Module 4

Question 1

what is residue?

Answer 1

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

Question 2

what are peptide bonds

Answer 2

covalent linkages between amino acids

Question 3

what is within the main chain of polypeptides

Answer 3

repeating pattern

Question 4

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

Answer 4

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

Question 5

what does steric exclusion mean?

Answer 5

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

Question 6

what is the primary structure of protein?

Answer 6

the linear sequence of amino acids

Question 7

what is the secondary structure of protein ?

Answer 7

the localized interactions within a polypeptide

Question 8

what is the tertiary structure of protein?

Answer 8

the final folding pattern of a single polypeptide

Question 9

what is the quaternary structure of protein ?

Answer 9

the folding pattern when multiple polypeptides are involved

Question 10

what order is the structure presented in a primary structure ?

Answer 10

N (amino) terminus to C (carboxyl) terminus

Question 11

what are examples of secondary structures?

Answer 11

a helix and b sheet

Question 12

how Is primary structure often determined?

Answer 12

through investigation of the corresponding gene

Question 13

how are secondary structures maintained?

Answer 13

through hydrogen bonds between main chain amide and carbonyl groups

Question 14

what are the two key roles for secondary structures?

Answer 14

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

Question 15

where can polypeptide chains of secondary structures rotate?

Answer 15

the Phi and Psi regions

Question 16

what is an a-helix?

Answer 16

a right handed helix with 3.6 residues/turn

Question 17

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

Answer 17

proline and glycine

Question 18

what residues hangout at the N terminus ?

Answer 18

Negatively charged residues (Asp, Glu)

Question 19

what residues hangout at the C terminus ?

Answer 19

positively charged residues (Lys, Arg, His)

Question 20

how is the dipole of a helix stabilized ?

Answer 20

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

Question 21

what is an amphipathic alpha helix

Answer 21

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

Question 22

what are beta (b) sheets?

Answer 22

multiple b strands arranged side by side

Question 23

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

Answer 23

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

Question 24

what is the starting point of polypeptides

Answer 24

N terminus

Question 25

what determines tertiary structure?

Answer 25

amino acid sequence

Question 26

what is stability defined as?

Answer 26

the tendency to maintain a native conformation

Question 27

what is protein folding and denaturation

Answer 27

a cooperative process

Question 28

what are the 3 words of denaturation ?

Answer 28

Rapid, cooperative, and reversible

Question 29

what does cooperative process mean?

Answer 29

that it is either folded or it isn't, there is no "in between"

Question 30

what does the function of a protein depend on

Answer 30

its structure

Question 31

what are the most important forces stabilizing protein structure ?

Answer 31

non covalent forces

Question 32

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

Answer 32

there are common structural patterns

Question 33

what are the 3 fibrous proteins?

Answer 33

keratin collagen silk

Question 34

what does keratin form at the primary structure?

Answer 34

a pseudo seven repeat

Question 35

what is keratin at the level of secondary structure?

Answer 35

an alpha helix

Question 36

what is a coiled coil?

Answer 36

two amphipathic helices interact to bury their hydrophobic faces together

Question 37

how are coiled coil formed?

Answer 37

when two or more helices entertwine to form a stable structure

Question 38

what does the cold coil of keratin involve ?

Answer 38

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

Question 39

how are the individual units of keratin linked together

Answer 39

disulfide bonds

Question 40

what is collagen?

Answer 40

a major protein of vertebrates

Question 41

what is collagen at secondary structure?

Answer 41

a left handed helix of three residues per turn

Question 42

what is collagens coiled coil

Answer 42

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

Question 43

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

Answer 43

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

Question 44

what do the enzymes performing post translational modification need?

Answer 44

Vitamin C

Question 45

what does silk have at the primary structure?

Answer 45

a six residue repeat

Question 46

what is silk at the level of secondary structure ?

Answer 46

composed primarily from beta sheets

Question 47

what does fully extended polypeptide chains indicate?

Answer 47

lots of strength

Question 48

The final folding pattern of a single polypeptide chain represents:

Answer 48

tertiary structure

Question 49

The strength of silk arises as a consequence of:

Answer 49

fully extended polypeptide chains

Question 50

what proteins contain coiled coils

Answer 50

Keratin and collagen

Question 51

what is responsible for scurvy

Answer 51

lack of vitamin C