Proteins

Question 1

Protein Structures
primary =
secondary =
tertiary =
quaternary =

Answer 1

• amino acid sequence
• a-helicies or b-sheets
• 3d folding of the protein (1chain)
• complex folding of the protein (many chains)

Question 2

Cysteines Specifically

undergo ________ chemistry
reduced form =
oxidized form =

Answer 2

redox chemistry
cysteine + cysteine (SH + SH)
disulphide bond (S—–S)

Question 3

what rxn breaks peptide bonds

Answer 3

hydrolysis

Question 4

what rxn makes peptide bonds

Answer 4

condensation

Question 5

what seconday structure has a dipole

Answer 5

a helix since all amides are on one side and all carbonyls are on the other side

Question 6

phi angle

Answer 6

bond angle between N——Calpha

Question 7

psi angle

Answer 7

bond angle between Calpha——Carbonyl C

Question 8

what are the two forms of B-sheets

Answer 8

parallel and antiparallel

Question 9

antiparallel B-sheets

Answer 9

both sheets run in opposite directions and H bonding is vertical/straight between amide and carbonyl

Question 10

parallel B-sheets

Answer 10

both sheets run in the same direction and H bonding is diagonal between amide and carbonyl

Question 11

salt bridge and example

Answer 11

electrostatic interaction between opposite charges
ex. Lys (+) ——— (-) Glutamate

Question 12

non polar residues =
charged residues =
polar residues =

Answer 12

inside of the portein (core)
surface of the protein
outside of the protein (periphery)

Question 13

stabilizing forces of proteins

Answer 13

electrostatic int, h bonding, wan ders wals forces, hydrophobic effects

Question 14

B-sheets

right handed twists result in ______ loops
left handed twists result in ________ loops

Answer 14

shorter
longer

Question 15

example of B-sheets

Answer 15

TIM barrel
- 8 stand B-barrel with right handed twists

Question 16

example of a-helicies

Answer 16

Leucine Zippers
- dimerization of 2 a-helicies with Leu repeats every 7 amino acids

Bacteriorhodopsin

Question 17

protein domains

Answer 17

independantly folded regions on a protein

Question 18

example of protein-carbohydrate complexes

Answer 18

Lectins

-functions in cell-cell recognition
- polyvalent affinity for polysaccharides not monosaccharides

Question 19

what are the 4 classes of proteins

Answer 19

• all a helical
• all b sheets
• mixed a/b
• mixed a+b

Question 20

mixed a/b proteins and example

Answer 20

have both a helicies and b sheets in the same domain
ex. Ricin (2 domains, a+b and another one)

Question 21

mixed a+b proteins and examples

Answer 21

have a helicies and b sheets in different domains
ex. Type 4 Pilin (2 domains, a helical (N term) and B sheets (C term))

Question 22

how many residues are there per turn in the a-helix

Answer 22

3.6 residues

Question 23

what atoms make up the phi angle

Answer 23

carboxyl C - amide N - alpha C - carboxyl C

Question 24

what atoms make up the psi angle

Answer 24

amide N - alpha C - carboxyl C - amide N

Question 25

what are helical wheels

Answer 25

a diagram that shows the arrangement/properties of amino acids in a a-helix and how it would look like in a protien

Question 26

each carbonyl is H-bonded to a amide _____ residues away

Answer 26

4 residues away
n+4

Question 27

what does the Ramacharan Plot show

Answer 27

shows the sterically allowed/not allowed conformations of the protein backbone through its phi and psi dihedral angles