Lecture 2: Amino Acids

Question 1

Basic Amino Acid formula… GO!

Answer 1

+H3N – C –COO- (Carbon has H, and R group)

Question 2

At physiological pH (7.4), what is the form for amino acids?

Answer 2

Zwitterion (amino pronated, carboxyl group depronated)

Question 3

Amino Acid: pH < pKa, group will be pronated, depronated, or mixture?

Answer 3

R-group will be pronated

Hint: Low pH = lots of H+ to go around, molecule wins and takes extra protons

Question 4

Amino Acid: pH > pKa, group will be pronated, depronated, or mixture?

Answer 4

R-group will be depronated

Hint: High pH = low H+ to go around, solution wins and takes protons

Question 5

Amino Acid: pH ~ pKa, group will be pronated, depronated, or mixture?

Answer 5

R-group will be mixture of two forms

Question 6

How do you calculate pI?

What if there are more than 2 pKa’s?

Answer 6

pI = 1/2 (pKa1 + pKa2)

Find isoionic species, use flanking pKa’s… aka find neutral species based on pH and pKa, go left and right–average pKa’s. Do NOT average all pKa’s!

Question 7

What are aliphatic amino acids?

Answer 7

Glycine (Gly), Alanine (Ala), Leucine (Leu), Isoleucine (ile), Valine (Val)

MNEUMONIC: VIGAL

Question 8

What are hydroxyl and sulfur containing amino acids?

Answer 8

Serine (Ser), Threonine (Thr), Tyrosine (Tyr), Methionine (Met), Cysteine (Cys), Selenocysteine (Set)*

Question 9

What are the acidic amino acids?

Answer 9

Aspartic Acid (Asp), Asparagine (Asn), Glutamic Acid (Glu), Glutamine (Gln)

Question 10

What are the basic amino acids?

Answer 10

Arginine (Arg), Lysine (Lys), Histidine (His)

Question 11

What are the aromatic amino acids?

Answer 11

Phenylalanine (Phe), Tyrosine (Tyr), Tryptophan (Trp)

Question 12

What is the only imino acid?

Answer 12

Proline (Pro)

Question 13

What amino acids can be used by UV-vis to determine protein concentration? Why? What region do they usually absorb in?

Answer 13

Tyr, Trp BEST, Phe OK

Aromatic R-groups absorb light in the UV region

275 - 280 nm

Question 14

How are extra functional groups added to amino acids?

Answer 14

Post-translation modification

Question 15

What are the hydrophic (non-polar) amino acids?

Answer 15

Glycine, Alanine, Leucine, Isoleucine, Valine

Phenylalanine, Tyrosine, Tryptophan, Histidine

Question 16

What are the hydrophilic (polar) amino acids?

Answer 16

Asparagine, Glutamine, Proline

Serine, Threonine, Tyrosine

Arginine, Lysine, Aspartic Acid, Glutamic Acid, Histidine

Methionine, Cysteine, Selenocysteine

Question 17

What type of Amino Acids cluster on interior of soluble proteins?

Answer 17

Non-polar (hydrophobic)

Question 18

What type of Amino Acids cluster on surface of soluble proteins?

Answer 18

Polar (hydrophilic)

Question 19

What type of Amino Acids cluster on the surface of membrane proteins?

Answer 19

Non-polar (hydrophobic)

Question 20

All human biological amino acids, except glycine, are what configuration?

Answer 20

L-configuration

Question 21

Where are D-amino acids usually found? Use?

Answer 21

Bacteria, used in drugs

Question 22

How are amino acid residues connected?

Answer 22

Peptide bond via dehydration synthesis (condensation)

Hint: Loss of water molecule

Question 23

Does a peptide bond have much mobility?

Answer 23

No, pseudo double bond prevents rotation

Question 24

What configuration is the peptide bond usually? Why?

Answer 24

Trans, steric hindrance from R-groups

Question 25

What is the distance between adjacent alpha-Carbons in a peptide bond?

Answer 25

0.36 nm or 3.6 Angstroms

Question 26

How are peptides named?

Answer 26

Start at free amine (NH3+), use -yl endings, last keeps amino acid name

Question 27

What factors contribute to tertiary structure?

Answer 27

1. Disulfide Bonds
2. Ionic Bonds
3. Hydrogen Bonding
4. Van der Waals Forces
5. Hydrophobic interactions
6. Proline Kinking

Question 28

At physiological pH (7.4), which Amino Acids are negatively charged?

Answer 28

Aspartic Acid - Asp - D

Glutamic Acid - Glu - E

Question 29

At physiological pH (7.4), which Amino Acids are positively charged?

Answer 29

Lysine - Lys - K
Arginine - Arg - R
Histidine - His - H