Exam 1 Lecture 4 Amino Acids and Peptides |
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Amino Acids and Peptides
Major concepts:
1. What is the basic structure of an amino acid, and how are amino acids classified?
2. What determines the net charge of an amino acid in solution?
3. How are amino acids bonded together to form peptides, and what type of bond is a peptide bond?
Core knowledge:
1. What are the structures, 3-letter abbreviations, and 1-letter abbreviations of the 20 amino acids commonly found in proteins?
2. How do you calculate the pI of an amino acid or a peptide, given the relevant pKa's?
Basic amino acid structure
A. α-carbon bonded to an α-amine and an α-carboxyl = the constant structure
B. side chain, which determines the amino acid character
C. For all amino acids but glycine, the α-carbon is chiral.
Naturally occurring amino acids are all L-amino acids.
CORN = clockwise around the α-carbon starting with the carboxyl (CO) → R → N.
D. At neutral pH, amino acids have two or more charges: α-COO- and α-NH3+
E. All amino acids have 3-letter and 1-letter abbreviations.
Nonpolar amino acids
Glycine (Gly, G): side chain = H. Least hydrophobic
Alanine (Ala, A): side chain = methyl
Valine (Val, V): simplest branched side chain
Leucine (Leu, L): one carbon more than valine before branching
Isoleucine (Ile, I): the only possible isomer for leucine
Methionine (Met, M): contains a sulfur but is not polar
Proline (Pro, P): an imino acid, because its side chain is bonded to its α-amine; rigid
Aromatic amino acids
Phenylalanine (Phe, F): alanine + a phenyl group
Tyrosine (Tyr, Y): phenylalanine + –OH
Tryptophan (Trp; W) includes an indole ring
Polar uncharged amino acids
Serine (Ser, S): alanine + –OH
Threonine (Thr, T): serine + a methyl group
Cysteine (Cys, C): alanine + –SH; two side chains can be oxidized to form - S - S -
Asparagine (Asn, N): alanine + an amide group
Glutamine (Gln, Q): like asparagine but with one more C in its side chain
Negatively charged amino acids
Aspartate (Asp, D): alanine + –COO-; (aspartic acid has –COOH)
Glutamate (Glu, E): like aspartate but with one more C.
Note that asparagine is the amide form of aspartate, and glutamine is the amide form of glutamate.
Positively charged amino acids
Histidine (His, H): alanine + an imidazole group;
important because the side chain pKa = 6.0
Lysine (Lys, K): four carbon chain + an amine
Arginine (Arg, R): three carbon chain + a guanidino group
These are the twenty amino acids used for protein synthesis. Others that are important:
A. formed by modification of these amino acids after protein synthesis
B. occur during metabolism
Titration curves and pI for amino acids
A. Amino acids are polyprotic acids, with at least two pKa's
B. Having adjacent ionizable groups influences pKa's
C. pI = the isoelectric point, when the amino acid has no net charge
This is the middle of the range in which the amino acid has no net charge.
For uncharged amino acids, the pI = the average of pKa1 (α-carboxyl) and pKa2 (α-amine).
For charged amino acids, the pI is the average of the two pKa's that bracket the pH range
for which the amino acid has no net charge.