Amino acids

Question 1

Draw the general structure of an amino acid

Answer 1

• NH2 on the left side
• COOH on the right side
• R group (side group) coming from the joining carbon group

Question 2

Dissociation constant and pKa

Answer 2

• Higher the Ka and lower the pKa, the stronger the acid
• The lower the Ka and higher the pKa, the weaker the acid
• pKa tells you the pH at which the molecule is 50% deprotonated (at this point the pKa = pH)
• When the pH is lower than the pKa it will be protonated, when the pH is higher than the pKa it will be deprotonated

Question 3

Amino acid stereochemistry

Answer 3

• All alpha-amino acids are chiral apart from glycine, they can exist as one of two enantiomers which are mirror images of each other
• Chiral = 4 different groups attached to a single carbon atom
• Natural state is usually an S designation (arrow to the left, anticlockwise) there is also R designation for clockwise
• L-amino acids = rotate plane polarised light to the left (natural state for most amino acids)
• D-amino acids = rotate plane polarised light to the right

Question 4

Naming enantiomers

Answer 4

1. Give a number to each of the groups, and number them according to the mass of the atom that is attached to the carbon, from heaviest to lightest
2. Arrange the molecule so that the smallest one is facing away from you (multiple lined line)
3. If the first atom is the same look at the next bonded atom
4. R designation if it goes clockwise and S for anticlockwise

Question 5

Side chains non-polar (alkyl)

Answer 5

• Alanine (Ala, A), Valine (Val, V), Leucine (Leu, L) and Isoleucine (Ile, I)
• CH2 or CH3
• Don’t react well with water which is why they are hydrophobic
• Get more hydrophobic from A to I because the carbon chain gets bigger

Question 6

Side chain non-polar

Answer 6

• Methionine (Met, M), Phenylalanine (Phe, F), Tryptophan (Trp, w) and Tyrosine (Tyr, Y)
• OH is a weak acid so the polarity is very small so still counts as non-polar
• Sulphur has the same electronegativity as carbon so Methionine is still non-polar

Question 7

Side chains polar

Answer 7

• Serine (Ser, S), Threonine (Thr, T), Asparagine (Asn, N) and Glutamine (Gln, Q)
• Engage in hydrogen bonding very easily
• Either have HBD or HBA

Question 8

Side chain charged

Answer 8

• Aspartic acid (Asp, D), Glutamic acid (Glu, E), Arginine (Arg, R), Histidine (His, H) and Lysine (Lys, K)
• A lot more polar because they are charged

Question 9

Isoelectric point (pl)

Answer 9

• The pH at which the amino acid exists largely in an overall neutral, Zwitterionic form
• Zwitterionic form is when the molecule has a double ion, both positive and negative charges
• Amino acids are amphoteric and can react as either an acid or a base
• To work out the pl for neutral amino acids you work out the average of the two pKa values
• To work out the pI for acidic amino acids you work out the average of the lower two pKa values
• To work out the pI for basic amino acids you work out the average of the two higher pKa values