amino acids Flashcards
Common structural features of amino acids
- alpha carbon attached to R group, amino group, and carboxyl group
- R group differentiates them
- alpha carbon is a chiral center
How can R groups vary
- size
- structure
- polarity
- solubility
stereoisomers vs constitutional isomers
- stereoisomers differ in the spatial orientation of the bond (ie. enantiomers)
- consitutional isomers are connected differently
why do amino acids tend to be the L conformer over the D conformer
- Overtime, things have evolved to favor the L isomer
- positive feedback - L-isomers interact better with L-isomers so more things will tend to evolve to be L
- don’t know specifically why L over D
properties of amino acids that make them well suited to carry out a variety of biological functions
- have useful acid-base properties
- capacity to polymerize
- diversity of amino acids –> many different proteins
Amino acids besides alpha
- some amino acids have different groups
- only alpha are used in making proteins
5 categories of amino acids
-nonpolar, aliphatic
- aromatic
- polar, uncharged (hydroxyl, sulfhydryl, and amido groups)
-positively charged
- negatively charged
- determined at biological pH
which amino acids can form disulfide bonds?
cystine
- disulfide bonds occur via the reversible oxidation of two cysteine molecules
How does the charge of the R group relate to acidity or basicity
- negatively charged R groups are acidic
- Positively charged R groups are basic
aromatic rings in amino acids
- generally nonpolar except tyrosine
- allow proteins to absorb light
cysteine
- SH oxidized to form disulfide bridges
- important in stabilizing tertiary and quaternary structures
glycine
- R group is H
- very small
- fits in tight places
- achiral
proline
- R group bends around to form a ring wby covalently bonding to the amino group of the alpha carbon
- introduces kink in folding of polypeptide chain
Proteinogenic amino acids
- amino acids in final form as protein components
are all amino acids used to make proteins
- no, but they can have other important functions
types of rare amino acids
- post-translational
- created by modification of common amino acids after they are incorporated into a protein
- proteinogenic
- amino acids in final form as protein components
- ex: methionine with formyl group attached to amino group
weak acid equilibrium
o Each reaction has Ke q as a fixed equilibrium constant
o If the chemical environment changes, [H+], [A-] and [HA] will adjust to return to equilibrium under the new conditions to satisfy Keq
buffer regions
o within a certain pH range, small amount of acid or base can be added without major changes in pH
o exist 1 pH above and below pKa
o surrounds area where pH=pKa
buffers
o Mixture of weak acids and conjugate bases
o Prevent major changes in pH around a specific pH
Amino acids as weak acids
o Amino acids have at least 2 protons
o Multiple buffer regions (pK1 and pK2)
o Ex in pic: glycine
o At 1 equiv, all carboxyl H+ will dissociate
isoelectric point (pI)
o pH where there is no net charge
o will be the average of two pK values
o occurs at one equivalence of OH
o ex: glycine – pI is where all carboxy groups have been deprotonated but amino groups have their proton
o pH higher that PI – aa has neg charge
o pH lower than PI – aa has pos charge
Titrations for amino acids with ionizable R group
o PI Average the pK values surrounding the molecule with net charge = 0
o Ex: PI is the average of pK1 and pKr
