topic 02 amino acids

Question 1

at physiological pH, what are the charges of the carboxyl group and amino group?

Answer 1

carboxyl: negative (unprotonated)

amino: positive (protonated)

Question 2

which of the two isomers is the only one present in proteins?

Answer 2

L - isomer

Question 3

which of the 20 amino acids are archiral?

Answer 3

glycine

Question 4

which type of amino acids are found in the interior? why? what does this indicate?

Answer 4

hydrophobic

to avoid water

hydrophobic side chains do not directly participate in chemical reactions

Question 5

how can polar amino acids interact with water?

Answer 5

due to the presence of hydroxyl, thiol, amide groups, or an imidazole ring (found in histidine)

Question 6

what is unique about glycine?

Answer 6

can’t form hydrogen bonds

not hydrophobic or charged

Question 7

what are the hydrophobic (non-polar) amino acids?

Answer 7

Glycine, Alanine, Valine, Leucine, Isoleucine, Proline, Phenylalanine, Tryptophan, Methionine

Question 8

what are the uncharged hydrophilic (polar) amino acids?

Answer 8

Asparagine, Glutamine, Serine, Threonine, Tyrosine, Cysteine

Question 9

what is the start codon?

Answer 9

AUG

codes for methionine

Question 10

what are the negatively charged hydrophilic (polar) amino acids?

Answer 10

Aspartate and Glutamate

Question 11

what are the positively charged hydrophilic (polar) amino acids?

Answer 11

Histidine, Lysine, Arginine

Question 12

which of the amino acids are aromatic?

Answer 12

Phenylalanine, Tryptophan, Tyrosine

Question 13

what is related to increasing hydrophobicity?

Answer 13

increasing number of carbon atoms in a hydrocarbon chain

Question 14

which of the amino acids contain a hydroxyl group?

Answer 14

serine, tyrosine, threonine

Question 15

which of the amino acids contain a thiol group?

Answer 15

cysteine

Question 16

which of the amino acids contain an amido group in the side chain?

Answer 16

asparagine, glutamine

Question 17

what is a guanido group? which of the amino acids contain one?

Answer 17

guanido group is a group of 3 nitrogen surrounding a carbon atom.

this is found arginine

Question 18

which of the amino acids contain a carboxyl group?

Answer 18

aspartate and glutamate

Question 19

which of the amino acids contain a primary amino group?

Answer 19

lysine

Question 20

differentiate between the charges of basic and acidic side chains at physiological pH. what about the uncharged amino acids?

Answer 20

basic side chains remain positively charged

acidic side chains become negatively charged

uncharged amino acids could become ionizied and develop a charge but not at physiological pH

Question 21

what will lowering the pH (or increasing the H ion concentration) lead to?

what about for basic groups?

Answer 21

lowering of the pH (or increasing the H ion concentration) will cause

• equilibrium to drive to the left (to the reactants)
• decreased concentration of RCOO-
• increased RCOOH
• fraction of ionized molecules decrease

for basic groups, lowering the pH, will have the opposite effect

• fraction of ionized molecules increase

Question 22

define amphoteric

Answer 22

possessing both a negative and positive charge and can exist as zwitterions. the net charge is the sum of positive and negative charges – changes due to pH. as pH decreases, net charge becomes more positive

Question 23

how does the affinity of group for a proton relate to Ka and pKa?

Answer 23

directly related to pKa
as affinity increases, so does pKa

inversely related to Ka
as affinity increases, Ka decreases

Question 24

how does the affinity of a group for a proton relate to the pKa and acidity/basic ness idk ?

Answer 24

acidic groups more readily give up protons and have a lower pKa

basic groups resist releasing protons and have a higher pKa

Question 25

what are the pKa of carboxyl and amino groups? what does this mean?

Answer 25

carboxyl groups have a lower pKa and readily release their protons amino groups have a higher pKa and release their protons at high pH

Question 26

what can be inferred when the concentration of the weak acid and conjugate base are equal?

Answer 26

log = 0 log10 of 1 = 0 pH = pKa 50% of the group is protonated and 50% is unprotonated

Question 27

if pH is 1 below pK, what do we assume? if pH is 2 below pK? if pH is 1 above pK? if pH is 2 above pK?

Answer 27

90% protonated 100% protonated 90% deprotonated 100% deprotonated

Question 28

what's the pK of the phenol group in Tyrosine?

Answer 28

10.46

Question 29

which of the uncharged amino acids could develop a charge at high pKs? what charge would they develop?

Answer 29

Tyrosine and Cysteine. they would develop a negative charge

Question 30

what's the pK of the sulfhydryl (thiol) group in Cysteine?

Answer 30

8.37

Question 31

what's the pK of the amine group in Lysine?

Answer 31

10.54

Question 32

what's the pK of the guanidino group in Arginine?

Answer 32

12.48

Question 33

what's the pK of the imidazole ring in histidine?

Answer 33

6.04

Question 34

what's the pK of the carboxyl group in aspartate?

Answer 34

3.90

Question 35

what's the pK of the carboxyl group in glutamate?

Answer 35

4.07

Question 36

what's the pK of the alpha-carboxyl group in amino acids?

Answer 36

2-3

Question 37

what's the pK of the alpha-amino group in amino acids?

Answer 37

8-9