3. amino acids Flashcards
T or F: the backbone is consistent for all amino acids
true
T or F: all R groups are similar
false; R groups vary in structure, size, charge, and solubility in water
how are proteins formed
a folded linear chain of covalently-bound amino acids forms a protein
describe an amino acid’s charge at physiological pH
the amino group is protonated and the carboxyl group is ionized
what is the amino group at physiological pH
NH3+
what is the carboxyl group at physiological pH
COO-
define zwitterions
dipolar ions. These refer to the amino and carboxyl groups when they’re charged (pH=7)
what is the NET charge of the zwitterions
zero (one is + and one is -)
in an amino acid, what is the alpha carbon
alpha carbon is the one attacked to the amino group, carboxyl group, R group, and H
T or F; the alpha carbon is chiral
true, but only in 19 of 20 amino acids
in which amino acid is carbon NOT chiral
glycine, whose R group is a hydrogen
what are the two configurations of amino acids called
L and D
do amino acids have conformations or configurations. Why?
configurations; bonds need to be broken to switch between L and D
describe the process on figuring out if an amino acid is L or D
place the chiral carbon in the center with the carboxyl above it and the R group below. If the amino group is on the left=L, on the right =D
T or F: if no configuration is designated, we can assume the amino acid is D
false; always assume L unless specifically designated D
T or F; switching between L and D is favourable
false; it requires breakage of bonds
why do we use greek letters instead of numbers to name amino acids
because then the carboxyl carbon would have to be denoted number 1, and we don’t want this
which are the non polar amino acids
glycine, alanine, proline, valine, leucine, isoleucine, methionine
why are non-polar amino acids non-polar?
their R groups have lots of hydrocarbons, so they cluster together due to the hydrophobic effect
why is proline a unique non-polar amino acid
it’s cyclic, so it often introduces kinks or bends in a polypeptide chain
which of the non-polar amino acids has the smallest contribution to the hydrophobic effect + why
glycine, because it’s R group is only an H
which of the non-polar amino acids are the most significant in terms of the hydrophobic effect + why?
alanine, valine, leucine, and isoleucine. This is because they are solely C and H
describe methionine (non-polar amino acid)
it has a slightly polar thioether in the side chain, but is still grouped as non-polar
list the polar amino acids
serine, threonine, cysteine, asparagine, and glutamine
why are the polar amino acids polar?
they contain functional groups that form hydrogen bonds with water (consist of mostly O’s or N’s)
which polar amino acid is the least polar + why
cysteine, it has a sulfhydryl group and is a weak acid
describe the role of cysteine in protein shape
2 cysteine residues can oxidize to form a disulfide bridge to form a dimeric amino acid called cystine
which amino acids are basic (+ charged)
lysine, arginine, and histidine
describe the R groups of the basic amino acids
positively charged residues all have some sort of N, but the protonated forms have different number of hydrogens
which amino acids are acidic (- charged)
aspartate and glutamate
which amino acids are aromatic rings and relatively non-polar
phenylalanine, tyrosine, tryptophan
T or F; the aromatic amino acids absorb ultraviolet light
true
what is the purpose of the aromatic amino acids being able to absorb uv light
used to help identify samples with protein
which aromatic amino acid is the best at uv absorption
tryptophan
alanine
Ala, A
arginine
Arg, R
asparagine
Asn, N
aspartate
Asp, D
cysteine
Cys, C
glutamate
Glu, E
glutamine
Gln, Q
glycine
Gly, G
histidine
His, H
isoleucine
Iso, I
leucine
Leu, L
lysine
Lys, K
methionine
Met, M
phenylalanine
Phe, F
proline
Pro, P
serine
Ser, S
threonine
Thr, T
tryptophan
Trp, W
tyrosine
Try, Y
valine
Val, V
Ala
alanine
Arg
arginine
Asn
asparagine
Asp
aspartate
Cys
cysteine
Glu
glutamate
Gln
glutamine
Gly
glycine
His
histidine
Iso
isoleucine
Leu
leucine
Lys
lysine
Met
methionine
Phe
phenylalanine
Pro
proline
Ser
serine
Thr
threonine
Trp
tryptophan
Try
tyrosine
Val
valine
A
alanine
R
arginine
N
asparagine
D
aspartate
C
cystine
E
glutamate
Q
glutamine
G
glycine
H
histidine
I
isoleucine
L
leucine
K
lysine
M
methionine
F
phenylalanine
P
proline
S
serine
T
threonine
W
tryptophan
Y
tyrosine
V
valine
how is hydropathy quantified
by measuring the free-energy difference (delta G) of the amino acid side chain as it moves from a hydrophobic solvent to water
what does a positive hydropathy value indicate
more positive=more hydrophobic side chain
what does a negative hydropathy value indicate
more negative=more hydrophilic
how many amino acids have been found
over 500
what is a post-translational modification
it’s when a common amino acid is permanently modified after being incorporated into the polypeptide chain
are the 500+ amino acids found in proteins? what is their purpose
no; they still have important metabolic roles though (ie urea cycle in the liver)
what are amino acid derivatives
common amino acids modified by enzymes to produce biologically important amines
list some of the amino acid derivatives
GABA, histamine, capsaicin, adrenaline, vanillin, auxin
T or F: amino acids can act as weak acids and bases
true; because they’re charged at pH=7
which group of the amino acid will donate protons
NH3+
which group of the amino acid will accept protons
COO-
why does each amino acid have two pKa values
two protons can be donated from a fully deprotonated backbone
how many inflection points should there be on an amino acid titration curve
at least 2
what is pI and what is the charge at this point
isoelectric point. The net charge is zero
what is the pI formula
(pK1+pK2)/2
how many of the amino acids have an ionizable side chain
7 of 20
what is the result of having an ionizable side chain
they have another value, pKR
define residue
residue describes one amino acid in a polypeptide chain
what type of reaction forms a peptide bond
condensation reaction (aka dehydration)
how do you name peptides
replace the -ine or -ate with -yl
for asparagine, glutamine, and cysteine: replace the -e with -yl
how do you name a full peptide
list all the residue names together as one word. Each gets the -yl ending except for the last one where the name doesn’t change
what components of the amino acids contribute to the charge of the peptide
only the amino and carboxyl groups are ionized at cellular pH. The remainder doesn’t contribute to the charge
how do you determine the overall charge of a peptide
sum any individual charges on: amino terminus, carboxyl terminus, and any ionizable R groups
