topic 02 amino acids Flashcards
at physiological pH, what are the charges of the carboxyl group and amino group?
carboxyl: negative (unprotonated)
amino: positive (protonated)
which of the two isomers is the only one present in proteins?
L - isomer
which of the 20 amino acids are archiral?
glycine
which type of amino acids are found in the interior? why? what does this indicate?
hydrophobic
to avoid water
hydrophobic side chains do not directly participate in chemical reactions
how can polar amino acids interact with water?
due to the presence of hydroxyl, thiol, amide groups, or an imidazole ring (found in histidine)
what is unique about glycine?
can’t form hydrogen bonds
not hydrophobic or charged
what are the hydrophobic (non-polar) amino acids?
Glycine, Alanine, Valine, Leucine, Isoleucine, Proline, Phenylalanine, Tryptophan, Methionine
what are the uncharged hydrophilic (polar) amino acids?
Asparagine, Glutamine, Serine, Threonine, Tyrosine, Cysteine
what is the start codon?
AUG
codes for methionine
what are the negatively charged hydrophilic (polar) amino acids?
Aspartate and Glutamate
what are the positively charged hydrophilic (polar) amino acids?
Histidine, Lysine, Arginine
which of the amino acids are aromatic?
Phenylalanine, Tryptophan, Tyrosine
what is related to increasing hydrophobicity?
increasing number of carbon atoms in a hydrocarbon chain
which of the amino acids contain a hydroxyl group?
serine, tyrosine, threonine
which of the amino acids contain a thiol group?
cysteine
which of the amino acids contain an amido group in the side chain?
asparagine, glutamine
what is a guanido group? which of the amino acids contain one?
guanido group is a group of 3 nitrogen surrounding a carbon atom.
this is found arginine
which of the amino acids contain a carboxyl group?
aspartate and glutamate
which of the amino acids contain a primary amino group?
lysine
differentiate between the charges of basic and acidic side chains at physiological pH. what about the uncharged amino acids?
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
what will lowering the pH (or increasing the H ion concentration) lead to?
what about for basic groups?
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
define amphoteric
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
how does the affinity of group for a proton relate to Ka and pKa?
directly related to pKa
as affinity increases, so does pKa
inversely related to Ka
as affinity increases, Ka decreases
how does the affinity of a group for a proton relate to the pKa and acidity/basic ness idk ?
acidic groups more readily give up protons and have a lower pKa
basic groups resist releasing protons and have a higher pKa
what are the pKa of carboxyl and amino groups? what does this mean?
carboxyl groups have a lower pKa and readily release their protons
amino groups have a higher pKa and release their protons at high pH
what can be inferred when the concentration of the weak acid and conjugate base are equal?
log = 0
log10 of 1 = 0
pH = pKa
50% of the group is protonated and 50% is unprotonated
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?
90% protonated
100% protonated
90% deprotonated
100% deprotonated
what’s the pK of the phenol group in Tyrosine?
10.46
which of the uncharged amino acids could develop a charge at high pKs? what charge would they develop?
Tyrosine and Cysteine.
they would develop a negative charge
what’s the pK of the sulfhydryl (thiol) group in Cysteine?
8.37
what’s the pK of the amine group in Lysine?
10.54
what’s the pK of the guanidino group in Arginine?
12.48
what’s the pK of the imidazole ring in histidine?
6.04
what’s the pK of the carboxyl group in aspartate?
3.90
what’s the pK of the carboxyl group in glutamate?
4.07
what’s the pK of the alpha-carboxyl group in amino acids?
2-3
what’s the pK of the alpha-amino group in amino acids?
8-9
