01 - Amino Acids & Proteins

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  1. Alipathic AAs
    • Nonpolar and uncharged at physiological pH; Glycine, alanine, valine, leucine, and
    • isoleucine
  2. Hydroxy AAs
    Polar and uncharged at physiological pH; AAs containing –OH; serine, threonine, and tyrosine
  3. What are the special characteristics of Hydroxy AAs?
    Can form –H bond with water or other polar groups; can form an ester with phosphoric acid (phosphorylation); the -OH on serine and threonine can also serve as an attachment site for oligosaccharides in glycoproteins (O-linked glycosylation)
  4. Sulfur-containing AAs
    Cysteine and methionine; uncharged at physiological pH
  5. What are the special characteristics of cysteine?
    Can form cystine; can be deprotonated and therefore is an important component in the active sites of many enzymes
  6. What are the special characteristics of methionine?
    Can be activated to form S-Adenosyl Methionine; serves as a methyl group donor in many transmethylation reactions
  7. Acidic AAs and their amide derivatives
    Aspartic acid and glutamic acid; their amide derivatives are asparagine and glutamine; polar and net negative charge on acidic AAs at physiological pH
  8. Basic AAs
    Lysine, arginine, and histidine; polar and net positive charge at physiological pH
  9. What are the basic characteristics of Histidine?
    Weakly basic and largely uncharged at physiological pH; in AAs it can be charged or neutral depending upon the neighboring AA residues and ionic environment of the PP chain
  10. Aromatic AAs
    Phenylalanine, tyrosine, and tryptophan; neutral at physiological pH
  11. What makes tyrosine and tryptophan special?
    They absorb light at 280nm, and can be used to determine protein concentration in an aqueous solution
  12. Imino acids
    Proline; nonpolar and neutral at physiological pH; very rigid and creates a fixed kink which limits how a protein can fold; also acts as a physiological pH because its pKR is close to physiological pH
  13. What are the ten essential AAs?
    PVT. TIM. HALL; phyenylalanine, valine, threonine, tryptophan, isoleucine, methionine, histidine, arginine, lysine, and leucine
  14. What happens to AAs, in regards to protonation, at a low pH?
    The carboxyl and amine groups are protonated; this gives a positive charge to the amino acid
  15. What is a zwitterion?
    Occurs when there is no net charge on the amino acid; typically occurs at neutral pH where the carboxyl group is deprotonated; the pH at which a zwitterion occurs is known as the isoelectric point (pK1 + pK2)/2
  16. How are AAs modified?
    Glycosylation, lipid addition, phosphorylation, acetylation, ADP-ribosylation, hydroxylation of Pro and Lys residues and γ carboxylation of Glu residues
  17. What is N-linked glycosylation and where is it seen?
    A carbohydrate is attached to the amino group in the side-chain of an Asn residue; this is seen in integral membrane proteins and the carbohydrate is exposed to the extracellular surface
  18. What is O-linked glycosylation and where is it seen?
    The carbohydrate is attached to the –OH group in Ser or Thr; seen in secreted proteins
  19. What is the purpose of lipid addition?
    Helps membrane proteins to hydrophobically anchor themselves to the membrane; 14 & 16 C atom Fatty acid molecules are often attached to the thio group of Cys or the amino group of N-terminal AAs of proteins in the lipid membranes of intracellular vesicles
  20. What is the purpose of regulatory modification?
    To change the activity of the protein
  21. How do cholera, pertussis, and diphtheria toxin regulate the activity of some enzymes?
    By attaching an ADP-ribosyl group to an Arg (most frequently), Gln, or Cys (rarely)
  22. Where is Hydroxylation of Pro and Lys residues seen?
    Seen in collagen where the –OH groups will provide extra polar groups for –H bonding between the collagen chains
  23. Where is γ-carboxylation seen?
    Proteins involved in chelating Ca2+ ions; this occurs because Glu already has one carboxy group in the γ position and the addition of a second carboxyl group will provide 2 negative charges that could bind Ca2+
  24. What are simple proteins?
    When they undergo hydrolysis they only yield AAs or their derivatives; examples are ribonuclease, chymotrypsinogen, etc.
  25. What are conjugated proteins?
    Proteins composed of simple protein/s combined with some non-protein substance; examples are hemoglobin, metalloproteins, casein, and flavoproteins
  26. What stabilizes the secondary structure of proteins?
    A repeating pattern of hydrogen bonds between the carbonyl oxygen and the amide hydrogen in the peptide bond
  27. What is the relationship between Pro and α-helices?
    Not commonly found in α-helices, because it limits how a polypeptide chain can fold, but it is often found at the end of an α-helix because it alters the direction of the PP chain and terminates the helix
  28. In what direction are the side chains in β-sheets?
    They are perpendicular to the plane of the peptide bond
  29. What are β-turns?
    Turns which allow PP chains to fold into a compact, spherical shape; Each β-turn consists of four amino acids two of which are usually Gly and Pro
  30. What are random coils?
    Regions of a polypeptide chain that do not have a definable repeat pattern, i.e. lack secondary structure
  31. What forces maintain the conformation of a protein?
    Ionic bonds, H-bonds, cystine bonds, van der Waals forces, and hydrophobic interactions
  32. What is nonenzymatic glycation?
    It is a process by which glucose is chemically bound to amino groups of proteins but without the help of enzymes; it is a covalent rxn in which the sugar-protein complex is formed through a series of chemical rxns
  33. How does glycation occur?
    First, glycation products are forms, which through a series of complex chemical rxns, leads to the formation of heterogenous, toxic and antigenic advanced glycation end products (AGEs)
  34. What are the major characteristics of AGEs?
    Protein modification with non-enzymatic glycation is irreversible and AGEs accumulate with age
  35. What signs would you see in an individual with excessive non-enzymatic glycation?
    Inactivation of enzymes, inhibition of regulatory molecule binding, crosslinking of glycated proteins and trapping of soluble proteins in said matrix, decreased susceptibility to proteolysis, altered macromolecular recognition and endocytosis, and an increased immunogenicity
  36. What is the link between diabetes and glycation?
    With a hyperglycemia, there are much higher levels of glycated proteins, this denaturation may lead to impaired protein function and contribute to long-term complications of diabetes; the rate of glycation is proportionate to the concentration of glucose present
  37. What is the role of PrPSC in prion diseases?
    The normal, non-infectious PrPC has a high α-helical content but little β-sheet, in the prion protein PrPSC a number of the α-helices are replaced by β-sheets; this disrupts and reforms H-bonds and causes PrPSC to be resistant to proteolysis and misfold abnormally forming insoluble aggregates; these aggregates act as a template and cause more PrPC to be converted
  38. What major neurodegenerative diseases are caused by protein aggregates?
    Alzheimer’s, Huntington, Amylotrophic Lateral Sclerosis, and Parkinsons; in all these aggregates with predominantly β-sheets are found
  39. How does gel filtration or size exclusion chromatography work?
    Balls with little holes are suspended in a solution, the proteins are added to the top of the column, and as the proteins filter down, the large ones can’t enter the balls and are immediately sent to the bottom, the small ones can enter the beads and move through the column more slowly
  40. How does ion exchange chromatography work?
    Proteins are separated on the basis of their overall charge; at pH values below the pI the protein will bear a net positive charge and at pH values above the pI the protein will be negatively charged; this works will on proteins with very different pIs; in anion exchange the balls are positively charged
  41. How is SDS-PAGE different from gel electrophoresis?
    Where as gel electrophoresis is dependent on mass:charge; SDS-PAGE has all denatured proteins so it is solely based on charge since all the proteins are denatured and given the same charge
  42. What is SDS-PAGE used to determine?
    Purity of a protein sample, molecular mass, and/or the number of PP subunits in a multimeric protein
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01 - Amino Acids & Proteins
CMBM Amino Acids & Proteins
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