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BMSC 200 > Module 4 > Flashcards

Module 4 Flashcards

1
Q

what is residue?

A

the residues are the amino acids that are left behind within the chain once the water goes away

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2
Q

what are peptide bonds

A

covalent linkages between amino acids

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3
Q

what is within the main chain of polypeptides

A

repeating pattern

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4
Q

which configuration of peptide bonds is favoured? Trans or cis? why?

A

trans because the cis configuration is more likely to cause steric interference between side chain groups

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5
Q

what does steric exclusion mean?

A

means that two groups can’t occupy the same space at the same time

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6
Q

what is the primary structure of protein?

A

the linear sequence of amino acids

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7
Q

what is the secondary structure of protein ?

A

the localized interactions within a polypeptide

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8
Q

what is the tertiary structure of protein?

A

the final folding pattern of a single polypeptide

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9
Q

what is the quaternary structure of protein ?

A

the folding pattern when multiple polypeptides are involved

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10
Q

what order is the structure presented in a primary structure ?

A

N (amino) terminus to C (carboxyl) terminus

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11
Q

what are examples of secondary structures?

A

a helix and b sheet

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12
Q

how Is primary structure often determined?

A

through investigation of the corresponding gene

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13
Q

how are secondary structures maintained?

A

through hydrogen bonds between main chain amide and carbonyl groups

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14
Q

what are the two key roles for secondary structures?

A
  • they must optimize the hydrogen bonding potential of main chain carbonyl and amide groups
  • they must represent a favoured conformation of the polypeptide chain
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15
Q

where can polypeptide chains of secondary structures rotate?

A

the Phi and Psi regions

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16
Q

what is an a-helix?

A

a right handed helix with 3.6 residues/turn

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17
Q

what are the two amino acids not found in a-helix?

A

proline and glycine

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18
Q

what residues hangout at the N terminus ?

A

Negatively charged residues (Asp, Glu)

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19
Q

what residues hangout at the C terminus ?

A

positively charged residues (Lys, Arg, His)

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20
Q

how is the dipole of a helix stabilized ?

A

by the residues at each termini who’s charge opposes the helix dipole

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21
Q

what is an amphipathic alpha helix

A

two different faces with different properties. one polar and one non polar

22
Q

what are beta (b) sheets?

A

multiple b strands arranged side by side

23
Q

which b sheets more stable? antiparallel or parallel ? Why?

A

anti parallel are more stable due to better geometry of hydrogen bonding

24
Q

what is the starting point of polypeptides

A

N terminus

25
Q

what determines tertiary structure?

A

amino acid sequence

26
Q

what is stability defined as?

A

the tendency to maintain a native conformation

27
Q

what is protein folding and denaturation

A

a cooperative process

28
Q

what are the 3 words of denaturation ?

A

Rapid, cooperative, and reversible

29
Q

what does cooperative process mean?

A

that it is either folded or it isn’t, there is no “in between”

30
Q

what does the function of a protein depend on

A

its structure

31
Q

what are the most important forces stabilizing protein structure ?

A

non covalent forces

32
Q

what is the only common thing amongst a huge number of unique protein structures?

A

there are common structural patterns

33
Q

what are the 3 fibrous proteins?

A

keratin
collagen
silk

34
Q

what does keratin form at the primary structure?

A

a pseudo seven repeat

35
Q

what is keratin at the level of secondary structure?

A

an alpha helix

36
Q

what is a coiled coil?

A

two amphipathic helices interact to bury their hydrophobic faces together

37
Q

how are coiled coil formed?

A

when two or more helices entertwine to form a stable structure

38
Q

what does the cold coil of keratin involve ?

A

two right handed helices wrapping around each other in a left handed fashion

39
Q

how are the individual units of keratin linked together

A

disulfide bonds

40
Q

what is collagen?

A

a major protein of vertebrates

41
Q

what is collagen at secondary structure?

A

a left handed helix of three residues per turn

42
Q

what is collagens coiled coil

A

three left handed helices wrap around each other in a right handed fashion

43
Q

how do the linkages in collagen occur? what are they?

A

residues that undergo post-transitional modification (hydroxyproline, hydroxylysine)

44
Q

what do the enzymes performing post translational modification need?

A

Vitamin C

45
Q

what does silk have at the primary structure?

A

a six residue repeat

46
Q

what is silk at the level of secondary structure ?

A

composed primarily from beta sheets

47
Q

what does fully extended polypeptide chains indicate?

A

lots of strength

48
Q

The final folding pattern of a single polypeptide chain represents:

A

tertiary structure

49
Q

The strength of silk arises as a consequence of:

A

fully extended polypeptide chains

50
Q

what proteins contain coiled coils

A

Keratin and collagen

51
Q

what is responsible for scurvy

A

lack of vitamin C

BMSC 200 (7 decks)

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