? Amino acids classification based on position of amino group and composition of
R-group and nutritional requirement.
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? Properties of Amino Acids.Introduction
? Proteins are made up of hundreds of smaller units called amino acids that are
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attached to one another by peptide bonds, forming a long chain.? Protein as a string of beads where each bead is an amino acid.
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Diverse Functions of Proteins
? Enzymes: Serve as biological catalysts.
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? Defense: Immunoglobulins and Interferon are proteins that protect the humanagainst bacterial and viral infections.
? Signaling: Provide recognition/markers on surface of cells or organelles and can
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illicit intracellular responses.
? Movement: Motor proteins provide contractile movement/energy transformation.
Cont---
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? Structural related proteins: Make up the structural-architecture of
the cell or tissues.
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? Storage related proteins: provide amino acids storage for growth andreproduction.
? Transport proteins: move molecules through membranes.
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Amino-Acids Classification Based on Standard and Non-
Standard Amino Acids
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? Standard amino-acids? Non-Standard amino-acids
General Structure of Common Amino Acids
? All proteins are composed of the 20 "standard "amino acids.
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? Common central alpha ()-carbon atom bound to a carboxylic acid group, an
amino group and a hydrogen atom are covalently bonded.
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? They have a primary amino group and a carboxylic acid group substituent on thesame carbon atom, with the exception of proline, (has a secondary amino
group).
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Fig.4.1. Biochemistry. 4th edition by Donald Voet and Judith G. Voet
Cont---
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? Proline classified as an imino acid, its -amine is a secondary amine with its anitrogen having two covalent bonds to carbon (to the -carbon and side chain
carbon), rather than primary amine.
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? Incorporation of the amino nitrogen into a five membered ring constrains the
rotational freedom around the ?N -C
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-bond in proline to specific rotational angle,reduces the structural flexibility of polypeptide regions containing proline.
Cont---
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? Ionized form of a common amino acid in solution atphysiological pH.
? Ionization state of an amino acid varies with pH.
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? -Amino group is protonated and in its ammonium
ion form
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? Carboxylic acid group is in its deprotonated orFig.4.2. Biochemistry. 4th edition by Donald Voet and Judith G. Voet
carboxylate ion form.
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Selenocysteine, the 21st Protein L--Amino Acids
? Selenocysteine are non-standard amino-acid.
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? Selenium atom replaces the sulfur of its elemental analog, cysteine.? Selenocysteine is not the product of a posttranslational modification, but is
inserted directly into a growing polypeptide during translation.
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? Incorporation of selenocysteine is specified by a large and complex genetic
element for the unusual tRNA called tRNA Sec which utilizes the UGA anticodon
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that normally signals STOP.L--Amino Acids Serve Additional Role
? L- amino acids and their derivatives participate in cellular functions (nerve
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transmission and biosynthesis of porphyrins, purines, pyrimidines, and urea).? Thyroid hormones are formed from tyrosine; glutamate serves as a
neurotransmitter as well as the precursor of g-aminobutyric acid (GABA).
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? Ornithine and citrulline are intermediates in urea biosynthesis.
Cont--
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? Homocysteine, homoserine, and glutamate--semialdehyde participate in theintermediary metabolism of the protein amino acids.
? The protein amino acids phenylalanine and tyrosine serve as precursors of
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epinephrine, norepinephrine, and DOPA (dihydroxyphenylalanine).
Amino Acids Classified on the Basis of Nutritional
Requirement
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? Essential proteinogenic amino acids.
? Non-essential proteinogenic amino acids.
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Amino-Acid Requirements of HumansTable 28.1. Harper's Il ustrated Biochemistry 26th edition
Amino-Acids Classification Based on Side Chain Groups
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? Based on the type of functional group (R group) present amino acids areclassified as: Aliphatic, aromatic, acidic, basic, acid amide, sulfur and cyclic amino
acids.
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? Based on the characteristic of the functional group amino acids are classified as:
polar and non-polar amino acids.
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? Based on the site of attachment of the functional group. They are also classifiedas: alpha, beta, gamma and delta amino acids.
Amino Acids Classification
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Cont--
Nonpolar/Hydrophobic
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Methyl R group
Isopropyl R group
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Branching in isobutyl side chain on carbon of aminoacid
Branching in isobutyl side chain on carbon of amino
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acid
Table 3.1. Harper's Il ustrated Biochemistry 30 edition
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Cont--Polar, uncharged-R group
Hydroxymethyl R group
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Polar, uncharged-R group
Secondary Alcohol structure
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Mentioned in amino acids with aromatic rings sectionPolar, uncharged-R group
Thiolmethyl/Sulfhydryl R group
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Nonpolar
Methyl ethyl thiol ether R group
Cont--
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Negatively charged R group
-COOH R group
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Polar, Uncharged-R groupNegatively charged R group
-COOH R group
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Polar, Uncharged-R group
Cont--
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Positively charged R groupsGuanidinium R group
-NH+3 R group
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Imidazolium R group
Cont--
Mentioned in amino acids with basic groups section
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Benzene ring R group
Phenol R group
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Heterocyclic structure, indole R groupImino group belongs to a five-member ring
Fig. 2.4. Textbook of Biochemistry with Clinical Correlations, 4th edition by Thomas M Devlin
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Fig. 2.5. Textbook of Biochemistry with Clinical Correlations, 4th edition by Thomas M DevlinFig. 2.6. Textbook of Biochemistry with Clinical Correlations, 4th edition by Thomas M Devlin
Properties of Amino Acids
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Genetic Code Specifies 20 L--Amino Acids? Proteins are synthesized from the set of 20 L--amino acids encoded by
nucleotide triplets called codons.
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? Common amino acids are those for which at least one specific codon exists in
the DNA genetic code.
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? Sequences of peptides and proteins represent by using one- and three letterabbreviations for each amino acid.
Cont---
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Genetic information is transcribed from a DNA sequence into mRNAand then translated to the amino acid sequence of a protein
Fig. 2.1. Textbook of Biochemistry with Clinical Correlations, 4th edition by Thomas M Devlin
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Summary
? Functions of Proteins: transport, defense, movement, storage, signaling etc.
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? Both -amino acids and non--amino acids occur in nature, but proteins aresynthesized using only L--amino acids.
? The R groups of amino acids determine their unique biochemical functions.
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? Amino acids are classified as basic, acidic, aromatic, aliphatic, or sulfur-containing
based on the composition and properties of their R groups.
Interaction with students
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? Distributed subtopics of class to students to participate in group
discussion in next class.
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Reference Books1) Harper 's Il ustrated Biochemistry-30th edition
2) Textbook of Biochemistry with Clinical Correlations. 4th edition. Thomas M.
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Devlin.3) Biochemistry. 4th edition. Donald Voet and Judith G. Voet.
4) Biochemistry 7th edition by Jeremy M. Berg, John L. Tymoczko and Lubert Stryer
5) Lehninger Principles of Biochemistry
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30
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