Foundations 2

Question 1

folding of cytosolic globular proteins is ___? why?

Answer 1

spontaneous: because of the hydrophobic effect

Question 2

prothestic groups definition - what level of structure? purpose?

Answer 2

additional non protein organic molecules which are permanently included in the protein’s tertiary structure; required for protein to function - confer additional chemical reactivity

Question 3

stabilization of the 3 D structure of soluble globular proteins is through what interactions?

Answer 3

almost entirely through non covalent interactions - folding driven by hydrophobic effect then stabilized by salt bridges, H bonds, vdw interactions

Question 4

the only covalent interaction for 3D structures (proteins)

Answer 4

disulphide bridges/bonds between cysteines

Question 5

sickle cell anemia: what mutation? result?

Answer 5

polar glu6 residue replaced with non polar val residue - which then associates with small hydrophobic patch on protein surface = occurs twice for each Hb molecule = enables formation of Hb fibers = distorts shape of RBCs

Question 6

fibrous proteins: critical roles in? solubility? structure?

Answer 6

critical roles in structure. low solubility in water. super secondary structure - packed layers of a helix or b sheets

Question 7

keratin found where

Answer 7

hair, nails, skin

Question 8

two families of keratins

Answer 8

alpha - hair, wool. beta - nails, beaks, horns

Question 9

structure of alpha keratins: individual keratins form? stabilized by?

Answer 9

individual keratin polypetides (Each an a-helix) interact to form coiled coil superhelical structures; stabilized by hydrophobic effect

Question 10

collagen: structure

Answer 10

3 polypeptide chains each of which is wound in a left handed helix - they twist around each other into a right handed superhelix = great tensile strength because of opposing twists

Question 11

all collagen types contain which 2 things repeated in tandem several hundred times? why?

Answer 11

gly pro Y or gly pro hydroxy proline - glycine because small, proline because rigid

Question 12

collagen specific secondary structure?

Answer 12

tightly twisted extended left handed helix with 3 aas per helical turn - proline help distorts geometry of backbone

Question 13

collagen: triplet of polypeptides form? what bonds?

Answer 13

right handed super helical structure. held together via H bonds = huge increase in melting temperatures

Question 14

why are gly residues important to collagen

Answer 14

the only ones small enough to allow individual fibers of the triple helix to meet closely

Question 15

two keys to understanding protein function

Answer 15

can bind to other molecules. have a flexible, dynamic structure

Question 16

1. proteins bind ___? reversibility? type of bonds

Answer 16

small organic molecules called ligands (or other proteins). almost always reversible - non covalent interactions

Question 17

ligand binding to proteins is an _____ reaction?

Answer 17

equilibrium reaction (so is reversible

Question 18

ligand binding: equilibrium position depends on?

Answer 18

ligand concentration and binding affinity

Question 19

how do enzymes speed up reactions

Answer 19

reducing activation energy barrier - ensure proximity and orientation of reactants, enable participation in the reaction by aa side chains and cofactors like prosthetic groups

Question 20

chemical reactivity of aa side chains?

Answer 20

quite limited - nucleophilic or acid base reactions

Question 21

cofactors: classification

Answer 21

coenzymes - cosubstrates (reversible) and poresthetic groups (permanently in active site). also have essential ions

Question 22

ability of an enzyme to catalyze a reaction depends on its:

Answer 22

binding affinity, aka its ability to bind the substrate/cosubstrate