Chapter 3: Amino Acids, Peptides, and Proteins

Question 1

What are proteins?

Answer 1

Linear macromolecular polymers (polypeptides) formed from amino acid monomers.

Question 2

What are the connections between amino acids called?

Answer 2

Amide linkages -> peptide bonds

Question 3

What are proteins synthesized by?

Answer 3

Ribosomes: large nucleoprotein particles which translate information from mRNA (nucleotide sequence) into protein (amino acid sequence).

Question 4

What α-amino acids?

Answer 4

When the carboxylic acid and the amino group are attached to the α-carbon.

Question 5

Are amino acids in proteins L-amino acids or D-amino acids?

Answer 5

L-amino acids.

Question 6

What are the 7 nonpolar, aliphatic amino acids?

Answer 6

Glycine (Gly, G), Alanine (Ala, A), Valine (Val, V), Leucine (Leu, L), Isoleucine (Ile, I), Methionine (Met, M), and Proline (Pro, P).

Question 7

What are the 3 aromatic amino acids?

Answer 7

Phenylalanine (Phe, F), Tyrosine (Tyr, Y), and Tryptophan (Trp, W).

Question 8

What are the five polar, uncharged amino acids?

Answer 8

Serine (Ser, S), Threonine (Thr, T), Cysteine (Cys, C), Asparagine (Asn, N), and Glutamine (Gln, Q).

Question 9

What are the 2 negatively charged (at pH=7) amino acids?

Answer 9

Aspartic Acid (Asp, D) or Aspartate, and Glutamic Acid (Glu, E) or Glutamate.

Question 10

What are the 3 positively charged (at pH=7) amino acids?

Answer 10

Lysine (Lys, K), Arginine (Arg, R), and Histidine (His, H).

Question 11

What form do we find amino acids in at physiological pH?

Answer 11

Zwitterionic form.

Question 12

Define zwitterion.

Answer 12

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).

Question 13

What is the isoelectric point (pI)?

Answer 13

The midpoint of a titration; when there is a net charge of zero on the amino acid.

Question 14

How do you calculate the isoelectric point?

Answer 14

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.

Question 15

What are amino acids linked by?

Answer 15

Peptide bonds

Question 16

What kind of reaction is peptide bond formation? What about peptide bond cleavage?

Answer 16

Formation: Condensation reaction (H2O lost)
Cleavage: Hydrolysis reaction (H2O added as nucleophile)

Question 17

What are amino acids that are linked together by peptide bonds called?

Answer 17

Amino acid residues, or residues

Question 18

What is a protein?

Answer 18

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.

Question 19

What is the primary protein structure?

Answer 19

The covalent linkage of the polypeptide chain (sequence of amino acids).

Question 20

What is the secondary protein structure?

Answer 20

The specific local stable conformation involving noncovalent interactions (usually H-bonds) between amino acid residues close together in sequence.

Question 21

What is tertiary protein structure?

Answer 21

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.

Question 22

What is quaternary protein structure?

Answer 22

The association of multiple polypeptide chains (monomers, protomers, subunits) by noncovalent interactions (and occasionally disulfide linkages).

Question 23

What are glycoproteins?

Answer 23

Proteins with oligosaccharides attached via a glycosidic linkage to Ser/Thr or Asn side chains.

Question 24

What does acid hydrolysis do to proteins?

Answer 24

Cleaves all peptide bonds, allowing determination of amino acid composition but not sequence.

Question 25

What is the Edman Degradation?

Answer 25

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.

Question 26

What are proteases?

Answer 26

They are enzymes which hydrolyze peptide bonds at precise and specific locations.