Amino Acids & Proteins

Question 1

Glycine

Answer 1

• Gly, G.

* Only achiral AA.

Question 2

Alanine

Answer 2

• Ala, A.

Question 3

Valine

Answer 3

• Val, V.

Question 4

Leucine

Answer 4

• Leu, L.

Question 5

Isoleucine

Answer 5

• Ile, I.

Question 6

Methionine

Answer 6

• Met, M.

* Sulfur in Side Chain (M & C).

Question 7

Proline

Answer 7

• Pro, P.
• Only Cyclic AA.
• Often found in the turns between chains of b-pleated sheets and at the start of a-helices.

Question 8

Tryptophan

Answer 8

• Trp, W.

Question 9

Phenylalanine

Answer 9

• Phe, F.

Question 10

Tyrosine

Answer 10

• Tyr, Y.

Question 11

Serine

Answer 11

• Ser, S.

Question 12

Threonine

Answer 12

• Thr, T.

Question 13

Asparagine

Answer 13

• Asn, N.

Question 14

Glutamine

Answer 14

• Gln, Q.

Question 15

Cysteine

Answer 15

• Cys, C.
• Sulfur in Side Chain (M & C).
• Only (R) Absolute Configuration.

Question 16

Aspartic Acid (Aspartate)

Answer 16

• Asp, D.

Question 17

Glutamic Acid (Glutamate)

Answer 17

• Glu, E.

Question 18

Arginine

Answer 18

• Arg, R.

Question 19

Lysine

Answer 19

• Lys, K.

Question 20

Histidine

Answer 20

• His, H.

Question 21

Nonpolar, Nonaromatic Side Chains

Answer 21

• G, A, V, L, I, M, P.

Question 22

Aromatic Side Chains

Answer 22

• W, Y, F.

Question 23

Polar Side Chains

Answer 23

• C, Q, N, T, S.

Question 24

Charged Side Chains

Answer 24

• H, E, R, D, K.

Question 25

Hydrophobic & Hydrophilic AAs

Answer 25

• Hydrophobic: A, L, I, V, F.

* Hydrophilic: H, E, R, D, K + Q, N

Question 26

If pH < pKa (or at low pH), a majority of the amino acid species will be ___. If pH > pKa (or at high pH), a majority of the amino acid species will be ___.

Answer 26

Protonated; Deprotonated.

Question 27

Peptide Bonds

Answer 27

• Are amide bonds [-C(O)NH-].
• Have delocalized pi electrons that produce resonance (partial double bond character) and restrict rotation around C-N bond.
• Form via condensation/dehydration reactions (acyl substitution reaction).

Question 28

Primary Structure of Proteins

Answer 28

• Linear arrangement of amino acids.

* Stabilized by covalent peptide bonds.

Question 29

Secondary Structure of Proteins

Answer 29

• Local structure of neighboring amino acids.
• a-helices & b-pleated sheets.
• Stabilized by intramolecular hydrogen bonds between backbone carbonyl oxygens and amide hydrogens.

Question 30

Tertiary Structure of Proteins

Answer 30

• Three-dimensional shape of protein.
• Stabilized by hydrophilic and hydrophobic interactions between R groups; hydrophobic residues in the interior and hydrophilic residues (polar/charged) on the exterior.
• Further stabilized by hydrogen bonds, salt bridge (acid-base) interactions between charged R groups, and disulfide bonds that create loops (2 cysteine are oxidized to form cystine).

Question 31

Quaternary Structure of Proteins

Answer 31

• Aggregate of more than one polypeptide subunit, representing the functional form of protein.
• Stabilized by hydrogen bonds and London dispersion forces.

Question 32

Denaturation

Answer 32

• Unfolding of protein that stops catalytic activity and is often irreversible.
• Caused by heat (disrupts hydrophobic interactions), solutes such as urea (disrupts tertiary structure), and detergents such as SDS (disrupts noncovalent bonds).

Question 33

Conjugated Proteins

Answer 33

• Proteins with covalently attached molecules called prosthetic groups.
• Can be metal ion, vitamin, lipid, carbohydrate, or nucleic acid.

Question 34

Define amphoteric species

Answer 34

• Species that can function as an acid or base (can either except a proton or donate a proton).
• Example: Carboxylic acid group of an amino acid can donate a proton and amino group of an amino acid can accept a proton.