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08 h3

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  • 1. Classification and Structure of Amino AcidBy:- Vivek KumarProgramme:- 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 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
  • 5. • 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!
  • 6. • 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
  • 7. (2) Amino Acids: Structural Classification (Table 3-1, p. 78)
  • 8. • Cystine residues provide structural stability of proteins through intramolecular or intermolecular disulfide bonds. Oxidation Reduction
  • 9. •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
  • 10. (a) Acidity and Basicity of amino acids
  • 11. • 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.
  • 12. (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
  • 13. • HistidineA good buffer at~ pH 6.pI =
  • 14. (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 .
  • 15. 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.
  • 16. [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.)
  • 17. Serylglycyltyrosylalanylleucine. Ser-Gly-Tyr-Ala-Leu SGTALN-terminus C-terminus
  • 18. • 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,
  • 19. (3) Deduced amino acid sequences from DNA sequences
  • 20. Protein function ⇐ 3-D structure ⇐ SequenceThe goal is to learn, from sequence, as muchinformation as possible on its structure,function, and its evolutionary history.
  • 21. [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
  • 22. • 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)
  • 23. •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.