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Flashcards

LS 3 Protein Structure

Anahita Sehgal English 52 cards

Cards in this deck (52)

  1. 1What are proteins made up of?Proteins are polymers made up of amino acids.
  2. 2List all the periodic table elements present in proteinsC, O, N, H and S
  3. 3Which element is found in DNA but NOT found in proteins? (Also helped in the Hershey Chase Experiment)Phosphorous
  4. 4What is the hydrophobic effect?A process wherein the non-polar groups in a protein align themselves away from the polar fluid.
  5. 5Which amino acid is unaffected by the hydrophobic effect?Glycine because it is found on the surface of many proteins.
  6. 6Which three amino acids have hydroxyl groups?Serine, Threonine and Tyrosine have hydroxyl groups
    (which are important for phosphorylation)
  7. 7Tyrosine has a special feature. Which characteristic does this feature enable?Tyrosine has a big benzene ring that contributes to its non-polar character.
  8. 8Which amino acid does not have a side chain?Glycine - simply has a hydrogen instead of a R group.
  9. 9Name two amino acids with a charged basic character. Where are these found heavily?Lysine and Arginine are charged basic amino acids. They are heavily found in histones.
  10. 10What is an example of dehydration synthesis?a Peptide bond
  11. 11Name the two terminus on an amino acidN terminus - Amino group
    C terminus- Carboxyl group
  12. 12Peptide Bonds have a _______ character. What does this enable?Partial Pi Bond Character. This restricts rotational freedom which causes the atoms to be coplanar.
  13. 13What advantage does being a coplanar amino acid give?all proteins have a similar skeletal structure, more so proteins can take cis and trans transformations.
  14. 14Describe the protein backbone1) Made up of repeating units.
    2) Uncharged except for the N and C terminals
    3) Has a directionality
    4) The amino group and Carboxyl group are available for hydrogen bonding.
  15. 15Which is the only cyclic amino acid?Proline; it has the least amount of rotational freedom.
  16. 16Which amino acid has the most conformational freedom and why?Glycine has the most conformational freedom because it has the smallest side group.
  17. 17Which amino acid has thiol bond? What does the presence of this group result in?Cysteine has thiol group and can make disulphide bonds.
  18. 18Why are disulphide bonds desirable?S-H + S-H = S-s bonds.
    They are desirable because they form covalent cross links, which stabilise the amino acid.
  19. 19Where are disulphide bonds found?They are found in proteins that roam in a oxidising environment in the body or in extracellular proteins; their function is to provide the cell with rigidity and stability. They are NOT found in intracellular proteins are they are present in reducing environments.
  20. 20What is a residue?An amino acid that has been incorporated into a polypeptide..
    This amino acid loses its own unique charge but still participates in Hydrogen Bonding.
  21. 21True or False: Proteins have a net positive or negative charge based on their side groups.True
  22. 22Describe the primary structure of a protein.it is a sequence of amino acids.
  23. 23Name two examples of the secondary structures known to you. Who were these structures first discovered by?Alpha helix and Beta Sheets. Linus Pauling in 1951
  24. 24True or False: Secondary Structures are responsible for the 3D folding of a proteinFalse. PRIMARY STRUCTURES are responsible for the 3D structure of a protein.
  25. 25True or False: Secondary structures are responsible for localised folding.True
  26. 26What feature makes the alpha helix and beta sheet particularly stabilising?H-bonding in the backbone.
  27. 27Describe the characteristics of alpha helix:1) Made from a single polypeptide.
    2) There exists hydrogen bonding between every four amino acids.
  28. 28Compare and contrast the positioning of H bonds and the alignment of R groups in a double helical structure (DNA) and alpha helical protein structure.Positioning of H bonds: In the DNA, the H bonds are perpendicular to the helical axis and in Alpha-helix, they are parallel to the helical axis.
    Alignment of the R groups: In DNA, the R groups point inward but in Alpha helix, the R groups point outwards. This is necessary because these R groups decide what is most stabilising for alpha helix.
  29. 29What are the two things the alpha helix structure avoids?Consecutive like charges and consecutive bulky R groups.
  30. 30Describe the characteristic features of the Beta Sheet.1) backbone H-bonds are formed between different segments of the polypeptide chain.
    2) Hydrogen bond donors and acceptors i.e.. the R groups are projecting outwards laterally and they interact between different segments.
  31. 31Differ between parallel and anti parallel beta strands. Why are the latter more commonly found?When the strands run in the same direction (both N to C terminus) - the sheets are parallel.
    When the strands run in opposite directions - the sheets are antiparallel.
    The latter are more commonly found because the hydrogen bonds formation is linear, which makes this pattern more stable.
  32. 32What does one third of the beta sheet structure comprise of?It comprises of turns and loops which allows the secondary structures to reverse themselves and loop. This is necessary to link them to one another.
  33. 33What feature of the secondary protein structures gives them a universal skeleton?Each backbone has one H bond donor and acceptor.
  34. 34What comprises the tertiary structure of a protein?The tertiary structure of a protein is its 3D folded structure and is dependent on its R groups. It comprises the secondary structure and all the loops and turns.
  35. 35What is the principal driving force of tertiary structures?The hydrophobic effect is the principal driving force. The non polar proteins are buried on the inside and the the polar proteins are exposed on the surface.
  36. 36While secondary structure focuses on localised folding, the 3D tertiary structure wants us to focus on ____________interactions between the side chains such as ionic boding.
  37. 37List three possible interactions that could exist between the side chains of a tertiary structure.1) H -bonds
    2) ionic bonds
    3) disulphide bonds
  38. 38Which enzyme breaks the phosphodiester bonds in the RNA molecule?RNAase
  39. 39True or False: The amino acid sequence is sufficient to determine the tertiary structure.True.
  40. 40Name the reducing agent used to break disulfide bonds.B-mercapethanol
  41. 41Name the two kinds of protein foldings that exist.1) Spontaneous folding: Proteins spontaneously take their native structure, which is largely driven by the hydrophobic effect.
    2) Chaperone assisted folding: Proteins need assistance in attaining their native shape.
  42. 42What are protein domains?structures that fold independently and often have specific functions. A polypeptide can have multiple domains or have 1 or 2 big domains.
  43. 43If a protein is insoluble, it is most likely ____________.denatured.
  44. 44Briefly explain Ligand BindingA ligand comes and binds at a protein at specific place called the 'binding site'. This site is complementary to the characteristics of the ligand.
  45. 45Proteins result in conformation change as a result in change of __________. This also impacts protein __________.environment, function.
  46. 46Differentiate between the two kinds of DNA binding proteins.1) Specific DNA binding proteins: These only bind to specific chemical patterns present in the major groove of DNA.
    2) Non-specific DNA binding proteins: These are independent of the sequences, and OFTEN RELIES ON THE POLY-ANIONIC BACKBONE.
  47. 47Alpha helix recognition sequence can form H bonds/ non polar contact via:insertion into major grove of DNA
  48. 48True or False: Post-translational modification impacts structure and functionTrue.
  49. 49What is phosphorylation? Which amino acids is phosphorylation possible on?Phosphorylation is the addition of a phosphate group to the hydroxyl group of Serine, Threonine and Tyrosine.
  50. 50Which enzyme adds a phosphate group? Which enzyme removes a phosphate group?1) kinase, 2) phosphatase.
  51. 51True or False: Phosphorylation doesn't lead to a conformational change.False.
  52. 52What are ribozymes?When RNA molecules behave like catalysts.

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Flashcards on LS 3 Protein Structure, created by Anahita Sehgal on 30/01/2018.
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Anahita Sehgal
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