WEEK 1

Question 1

What are the 20 essential amino acids ? (list if they are non-polar, polar, + charged or - charged)

Answer 1

Non-polar:
Glycine
Alanine
Valine
Phenylalanine
Leucine
Isoleucine
Tryptophan
Cysteine
Proline
Methionine

Polar:
Serine
Threonine
Tyrosine
Asparagine
Glutamine

Acidic:
Aspartic Acid
Glutamic Acid

Basic:
Lysine
Histidine
Arginine

Question 2

What is pI?

Answer 2

Isoelectric point. It is the point at which an amino acid is electrically neutral.

Question 3

Describe the concept of acid-base chemistry (pH of solution to the pKa of the amino acid chain)

Answer 3

If the pH of the solution is less than the pKa of a functional group or side chain, then it will be PROTONATED.
If the pH of the solution is greater than the pKa of a functional group or side chain, then it will be DEPROTONATED

Question 4

What is the pKa of the amino and carboxyl group of an amino acid ?

Answer 4

pKa amino group: ~9-10
pKa carboxyl group: ~2

Question 5

What is a buffer ?

Answer 5

a solution that resists changes in pH when an acid or base is added

Question 6

What are peptides?

Answer 6

a chain of multiple amino acids connected to each other via a dehydration reaction

Question 7

What is a dehydration reaction? Describe its mechanism

Answer 7

a reaction that forms a bond while water is lost
mechanism: the carbon on the amino group nucleophilic attacks the carboxyl oxygen on the carboxyl group of the second amino acid forming a bond.

Question 8

Is there any rotation about a peptide bond?

Question 9

What are oligopeptides ?

Question 10

What is hydrolysis ?

Question 11

How do hydrolytic enzymes work ?

Question 12

What does the primary structure of a protein tell us ?

Question 13

How is the primary structure of a protein stabilized ?

Question 14

What are covalent bonds ?

Question 15

What does the secondary structure of an amino acid tell us?

Question 16

How is the secondary structure of a protein stabilized ?

Question 17

What are hydrogen bonds ?

Question 18

What are the most common secondary structures of a protein and how are they stabilized ?

Question 19

Describe the key structural differences between alpha helices and beta pleated sheets.

Question 20

What is the function of proline in the secondary structure of a protein?

Question 21

What does the tertiary structure of a protein tell us?

Question 22

How is the tertiary structure of a protein stabilized ?

Question 23

The 3D shape of a protein can be determined by ?

Question 24

What is the important component found in the tertiary structure of a protein ?

Question 25

What are disulfide bonds ? What reaction occurs during this process ?

Question 26

What intermediate forms as the protein “collapses” into its tertiary structure ?

Question 27

What process causes a protein to lose its function ?

Question 28

Why do hydrophobic residues occupy the inferior part of a protein, while hydrophilic residues tend to accumulate on the exterior portion ?

Question 29

What is a solvation layer ?

Question 30

What would ΔS be if a hydrophobic side chain is placed in an aqueous solution ?