Chapter 4 Lecture

Question 1

Proteins are composed of ______

Answer 1

amino acids

Question 2

Amino acid

Answer 2

Question 3

How many amino acids are there and how do you tell them apart?

Answer 3

20 amino acids

Each has a 3-letter and 1-letter abbreviation

alanine = Ala = A

Question 4

Basic amino acids, what are they and how do they differ from others?

Answer 4

Basic amino acids are polar and positively charged

Lysine (Lys, or K)

Arginine (Arg, or R)

Histidine (His, or H)

Question 5

Acidic amino acids, what are they and how do they differ from others?

Answer 5

Acidic amino acids are polar and negatively charged.

Aspartic acid (Asp, or D)

Glutamic acid (Glu, or E)

Question 6

Are aromatic amino acids polar or non-polar?

Answer 6

Aromatic amino acids (tyr, trp, phe) are relatively nonpolar

Question 7

Which is the only aromatic amino acid with an ionizable side chain?

Answer 7

Tyrosine is the only one of the aromatic amino acids with an ionizable side chain.

Question 8

Polar side chains can participate in what kind of binding?

Answer 8

H-bonding and electrostatic interactions if ionized

Question 9

Are non-polar side chains hydrophilic or hydrophobic?

Answer 9

hydrophobic

Question 10

Where do you expect to find non-polar side chains in the final folded protein?

Answer 10

On the inside

Question 11

Diversity amongst non-polar side chains

Answer 11

• Hydrophobicity increases with increasing number of C atoms in the hydrocarbon chain.
• Although these amino acids prefer to remain inside protein molecules, alanine and glycine are ambivalent, meaning that they can be inside or outside the protein molecule.
• Glycine has such a small side chain that it does not have much effect on the hydrophobic interactions.

Question 12

What’s special about cysteine side chains?

Answer 12

• Can form disulfide bonds (covalent bonds)
• Can be used to join two cysteines in the same or different polypeptides

•Stabilize the favored conformation of a protein
“atomic staple”

• Often used in proteins exported from cells
• Disulfide bonds form in the ER

Question 13

Where are disulfide bonds formed?

Answer 13

ER’s oxidizing environment – allows S-S bonds to form (as hydride ion is lost from cysteine’s R-group)

S-S bonds don’t generally form in cytosol due to the high concentration of reducing agents

Question 14

Why are disulfide bonds critical to antibodies?

Answer 14

Without disulfide bonds antibodies would be useless: they are critical to maintaining the proper structure for antigen binding

Question 15

Peptide bond formation

Answer 15

Question 16

Hydrophobic/Hydrophilic Interactions of side chains

Answer 16

Question 17

How different types of non-covalent bonds help proteins fold (picture)

Answer 17