Module 4

Question 1

what are peptide bonds

Answer 1

covalent linkages between carboxyl + amino group of 2 separate amino acids

Question 2

what is the repeating pattern of polypeptide main chains?

Answer 2

NCCNCC

Question 3

what is primary structure?

Answer 3

linear sequence of amino acids
N-> C terminus

Question 4

what is the primary structure pattern?

Answer 4

YGGFL

Question 5

what is ramachadran plots?

Answer 5

illustrate possible configurations of phi + psi

Question 6

what is the secondary structure?

Answer 6

localized folding within polypeptide

Question 7

how is secondary structure maintained?

Answer 7

H+ bonds between main chain amide + carbonyl groups

Question 8

what are the 2 key rules of secondary structure?

Answer 8

1. optimize potential
2. represent a favoured configuration

Question 9

why are hydrogen acceptors/donors important in secondary structure?

Answer 9

for optimization

Question 10

how are PHI bonds attached to alpha carbons?

Answer 10

on the N terminus

Question 11

how are PSI bonds attached to alpha carbons?

Answer 11

on the C terminus
think “C for Psi”

Question 12

what are the 2 characteristics of Alpha Helices?

Answer 12

1. right handed
2. have 3.6 residues per turn

Question 13

what 4 amino acids are not found in alpha helices?

Answer 13

1. proline
2. glycine
3. amino acids with side branches
4. amino acids with H+ groups near main chain

Question 14

why is proline not found in alpha helices?

Answer 14

its too rigid

Question 15

why is glycine not found in alpha helices?

Answer 15

too flexible

Question 16

what charge does the N terminus carry?

Answer 16

partial positive charge with negative residues (asp, glu)

Question 17

what charge does the C terminus carry?

Answer 17

partial negative charge with positive residues

Question 18

what are beta sheets made of?

Answer 18

4 or 5 B strands arranged side by side

Question 19

configuration of B sheets?

Answer 19

fully extended polypeptide chain

Question 20

true or false: antiparallel beta sheets are more stable than parallel sheets

Answer 20

true, they have better alignment of H+ donors + acceptors

Question 21

what are mixed beta sheets?

Answer 21

both parallel + antiparallel strands

Question 22

what is the pattern of side chains in amphipathic B sheets?

Answer 22

alternating pattern above & below polypeptide chain, they attach polar face to the non-polar face

Question 23

what is denaturation?

Answer 23

adding heat to a protein to disrupt structure (is reversible)

Question 24

what is tertiary structure?

Answer 24

the final folding pattern of a single polypeptide

Question 25

what is native confirmation of tertiary structure?

Answer 25

biological active folding pattern

Question 26

true or false: primary structure dictates tertiary structure

Answer 26

true

Question 27

what is stability?

Answer 27

tendency to maintain native conformation

Question 28

what does stability reflect?

Answer 28

the difference in free energy of folded/unfolded states

Question 29

what amount of free energy is most stable?

Answer 29

lowest free energy

Question 30

2 characteristics of folded proteins?

Answer 30

1. low energy state 2. greatest stability

Question 31

is protein folding a slow or rapid process?

Answer 31

rapid

Question 32

what are chaperones?

Answer 32

heat shock proteins that help the protein perform complex functions

Question 33

why are chaperones often called heat shock proteins?

Answer 33

b/c they are induced by shock

Question 34

what are quaternary structures?

Answer 34

subset of proteins

Question 35

how are quaternary structures formed?

Answer 35

when 4 subunits non-covalently join together and create a binding site

Question 36

what are 3 advantages of quaternary structure?

Answer 36

1. stability 2. produce active sites 3. produce complex combinations

Question 37

how big are proteins?

Answer 37

100-1000 amino acids in length

Question 38

at 51 amino acids ( ) is used as a threshold of when a polypeptide becomes a protein

Answer 38

insulin

Question 39

what is the smallest protein?

Answer 39

insulin

Question 40

what is the largest protein?

Answer 40

Titin

Question 41

how to calculate the number of amino acids a protein has?

Answer 41

molecular weight / 110

Question 42

what is the most important force & why?

Answer 42

non-covalent b/c they stabilize structure

Question 43

what are fibrous proteins?

Answer 43

simple proteins that hold your body together

Question 44

what are the 3 fibrous proteins?

Answer 44

1. keratin 2. collagen 3. Silk

Question 45

what are Globular Proteins?

Answer 45

proteins that perform highly complex functions & structures

Question 46

role of hemoglobin

Answer 46

transporting O2 in bloodstream

Question 47

role of myglobin

Answer 47

storage of O2 in the lungs

Question 48

what is keratin?

Answer 48

primary component in hair, nails & horns

Question 49

what does a pseudo trend mean in keratin?

Answer 49

positions a & d are hydrophobic residues

Question 50

where is the hydrophobic strip located in keratin?

Answer 50

along the length of the helix

Question 51

what are keratin coiled coils?

Answer 51

when 2 amphipathic keratin helices put their hydrophobic faces together

Question 52

when are coiled coils formed?

Answer 52

when 2 or more helices entwine to form a stable structure

Question 53

what are the 2 reasons for coiled coils?

Answer 53

1. greater strength 2. greater durability

Question 54

what kind of helices are involved in keratin coiled coils?

Answer 54

2 right handed wrapped to the left

Question 55

what is post translational stabilization?

Answer 55

covalently modified structures through the use of disulphide bonds

Question 56

how much protein does collagen make up in the body?

Answer 56

25%

Question 57

where is collagen found?

Answer 57

skin, tendons & vascular system

Question 58

primary structure of collagen

Answer 58

GLY-X-Y pattern (X is often proline)

Question 59

1/3 of residues in collagen is ( ) and the other 1/3 is ( )

Answer 59

glycine and proline

Question 60

how many residues per turn does collagen have?

Answer 60

3

Question 61

how are collagen coiled coils formed?

Answer 61

when 3 left handed helices join together & wrap to the right

Question 62

where are proline side chains located on collagen coiled coils?

Answer 62

on the outside

Question 63

what is post-translational modification in collagen?

Answer 63

occur from hydroxyproline & hydroxylysine

Question 64

what vitamin is required for collagen post-translational modifcation?

Answer 64

vitamin C, is needed for stable crosslinks

Question 65

What is silk's primary structure?

Answer 65

has a 6 residue repeat (GSGAGA)

Question 66

what is silk's secondary structure?

Answer 66

beta sheets

Question 67

what is the strongest silk material?

Answer 67

cross sectional

Question 68

what do fully extended polypeptide chains give?

Answer 68

strength

Question 69

what does association of strands by hydrogen bonding allow for?

Answer 69

flexibility

Question 70

what 2 amino acids come together & form a zipper?

Answer 70

alanine & glycine

Question 71

is silk non-immuniogenetic or immunogenetic?

Answer 71

non-immuniogenetic

Question 72

what does non-immuniogenetic mean?

Answer 72

when the body can recognize the molecule has not itself and provokes an immune response

Question 73

what is a steric interference

Answer 73

2 groups cannot occupy the same space at the same time