Chapter 2: Amino Acids

Name all 20 amino acids and their abbreviations

Glycine (Gly, G)

Alanine (Ala, A)

Valine (Val, V)

Leucine (Leu, L)

Isoleucine (Ile, I)

Proline (Pro, P)

Methionine (Met, M)

Phenylalanine (Phe, F)

Tyrosine (Tyr, Y)

Tryptophan (Trp, W)

Serine (Ser, S)

Threonine (Thr, T)

Cysteine (Cys, C)

Asparagine (Asn, N)

Glutamine (Glen, Q)

Aspartic Acid/ Aspartate (Asp, D)

Glutamic Acid/Glutamate (Glu, E)

Lysine (Lys, K)

Arginine (Arg, R)

Histidine (His, H)

Describe Glycine

• Gly, G

• Non-polar (aliphatic, hydrophobic)

• R= H

• Only amino acid that is not chiral

• Affected by hydrophobic effect

• Only amino acid that has two protons bonded to alpha carbon

• Key feature:

  • ammonia (NH3+)

  • Carboxygroup (COO-)

  • Hydrogen (H) on alpha carbon

Describe Alanine

• Ala, A

• Non-polar (aliphatic, hydrophobic)

• Slightly hydrophobic

• R= CH3

• Key features

  • Ammonia (NH3+)

  • Carboxygroup (COO-)

  • Methyl (CH3)

Describe Valine

• Val, V

• R= CH3-CH-CH3

• Non-polar (aliphatic, hydrophobic)

• More hydrophobic, more bulky

• Key Features:

  • Ammonia (NH3+)

  • Carboxy group (COO-)

  • Isopropyl group (C3H7) (CH3-CH-CH3)

Describe Leucine

• Leu, L

• non-polar (aliphatic, hydrophobic)

• Very compact compared to valine

• key features:

  • Ammonia (NH3+)

  • Carboxy group (COO-)

  • Isobutyl group (C4H9) (CH3 - CH - CH2 - CH3)

Describe Isoleucine

• Ile, I

• non-polar (aliphatic, hydrophobic)

• Has TWO chiral centers

  • Alpha carbon

  • CH

• Packing and hydrophobicity are affected

• Key features:

  • ammonia (NH3+)

  • carboxyl group (COO-)

  • Isobutyl group (C4H9) (CH3-CH-CH2-CH3)

Describe Proline

• Pro, P

• Non-polar (aliphatic, hydrophobic)

• A cyclic alpha-imino acid

• Has two covalent interactions

• Key features:

  • Ammonia (NH3+)

  • Carboxyl group (COO-)

  • Cyclic 5-membered rings with NH2+

Describe Methionine

• Met, M

• Non-polar (aliphatic, hydrophobic)

• Doesn’t do anything since Sulfer (S) is not at the end of the chain

• Key feature:

  • NH3

  • COO

  • CH3-S-CH2-CH2

Describe Phenylalanine

• Phe, F

• Aromatic, however absorbs the least amount of light compared to other aromatic amino acids

• Very rigid and hydrophobic

• Key features:

  • NH3

  • COO

  • CH2-6 carbon ring

Describe Tyrosine

• Tyr, Y

• Aromatic

• The OH group on the top can hydrogen bond, as it is a hydrophilic tip

• OH can have phosphate attached/replaced

• Very weak acid

• Phenolic hydroxyl pKa = 10.1

• Key features

  • NH3

  • COO

  • CH2-Carbon ring-OH

Describe tryptophan

• Trp, W

• Aromatic, can absorb light very well and fluoresce

• Rigid, biggest and largest amino acid

• Has polarity

• H on the NH is not stable, will not lose or gain protons

• Key feature:

  • NH3

  • COO

  • Indole rung

Describe Serine

• Ser, S

• Polar, uncharged, hydrophilic

• Alcohol pKa = 13.6

• OH on the R group can be replaced by phosphate

• Polar side changes, has polarity, can form H+ bonds

• Key feature

  • NH3

  • COO

  • CH2OH

Describe Threonine

• Thr, T

• Polar, uncharged, hydrophilic

• Alcohol pKa = 13.6

• Not as polar than Serine

• Key feature:

  • NH3

  • COO

  • H-C-OH
    |
    CH3

Describe Cysteine

• Cys, C

• Polar, uncharged, hydrophilic

• Thiol pKa ~ 8.3

• Can use H+ in oxidizing conditions

• Two nearby Cys can form a disulfide bond in an oxidizing environment

  • Only Cysteine can do thiS

• SH <—> S;

• Disulfide bonds help stabilize protein structure

  • Brings two parts of proteins together (covalent bonds)

• Key feature:

  • SH-CH2-

Describe Asparagine

• Asn, N

• Amide side-chain

• Polar, uncharged, hydrophilic

• Key features:

  • NH3

  • COO

  • O=C-NH2
    |
    CH2

Describe Glutamine

• Glen, Q

• Amide side-chain

• Polar, uncharged, hydrophilic

• Key feature:

  • NH3

  • COO

  • O=C-NH2
    |
    CH2
    |
    CH2

Aspartic Acid/Aspartate

• Aspartic Acid (protonated)

• Aspartate (deprotonated)

• Asp, D

• Negative at pH 7 (acidic)

• Carboxyl pKa = 3.9

• Most of the time it is aspartame due to the low pKa

• Key feature:

  • O=C-O-
    |
    CH2

Glutamic Acid/Glutamate

• Glutamic Acid (protonated)

• Glutamate (deprotonated)

• Glu, E

• Negative at pH 7 (acidic)

• Carboxylic pKa = 4.2

• Key feature:

  • NH3

  • COO

  • O=C-O-
    |
    CH2
    |
    CH2

Describe Lysine

• Lys, K

• Positive at pH 7 (basic)

• E-amino pKa = 10.5

• Very weak acid

• Protonated (positive charge)

• Hydrophobic

• Bulky

• Key feature:

  • NH3

  • COO

  • NH3-CH2-CH2-CH2-CH2

Describe Arginine

• Arg, R

• Guanidino pKa = 12.5

• NH2 can Gain or lose proton

• Key feature:

  • NH2-C-NH-CH2-CH2-CH2
    ||
    NH2+

Describe Histidine

• His, H

• Imidazole pKa = 6.0

  • Close to physiological pH = 7

• N double bonded to NH is acidic, can have proton, can buffer, 10% would be charged

• Key feature:

  • NH3

  • COO

  • imidazole side chain

When do acidic amino acids lose a proton and what are they?

Lose a proton before pH 7 and are anionic

When do basic amino acids bind to a H+ and what are they?

It can bind at whichever pH but around 7 best? They are cationic

What is molecular conformation?

Refers to differences in spatial arrangement of groups joined by covalent bonds due to bond rotation
no breaking/forming bonds, just rotating

What is molecular configuration?

Refers to isomers that can be interchanged only by breaking bonds

Arrangement of atom, must break and form bonds

What is an isomer?

Have the same molecular formula but a different arragement of the groups.

Ex. would be Leucine and isoleucine

What is a stereoisomer

When there are 2 possible arrangements of the 4 groups (not including H)

They are non-superimposable mirror images or enantiomers

In terms of enantiormers, what is D and L

D and L are defined as the absolute configuration and are derived from carbohydrate nomenclature
no matter how they are rotated, they cannot be superimposed in 3D

D = Right/dextro

L = Left/levo

Which isomeric form is most naturally occurring

The most naturally occuring amino acids are in the L-isomeric form

At what pH, what occurs to amino and carboxyl groups

At pH 7, the amino and carboxyl groups of amino acids are ionized.
Side chains in group A (non-polar), B (aromatic), C (polar) carry no net electric charge at pH 7 and remaain stationary in electric field.

What is a Zwitterion

It is a hybrid ion, meaning it carries both a positive and negative charge, it is electrically neutral.
They can act as both an acid or a base

If the zwitterion acts as an acid what happens?

Donates a proton so acid forms

If the zwitterion acts as a base what happens?

Accept proton, base is formed

how is pH important to an amino acid solution

By varying the pH of an amino acid solution, the charge on the amino acid can be changed

protons are added or removed

What can be said about amino acids and proteins in terms of pH

Amino acids and proteins are very sensitive to changes in pH. Outside the optimal pH range, structures may not function because charge is incorrect.

What happens to an amino acid under ionization?

Low pH (+)

• CooH lose proton

Neutrality (zwitter)

• Coo-

High pH (-)

• NH3+ donates H+ and becomes NH2

What happens when an amino acid with non-ionizable R-groups?

Since Glycine is non-ionizable the reaction will look like this

From the titration curve, describe it

It has two distinct stages, each corresponding to the removal of a proton

When titrating, what can be seen in the first stage

COOH converted to COO-

It is initially fully protonated. At the midpoint, equal amounts of 1st acid-base pair exist - this is the pKa for the COOH group
The removal of the proton continues with addition of NaOH. When the pH increases to 6, the protons from the COOH group are lost completely

When titrating, describe the second stage

NH3+ is converted to NH2

Midpoint: the pH = pKa of the NH3+ group. Equal amounts of the acid-base pair exist. Then, at pH 12 the titration is complete (the last plateau, as the pH fo the NaOH itself is approached).

What are 3 key information gained from titration

1. Pka values of the two ionizable groups determiend

2. SHows the two buffering regions; one around the first pKa and one around the second pKa

3. The curve shows the relationship between the charge of the species and the pH. At pH 6, the point of inflection between the two stages, the amino acid is present as its dipolar or zwitterion. ie. ionized but no net charge. This pH is called the ISOELECTRIC POINT or pI. It is the arithmetic mean of the 2 pKa values

For all 20 amino acids, what is the pKA values for alpha-COOH and alpha-NH3+

COOH: Fall in the range of 1.7 - 2.6

NH3+: 8.9 - 10.8

What can be said about non-ionizable R-groups titration curve and ionizable R group titration curves?

All amino acids with non-ionable R groups will have titration curves like Glycine (2 peaks, very simple) 13 of the 20 common amino acids fall into this category

An amino acid with an ionizable R group has more complex titration curve. The different R groups ionzie at acidic, neutral or basic pHs (7 in total)