Lecture 3: protein structure

Question 1

protein is a linear polymer of _____ linked to one another by peptide bonds

Answer 1

protein is a linear polymer of L-alpha-AA’s linked to one another by peptide bonds

Question 2

primary structure (1)

Answer 2

• linear sequence of AA’s with no higher order structure

Question 3

secondary structure [define; how is it stabilized? ex (2)]

Answer 3

• spatial arrangement of AA’s that are close to each other in the primary sequence
• structure stabilized by backbone H-bonds
  ex) alpha-helix and beta-strand

Question 4

tertiary structure [define; how is it stabilized? (3)]

Answer 4

• folding of secondary structural units to minimize molecular volume and pack interior
• stabilized by side-chain H-bonding, salt bridges and hydrophobic effect

Question 5

quaternary structure [define]

Answer 5

interaction of multiple individual polypeptide chains in a multi-subunit protein complex

Question 6

from primary to quaternary the structure becomes more ____ and ____

Answer 6

the structure becomes more compact and ordered

Question 7

what kind of rxn is a peptide bond formation?

Answer 7

dehydration rxn

Question 8

the Ramachandran plot identifies ____, with the white regions showing _____

Answer 8

identifies different allowed geometries, with the white regions showing the range of the most favorable

Question 9

secondary structure requires the ____ geometry

Answer 9

requires the trans geometry

Question 10

how is the alpha helix structure stabilized? [n+?]

Answer 10

stabilized by backbone H-bonds between residues within the helix chain [n+4]

Question 11

all side chains of the alpha helix face (in/outwards)

Answer 11

all side chains face outwards

Question 12

why does proline disrupt the alpha helix? what can it identify?

Answer 12

• during the dehydration rxn, the N loses both of its H’s so it has no stable backbone
• identifies 2 separate alpha helices

Question 13

hydrophobic effect drives ____ regions together to establish the overall protein fold

Answer 13

hydrophobic effect drives non-polar regions together to establish overall protein fold

Question 14

alternate side chains in a beta chain points in ____ directions

Answer 14

alternate side chains point in opposite directions

Question 15

difference in type 1 and 2 beta turn

Answer 15

the change in orientation

Question 16

how is a beta turn stabilized? [n+?]

Answer 16

stabilized by H-bonds between residues [n+3]

Question 17

where are beta turns and what is their purpose?

Answer 17

beta turns are on the edges of globular proteins and allow for a change in direction (180° turn) of the polypeptide chain

Question 18

what amino acids will not form an alpha helix or a beta sheet and why? (2)

Answer 18

• proline; rigid, forms a covalent bond with itself

- glycine; has too small of a side chain, not able to interact with other residues to stabilize either forms

Question 19

intrinsically disordered proteins (IDP’s) [define; ex (1)]

Answer 19

• protein that can’t retain a structure past primary or secondary [very little overall fold]
  ex. protein tau = stabilizes protein structure of tubule