2. P. Amino Acids

Question 1

AAs

Answer 1

Basic building blocks of proteins
Precursors of many biomolecules
> 300 described in nature
Only 20 are commonly found in proteins
Most AA’s are asymmetric except glycine (H in R group)

chiral C alpha w 4 gps attached
carboxyl (COOH), amino (NH2), H, R (side chain)

In amino acids with asymmetric α carbon, two stereospecific configurations are possible (mirror images=nonsuperimposable)

• Project polarized light on mixtures, light gets rotated
• Capacity to rotate light=optical activity/optical rotation

All amino acids that occur in proteins (in human bodies, plants, animals) are L isomers (enantiomer that rotates plane polarized light CCW (-))
Bacteria-D isomers (enantiomer that rotates plane polarized light clockwise (+))

Question 2

Classification of amino acids

Answer 2

(pic of AAs)
Based on the chemical nature of the  side chain R group
Hydrophobic (nonpolar)
-Aliphatic
-Aromatic
-Imino

Hydrophilic (polar)

• Uncharged
• Charged
• -Acidic
• -Basic

notes-
Hydrocarbonswhich do not contain a benzenering are called aliphatic hydrocarbons.
They cannot H-bond with water and these side chains have a characteristic hydrophobic effect in water.
Polarity is defined as the magnitude of the dipole induced in the presence of external electromagnetic field.

Question 3

Hydrophobic/Aliphatic AAs

Answer 3

GAVLI, CM
Gly, Ala, Val, Leu, Ile, Cys, Met

*just rmbr 3-letter names*
Groups:
-CH3=methyl
-CH2-SH=thiol
Valine-ethyl
Leucine-isobutyl
Isoleucine-butyl
Methionine-thioether

Question 4

Hydrophobic/Aromatic AAs

Answer 4

FYW
Phe, Tyr, Trp

Phe-phenyl on alanine, hydrophobic bc no active gps on phenyl (ring) to react w water
Though Tyr has a polar hydroxyl group that can form hydrogen bonds, it is mainly hydrophobic
The indole nitrogen (to methylene) of Trp does not form hydrogen bonds

Question 5

Hydrophobic/cyclic α-imino acid

Answer 5

Pro (P) markedly influences protein structure because its ring structure makes it more conformationally restricted
Often found in the bends of folded protein chains
Alpha gp is secondary to primary gp
-Side chain bonded to N and alpha-C
-Normally, N is free

Question 6

Hydrophilic/uncharged AAs

Answer 6

Ser, Thr, Asn, Gln (STNQ)

Can form hydrogen bonds

Ser- hydroxyl gp to aliphatic side chain
Thr- secondary alcohol gp
Asn-carboxamide gp attached to another AA, aspartic acid
Gln-carboxamide gp attached to another AA, glutamic acid

Question 7

Hydrophilic/Charged AAs

Answer 7

Asp, Glu, Lys, Arg, His (DEKRH)

Have a net positive charge at physiological pH

Imidazole nitrogen (attached to methyl gp) of His is weakly basic at physiological pH

Arg- guanidinium side chain attached to aliphatic side chain

Question 8

Ionization of amino acids

Answer 8

Each amino acid possesses at least two ionizable groups
-α-COOH (pKa ~2.2)
-α-NH2 (pKa ~9.4)
At the physiological pH of 7.4, α-COOH is deprotonated (COO-) and α-NH2 is protonated (NH3+)

Cation=    molecule with a (+) charge
Anion  =    molecule with a (-) charge
Zwitterion =   neutral molecule with an 			 equal number of (+) and (-) charges

Question 9

Isoelectric point (pI)

Answer 9

pI is the pH at which an amino acid exists as a zwitterion (neutral)
-for 2 ionizable gps, take avg of 2 pK’s

-for 3 ionizable gps, pI is the average of the two nearest pKas
For Asp, pI = (pK1 + pK2)/2 = 3.0
For Arg, pI = (pK2 + pK3)/2 = 10.75

Eg Asp-take 2 lowest pK’s (closest)
Arg-take 2 highest pK’s (closest)