This document discusses the classification and structure of amino acids. It begins by describing the standard amino acids as α-amino acids containing an amino group and a carboxyl group. Amino acids exist in a zwitterionic form at physiological pH. They differ in their side chains and have L or D configurations. Amino acids are classified based on their side chains and functions include roles as neurotransmitters, protein subunits, and energy metabolites. Peptides and proteins are polymers of amino acids joined by peptide bonds. Protein sequences can be deduced from DNA and provide insight into structure, function, and evolution through sequence comparisons.

1. Classification and Structure of
Amino Acid
By:- Vivek Kumar
Programme:- Bs-Ms (Physics)
School:- School Of Basic Sciences and Researches

2. [1] Amino Acids
(1) Description
• The “standard” amino acids are α-amino acids.
‒ primary amino group (−NH2)
‒ carboxylic acid group (−COOH)
•Proline is an exception
with a secondary amino group,
but, it is still referred to
as an α-amino acid.

3. • Amino acids also exist in a zwitterionic form at pH 7.
The amino group is protonated (pKa ~9.4).
The carboylic acid group is deprotonated
(carboxylate; pKa ~2.2).
• Amino acid structures differ at the side chain (R-groups).
• Abbreviations: three or one letter codes
• Amino acids (except glycine)
have chiral centers:
- Rotate the plane of
plane-polarized light
and are optically active.

4. Amino acid carbons are named in sequence
using the Greek alphabet (α, β, γ, δ, ε)
starting at the carbon COO
between the carboxyl and amino groups. H N CH α
3
CH2 β
CH2 γ
CH2 δ
CH2 ε
NH3

5. • Configuration of biological chiral compounds is defined in
relation to glyceraldehyde (L- & D-)
D - dextrorotatory (rotating light to the right)
L - levorotatory (rotating light to the left)
BUT L or D designation for an amino acid does NOT reflect its
ability to rotate plane polarized light in a particular direction!

7. • The amino acids in proteins are L isomers.
COO COO H
3 2
H3N C H H3N C H H3C C COO
CH3 CH3 S 1 NH3
L-Alanine (S)-Alanine

8. (2) Amino Acids: Structural Classification (Table 3-1, p. 78)

13. • Cystine residues provide structural stability of proteins
through intramolecular or intermolecular disulfide bonds.
Oxidation
Reduction

14. •D-amino acids are found in a few small peptides, including
some peptides of bacterial cell walls and certain antibiotics
(such as penicillin).
D-Glu
D-Ala

15. (a) Acidity and Basicity of amino acids

16. • pKa for the –COOH group in amino acids is 2 ~ 2.3, two
pH units lower than that of ordinary aliphatic carboxylic
acid (pKa of CH3COOH = 4.6).
Glycine is 100 times more acidic than acetic acid.
•ppKa for the –NH3+ group in amino acids is 9 ~ 10, one
pH unit lower than that of ordinary aliphatic amine (pKa of
CH3NH3+ = 10.6).
TThe amino group of glycine is 10 times less basic than
the amino groups of methylamine.

17. (b) Titration Curve of Amino Acids
• The pH at which a molecule’s net
charge is zero is called
the isoelectric point or the pI
• For two ionizable groups: pI = ?
(such as carboxyl & amino)
pKa1 + pKa2
pI =
2

19. • Histidine
A good buffer at
~ pH 6.
pI =

20. (4) Functions
1. Chemical Messengers: Neurotransmitters are roughly divided
into small molecules & peptidic (neuropetides), these are further
classified as inhibitor and excitatory.
(A) Inhibitory Neurotransmitters
• Glycine (-OOC-CH2-NH3+)
– binds a receptor that depolarizes the synapse by Cl- release
– involved in motor and sensory functions
• γ-Aminobutyric acid (-OOC-(CH2)3-NH3+) – GABA
– Glutamic acid derivative
– Most common neurotransmitter in brain
– Huntington’s disease - altered levels
(B) Excitatory Neurotransmitters
• Glutamic acid and Aspartic acid: learning and memory
• Epinephrine (=adrenaline) and norepinephrine
are derived from tyrosine .

21. 2. Monomeric subunits of proteins
All proteins are composed of some or all of the 20 "standard"
amino acids
‒ two new amino acids have been recently discovered!
Discovery of 21st amino acid: (Selenocystein)
Discovery of 22nd amino acid: (Pyrrollysine)
3. Energy metabolites – many are essential nutrients and
can be used as precursors to other molecules.

22. [2] Peptides and Proteins (MW > 10,000):
Polymers of amino acids
Peptide synthesis:
Energetically unfavourable
(∆G > 0)
→ Couple with energetically
favourable reaction(s)
(Leaving group activation)
(Lehninger Fig 27-14, p.1052.)

23. Serylglycyltyrosylalanylleucine.
Ser-Gly-Tyr-Ala-Leu
SGTAL
N-terminus C-terminus

24. • Peptide bonds are stable:
t1/2 = 7 yrs in cells due to high ∆G‡ of the hydrolysis reaction.
• Peptides (and proteins) have their unique pI values
depending on the a.a. compositions.
• Biologically active peptides:
oxytocin, bradykinin, vasopressin, etc.
insulin, glucagon,

25. (3) Deduced amino acid sequences from DNA sequences

26. Protein function ⇐ 3-D structure ⇐ Sequence
The goal is to learn, from sequence, as much
information as possible on its structure,
function, and its evolutionary history.

27. [4] Protein Sequences and Evolution
• Genes and proteins from closely related organisms
should be similar.
• The sequences increasingly diverge as the evolutionary
distance between two organisms increases.
• Conserved a.a. residues: amino acid residues essential
for function and structure are conserved throughout the
evolution.
• Variable residues: Those less important vary over time.
⇒ polymorphism

28. • Protein family: A group of proteins with significant
sequence similarity (>25%), and/or with similar
structure and function.
• Likely share common evolutionary origin.
Ser proteinases: chymotrypsin, trypsin, elastase, etc.
Cytochrome P450 family.
• Homologs, paralogs (gene duplication), orthologs (speciation)

29. •Multiple sequence alignment & Conservative Substitution
Homologs are identified by comparing multiple sequences of a
protein from different organisms.
Multiple sequences are aligned to maximize the sequence
similarity.
Conservative substitution by a chemically similar a.a. residue
(Asp and Glu, Lys and Arg, Trp and Phe, etc) is given a high
score during alignment according to the scoring system
such as Blosum62.