Protein Structure

Question 1

T/F nearly all protein functions have been discovered

Answer 1

FALSE.

Question 2

levels of protein structure

Answer 2

Primary-linear sequence of AA
Secondary: local arrangements of polypeptide backbone
Tertiary: 3D structure including side chains
Quaternary: subunit organization

Question 3

Prosthetic group

Answer 3

non AA but still needed for structure/function of polypeptide

Question 3

what bond type are primary structures determined by

Answer 3

covalent bonds

Question 4

what bond are secondary structures determined by

Answer 4

Hydrogen bonds

Question 5

what bond are tertiary and quaternary structures determined by

Answer 5

non covalent bonds

Question 6

what makes a peptide bond rigid

Answer 6

it exists between its two resonance structures(40% double bond character)

Question 6

T/F peptide bonds hold a formal charge

Answer 6

FALSE. they are uncharged but polar

Question 7

T/F peptide bonds are always planar

Answer 7

TRUE

Question 8

which confirmation is almost always favored by peptide bonds? who is the exception

Answer 8

trans conformation
Proline is 10% cis

Question 9

torsion angles

Answer 9

describe conformation of the backbone
-phi: C-N
-psi: C-C

Question 10

what determines how much the phi and psi bonds can rotate

Answer 10

the side chain size

Question 11

Ramachandran diagram

Answer 11

describe what angles bonds will prefer to be in
-white areas detail unfavorable bond angles

Question 12

characteristics of the a-helix

Answer 12

3.6 residues per turn
1.5A rise per residue
rise per turn: 3.6 x 1.5 = 5.4A
average 12 residues per helix

Question 13

hydrogen bonding of the a-helix

Answer 13

carboxyl of the nth residue h bonds with NH group on (n+4)th residue

Question 14

what is the optimal h bond length

Answer 14

2.8 A

Question 15

net dipole of the a-helix

Answer 15

partial negative towards C terminal
partial positive towards N terminal

Question 16

B-sheets

Answer 16

forms backbone H bonds to neighboring polypeptide chain

Antiparallel: polypeptides run in opposite directions
Parallel: polypeptides run in the same direction

Question 17

large B-sheets

Answer 17

parallel forms structures >5 strands

antiparallel forms smaller structures
(anywhere from 2-22 strands, strands average 6 residues)

Question 18

what causes large B-sheets to exhibit a right hand twist

Answer 18

interactions between chiral L-AA

Question 19

does parallel or antiparallel cause more complicated loops

Answer 19

parallel

Question 20

turns and loops

Answer 20

-allows peptide chains to reverse direction
-proline and glycine are common ones
-occur on surface of protein

Question 21

what stabilizes tertiary structures

Answer 21

AA side chains interacting with each other

Question 22

T/F side chains are involved in H bonds in the secondary structure

Answer 22

FALSE

Question 23

what AAs destabilize the a-helix

Answer 23

-proline -glycine -strings of Asp, Glu, Lys, Arg(have charged side chins that ionically interact)

Question 24

what type of AA dont like to be in B-sheets

Answer 24

charged AA

Question 25

oligomers

Answer 25

proteins with more than one subunit(polypeptide chains)

Question 26

T/F domains can be structurally and functionally independent

Answer 26

TRUE

Question 27

what is a domain

Answer 27

two or more unique clusters within the same polypeptide chain

Question 28

what is the purpose of domains

Answer 28

they allow for different interactions EX: part of chain is extracellular and part is in cytosol

Question 29

domains of phenylalanine hydroxylase

Answer 29

tetramerization domain regulatory domain catalytic domain

Question 30

what would happen if pheHase did not form properly

Answer 30

Phe would build up and be converted to a toxic substance leading to brain damage, siezures, death

Question 31

globular proteins

Answer 31

folded in a spherical shape very common high amt of a-helix and B-sheet

Question 32

fibrous proteins

Answer 32

structural proteins made in bulk

Question 33

keratin characteristics

Answer 33

"coiled coil" 5.1 A pitch left handed coil rich in Cys

Question 34

building of keratin

Answer 34

keratin a-helix two-chain coiled coil protofilament protofibril microfibril macrofibril

Question 35

what makes keratin hard vs. soft

Answer 35

amount of Cys /sulfur presense

Question 36

collagen characteristics

Answer 36

collagen triple helix right handed twist 1/3 is glycine found in connective tissue

Question 37

how much of the human body is made of collagen

Answer 37

30%

Question 38

what amino acid and its modified counterpart make up 30% of collagen

Answer 38

proline and hydroxyproline

Question 38

when are non standard AA formed

Answer 38

after the parent AA are incorperated

Question 39

what is required to add the hydroxyl group to proline

Answer 39

ascorbate(comes from vitamin C)

Question 40

why is hydroxylized proline so important for collagen

Answer 40

triple helix is stabilized by H bonding

Question 41

cause of scurvy

Answer 41

lack of vitamin C leads to weak collagen

Question 42

how are collagen fibrils stabilized

Answer 42

covalent crosslinks between Lys and His at N and C terminals

Question 43

T/F collagen stabilization relies heavily on disulfide bonds from Cys

Answer 43

FALSE. collagen contains very little Cys

Question 44

collagen disease

Answer 44

Ehlers Danlos brittle bone disease

Question 45

cause of Ehlers Danlos

Answer 45

Lysly-hydroxylase not made in high enough amounts leading to weak collagen

Question 46

cause of brittle bone disease

Answer 46

mild cases: gly is replaced with a bulkier residue, preventing proper formation of collagen severe cases: large base deletion in gene

Question 47

cofactor

Answer 47

similar to prosthetic group but not permanently attached to protein

Question 48

motif

Answer 48

small segment of polypeptide chain, usually to allow for cofactors

Question 49

T/F motifs allow side chains to rearrange to stabilize a cofactor when needed

Answer 49

TRUE

Question 50

example of enzyme using a motif and cofactor and its purpose

Answer 50

phosphofructokinase-breaks down sugar. when sugar breakdown is needed signaling structure appears and changes structure of motif to conformation that allows for sugar breakdown. when it is no longer needed motif goes to conformation not allowing sugar breakdown

Question 51

are folded proteins more stable than unfolded proteins

Answer 51

slightly(.4 kJ mol-1 AA