Chapter 3: Amino Acids, Peptides, and Proteins Flashcards
What are proteins?
Linear macromolecular polymers (polypeptides) formed from amino acid monomers.
What are the connections between amino acids called?
Amide linkages -> peptide bonds
What are proteins synthesized by?
Ribosomes: large nucleoprotein particles which translate information from mRNA (nucleotide sequence) into protein (amino acid sequence).
What α-amino acids?
When the carboxylic acid and the amino group are attached to the α-carbon.
Are amino acids in proteins L-amino acids or D-amino acids?
L-amino acids.
What are the 7 nonpolar, aliphatic amino acids?
Glycine (Gly, G), Alanine (Ala, A), Valine (Val, V), Leucine (Leu, L), Isoleucine (Ile, I), Methionine (Met, M), and Proline (Pro, P).
What are the 3 aromatic amino acids?
Phenylalanine (Phe, F), Tyrosine (Tyr, Y), and Tryptophan (Trp, W).
What are the five polar, uncharged amino acids?
Serine (Ser, S), Threonine (Thr, T), Cysteine (Cys, C), Asparagine (Asn, N), and Glutamine (Gln, Q).
What are the 2 negatively charged (at pH=7) amino acids?
Aspartic Acid (Asp, D) or Aspartate, and Glutamic Acid (Glu, E) or Glutamate.
What are the 3 positively charged (at pH=7) amino acids?
Lysine (Lys, K), Arginine (Arg, R), and Histidine (His, H).
What form do we find amino acids in at physiological pH?
Zwitterionic form.
Define zwitterion.
A molecule that contains both a positive and a negative charge.
- For the zwitterion amino acid, the negative charge comes from the carboxylate ion while the positive charge comes from the ammonium ion.
- The zwitterionic form is amphoteric (can act as an acid or a base).
What is the isoelectric point (pI)?
The midpoint of a titration; when there is a net charge of zero on the amino acid.
How do you calculate the isoelectric point?
pI = (pK1 + pK2) / 2
For those with more than two pKa values, you’ll take the two pKa values on either side of the point where the molecule has a net charge of zero.
What are amino acids linked by?
Peptide bonds
What kind of reaction is peptide bond formation? What about peptide bond cleavage?
Formation: Condensation reaction (H2O lost)
Cleavage: Hydrolysis reaction (H2O added as nucleophile)
What are amino acids that are linked together by peptide bonds called?
Amino acid residues, or residues
What is a protein?
A genetically encoded functional biological macromolecule consisting of one or more polypeptide chains (polypeptide consists of more than 10 amino acids).
- Contains 50-30,000 amino acid residues.
What is the primary protein structure?
The covalent linkage of the polypeptide chain (sequence of amino acids).
What is the secondary protein structure?
The specific local stable conformation involving noncovalent interactions (usually H-bonds) between amino acid residues close together in sequence.
What is tertiary protein structure?
The 3D structure formed as secondary structural units pack together (“fold”)
- If the protein is only one polypeptide chain, this is the last level the protein will reach.
What is quaternary protein structure?
The association of multiple polypeptide chains (monomers, protomers, subunits) by noncovalent interactions (and occasionally disulfide linkages).
What are glycoproteins?
Proteins with oligosaccharides attached via a glycosidic linkage to Ser/Thr or Asn side chains.
What does acid hydrolysis do to proteins?
Cleaves all peptide bonds, allowing determination of amino acid composition but not sequence.
What is the Edman Degradation?
The Edman Degradation derivatizes and selectively cleaves the N-terminal amino acid, allowing the protein to be sequenced stepwise by removal and identification of residues one at a time from the N-terminus.
What are proteases?
They are enzymes which hydrolyze peptide bonds at precise and specific locations.
