Motifs

Question 1

Importance of structure irregularity

Answer 1

helps proteins fulfill diverse functions, able to recognize thousands types of molec

Question 2

Interior of proteins

Answer 2

hydrophobic core

Question 3

Driving force of folding water soluble proteins

Answer 3

To pack HPhob side chains into interior of molec

Question 4

Folding HPhob side chains into center -> main chain (polar/HPhil due to -NH and -COOH groups) must fold into center as well; how to stabilize?

Answer 4

secondary structures: forms H-bonds to neutralize polarity, forms btwn H of the -NH and carbonyl oxygen of the -COO

Question 5

Residues per turn in A helix

Answer 5

3.6 residues (5.4 A)

Question 6

Angstroms per turn in A helix

Answer 6

3.6 residues/5.4 A = 1.5 A

Question 7

In A helices, H bonds form every

Answer 7

4th AA, btwn n and n+4

Question 8

Ends of A helices are

Answer 8

polar, almost always towards surface

Question 9

Why are the ends of A helices more polar?

Answer 9

first -NH group and last -COO group not H bonded

Question 10

how are H bonds in A helices oriented?

Answer 10

parallel to helical axis, between nearby residues, forms btwn H of the -NH and carbonyl oxygen of the -COO

Question 11

how are side chains in A helices oriented?

Answer 11

perpendicular to helical axis

Question 12

Why does A helix exhibit a dipole moment?

Answer 12

peptide units and H bonds aligned in the same orientation as helical axis, peptide bonds have dipole (N term is pos, C term is neg), whole helix has a macroscopic dipole moment

Question 13

ligands attracted to N terminus of A helix

Answer 13

negative groups, especially phosphate groups

Question 14

preferred AA’s in A helices

Answer 14

small HPhob residues, eg Ala, Leu (other good choices are in Tooze 17)

Question 15

helix breakers

Answer 15

Pro, Gly (other bad choices are in Tooze 17)

Question 16

Why is Pro is helix breaker?

Answer 16

rotation around the N-Ca bond is impossible

Question 17

Why is Gly is helix breaker?

Answer 17

tiny R-group supports other conformations

Question 18

how are H bonds in B sheets oriented?

Answer 18

perpendicular to the direction of the strand, between dif strands, forms btwn H of the -NH and carbonyl oxygen of the -COO

Question 19

H bonding in parallel B sheets

Answer 19

H-bonded strands run in the same direction, H bonds bent/weaker

Question 20

H bonding in antiparallel B sheets

Answer 20

H-bonded strands run in opposite directions, H bonds linear/stronger

Question 21

What connects A helices and B sheets?

Answer 21

loop regions

Question 22

location of loop regions

Answer 22

surface of proteins

Question 23

Loop regions also commonly found in

Answer 23

binding sites and enzyme active sites

Question 24

Loops regions that connect adjacent antiparallel B strands

Answer 24

B hairpin loops or B turns

Tooze 21

Question 25

180 deg B turn occurs over how many AA?

Answer 25

4 AA

Question 26

How are B turns stab?

Answer 26

stabilized by a H-bond from a carbonyl oxygen to amide

proton three residues down the sequence

Question 27

Common AA positions in B turn

Answer 27

Pro in position 2 or Gly in position 3

Question 28

motifs def

Answer 28

frequent simple combinations of secondary structure elements w/specific geometric arrangement

Question 29

helix turn helix usage

Answer 29

usually found in DNA binding and calcium binding motifs

Question 30

Loops regions that connect adjacent parallel B strands

Answer 30

B-A-B motif

Tooze 27

Question 31

coiled coiled

Answer 31

2 A helices coiled onto each other, more stable than a straight A helix chaib

Question 32

heptad repeat

Answer 32

repeat of 7 AA, labeled A-G, E/G are charged, A/D are HPhob, the rest are polar

eg. D is Leu in Leu zipper

Question 33

knobs in holes model

Answer 33

how A helices pack against each other, each HPhob residue of one helix fits into a hole made by 4 side chains in the second

every other A helix motif uses ridges and grooves model

Question 34

4 helix bundle

Answer 34

HPhob side chains buried on the interior

Question 35

eg of 4 helix bundle

Answer 35

human growth hormone (up, up, down, down)

Tooze 38

Question 36

globin fold

Answer 36

8 A helices, connected by short loop regions

pocket for heme group

Question 37

eg of globin fold

Answer 37

myoglobin, hemoglobin

Question 38

3 classes of A/B structures

Answer 38

TIM barrel (closed B barrel), Rossman Fold (open B barrel), Leu rich motifs/horseshoe fold

Question 39

TIM barrel (closed B barrel)

Answer 39

closed barrel, 8 parallel B strands inside, 8 A helices that connect on outside

Question 40

Rossman Fold (open B barrel)

Answer 40

open twisted B parallel sheet surrounded by A helices on both sides

Question 41

Leu rich motifs

Answer 41

repetitive regions of Leu. , B strands form curved parallel sheet, A helices on outside

Question 42

TIM barrel (closed B barrel) active site

Answer 42

loops at C term of B sheet

Question 43

Rossman Fold (open B barrel) active site

Answer 43

crevice at C term of B strand, formed by 2 loop regions that connect the two A helices on opp of B sheet

Question 44

3 most common B structures

Answer 44

up and down B barrel, Greek key, jelly roll

Question 45

up and down B barrel

Answer 45

sim to A/B barrels but all B strands are antiparallel, all connections are B hairpins

Question 46

eg of up and down B barrel

Answer 46

retinol binding protein

Question 47

eg of Rossman Fold (open B barrel)

Answer 47

MHC receptor