Proteins I

Question 1

Name the 3 aromatic side chain Amino Acids as well as their 3 letter/ 1 letter abbreviations.

Answer 1

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

Question 2

Which amino acid chemical configuration is associated with clockwise rotation?

Answer 2

L-configuration

Question 3

Which of the amino acids are optically active? What is required for optical activity?

Answer 3

All but Glycine (Gly, G) because it doesnt have at least one asymmetric carbon

Question 4

Which amino acids contain an imino group?

Answer 4

Only proline

Question 5

Vanderwaals forces are weak charges between _____ but ____ groups. (They have both attractive and repulsive terms.)

Answer 5

Uncharged but Polarizable groups

Question 6

Oppositely charged species are involved in ______ interactions and form a ______ between residues of opposite charge.

Answer 6

• Ionic

- salt-bridge

Question 7

List the 6 processes non-covalent bonding forces are important for

Answer 7

1- Protein Folding
2- Protein-Protein Interactions
3- DNA Structure formation
4- Protein-DNA interactions
5- Enzyme Substrate Interactions
6- Drug Interactions with a target protein

Question 8

_______ polymers do not have the rigidity to fold into unique 3D structures.

Answer 8

Random Coil polymers

Question 9

List the nonpolar, aliphatic amino acids and their 3 letter/1 letter abbreviations.

Answer 9

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

Question 10

Name the polar, uncharged Amino acids and their 3 letter/1 letter abbreviations.

Answer 10

• Serine (Ser, S)
• Threonine (Thr, T)
• Cysteine (Cys, C)
• Asparagine (Asn, N)
• Glutamine (Gln, G)

Question 11

Name the positively charged Amino Acids as well as their 3 letter/ 1 letter abbreviations

Answer 11

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

Question 12

Name the negatively charged amino acids as well as their 3 letter/ 1 letter abbreviations.

Answer 12

• Glutamate (Glu, E)

- Aspartate (Asp, D)

Question 13

The ____ is the pH at which an amino acid has a charge of zero.

Answer 13

pI OR isoelectric point

Question 14

Peptide bonds form between two amino acids with the elimination of 1 ______ per bond. Is this reaction spontaneous or non-spontaneous in vitro?

Answer 14

• H20 molecule

- Non-spontaneous

Question 15

Hydrogen bonding occurs due to the high _____ of the H-X bond. What are its characteristics compared to a covalent bond?

Answer 15

• Polarity

- longer/weaker

Question 16

Which type of bonding is most important for the structure and function of proteins in a DNA double helix?

Answer 16

Hydrogen Bonding

Question 17

Where is rotation possible within a peptide bond? This allows for several different conformations.

Answer 17

At bonds flanking the alpha-Carbon

Question 18

What angles determine the path of the polypeptide chain in 3D space?

Answer 18

Pi and Phi angles

Question 19

Due to _________, poly-peptide chains are flexible but conformationally restricted.

Answer 19

Partial double bond character

Question 20

Most amino acid residues adopt a(n) ______ configuration except which?

Answer 20

• trans

- Proline (cis)

Question 21

Peptide bonds can be broke by heating in the presence of __N of HCl @ ___ celsius for ____ hours.

Answer 21

• 6N
• 110 degrees C
• 18

Question 22

The hydrophobic effect drives the folding of _________ and promotes _________.

Answer 22

• Globular proteins

- Intermolecular interactions

Question 23

The hydrophobic effect is an indirect effect of the high polarity of water. This causes entropy to _______ when non-polar molecules are dispersed.

Answer 23

Decrease

Question 24

What determines the optimal Vanderwaals contact distance? What is this contact distance referred to as?

Answer 24

• The balance between attractive and repulsive forces

- Vanderwaals radius