Proteins

Question 1

functional part of the cell

Answer 1

proteins

Question 2

describe AA structure

Answer 2

central C atom
amino group (-NH3+)
carboxylate group (-COO-)
R side chain

Question 3

how many AA are there

Answer 3

20 ( hydrophobic, hydrophilic, and amphipathic)

Question 4

when is an AA considered protonated or unprotonated

Answer 4

protonated- below pKa

unprotonated- above pKa

Question 5

pKa of carboxyl and amino goups

Answer 5

carboxyl ~2

amino ~9.0-9.5

Question 6

L vs D AA

Answer 6

L-AA is natural form

D-AA is mirror image of L form

Question 7

describe how a peptide bond is formed

Answer 7

dehydration synthesis
-on one AA, the OH from carboxyl and an H from the amino form water and Is released

the remaining central C w/ double bonded O attached from carboxyl BINDS to N w/ H attached from amino

Question 8

which AA are found in alpha helices

Answer 8

leucine, methionine, glutamine, and glutamic acid

Question 9

which AA are found in beta sheets

Answer 9

valine, isoleucine, phenylalanine

Question 10

which AA are found in beta turns and why

Answer 10

glycine- very small side chain (-H) and very flexible

proline- has unusual structure that introduces kinks in th polypeptide chain (wide, big turn)

Question 11

links helices and sheets

Answer 11

beta turns

Question 12

describe protein folding

Answer 12

driven by hydrophobic interactions

energetically favorable- entropy inc as water molecules become more disordered

hydrophobic (polar) residues are on outside of folded protein

internal protein structures tightly packed with few gaps (hydrophobic)

Question 13

where does protein folding occur in the cell

Answer 13

ER

Question 14

describe protein DNA interactions

Answer 14

chemical groups exposed in major and minor grooves

DNA binding proteins most frequently bind in the major groove (TATA binding protein)

alpha helices and beta sheets can fit in major groove

binding in minor groove introduces a distortion to the DNA that can benefit certain reactions

Question 15

which groove have more variation

Answer 15

major groove has more variation than minor groove

major groove has acceptors, donors and methyl group
minor groove has acceptors and donors

Question 16

specific DNA and protein interaction is deteremined by

Answer 16

DNA sequence and protein shape/available binding groups

Question 17

binds 3 operator sites in the double stranded phage DNA (controls lytic/lysogenic switch)

17 bp sequences in operator sites that are similar

Answer 17

Lambda Cro

Question 18

lambda cro competes w/ _____ for operator sites

Answer 18

lambda repressor

Question 19

66 AA monomer that exists as a dimer

Answer 19

Cro

Question 20

describe lambda cro structure

Answer 20

each monomer has 3 antiparallel beta sheets and 3 alpha helices

the alpha helix 3 form protruding ridges separated by 34 Angstrom of beta sheets

Question 21

how does lambda cro bind to DNA

Answer 21

binds to DNA from alpha helices