OBJ - Amino Acids in Proteins

Question 1

Draw the general structural plan of amino acid molecules and identify the α-carbon, the carboxylic carbon, the amino nitrogen and the position of the side chain

Answer 1

@ physiological pH COOH -> COO- NH2 -> NH3+ becomes zwitterion

Ionization state of SIDE CHAIN determines its chemical nature

how the protein will fold, bind & interact with its environment

Question 2

Classify amino acids based on the physicochemical properties of their side chains into nonpolar, aromatic, polar positively charged, polar negatively charged, and polar uncharged

Answer 2

Nonpolar Aliphatic (7 - VIMPGAL)

Nonpolar Ar (3 - PTT)

Polar Uncharged (5)

Polar Charged - Neg (2 - E,R)

Polar Charged - Pos (3 - HAL)

Question 3

Recognize the sulfur-containing amino acid side chains, and explain formation of disulfide bond between two cysteine residues

Answer 3

Methionine

Cysteine (R = S-H)

• Disulfide bond: oxidation of 2 Cysteine side chains -> 2 H+ & R-S-S-R
• weaker than C-C; vulnerable to Nu attach; weak link in a molecule -disulfide bonds shape tertiary structure of proteins in folding -disulfide bonds: prefer hydrophobic environment
• Cysteine residues = hydrophilic Makes a huge change in protein folding

Question 4

Recognize potential hydrogen bond donors and acceptors in amino acids side chains

Answer 4

anything with OH, NH

Tyrosine

Tryptophan

Serine

Threonine

Asparagine

Glutamine

Arginine

Lysine

Histadine

**Tyrosine, cysteine, serine, Histidine, Lysine, aspartate present in some enzyme active sites

** 2 OH groups that have pKa’s too hight (Serine/Threonine), but still can H bond

Question 5

List the amino acid side chains with dissociable groups, and identify their ionized and deionized states

Answer 5

AA with Ionizable Side Chains:

• **Tyrosine = OH
• **Cysteine = SH
• Polar Neg
  
  • Aspartate = COO-
  • Glutamate = COO-
• Polar +
  
  • Histidine = N=C
  • Arginine = C=NH2+
  • Lysine = NH3+ PIC

Question 6

Explain how the pKa of dissociation for a particular side chain dictates the ionization status of its dissociable group at a given pH

Answer 6

PIC

Question 7

**Peptide bond

Answer 7

Amide linkage; bond between COOH & Amide group with the loss of H2O picture

Question 8

**3 letter abbreviations for 20 Amino Acids

Answer 8

picture

Question 9

**Properties of side chains

Answer 9

• determines how the protein is going to be folded
• what molecule it will bind to how it will interact with its enviornment

Question 10

**Sickle Cell Anemia

Answer 10

-mutation of 1 AA in beta subunit of Hb causes proteins to aggregate with each other & RBC sickles -AA mutates from Polar Neg -> aliphatic

Question 11

**Osteogenesis Imperfecta (Type II)

Answer 11

-mutation of Gly-> Asparate @ any of 6 positions causes collagen deformation & perinatal lethality -AA mutates from Aliphatic -> Polar Neg changes/ruins the collagen triple helix -> why cartilage/bone matrix, tendons, cornea can’t form

Question 12

**Testicular feminization

Answer 12

substitute 1 AA at either of 2 positions -> Angrogen Receptor (AR) protein

AR have 2 DNA binding Zinc fingers, but mutation can’t coordinate with Zinc -> unable to interact with DNA preventing transcription activation of many genes

• males develop female secondary sexual characterisitics
• AA mutates from Sulfur containing/disulfide forming Polar uncharged -> Ar