3. Amino Acids and Peptides
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52 Terms
What are amino acids?
The monomers that make up proteins.
How many common amino acids are found in proteins?
20.
What is the basic structure of an amino acid?
An alpha carbon bonded to an amino group, carboxyl group, hydrogen, and side chain (R group).
Why are most amino acids chiral?
The alpha carbon is bonded to four different groups.
Which amino acid is not chiral?
Glycine.
What determines the identity of an amino acid?
The side chain (R group).
What is a zwitterion?
A molecule with both positive and negative charges.
What form do amino acids exist in at physiological pH?
Zwitterionic form.
Why are zwitterions water-soluble?
They contain charged groups that interact with water.
What are the four major classes of amino acids?
Nonpolar, polar uncharged, acidic, and basic.
Which amino acids are nonpolar (hydrophobic)?
Ala, Val, Leu, Ile, Met, Phe, Trp, Pro.
Which amino acids are polar but uncharged?
Gly, Ser, Thr, Asn, Gln, Tyr, Cys, His.
Which amino acids are acidic at pH 7?
Aspartate and Glutamate.
Which amino acids are basic at pH 7?
Lysine and Arginine.
Why is histidine special?
Its pKa (~6.0) allows it to gain or lose protons near physiological pH.
What role does histidine often play in enzymes?
Proton transfer and catalysis.
What does amphipathic mean when describing amino acids?
Having both hydrophobic and hydrophilic properties.
Where are hydrophobic amino acids usually found in proteins?
Buried in the protein interior.
What are essential amino acids?
Amino acids that humans cannot synthesize.
Which amino acids are essential?
His, Ile, Leu, Lys, Met, Phe, Thr, Trp, Val.
What does L-configuration mean?
The stereochemistry of amino acids found in proteins.
Are proteins made of L- or D-amino acids?
L-amino acids.
What is a peptide bond?
An amide bond linking amino acids.
How is a peptide bond formed?
By condensation between the carboxyl group of one amino acid and the amino group of another.
What molecule is released during peptide bond formation?
Water.
Why does peptide bond formation require energy?
The reaction is not thermodynamically favorable.
What type of bond is a peptide bond?
Covalent amide bond.
What gives the peptide bond partial double-bond character?
Resonance between the C=O and C–N bonds.
What is a consequence of peptide bond resonance?
Restricted rotation around the peptide bond.
What is the amide plane?
The six coplanar atoms involved in the peptide bond.
Which bonds allow rotation in a polypeptide backbone?
The N–Cα (phi) and Cα–C (psi) bonds.
What is the N-terminus of a peptide?
The end with a free amino group.
What is the C-terminus of a peptide?
The end with a free carboxyl group.
What is the directionality of protein sequences?
N-terminus to C-terminus.
What is a dipeptide?
Two amino acids linked by one peptide bond.
What is a tripeptide?
Three amino acids linked by peptide bonds.
What is an oligopeptide?
A short peptide of up to ~20 amino acids.
What is a polypeptide?
A long chain of amino acids.
When is a polypeptide considered a protein?
When it folds into a functional structure.
What is the isoelectric point (pI)?
The pH at which a molecule has no net charge.
What happens to amino acids at pH < pI?
They have a net positive charge.
What happens to amino acids at pH > pI?
They have a net negative charge.
How is pI calculated for amino acids without ionizable side chains?
pI = (pKa₁ + pKa₂)/2.
Which amino acids have ionizable side chains?
Asp, Glu, His, Cys, Tyr, Lys, Arg.
Why can pKa values shift in proteins?
The local microenvironment alters ionization.
What is a disulfide bond?
A covalent bond between two cysteine residues.
Why are disulfide bonds important?
They stabilize protein structure.
Which amino acids absorb UV light?
Phenylalanine, tyrosine, and tryptophan.
Which amino acid contributes most to protein UV absorbance?
Tryptophan.
What reaction is used to detect amino acids?
Ninhydrin reaction.
What color is produced in the ninhydrin reaction?
Purple (Ruhemann’s purple).
Which amino acid does not react strongly with ninhydrin?
Proline.
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