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Flashcards

Biochemistry

Gabrielle Daniels Biology Inglês 45 flashcards

Flashcards do conjunto (45)

  1. 1ZwitterionDipolar Ion -- can be an Acid or a Base. Also has a 'net charge' of 0.
  2. 2What is at the N and C termini of a Protein?The N terminal is the NH2 terminus & beginning of the Protein. The C terminus is the carboxyl Terminus and the end of the protein. Each is a part of the amino acid first and last in the protein.
  3. 3Which Amino Acids can be phosphorylated?Serine, Threoinine, Tyrosine (Eukaryotes) and Histidine (Prokaryotes)
  4. 4What is the importance of disulfide bonds in polypeptides?They are linked covalently and determine the quaternary structure of many proteins.
  5. 5What is polymorphism?Proteins that have variance in the human population.
  6. 6What are native proteins?When proteins are in any of their functional, folded conformations.
  7. 7What contributes to stability of a protein/polypeptide?Since it is the tendency to maintain native conformation, disulfide and non-covalent interactions (such as H-bonds, hydrophobic interactions, and ionic interactions) help this maintenance.
  8. 8Where do hydrophobic Amino Acids tend to cluster?These Amino Acids tend to cluster in the proteins interior to protect it from water.
  9. 9Why do some polar molecules cluster in the proteins interior?1. Because they are solvent.
    2. The non-polar molecules need H-bonding partners.
  10. 10How would you describe a peptide bond?Rigid and Planar
  11. 11What does the Ramachandran Plot show?It shows the ability of a steroisomer to make a conformation -- its tendency w/regard to steric qualities.
  12. 12Which Amino Acids tend to form Alpha Helices?Methionine, Alanine, Leucine, Glutamate and Lysine.
  13. 13Which have a poor tendency to form Alpha Helices?Proline and Glycine
  14. 14Which AA residue do you expect to see at a Beta Turn?Proline
  15. 15What causes Alpha Helices to Form and what causes Beta Sheets to form?Alpha Helix -- Makes optimal use of internal H-bonds. It is also stabilized by an H-bond between the N and the O on the carnoyl group of the 4th AA.
    Beta sheet -- antiparallel more common and the H-bonds are between adjacent segments of polypeptide chain.
  16. 16What is proteolysis?The breakdown of proteins into Amino Acids or smaller peptides.
  17. 17What is a Protease?An enzyme that causes protein catabolism by hydrolysis of peptide bonds.
  18. 18What is Salting Out? Explain the Process.Method of separating proteins:
    1. Salt concentration used to precipitate proteins
    2. If enough of the surface of a protein is hydrophilic, it can be dissolved in water.
    3. Proteins coagulate when the salt is added b/c the water is interacting with the salt and not the protein.
    4. The protein aggregates and you can then remove the protein by filtration or centrifugation.
  19. 19What is Salting In? Explain the Process.Increasing the solubility of a protein:
    1. Proteins are surrounded by the salt counter ions (of opposite net charge)
    2. This lowers the electrostatic free energy of the protein
    3. Raising the activity of the solvent
    4. Increasing the protein's solubility
  20. 20What is dialysis? Explain the Process.Process of separating molecules in solution by the difference in their rates of diffusion through a semi-permeable membrane.
    1. Remove unwanted small molecules (i.e. salts) from larger macromolecules
    2. Allow small molecules to diffuse into dialysate, reducing its concentration in the original size.
    3. Takes advantage of proteins' large size.
  21. 21Explain Column ChromatographyTakes advantage of differences in the protein charge, size, binding affinity and other properties.
    1. Need solid, porous material (matrix) supported in a column
    2. Solution flows through matrix
    3. Proteins have different interactions with matrix material
    4. Proteins separate according to their individual properties
  22. 22Explain Ion Exchange ChromatographyExploits differences in he sign and magnitude of the net electric charge of proteins at a given pH.
    *Separation can occur by changing pH or salt (gradient)
  23. 23Explain the difference between Cation and Anion Exchange Chromatography*Cation exchange = negatively charged, meaning it attracts positive and repels negatively (negative moves faster)
    *Anion exchange = positively charged, vice versa as above
  24. 24Size Exclusion ChromatographyAKA GEL FILTRATION
    1. Separates according to size
    2. Large proteins leave faster than smaller because they go around the beads, which is a quicker way.
    3. Can approximate size of protein being purified by comparison.
  25. 25Affinity ChromatographyBased on binding affinity
    1. Have a covalently attached ligand
    2. Add salt or ligand and the free ligand competes with the attached one
    3. Ligand is released
    4. New ligand is bound to protein when elutes
  26. 26ElectrophoresisSeparation of proteins based on the migration of charged proteins in an electric field
  27. 27What are the advantages and disadvantages of electrophoresis?Adv: Can determine isoelectric point, Mw, visualize and separate the proteins and understand the purity of a mixture
    Dis: Can affect the structure & function of the protein -- which is why it is mainly used for analysis.
  28. 28What kind of matrix is used in electrophoresis? What do you look at?1. Agarose matrix which causes sieving and the smaller molecules migrate more easily through the gel.
    2. SDS in the presence of proteins separates them almost exclusively by mass -- thus look at the relative migration of an unknown protein to find its Mw.
  29. 29What is isoelectric focusing?Determines the pI of the protein by establishing a pH gradient, adding protein and then each protein migrates and aggregates according to it pI.
  30. 30What is Edman degradation?Labels and removes only the N terminal from a peptide, leaving the rest of the peptide intact.
  31. 31What is mass spectrometry?Can help measure accurate Mw as well as polypeptide segments by utilizing a light absorbing matrix.
  32. 32Difference between a paralog and an ortholog?1. Paralogs are two proteins in a family (two homologs) that are present in the same species. Usually different functions.
    2. Orthologs are two proteins that are not in the same species but have similar functions.
  33. 33What is Sanger's reagent?Uses DFNB in order to cleave the amino end of the N-terminus of a protein and then mix a weak acid and a strong base and water at room temp.
  34. 34Which kinase is involved in the first step of Glycolysis?Hexokinase -- it phosphorylates glucose to glucose 6-phosphate (via induced fit -- meaning it closes around the glucose when it enters).
  35. 35What occurs in the second stage of Glycolysis?Binding and opening of the glucose 6-phosphate ring --> dissociation and closing of the fructose 6-phosphate ring. (1 - ring opening; 2 - isomerization). Occurs by Phosphohexose isomerase.
  36. 36What is the committed step of Glycolysis and why?Step 3, when Fructose 6-Phosphate --> Fructose 1-6 Bi-Phosphate by Phosphofructokinase. This is because the previous step is actually an "isomer" b/t glucose 6-phosphate and fructose 6-phosphate (where the former can go on to glycogenesis or pentose phosphate pathway). When it becomes F16BP, it has officially committed to continuing to glycolysis. (MOST IMPORTANT STEP!)
  37. 37What happens in Step 4 of Glycolysis?F16BP is cleaved by aldolase (aldol cleavage) into dihydroxyacetone phosphate and glyceraldehyde 3-phosphate. Only the latter goes to the next step (the payoff).
  38. 38What happens in Step 5 of Glycolysis?The dihydroxyacetone phosphate produced in step 4 is isomerized into glyveraldehyde 3-phosphate and contributes to the next stages.
  39. 39What is aldol condensation?When an enol/enolate react w/a carbonyl in order to create a bond and release a H20 as a result.
    (Aldol cleavage is the opposite, utilizing H2O)
  40. 40What happens in Step 6 of Glycolysis?First energy yielding stage in glycolysis. When you couple favorable oxidation w/unfavorable phosphorylation (using glyceraldehyde 3-phosphate dehydrogenase). Enzyme substrate complex intermediate is oxidized by NAD+ (bound to active site), NADH is released, when another NAD+ comes in and covalent linker btw enzyme and substrate undergoes phosphorlysis (attack by P) and releases second product.
  41. 41What is a dehydrogenase? Give an example when it is used?The removal of hydrogens from a molecules. Glucose 6-phosphate dehydrogenase in Pentose Phosphate Pathway, which will rid the glucose of the hydrogen and reduce the NADP+-->NADPH (important in preventing oxidative damage to cells).
  42. 42What is Hydrolysis?Adding a H2O molecule in order to cleave bonds.
  43. 43What happens in Step 7 of Glycolysis?The glyceraldehyde 3-phosphate utilized NAD+-->NADH + H+ (which contributes to the proton gradient) via the glyceraldehyde 3-phosphate dehydrogenase enzyme to get 1,3 Biphosphoglycerate.
  44. 44Why are some reactions in glycolysis with a positive delta G?The reason for this is that these are just steps in a reaction and the overall reaction is negative, meaning it will happen.
  45. 45What happens in Step 7 of Glycolysis?

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Biology FlashCards sobre Biochemistry, criado por Gabrielle Daniels em 10-01-2017.
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