module 2: amino acids Flashcards
four levels of protein structure
primary - amino acid sequence
secondary - local structures such alpha helix
tertiary - 3D structure
quarternary - polypeptide 3D structure
anatomy of amino acid
composed of protonated amine (NH3+), an acid (COO-), and a central alpha carbon which all groups are bonded to
alpha carbon is also bound to a side chain and an H atom
enantiomer
two mirror images of a chiral molecule
how are amino acids categorized?
based on size and shape, types of interactions, and conformational flexibility
distinguished between non polar and polar
types of polar amino acids
neutral, acidic, basic
non polar amino acids
glycine (G, gly) -
alanine (A, ala) -
valine (V, val)
leucine (L, leu) -
isoleucine (I, ile) -
phenylalanine (F, phe) -
methionine (M, Met) -
proline (P, Pro) -
tryptophan (W, trp)
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F and W have aromatic side chains, the rest have alkyl side chains (CH)
methionine contains sulfur
proline’s amino group is covalently bound to its non polar side chain, disrupting backbone hydrogen bonding in secondary structure
polar amino acids
serine (S, Ser) -
threonine (T, Thr) -
tyrosine (Y, Tyr) -
asparagine (N, Asp) -
glutamine (Q, Gln) -
cysteine (C, cys) -
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polar enough to form hydrogen bonds with water but don’t act as an acid or a base
cysteine contains sulfur
tyrosine may be non polar
acidic amino acids
Aspartic acid (D, Asp) -
Glutamic acid (E, Glu) -
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both contain carboxylic acid R groups
basic amino acids
lysine (K, lys) -
arginine (R, arg) -
histidine (H, his) -
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-histidine can sometimes act as an acid
characteristics of non polar amino acids
glycine - R group is hydrogen
alanine - methyl R group
valine - two methyl groups
leucine - CH attached to two methyl groups
isoleucine - methyl and ethyl group
phenylalanine - methyl attached to phenyl group
tryptophan - two aromatic rings, one ring contains NH, one is just a 6 membered carbon ring
methionine - S attached to methyl
proline - Nitrogen is part of side chain, three CH2 are part of R group with last one attaching to NH2+
characteristics of polar amino acids
serine - OH
threonine - methyl and OH
tyrosine - phenyl which has a hydroxy group attached to it
asparagine - amide functional group
glutamine - CH2 attached to amide functional group
cysteine - SH
characteristics of acidic amino acids
Aspartic acid - CH2 attached to COO-
Glutamic acid - CH2 attached to CH2 attached to COO-
characteristics of basic amino acids
lysine - 3 CH2 attached to an amine
arginine - 2CH2 attached to NH which attaches to a carbon that has two NH2 groups attached to it, one NH2 has a positive charge
histidine - 5 membered aromatic ring including NH and NH+
zwitterion
ionic form containing no net charge
equivalence point
when moles of acid = moles of base
relation of ph and pKa to deprotonation and protonation
when ph>pKa, there is more deprotonation
pKa values of carboxyl and amine groups
carboxyl - around 2
amine - around 9
tyrosine side chain pKa
10.07
cysteine side chain pKa
8.33
side chain pKas of acids
aspartic - 3.86
glutamic - 4.25
side chain pKas of bases
arginine - 12.48
histidine - 6
lysine - 10.53
isoelectric point
when pH is equal to pI, amino acid is electrically neutral and zwitterion concentration is at its max
pI formula
1/2(pka1 +pka2)
what happens to amino acids at physiological pH?
acids are deprotonated and bases are protonated
essential amino acids
not produced by our body
function of disulfide bonds
provide stability between and within polypeptides