Classification and Structure of Amino AcidBy:- Vivek KumarProgramme:- Bs-Ms (Physics)School:- School Of Basic Sciences and Researches
 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.
• 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.
Amino acid carbons are named in sequenceusing the Greek alphabet (α, β, γ, δ, ε)starting at the carbon COObetween the carboxyl and amino groups. H N CH α 3 CH2 β CH2 γ CH2 δ CH2 ε NH3
• Configuration of biological chiral compounds is defined inrelation 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 itsability to rotate plane polarized light in a particular direction!
• The amino acids in proteins are L isomers. COO COO H 3 2H3N C H H3N C H H3C C COO CH3 CH3 S 1 NH3L-Alanine (S)-Alanine
(2) Amino Acids: Structural Classification (Table 3-1, p. 78)
• Cystine residues provide structural stability of proteins through intramolecular or intermolecular disulfide bonds. Oxidation Reduction
•D-amino acids are found in a few small peptides, includingsome peptides of bacterial cell walls and certain antibiotics(such as penicillin). D-Glu D-Ala
• pKa for the –COOH group in amino acids is 2 ~ 2.3, twopH units lower than that of ordinary aliphatic carboxylicacid (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, onepH unit lower than that of ordinary aliphatic amine (pKa ofCH3NH3+ = 10.6).TThe amino group of glycine is 10 times less basic thanthe amino groups of methylamine.
(b) Titration Curve of Amino Acids• The pH at which a molecule’s netcharge is zero is called the isoelectric point or the pI• For two ionizable groups: pI = ?(such as carboxyl & amino) pKa1 + pKa2 pI = 2
(4) Functions1. Chemical Messengers: Neurotransmitters are roughly dividedinto small molecules & peptidic (neuropetides), these are furtherclassified 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 .
2. Monomeric subunits of proteinsAll 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.
 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.)
• 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,
(3) Deduced amino acid sequences from DNA sequences
Protein function ⇐ 3-D structure ⇐ SequenceThe goal is to learn, from sequence, as muchinformation as possible on its structure,function, and its evolutionary history.
 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
• 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)
•Multiple sequence alignment & Conservative SubstitutionHomologs are identified by comparing multiple sequences of aprotein from different organisms.Multiple sequences are aligned to maximize the sequencesimilarity.Conservative substitution by a chemically similar a.a. residue(Asp and Glu, Lys and Arg, Trp and Phe, etc) is given a highscore during alignment according to the scoring systemsuch as Blosum62.