Chapter 1: Amino Acids, Peptides, and Proteins

Question 1

What are the four groups attached to the central (Alpha) carbon of a proteinogenic amino acid.

Answer 1

1. Amino Group (-NH₂)
2. A Carboxylic Acid Group (-COOH)
3. Hydrogen atom
4. An R group (Side Chain)

Question 2

What is the stereochemistry of the chiral amino acid that appears in eukaryotic proteins?

• L or D?
• (R) or (S)? (Exception:)_____

Answer 2

• All chiral eukaryotic amino acids are L
• All chiral eukaryotic amino acids are (S), with the exception of cysteine (because cysteine is the only amino acid with an R group that has a higher priority than a carboxylic acid according to Cahn-Ingold-Prelog rules)

Question 3

Amino Acids

Nonpolar, nonaromatic

There are seven of them

Answer 3

1. Glycine
2. Alanine
3. Valine
4. Leucine
5. Isoleucine
6. Methionine
7. Proline

Question 4

Amino Acids

Aromatic

There are three of them

Answer 4

1. Tryptophan
2. Phenylalanine
3. Tyrosine

Question 5

Amino Acids

Polar

There are five of them

Answer 5

1. Serine
2. Threonine
3. Asparagine
4. Glutamine
5. Cysteine

Question 6

Amino Acids

Negatively Charged/Acidic

There are two of them

Answer 6

1. Asparagine
2. Glutamate

Question 7

Amino Acids

Positively Charged/Basic

There are three of them

Answer 7

1. Lysine
2. Arginine
3. Histidine

Question 8

Where do hydrophobic amino acids tend to reside with a protein? What about hydrophillic ones?

Answer 8

• Hydrophobic
  
  • Tend to reside in the interior of a protein, away from water
• Hydrophilic
  
  • Tend to remain on the surface if the protein, in cotact with water

Question 9

Except for ___, all amino acids are chiral.

Except for ____, all amino acids have an (S) absolute configuration.

Answer 9

Glycine

Cysteine

Question 10

Describe the mechanism for trypsin and chymotrypsin.

Answer 10

They break apart the amide bond by adding a hydrogenatom to the amide nitrogen and an OH group to the carbonyl carbon.

Question 11

Describe the mechanism of a peptide bond formation

Answer 11

1. The electrophilic carbonyl carbon on the first amino acid is attacked by the nucleophile amino group on the second amino acid.
2. The hydrocy group of the carboxylic acid is kicked off.
3. Amid Peptide Bond formation.

Question 12

What is the difference between an amino a cid, a dipeptide, a tripeptide, an oligopeptide, and a polypeptide?

Answer 12

These species differ by the number of amino acids that make them up:

• Amino Acid = 1
• Dipeptide = 2
• Tripeptide = 3
  
  • Oligopeptide = Few ( Less than 20)
  • Poplypeptide = Many (more than 20)

Question 13

What molecule is released during formation of a peptide bond?

Answer 13

Water

Question 14

Answer 14

Question 15

The primary structure of a protein is the order of its amino acids. The two main secindary structures are the ____ and _____, which both result from ______.

Answer 15

Alpha-Helix

Beta Pleated Sheet

Hydrogen Bonding

Question 16

Answer 16

Question 17

What role does proline serve in secondary structure?

Answer 17

Prolines rigid structure causes it to introduce kinks in alpha-helices or create turns in Beta pleated sheets

Question 18

Which structure is this and describe its features.

Answer 18

• Alpha-Helix
  
  • A rod like structure in which the peptide chain coils clockwise around a central axis.

Question 19

Which structure is this and describe its features.

Answer 19

The peptide chains lie alongside one another, forming rows or strands held together by intramolecular hydrogen bons between carbonyl oxygen atoms on one chain and amide hydrogen atoms in an adjacent chain.

Question 20

How is a tertiarty structure made?

Answer 20

By moving hydrophobic amino acid side chains into the interior of the protein.

Question 21

Answer 21

Question 22

What is the primary motivation for hydrophobic residues in polypeptide to move to the interior of the protein?

Answer 22

Increases the intropy by allowing water molecules on the surface of the protein to have more possible positions and configurations, The positive Delta S makes Delta G < 0, stabilizing the protein.

Question 23

List the three different prosthetic groups that an be attached to a protein and name the conjugated protein.

Answer 23

1. Lipids
2. Carbohydrates
3. Nucleic Acids
4. They are known as lipoproteins, glycoproteins, and nucleoproteines.

Question 24

What are the two main ways proteins are denatured?

Answer 24

1. Heat
2. Solutes
   
   1. Urea as such