Lecture 3 amino acids

what can amino acids function as?

Amino acids can also function as neurotransmitters
(glutamate, -aminobutyric acid (GABA), hormones
(thyroxine), as bacterial cell wall components (D-
alanine) and as intermediates in many metabolic
pathways

what defines an a-amino acid

common a-amino acid in which the carboxylic acid
and amino groups are attached to the same
carbon - the a-carbon

all 20 amino acids share a common strucuture, name them.

All standard 20 amino acids used in genetic coding share a core structure:

• A central carbon (called the α-carbon)

• Attached to:

  • Amino group (–NH₃⁺)

  • Carboxyl group (–COO⁻)

  • Hydrogen atom (H)

  • An R group (or side chain) that varies between amino acids

what is happening to the amino acid at At physiological pH (~7.0):

• The amino group is protonated (+)

• The carboxyl group is deprotonated (–)
  → making the amino acid a zwitterion (has both + and – charges)

what differentiates amino acids?

• The R group is what differentiates each amino acid.

• It determines:

  • Chemical properties (e.g., polar, non-polar, acidic, basic)

  • Behavior in proteins

  • Hydrophobic/hydrophilic interactions

what are examples of Non-polar (aliphatic, hydrophobic) (7)

1. Glycine (Gly, G)

2. Alanine (Ala, A)

3. Valine (Val, V)

4. Leucine (Leu, L)

5. Isoleucine (Ile, I)

6. Proline (Pro, P)

7. Methionine (Met, M)

what are examples of aromatic amino acids?

8. Phenylalanine (Phe, F)

9. Tyrosine (Tyr, Y)

10. Tryptophan (Trp, W)

what are examples of Polar, uncharged, hydrophilic amino acids? (5)

11. Serine (Ser, S)

12. Threonine (Thr, T)

13. Cysteine (Cys, C)

14. Asparagine (Asn, N)

15. Glutamine (Gln, Q)

what are examples of negative (acidic) amino acids?

16. Aspartic Acid (protonated) Aspartate (deprotonated)
    (Asp, D)

17. Glutamic Acid (protonated) Glutamate (deprotonated)
    (Glu, E)

what are examples of amino acids that are positive at ph 7 (basic)

18. Lysine (Lys, K)

19. Arginine (Arg, R)

20. Histidine (His, H)

what do acidic amino acids do?

Acidic amino acids lose a proton at pH 7 and are anionic

what do basic amino acids do?

Basic amino acids bind a H+ at pH 7 and are cationic

properties of Nonpolar (Hydrophobic)

Hydrophobic; found in protein interiors; do not form H-bonds easily

properties of Aromatic r groups

Contain benzene-like rings; Tyrosine is polar; Tryptophan has a large, bulky ring

• absorb uv rays with tryptophan absorbing the most

properties of Polar, Uncharged

Can form H-bonds; hydrophilic; Cysteine can form disulfide bonds

properties of polar, Positively Charged r groups?

Basic; hydrophilic; often found on protein surfaces; can form ionic bonds

properties of Polar, Negatively Charged r groups

Acidic; hydrophilic; can donate protons and form salt bridges

what is Molecular Configuration?

Configuration refers to the 3D spatial arrangement of atoms.

• refers to isomers that can be interconverted only by breaking bonds
  

what are isomers?

Isomers are molecules with the same molecular formula (same atoms and number of atoms) but different arrangements of those atoms.

what are the two types of isomers

1. structural isomers - compounds that have the same structural formula but diff connectivity of atoms

2. Stereoisomers - compounds that have identical formula and connectivity but differ in arrangements of atoms in space.

   • two types of sterioisomers

two types of categories of stereoisomers

1. enantiomers - non-superimposable mirror images of one another

2. diastereomers - that are not mirror images of one another

   • Non-superimposable" means two objects are not identical and cannot be aligned in a way that they perfectly match

what is Chirality

• Chirality happens when the α-carbon (central carbon) has four different substituents — common in all amino acids except glycine.

• This allows the molecule to exist in two mirror-image forms, called enantiomers.

example of enantiomers.?

L-Alanine and D-Alanine

• These are stereoisomers: same formula, same connections, but different 3D spatial arrangement.

• They are non-superimposable — like your left and right hands.

where does D- and L- naming come from?

• D- and L- naming comes from carbohydrate chemistry, not from the direction of light rotation (which is + or –, or dextrorotatory/levo).

• They describe absolute configuration — how the atoms are arranged in space.

how is D and L naming correlated with amino acids?

• For amino acids, the molecule is drawn in a Fischer projection with:

  • COO⁻ on top

  • R group on the bottom

• Then:

  • If the amino group (NH₃⁺) is on the left, it's L-amino acid

  • If it's on the right, it's D-amino acid

All naturally occurring amino acids in proteins are L-amino acids.
D-amino acids are rare, found in bacteria and some antibiotics.

D- and L- vs (+) and (–):

D- / L- System (Fischer Projection Configuration)

• Based on the structure of glyceraldehyde, used for naming amino acids and sugars.

• Refers to the spatial arrangement of groups around the chiral center in a Fischer projection.

• For amino acids:

  • L-amino acids: the –NH₂ group is on the left in a Fischer projection.

  • D-amino acids: the –NH₂ group is on the right.

(+)/ (–) System (Optical Rotation):

• Refers to how a compound rotates plane-polarized light:

  • (+) or dextrorotatory: rotates light to the right

  • (–) or levorotatory: rotates light to the left

This is an experimental property measured using a polarimeter.

what is plane polarized light and Why it matters in chemistry:

Plane-polarized light is a type of light wave in which the electric field oscillates in only one plane as it travels through space.

Why it matters in chemistry:

• Chiral molecules (like most amino acids) can rotate the plane of plane-polarized light.

• This is the basis for optical activity:

  • Clockwise rotation → (+) or dextrorotatory

  • Counterclockwise rotation → (–) or levorotatory

what does Normal (Unpolarized) Light: do?

In regular light (like sunlight or from a bulb), the electric field vectors vibrate in all directions perpendicular to the direction of travel.

how is D and L naming work for sugars?

For sugars (like glyceraldehyde):

• We look at the chiral carbon farthest from the aldehyde or ketone group.

• If the OH is on the right → it’s D-sugar

• If the OH is on the left → it’s L-sugar

how many chiral centers and stereoisomers does threonine and isoleucine have

have two chiral centres and 4 stereoisomers