Amino acid residue structures, pKa's

Question 1

Glycine

Answer 1

Gly, G

Hydrophobic

simplest structure

-H

pKas: 2.35, 9.78

Question 2

Alanine

Answer 2

Ala, A

hydrophobic

One of the simplest structures

-CH₃

pKas: 2,9

Question 3

Leucine

Answer 3

Leu, L

Hydrophobic

“Dad” of the family

-CH₂CH(CH₃)₂

pKas: 2,9

Question 4

Arginine

Answer 4

Arg, R

Charged, positive charge on double bond N

Mom of family, 3-time swimming champion

-CH₂CH₂CH₂NH(=NH₂)(NH₂)

pKas: 2, 9, 12.5

Question 5

Isoleucine

Answer 5

Ile, I

Hydrophobic

One of the kids, isomer of dad

-CH(CH₂CH₃)CH₃

pKas: 2,9

Question 6

Valine

Answer 6

Val, V

Hydrophobic

Second child, shorter than dad

-CH(CH₃)CH₃

pKas: 2,9

Question 7

Threonine

Answer 7

Thr, T

Polar (may participate in hydrogen bonds)

similar 2 mom because likes water,but looks like dad

-CH(CH₃)OH

pKas: 2,9

Question 8

Cysteine

Answer 8

Cys, S

Polar

One of the sisters

-CH₂SH

pKas: 2, 10.25, 8

Question 9

Serine

Answer 9

Ser, S

Polar

One of the sisters

CH₂OH

pKas: 2,9

Question 10

Proline

Answer 10

Pro, P

One of the random structures, sort of cyclic

Hydrophobic

amino group and alpha C part of 5 membered ring

Question 11

Methionine

Answer 11

Met, M

Polar

Random structure, Meth -> Eth -> Thio -> M

-CH₂CH₂SCH₃

pKas: 2,9

Question 12

Tryptophan

Answer 12

Trp, W

Polar

Looks like a turkey, pentagon on top of benzene

-CH₂-pentagon w/N-benzene

pKas: 2,9

Question 13

Tyrosine

Answer 13

Tyr, Y

Polar

looks like a tire “tyr”

CH₂-benzene-OH

pKas: 2,9,10

Question 14

Phenylalanine

Answer 14

Phe, F

Hydrophobic

Phenyl group + alanine residue

CH₂-benzene

pKas: 2,9

Question 15

Aspartic Acid

Answer 15

Asp, D

charged, acidic

One carbon +carboxilic acid “acid”

-CH₂-COO^-

pKas: 2, 9, 3.8

Question 16

Glutamic acid

Answer 16

Glu, E

Charged, acidic

Two carbons, carboxilic acid “acid”

-CH₂-CH₂-COO^-

pKas: 2,9,4

Question 17

Asparagine

Answer 17

Asn, N

Polar

Looks like Asp, but replace COO with amide

-CH₂-C(NH₂)=O

pKas: 2,9

Question 18

Glutamine

Answer 18

Gln, Q

Polar

Looks like Glu, but replace COO^- with amide

-CH₂CH₂C(NH₂)=O

Question 19

Lysine

Answer 19

Lys, K

Charged

“e” at the end of lysine = epsilon C amino group

-CH₂CH₂CH₂CH₂NH₃

pKas: 2,9,10.5

Question 20

Histidine

Answer 20

His, H

Polar

Aromatic with 2 N’s

CH-Pentagon with 2 N’s, one lone pair, one (=)

pKas: 2,9,6

Question 21

Charged amino acids

Answer 21

Lysine

Glutamic Acid

Aspartic Acid

Arginine

Question 22

Polar amino acids

Answer 22

Cysteine

Serine

Threonine

Tryptophan

Tyrosine

Methionine

Asparagine

Glutamine

Histidine

Question 23

Hydrophobic amino acids

Answer 23

Glycine

Alanine

Leucine

Isoleucine

Valine

Phenylalanine

Proline

Question 24

Chirality of amino acids

Answer 24

• All amino acids besides Glycine have chiral alpha carbon centers
• Most amino acids exist in L- form
• Enzymes have active sites that have specific chiralities, so their substrates must match with that chirality
• D- vs. L- determined by CO-R-N in clockwise fashion when looking down C-H bond

Question 25

pKa shift of amino acids

Answer 25

pKa's can shift on amino acid reactive sites when conformation is changed i.e histidine-\>imidazole pKa range 6.5-7.4

Question 26

What kind of bond are aa's linked with?

Answer 26

amide bond