin, NOT fibrillin
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What AA has a high capacity to form alpha helixes and is abundant in elastic fibers?
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Lysine
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What is a desmosine?
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A stable six membered ring that cross links elastic fibers, requires lysyl oxidase, and therefore copper to form
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What type of reaction crosslinks collagen?
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Aldol reaction
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What does heparin bind to in order to inhibit clotting?
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anti-thrombin
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What does adding a strongly cationic polypeptide to heparin do?
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inhibits its anti-coagulation activity
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What function does fibriongen have in the body?
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aids blood clotting
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What does fibronectine do?
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Aids in cell adhesion/migration
Wound healing |
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Where is tenascin expressed?
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Tendon, mesenchyme
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What is the factor that activates clotting?
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von Willebrand's factor
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What transmembrane receptor does fibronectin regularly bind to?
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integrin
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What are the two different pools of fibronectins?
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Tissue fibronectins and plasma fibronectin
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What is the major matrix adhesive glycoprotein of the basal lamina?
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Laminin
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What type of disease results from defects in tenascins?
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Ehler-Danlos syndrome
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What are the four major families of cell adhesion receptors?
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Ig-CAM, Cadherins, Integrins, Selectins
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What cell adhesion molecule is important in the formation of the neural tube?
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Cadherin
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What does B-catenin do?
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Activates gene expression
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How does snake venom inhibit blood clotting?
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The venom contains RGD proteins that block binding of integrin to fibrinogen
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Where are selectin molecules commonly found?
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Endothelial cells, at sites of inflammation
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What heavily glycosylated protein does selectin normally interact with?
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Mucin
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What cell adhesion molecules is important in the initial attachment of WBCs to sites of inflammation?
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Selectin
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What carbohydrate rich layer must sperm digest in order to fertilize an egg?
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Glycocalyx
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What 5 types of cells are indigenous to the ECM?
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fat cell, chondrocyte, osteoblast, mast cell, fibroblast
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What degenerative disease can arise from uncontrolled destruction of ECM?
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arthritis and emphysema
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What inhibits MMPs?
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TEMPS (tissue inhibitors of matelloproteinases)
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What disease is observed in mutations of Type I collagen?
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Osteogenesis Imperfects or brittle bone disease
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What AA is usually mutated in Osteogenesis Imperfecta?
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Glycine
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When a patient exhibits dark blue sclera, what disease can one suspect?
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Osteogenesis Imperfecta
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When a patient has stretchy skin, loose joints, and bulging eyeballs, what genetic disease might one suspect?
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Ehlers-Danlos
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What might a cardiologist worry about in Ehlers-Danlos patients?
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Mitral valve prolapse
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When a patient has dark purplish spots on their skin and also gum disease what might they be suffering from?
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Scurvy
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What mutation causes Marfan syndrome?
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mutation in fibrillin-1
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When a patient is tall, has long arms, legs, and fingers, along with chest deformity, what disease might one suspect them of having?
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Marfan syndrome
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What can be caused by chronic ingestion of sweat peas? What enzyme is not functioning?
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Lathyrism, lysyl oxidase
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What 3 types of mutations can occur with changes in nucleotide sequence?
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missense, frameshift, nonsense
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Changes in DNA methylation, histone acetylation and environmental factors can lead to what type of gene variation?
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Epigenetic changes
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What chromosomal abnormality causes Down Syndrome?
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Trisomy 21
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What does deletion of a region of chromosome 7 cause?
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William-Beuren sydrome
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A person has an out-going personality but has mild mental retardation and Elfin-like facial appearance? What disease might they be suffering from
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William-Beuren syndrome
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Name 5 ways chromosomes can be rearranged
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deletion, insertion, translocation, duplication, inversion
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What cytogenetic technique is commonly used to visualize specific genes on chromosomes?
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FISH
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Less active genes are usually located where in the nucleus?
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periphery
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Are chromosomes randomly organized in the nucleus?
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No
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Southern blotting, restriction enzyme mapping, and DNA sequencing is used to identify which type of genetic mutations?
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nucleotide sequence on DNA
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What type of mutation is characterized by a premature stop codon?
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Nonsense
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Consecutive generations are affected by a genetic disease, both male and female. What is the mostly likely inheritance pattern of this gene?
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Autosomal dominant
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Mitochondria DNA is passed down from the father or mother?
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mother
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What gene is mutated in autosomal dominant retinitis pigmentosa?
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rhodopsin
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For patients suffering from leukemia and wanting to use the drug thiopurine, what test should be performed prior to drug administration?
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SNP analysis of TMPT allele to avoid dose-limiting hematopoietic toxicity
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When a region of DNA is very acetylated, what is likely happening to the DNA?
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It is being actively transcribed
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On what structure does acetylation, methylation, and phosphorylation usually occur in terms of chromatin?
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histone tails
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What enzyme is used to reverse histone acetylation?
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histone deacetylase
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On what nucleotide base does methylation usually occur?
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Cytosine
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What two organs play a major role in acid/base balance?
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Lung/Kidney
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What is the normal pH of the blood?
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7.35-7.46 in ECF
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What is normal serum concentration of H+?
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40 nEq/L
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What is normal serum partial pressure of carbon dioxide?
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40 mm Hg
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Metabolic acidosis will usually compensate with?
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Respiratory alkalosis, hyperventilation
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pCO2 rises, the person will likely suffer from?
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Respiratory acidosis
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Should one draw blood from the artery or vein for blood gas analysis?
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artery
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Bicarbonate falls, the person is suffering from what acid-base imbalance?
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metabolic acidosis
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What does the Band 3 anion transporter do?
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transport chloride into cell
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How does the kidney increase the buffering capacity of blood?
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increase the concentration of bicarbonate in the blood
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pH is dependent on what two parameters?
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concentration of bicarbonate and carbon dioxide
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A person has low blood pH, but little change in pCO2, what acid base imbalance are they likely suffering from?
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metabolic acidosis
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How does the body usually compensate for respiratory acidosis? What organ is involved?
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By metabolic alkalosis through excretion of H+ via kidney
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A person is hyperventilating as a form of compensation. What was the original acid/base disorder?
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Metabolic acidosis
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A person is choking. What acid-base disorder should one expect?
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Respiratory Acidosis
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What acid-base disorder is commonly seen in diabetic patients?
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Keto-acidosis
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What acid/base imbalance occurs after prolonged vomiting?
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Metabolic alkalosis, lose H+ in vomit
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When pCO2 decrease by 10 mm Hg, what change in pH should one expect if the problem is an acute respiratory disorder? chronic?
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0.08 increase for acute
0.03 for chronic |
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What is the normal anion gap?
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12-16
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What can increase the anion gap?
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organic acids, aspirin intake
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What is the normal serum osmolality?
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280-300 mOsm/kg
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What can causes changes in serum osmolality?
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ethylene glycol, methanol, hyperlipidemia, hyperproteinemia
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What is the normal pH of urine?
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<5.0
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How does one treat Bartter's syndrome, a form of saline responsive metabolic alkalosis?
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K+ repletion
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What organ is mostly likely malfunctioning in cases of saline non-responsive metabolic alkalosis?
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reduced kidney function
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What type of acid base imbalance should one watch out for in a patient with emphysema?
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Respiratory acidosis
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What acid/base disorder can hypoxia induce?
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Respiratory alkalosis, due to increased respiratory rate to remove carbon dioxide, hypoxia in the tissue level will increase lactic acid leading to metabolic acidosis, causing a mixed acid base disorder
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Cushings syndrome, hyperaldosteronism, and exogenous steriods can all lead to what type of acid/base disorder?
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metabolic alkalosis
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A person has lots of CAG trinucleotide repeats. What disease should they look out for?
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Huntington's Disease
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What conformation is a bad sign that a protein may aggregate and form a plaque?
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Beta sheet
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When a protein aggregates, is the pathway reversible?
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No
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What gene involved in cholesterol metabolism is linked to Alzheimer's disease?
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APO-E
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What forms aggregates in Alzheimer's disease
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amyloid beta peptide
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Endopeptidase processes what to form amyloid beta peptide?
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amyloid precursor protein
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What cuts amyloid precursor protein?
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Presenilin complex
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Is 1 or 2 cuts by presenilin of APP normal?
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2 cuts, 1 leads to generation of AB peptide
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Can you catch Kuru from eating beef?
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No, kuru is a human transmissible disease that results from cannibalism and not cross-species transmissble
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You catch a prion disease from corneal transplantion. What form is it?
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Creutzfeld-Jakob disease
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Is the misfolded prion protein Protease K sensitive?
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No
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What stain can be used to visualize plaques?
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PAS stain
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What types of neurons are depleted in Parkinson's patients?
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dopaminergic neurons
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What type of plaque is commonly seen in Parkinson's patients?
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Lewy body
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What protein is associated with Lewy bodies?
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alpha-synuclein
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Name 4 genes associated with Parkinson's Disease
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PARKIN, UCHL1, PINK1, DJ1
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What is hypothesized about how dopamine affects alpha-synuclein
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Dopamine stabilizes alpha-synuclein, lack of dopamine may lead to fibril formation, eventually leading to the formation of Lewy bodies
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What does PINK-1 do?
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mitochondrial kinase
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Lack of what protein blocks axonal transport, leading to cell death?
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alpha-synuclein, over expression of alpha-synuclein can lead to increase clustering of vesicles near synapse
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What is "Anticipation" in relation to HD?
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with each generation, CAG repeats increase and there is earlier onset of disease
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RNA splicing is affected by trinucleotide repeats in which DNA region?
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introns
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Accumulation of SOD1 can lead to?
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ALS
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Gene defect in androgen receptor leading to CAG/polyglutamine repeat leads to?
|
Bulbospinal Atrophy (Kennedy Syndrome)
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Fatty acid synthesis occurs where?
|
Cytosol
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Anabolic process does what?
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Build up molecules from smaller parts
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Myelin contains which phospholipid in high quantities?
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Sphingolipids
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What amino acid links head group and acyl chain of sphinglipids?
|
Serine
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What is the term for sphingolipids with a sugar head group?
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glycolipids
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Where are glycolipids recycles?
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Lysosome, malfunction can lead to lysosomal diseases
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What is the common terminal residue on cell surface glycoproteins?
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Sialic acid
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Does cholesterol increase or decrease the rigidity of the PM?
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Increase
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Is phosphatidylcholine found more on the inner or outer leaflet of PM?
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outer
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Why is there asymmetric distribution of phospholipids in the bilayer?
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Allows for curvature of membrane
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The diffusion rate of proteins can be measured by what technique?
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FRAP, fluids that do not diffuse are usually anchored to cytoskeleton
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What type of modification allows soluable proteins to anchor to the outer surface of PM
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GPI anchor
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What cleaves GPI anchor?
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phospholipase
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Does dynamin use GTP or ATP to pinch off clathrin vesicles?
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GTP
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Viruses enter the cell via?
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Receptor mediated membrane fusion, usually followed by fusion to endosome, low pH allows the breakdown of viral coat, releasing genomic material
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NSF, Rab, and SNAREs are involved in?
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Exocytosis of secretary vesicles
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Ran is bound to GTP, the cargo is moving into or out of nucleus?
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out of nucleus
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Approximately how much of the human body is composed of water?
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60-70%
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Do strong acids or bases have buffering activity?
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No
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What is the value used to describe when a acid is half dissociated, half associated?
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pKa
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The pKa is equal to what at equilibrium?
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pH
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a small pKa indicates the acid is strong or weak?
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strong
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At what value does an acid have its highest buffering capacity?
|
pKa
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Would a compound with multiple ionizing groups have a higher or lower buffering capacity compared to compound with only one ionizing group?
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Higher
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What is the Henderson-Hasselbalch Equation?
|
pH= pKa + log [(A-)/ (HA)]
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Aspirin has a pKa of 3.5. If the pH of cytoplasm is 7.4, will aspirin present in the cytoplasm be in the protonated or unprotonated form?
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unprotonated
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Is it true that only the protonated form of aspirin can be absorbed by the cell?
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yes, therefore only in stomach fluid, where pH is low will aspirin be absorbed
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When the number of negatively charged groups are equal to the number of positively charged groups on a molecule, the molecule is at what point?
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Isoelectric point (PI)
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At pH above PI, the protein is positively or negatively charged?
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negatively
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What is a technique that can separate proteins based on PI and molecular weight?
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Two Dimensional Gel Electrophoresis
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What is the oxidation state of carbon in CO2?
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+4
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Do ingested carbons get oxidized or reduced in the body?
|
Oxidized to Carbon Dioxide and breathed out
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In what direction is bicarbonate flowing in the parietal cell? Into or out of cell?
|
bicarbonate is coming out of parietal cell into extracellular fluid. this occurs because carbon dioxide enters the parietal cells and is converted to bicarbonate via carbonic anhydrase and bicarbonate then flows out of parietal cell
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What ATPases are important in the secretion of HCL into stomach parietal cell?
|
Sodium Potassium and H+/K+
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What is the main buffer in RBC's?
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hemoglobin
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What is the main buffer in extracellular fluid?
|
bicarbonate
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What are the 2 buffers in intracellular fluid?
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albumin and phosphate
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cellular edema is caused by increased or decreased ECF osmolarity?
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decreased
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If the hydrostatic pressure in a blood vessel exceeds the oncotic pressure what occurs: reabsorption or filtration?
|
Filtration
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What protein is important in maintaining oncotic pressure?
|
albumin
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What does vasopressin do?
|
Increases blood pressure by increasing concentration of aquaporins in collecting duct
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IV solution must maintain what concentration of salt?
|
150 mM
|
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Nutrient absorption is driven by which gradient?
|
Sodium gradient
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hypokalemia and dehydration results from what?
|
loss of intestinal fluid due to diarrhea
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Malnutrition can lead to what as a result of protein loss?
|
edema
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Will giving a patient an IV that contains only saline affect the intracellular compartment?
|
No
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A patient has lack of nutrient uptake. What type of IV should you give them?
|
5% dextrose
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The secondary structure of proteins includes?
|
alpha helixes and beta sheets super secondary structures: folds, domains, topology
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Naturally occuring amino acids are in the L or R configuration?
|
L
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Symbol A stands for what AA?
|
Alanine
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Tyrosine is represented by what letter?
|
Y, Tyr
|
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Arginine letter?
|
R
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H is what AA?
|
Histidine
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Cysteine is what letter?
|
C
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Q is what amino acid?
|
Glutamine
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Aspartic Acid is what letter?
|
D
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Proline is what letter?
|
P
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S represents what AA?
|
Serine
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T represents what AA?
|
Threonine
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W represents what AA?
|
Tryptophan
|
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Valine is what letter?
|
V, Val
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Leucine is what letter?
|
L
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Phenylalanine is what letter?
|
F
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K represents what amino acid?
|
Lysine
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N represents what amino acid
|
Asparagine
|
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Isoleucine is what letter?
|
I
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Methionine is what letter?
|
M
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What two AA have no asymmetric center?
|
Proline and glycine
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What two proteins are hydroxylic?
|
serine, threonine
|
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What two amino acids are sulfur containing?
|
cysteine and methionine
|
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Aromatic AA?
|
Tryptophan, tyrosine, phenylalanine
|
|
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Acidic AA?
|
glutamic and aspartic acid
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|
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Basic AA?
|
histidine, lysine, arginine
|
|
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Aliphatic amino acids are located on the interior or exterior of protein?
|
interior, they are hydrophobic
|
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Which amino acid is an alpha helix breaker?
|
Proline
|
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What enzyme regulates the conformation of proline?
|
prolyl isomerase
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What amino acid is the initiation codon of translation?
|
methionine
|
|
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Which amino acid facililates methyl donation?
|
methionine
|
|
|
UV absorption for a protein is around 280 nm. This protein must have a lot of what class of AA?
|
aromatic
|
|
|
Amino acids are linked via which type of bond? How is this bond formed?
|
Peptide bond, dehydration of water
|
|
|
AA sequence is FSEK. What are the AA?
|
Phenylalanine, serine, glutamic acid, lysine
|
|
|
The angle of rotation between the carbonyl carbon and the alpha carbon in polypeptides is?
|
psi angle
|
|
|
What is the most important driving force in protein folding?
|
Hydrophobicity
|
|
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What are the three non-covalent interactions in protein folding?
|
charge-charge, hydrogen bonding, van der waals
|
|
|
What reverses disulfide bonds?
|
Reducing agents like glutathione
|
|
|
Beta-alpha-Beta-alpha-Beta is given what common name?
|
Rossman fold
|
|
|
Do alpha helixes have a dipole moment?
|
Yes, called macrodipole since all carbonyl groups point in one direction while N-H groups point in other direction
|
|
|
Is hydrogen bonding in beta sheets parallel or perpendicular to the peptide backbone?
|
perpendicular
|
|
|
Leber hereditary optic neuropathy is caused by a genetic defect where?
|
Mitochondrial DNA
|
|
|
Are anti-parallel beta sheets more stable or parallel beta sheets?
|
anti-parallel
|
|
|
What motif is found in anti-parallel sheets?
|
Greek Key
|
|
|
What molecule does the E-F hand motif usually bind?
|
Calcium
|
|
|
The Rossman Fold motif is commonly found in?
|
Nucleotide binding sites of proteins
|
|
|
What does wobbling lead to?
|
Degeneracy of genetic code
|
|
|
Which type of nucleotide mutation is usually most deleterious?
|
frameshift mutation
|
|
|
What are the three sites on a ribosome?
|
EPA
|
|
|
Is prokaryote DNA 5` capped and have a poly-A tail at the 3` end?
|
No
|
|
|
Does prokaryote DNA have introns?
|
No
|
|
|
Is the amino acid acceptor arm on the 5` or 3` end of tRNA?
|
3` end
|
|
|
How many high energy bonds is required to put on amino acid to tRNA?
|
2
|
|
|
What compound controls the accuracy of translation by recognizing specific tRNAs and catalyzing the addition of the amino acid to the 3` end?
|
aminoacyl-tRNA synthetase
|
|
|
What is the only amino acyl-tRNA that binds to the P-site?
|
Methionine-tRNA
|
|
|
The virus contains what types of sites which act as initiation sites for recruitment of cap proteins?
|
IRES sites
|
|
|
Peptide bond formation is catalyzed by?
|
rRNA, not protein
|
|
|
Transfer of the peptidyl-t-RNA to P site and the empty tRNA to E site is mediated by what factor?
|
EF-G
|
|
|
What does EF-Ts do?
|
Displaces GDP from EF-Tu
|
|
|
When there is a stop codon and protein translation terminates, what is the last thing added onto amino acid chain?
|
water
|
|
|
Does transcription and translation occur at the same time in a prokaryote? eukaryote?
|
Yes, No
|
|
|
What are the two components of a eukaryotic ribosome? prokaryotic?
|
60S + 40S
50S + 30S |
|
|
What prevents binding of charged tRNAs in eukaryotic ribosomes, preventing translation?
|
Shiga toxin, ricin
|
|
|
How does the antibiotic tetracycline work?
|
binds to 30S subunit and blocks access to ribosome
|
|
|
What does diptheria toxin do?
|
catalyzes ADP ribosylation of eEF-2 using NAD as substrate
|
|
|
What compound blocks peptidyl transferase reaction in eukaryotic protein synthesis only?
|
Cycloheximide
|
|
|
If the temperature in the cell increases, one could expect increased expression of what type of protein?
|
Heat shock proteins
|
|
|
What types of proteins are used to prevent peptide aggregation and assist in regular protein folding?
|
chaperones and chaperonin
|
|
|
Are chaperones and chaperonins GTPases or ATPases?
|
ATPases, require 7 ATP per protein
|
|
|
Is the protein properly folded by DNAJ or DNAK?
|
DNA-K, DNAK-ADP form assists in proper protein folding. DNA-J delivers new polypeptide to DNAK-ATP complex
|
|
|
Does GroES or GroEL hydrolyze ATP to ADP in the chaperonin protein?
|
GroES
|
|
|
When a protein wished to transverse a channel, is it more favorable for it to be in the folded or unfolded form?
|
unfolded, or it won't fit through channel
|
|
|
Where are TOM and TIM located?
|
mitochondrial membrane
|
|
|
Is the barbed or pointed end favorable for actin assembly?
|
barbed
|
|
|
Actin assembly is driven by ATP or GTP?
|
ATP
|
|
|
Ran GTPase controls transport in and out of where?
|
nucleus
|
|
|
A protein has the sequence Pro-Pro-Lys-Lys-Lys-Arg-Lys-Val
Where is it headed? |
Into nucleus
|
|
|
What translocon recognizes signal sequences associated with entry into Peroxisome?
|
PEX protein
|
|
|
The membrane has a Sec translocon. Which organelle is this?
|
ER
|
|
|
What is exported out of the nucleus?
|
tRNAs, mRNAs, ribosomes (partially assembled)
|
|
|
Is the N-Terminal or C-terminal generally cleaved by signal peptidase?
|
N-terminal
|
|
|
Where does asparagine linked glycosylation occur?
|
ER lumen
|
|
|
A vesicle is moving for the ER to Golgi. It should be coated with COP I or II?
|
COP II
|
|
|
What is put on a protein targeted towards the lysosome?
|
Mannose 6-Phosphate
|
|
|
A protein is ubiquinated. Where is it headed?
|
Proteasome for degradation
|
|
|
When the cell is starving for nutrients which autophagy pathway is it more likely to chose? The selective or non-selective pathway?
|
Non-selective
|
|
|
What process is important to mammalian newborn survival before external nutrients are available?
|
autophagy
|
|
|
How many ATP are required by the proteasome to degrade a protein?
|
7
|
|
|
Is ubiquitin recycled or degraded after the protein is degraded in proteasome?
|
Recycled
|
|
|
What antibiotic binds to bacterial isoleucyl-tRNA synthase and prevents the incorporation of isoleucine?
|
Mupirocin
|
|
|
A patient is very shy, has an elongated face, protruding ears, and flat feet. What genetic disorder might you suspect?
|
Fragile X
|
|
|
Which trinucleotide repeat is in an untranslated region? Huntington's or Fragile X
|
Fragile X
|
|
|
Which gene is inhibited in Fragile X syndrome?
|
FMR1
|
|
|
Where is FMR1 widely expressed?
|
Brain and testis
|
|
|
Are genes overexpressed or underexpressed when FMRP is not modulating activity?
|
overexpressed
|
|
|
What technique is used to determine whether a person is suffering from Fragile X syndrome?
|
Southern Blot
|
|
|
Glucose concentration can be measured via coupling to what enzyme?
|
NADPH
|
|
|
When there is a high amount of creatine kinase in the serum what can one suspect is wrong with the patient?
|
The patient is having a heart attack
|
|
|
Levels of CK-MB, AST, and LDH in serum can be used to deduce what?
|
If a heart attack occurred and how long it has been since the heart attack occurred
|
|
|
If a patient's serum protein shows only one band for gamma globulins rather than a smear, what disease could this be an indication of?
|
myeloma
|
|
|
What protein is a very strong marker of infection and inflammation?
|
C-reactive protein
|
|
|
You want to know whether a patient is producing antibodies against HIV in their serum. Name one technique you could use to do this?
|
ELISA, Western would work as well
|
|
|
How is one way that indirect ELISAs are not as accurate as sandwich ELISAs?
|
In indirect ELISAs the antigen may denature and lose its conformation and therefore the detection is not as sensitive
|
|
|
Will immuno-precipitation occur when the antibody and the antigen are in equivalent ratios and one is dealing with polyclonal antibodies?
|
Yes
|
|
|
If a person with Type B blood is transfused with blood from someone with Type A blood, what will happen?
|
Agglutination
|
|
|
In rocket immuno-electrophoresis, if the sample on the left has a higher column than the one on the right, which sample has more antigen?
|
the one on the left
|
|
|
Will a shorter or longer palindromic sequence generate more cleavage sites in the genome via restriction enzymes?
|
shorter
|
|
|
What type of library is only made up of the expressed genes, or genes that contain only introns, no exons?
|
cDNA library
|
|
|
In Sanger sequencing what is the inhibitor used?
|
dideoxynucleotides
|
|
|
What blot should you use if you want to know whether your gene is expressed in the mammary gland or spleen?
|
Northern Blot
|
|
|
Which region do crime labs usually use for DNA testing?
|
hypervariable region, have variable tandem repeats that are different in each peson
|
|
|
You have a polymerase that denatures at 60 degrees. Is this a good polymerase to use for PCR?
|
No, need a heat stable polymerase that can survive denaturing temperatures
|
|
|
In the PCR cycle, what is occuring around 80 degrees?
|
Synthesis, elongation
|
|
|
In the PCR cycle, what is occuring around 65 degrees?
|
Annealing
|
|
|
What is a special type of PCR that can be used to detect gene expression level at the mRNA level?
|
RT-PCR
|
|
|
Name the purines
|
Guanine and Adenosine
|
|
|
Which purine has a carbonyl group?
|
Guanine
|
|
|
How is thymine different from uracil structurally?
|
In Thymine the C5 carbon has a methyl group while in uracil there is just a hydrogen attached to the carbon
|
|
|
How many hydrogen bonds occur when G binds to C? A to T?
|
3, 2
|
|
|
Is the DNA helix in humans usually right or left handed?
|
right
|
|
|
Are the phosphate groups located on the inside or outside of the DNA helical structure?
|
outside
|
|
|
Is the A, B, or Z form of the double helix most prevelant?
|
B form
|
|
|
Does the RNA transcript that results after transcription look like the template or coding strand of DNA?
|
coding
|
|
|
A strand of DNA has lot of CG content. Will it be stronger or weaker compared to a strand of DNA that has AT content?
|
stronger, GC has 3 hydrogen bonds compared to only two on AT
|
|
|
At what UV absorption rate does one test for DNA? protein?
|
260 nm, 280 nm
|
|
|
When the DNA strand is denatured, will its UV absorbence be greater or less than the undenatured version?
|
Greater, Hyperchromicity
|
|
|
Which enzyme opens up the double helical structures of DNA for replication or transcription?
|
Helicase
|
|
|
Does helicase action require ATP?
|
Yes
|
|
|
What enzyme is used to counter supercoiling of DNA?
|
topoisomerases
|
|
|
Which base is usually methylated in order to shut down gene expression?
|
cytosine
|
|
|
Which is more stable: DNA or RNA?
|
DNA by far, RNA degrades rapidly due to having 2` OH group
|
|
|
DNA packing and extension is controlled by which histone?
|
H1
|
|
|
Heterochromatin is stabilized by what protein complex
|
Sir proteins
|
|
|
What must happen to lamins in order to allow the nuclear envelope to disintegrate in cell division?
|
Phosphorylation
|
|
|
Condensin and Cohesin contribute to what?
|
Forming the loop structure of chromatin
|
|
|
During DNA replication, two sister chromosomes are held together by what complex?
|
Cohesin complex with SMC proteins
|
|
|
Does the centromere containing any gene coding sequences
|
No, just a lot of repeats
|
|
|
When diseases can result from alpha-1-antitrypsin deficiency?
|
emphysema and liver cirrhosis
|
|
|
Where does alpha1-antitrypsin aggregate if it is mutated and cannot be released from this organ?
|
liver
|
|
|
Nucleosomes in centromeres is formed with which histone?
|
H3
|
|
|
What enzyme helps replicate telomeres? What type of primer does it use? DNA or RNA?
|
telomerase, RNA primer
|
|
|
Kinetochores are attached to what part of the chromosome during mitosis?
|
centromeres
|
|
|
Does eukaryotic chromosomes have single or multiple origins of replication?
|
multiple
|
|
|
DNA polymerase has 3` to 5` exonuclease activity. What does this allow it to do?
|
Edit out wrong nucleotides, proofreading mechanism
|
|
|
DNA primase generates what?
|
RNA primer for lagging strand synthesis
|
|
|
Moving on from what cell cycle stage requires a check for favorable enviromental conditions and check for nutritional status and cell size?
|
G1
|
|
|
What is at the 5` end of a DNA molecule, the phosphate group or OH group?
|
phosphate group
|
|
|
lagging strand is made up of what short fragments?
|
Okazaki fragments
|
|
|
The lagging strand uses a DNA or RNA primer?
|
RNA
|
|
|
How many origins of replication does a prokaryote cell have?
|
One
|
|
|
What direction does the proofreading activity of DNA polymerase run?
|
3` to 5` exonuclease
|
|
|
What protein removes the hairpin structure on DNA?
|
single strand DNA binding protein
|
|
|
What does the clamp loader do?
|
Maintains contact of DNA polymerase with DNA template and prevents slipping, also capable of conducting surveillance for DNA damage
|
|
|
What generates the short RNA primer on the lagging strand?
|
DNA primase
|
|
|
The RNA primer on lagging strands are eventually removed by?
|
5` to 3` exonuclease
|
|
|
What DNA polymerase is responsible for the synthesis of the lagging strand?
|
DNA polymerase I or alpha
|
|
|
What DNA polymerase is responsible for DNA proofreading and repair?
|
DNA polymerase II/ epsilon
|
|
|
What DNA polymerase is responsible for DNA repair only?
|
DNA polymerase II/ beta
|
|
|
What DNA polymerase is responsible for mitochondrial DNA synthesis?
|
DNA polymerase II/ gamma
|
|
|
What DNA polymerase is responsible for leading strand synthesis?
|
DNA polymerase III
|
|
|
DNA gyrase is a?
|
topoisomerase and ATP binding protein which removes supercoils by making breaks in DNA
|
|
|
Replication of the ends of eukaryotic chromosomes is added by what enzyme?
|
Telomerase
|
|
|
Do somatic cells have active or inactive telomerases?
|
inactive, therefore chromosomes shorten with each replication cycle, and eventually the cell will go through senescence and apoptosis
|
|
|
What drug is an analog of deoxythymidine and is used to treat AIDs patients?
|
AZT
|
|
|
What drug targets viral thymine kinase?
|
Acyclovir
|
|
|
What drugs inhibit topoisomerases and therefore DNA replication?
|
Quinolones: Fluoroquinolones, Nalidixic acid, teniposide
|
|
|
What checkpoint is used to check the accuracy of DNA replication?
|
G2
|
|
|
What type of damage does UV irradiation due to cell?
|
Cause the formation of thymine dimers
|
|
|
Deamination of cytosine leads to what base? What chemical can cause this change?
|
Uracil, Nitrous acid
|
|
|
ATM kinase, ATR kinase, and the 9-1-1 complex are important for what?
|
DNA repair/surveillance, activate checkpoint kinases at G2 checkpoint
Something wrong with them can lead to ataxia (mental retardation) |
|
|
Formation of thymidine dimers from UV damage can be repaired with which DNA repair mechanism?
|
Nucleotide excision repair
|
|
|
Deamination damage can be repaired with which DNA repair mechanism?
|
base excision repair
|
|
|
Glycosylase is involved in what type of DNA repair mechanism?
|
base excision repair
|
|
|
What are the two different way that one can repair double strand breaks?
|
homologous end joining (homologous recombination) or nonhomologous end joining
|
|
|
Holiday junctions are part of what type of DNA repair mechanism?
|
Homologous recombination
|
|
|
What gene is mutated with patients suffering from Xeroderma pigmentosum? What do patients suffer from?
|
DDB2 (Damaged DNA binding protein 2) , high sun sensitivity due to inability to repair UV damage to DNA
|
|
|
What event is the most important mechanism that generates genetic diversity in the human population?
|
homologous recombination
|
|
|
What enzyme facilitates strand crossover in homologous recombination?
|
RecA protein
|
|
|
What enzyme mediates the opening of the ring and the correct release of sister chromatids?
|
Separase
|
|
|
What type of virus can add viral genetic material to chromosome?
|
RNA virus via reverse transcriptase
|
|
|
Cornelia de Lange Syndrome is caused by a defect of what?
|
Cohesin
|
|
|
What type of virus can add viral genetic material to chromosome?
|
RNA virus via reverse transcriptase
|
|
|
Cornelia de Lange Syndrome is caused by a defect of what?
|
Cohesin
|
|
|
Robert's Syndrome is caused by a mutation where?
|
ESCO2, which stabilizes sister chromatids and possesses acetyltransferase activity
|
|
|
alpha-Thalassemia/Mental Retardation sydrome is cause by a mutation of what gene?
|
ATRX, leads to cohesin defect
|
|
|
Robert's Syndrome is caused by a mutation where?
|
ESCO2, which stabilizes sister chromatids and possesses acetyltransferase activity
|
|
|
Hammerhead ribozymes are important for what process?
|
RNA splicing
|
|
|
alpha-Thalassemia/Mental Retardation sydrome is cause by a mutation of what gene?
|
ATRX, leads to cohesin defect
|
|
|
Hammerhead ribozymes are important for what process?
|
RNA splicing
|
|
|
When there is a high level of AST (aspartate amino transferase) in the plasma what can one suspect?
|
Liver disease
|
|
|
If there is a spike of creatine phosphokinase in a patient's serum, what might the patient has just suffered?
|
Heart attack
|
|
|
Acid phosphatase is high in a patient's serum. Where might they have an issue?
|
Prostate
|
|
|
Alkaline phosphatase is high in a patient's serum. Where might they have an issue?
|
Bone disease/tumor
|
|
|
What three AA's are involved in the charge relay system of serine proteases?
|
Aspartic Acid, Histidne, Serine
|
|
|
Covalent catalysis is used by which type of protease?
|
Cysteine/Serine
|
|
|
Acid-Base catalysis is used by which type of protease
|
Aspartyl proteases
|
|
|
Electrophilic catalysis is used by which type of protease
|
Metalloproteases
|
|
|
Does the enzyme bind the transition state structure well?
|
Yes
|
|
|
How do enzymes make the reaction quicker/more favorable?
|
Lowers activation energy
|
|
|
Inhibitors of enzymes usually mimick what structure?
|
transition state
|
|
|
Irreversible changes to enzymes, such as by cleaving, are the job of what enzymes?
|
zymogens
|
|
|
Inside the cell is there a reduced or oxidized environment?
|
reduced, therefore less disulfide bonds due to high concentration of reduced glutathione
|
|
|
Is phosphorylation as modulation of enzyme activity reversible or irreversible?
|
reversible
|
|
|
Genetic variants of an enzyme of the same allele is called what?
|
Isozyme
|
|
|
Reduction in active G6P leads to what?
|
hemolytic anemia
|
|
|
What might happen if one has too many fava beans?
|
hemolytic anemia because fava beans have an enzyme that inhibits G6P dehydrogenase, leading to decrease of NADPH, and inability to maintain high levels of reduced glutathione in the cell
|
|
|
If a patient shows lots of LDH 1 in blood, what might this suggest they are suffering from?
|
heart attack
|
|
|
If a patient shows lots of LDH 5 in blood, what might this suggest they are suffering from?
|
liver disease such as hepatitis
|
|
|
Is CPK expressed early on after a heart attack or later?
|
early on
|
|
|
What do ACE-inhibitors do?
|
reduce blood pressure
|
|
|
What does captopril do?
|
Inhibit ACE and therefore reduces blood pressure
|
|
|
What drug inhibits HIV protease?
|
Crixivan
|
|
|
What treats gout?
|
allopurinol
|
|
|
What enzyme does statin inhibit?
|
HMG CoA reductase
|
|
|
Lovastatin acts as what type of inhibitor of HMG?
|
competitive
|
|
|
Organophosphorus compounds such as nerve gas inhibit what?
|
acetylcholine esterase causing muscle paralysis because ACh causes muscles to contract and will remain at high concentrations without acetylcholine esterase
|
|
|
What is an antidote for Organophosphorus compounds?
|
Parlidoxime, and atropine which competively blocks acetylcholine binding of NMJ
|
|
|
Can enzyme kinetics confirm the right mechanism or only eliminate wrong mechanisms?
|
Only confirm wrong mechanisms
|
|
|
Binding affinity is measure by what value?
|
Km
|
|
|
What is the Michaelis Menton complex?
|
[ES]
|
|
|
When the enzyme is saturated what value have we reached? What is term given to 1/2 this value?
|
Vmax, Km
|
|
|
Is Km dependent or independent of enzyme concentration?
|
independent
|
|
|
Does a low Km indicate high or low affinity binding?
|
High
|
|
|
If [S] >>>Km then will there be rapid or slow turnover of substrate?
|
rapid, reaction always at Vmax
|
|
|
If [S] <<<Km then will there be rapid or slow turnover of substrate?
|
Slow, basically no reaction
|
|
|
If an enzyme has a high Km will the substrate likely have a slow or rapid turnover?
|
rapid because the binding is not specific and therefore the enzyme is designed for fast turnover and not for specificity
|
|
|
Gluokinase has a high Km and Vmax. It is more likely to be active after intake of a meal or will hexokinase be more active? Hexokinase has a low Km and Vmax. Both phosphorylate glucose
|
Glucokinase because hexokinase is already saturated
|
|
|
What type of curve is observed with allosteric enzymes?
|
sigmoidal
|
|
|
With allosteric enzymes does Vmax and Km change?
|
Vmax does not change, but Km varies with substrate concentration
|
|
|
In the concerted model, is T the low affinity or high affinity conformation of the enzyme?
|
Low affinity, R is high affinity
|
|
|
If the Hill coefficient is greater than 1, is there positive or negative cooperativity ?
|
positive
|
|
|
If an inhibitor has a high Ki, is it a potent inhibitor?
|
No, the smaller the Ki the tighter the binding and the higher potency of the drug
|
|
|
How is a non-competitive inhibitor different from a un-competitive inhibitor?
|
Un-competitive inhibitors only bind to the ES complex, whereas non-competitive inhibitors can bind to both ES and E
|
|
|
For competitive inhibitors does Vmax change with increasing inhibition? Does Km?
|
Vmax does not change, but Km does
|
|
|
What can the Dixon plot tell you?
|
Ki
|
|
|
Only ES and EI are formed. What type of competitor is this?
|
competitive
|
|
|
2,3 BPG shift hemoglobin curve left or right?
|
Right, makes it easier to release oxygen in tissue
|
|
|
Myogoblin is found where?
|
muscle
|
|
|
Does hemoglobin or myoglobin have higher oxygen binding affinity?
|
myoglobin
|
|
|
In the T state, what is hemoglobin doing, releasing or binding oxygen?
|
releasing, low affinity state
|
|
|
2,3 BPG originates from where?
|
glycolytic pathway
|
|
|
Does fetal hemoglobin bind BPG?
|
no, histidine is replaced by serine
|
|
|
Does fetal hemoglobin cause the curve to shift left or right?
|
Left, higher affinity for oxygen than maternal hemoglobin
|
|
|
At high altitude what adaption allows for compensation of low oxygen?
|
increased 2,3 BPG
|
|
|
If pH is lower, does hemoglobin curve shift left or right?
|
Right
|
|
|
If temperature is lower, does hemoglobin curve shift left or right?
|
Left
|
|
|
Carbon dioxide is transported through the blood mostly via what form?
|
bicarbonate
|
|
|
Carbon dioxide can affect oxygen binding to Hb in two ways. What ways?
|
1) Bohr effect, carbon dioxide generates H+ and bicarbonate
2) Form carbamates, stimulates release of oxygen as Hb binds CO2 rather than oxygen |
|
|
Can bicarbonate cross the red cell membrane by itself?
|
No, it must be transported. The transporter is Band 3 antiporter, which sends Cl- into the cell and bicarbonate out of the cell
|
|
|
What is the inheritance pattern of sickle cell anemia?
|
autosomal recessive
|
|
|
In Beta-thalassemia do you have an excess of alpha chains or beta chains?
|
alpha
|
|
|
You want to get a general idea of what type of gene clustering is occuring in a cancer patient. What test could you do?
|
Microarray looking for gene expression patterns
|
|
|
If you want to make a structural determination of a molecule, what technique could you use?
|
Mass spectrometry
|
|
|
What disease might one suspect if there is an increase in phenylalanine via mass spec?
|
phenylketonuria
|
|
|
If there are indinavir crystals in a patient's urine, what disease might one suspect?
|
HIV
|
|
|
What compound can be used as a test of kidney function?
|
Creatinine
|
|
|
Are reducing metabolites usually present or absent in the urine?
|
Absent, therefore reduced metabolites in urine could be indication of problem, such as too much glucose, ketones, bilirubin
|
|
|
What is the apoptosis signal that mitochondria excrete?
|
cytochrome C
|
|
|
Does mitochondrial disease occur at birth?
|
seldomly, disease ins more progressive because there are many many copies of mitochondrial dna, and mtDNA divides randomly to daughter cells, and therefore the effect is variable
|
|
|
Mutations of nuclear genes that affect mitochondria show what type of inheritance pattern?
|
Mendelian
|
|
|
Does the human mitochondrial genome contain any genes related to DNA replication?
|
Nope
|
|
|
Do nuclear gene defects on mitochondrial diseases have an early or late onset of disease compared to defects in mitochondria DNA?
|
early, because there is no heteroplasmy unlike the mitochondrial DNA in the cell
|
|
|
Leber hereditary optic neuropathy is a disease of which mitochondria complex?
|
Complex I, loss of transport from NADH to ubiqunone
|
|
|
What mitochondrial disease is caused by a mutation of mitochondrial tRNA-Lys gene?
|
MERRG (myoclonic epilepsy and ragged red fiber disease)
|
|
|
What mitochondrial disease is due to mutation of complex I subunits that are encoded in the nuclear genome?
|
Leigh syndrome
|
|
|
Release of insulin from the pancreas can be affected by mitochondrial disease because mitochondria is important for generating what?
|
ATP
|
