Download MBBS Biochemistry PPT 85 Structures Of Amino Acids Lecture Notes

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Structure of Amino Acids

Specific learning objectives

? Diverse functions of Proteins.
? Amino acids classification based on position of amino group and composition of

R-group and nutritional requirement.

? Properties of Amino Acids.
Introduction

? Proteins are made up of hundreds of smaller units called amino acids that are

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.

? Defense: Immunoglobulins and Interferon are proteins that protect the human

against bacterial and viral infections.

? Signaling: Provide recognition/markers on surface of cells or organelles and can

illicit intracellular responses.

? Movement: Motor proteins provide contractile movement/energy transformation.
Cont---

? Structural related proteins: Make up the structural-architecture of

the cell or tissues.

? Storage related proteins: provide amino acids storage for growth and

reproduction.

? Transport proteins: move molecules through membranes.

Amino-Acids Classification Based on Standard and Non-

Standard Amino Acids

? Standard amino-acids
? Non-Standard amino-acids
General Structure of Common Amino Acids

? All proteins are composed of the 20 "standard "amino acids.

? Common central alpha ()-carbon atom bound to a carboxylic acid group, an

amino group and a hydrogen atom are covalently bonded.

? They have a primary amino group and a carboxylic acid group substituent on the

same carbon atom, with the exception of proline, (has a secondary amino

group).

Fig.4.1. Biochemistry. 4th edition by Donald Voet and Judith G. Voet

Cont---

? Proline classified as an imino acid, its -amine is a secondary amine with its a

nitrogen having two covalent bonds to carbon (to the -carbon and side chain

carbon), rather than primary amine.

? Incorporation of the amino nitrogen into a five membered ring constrains the

rotational freedom around the ?N -C

-bond in proline to specific rotational angle,

reduces the structural flexibility of polypeptide regions containing proline.
Cont---

? Ionized form of a common amino acid in solution at

physiological pH.

? Ionization state of an amino acid varies with pH.

? -Amino group is protonated and in its ammonium

ion form

? Carboxylic acid group is in its deprotonated or

Fig.4.2. Biochemistry. 4th edition by Donald Voet and Judith G. Voet

carboxylate ion form.

Selenocysteine, the 21st Protein L--Amino Acids

? Selenocysteine are non-standard amino-acid.

? 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.

? Incorporation of selenocysteine is specified by a large and complex genetic

element for the unusual tRNA called tRNA Sec which utilizes the UGA anticodon

that normally signals STOP.
L--Amino Acids Serve Additional Role

? L- amino acids and their derivatives participate in cellular functions (nerve

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).

? Ornithine and citrulline are intermediates in urea biosynthesis.

Cont--

? Homocysteine, homoserine, and glutamate--semialdehyde participate in the

intermediary metabolism of the protein amino acids.

? The protein amino acids phenylalanine and tyrosine serve as precursors of

epinephrine, norepinephrine, and DOPA (dihydroxyphenylalanine).
Amino Acids Classified on the Basis of Nutritional

Requirement

? Essential proteinogenic amino acids.

? Non-essential proteinogenic amino acids.

Amino-Acid Requirements of Humans

Table 28.1. Harper's Il ustrated Biochemistry 26th edition
Amino-Acids Classification Based on Side Chain Groups

? Based on the type of functional group (R group) present amino acids are

classified as: Aliphatic, aromatic, acidic, basic, acid amide, sulfur and cyclic amino

acids.

? Based on the characteristic of the functional group amino acids are classified as:

polar and non-polar amino acids.

? Based on the site of attachment of the functional group. They are also classified

as: alpha, beta, gamma and delta amino acids.

Amino Acids Classification

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Cont--

Nonpolar/Hydrophobic

Methyl R group

Isopropyl R group

Branching in isobutyl side chain on carbon of amino

acid

Branching in isobutyl side chain on carbon of amino

acid

Table 3.1. Harper's Il ustrated Biochemistry 30 edition

Cont--

Polar, uncharged-R group

Hydroxymethyl R group

Polar, uncharged-R group

Secondary Alcohol structure

Mentioned in amino acids with aromatic rings section

Polar, uncharged-R group

Thiolmethyl/Sulfhydryl R group

Nonpolar

Methyl ethyl thiol ether R group
Cont--

Negatively charged R group

-COOH R group

Polar, Uncharged-R group

Negatively charged R group

-COOH R group

Polar, Uncharged-R group

Cont--

Positively charged R groups

Guanidinium R group

-NH+3 R group

Imidazolium R group
Cont--

Mentioned in amino acids with basic groups section

Benzene ring R group

Phenol R group

Heterocyclic structure, indole R group

Imino group belongs to a five-member ring

Fig. 2.4. Textbook of Biochemistry with Clinical Correlations, 4th edition by Thomas M Devlin
Fig. 2.5. Textbook of Biochemistry with Clinical Correlations, 4th edition by Thomas M Devlin

Fig. 2.6. Textbook of Biochemistry with Clinical Correlations, 4th edition by Thomas M Devlin
Properties of Amino Acids

Genetic Code Specifies 20 L--Amino Acids

? Proteins are synthesized from the set of 20 L--amino acids encoded by

nucleotide triplets called codons.

? Common amino acids are those for which at least one specific codon exists in

the DNA genetic code.

? Sequences of peptides and proteins represent by using one- and three letter

abbreviations for each amino acid.
Cont---

Genetic information is transcribed from a DNA sequence into mRNA

and 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

Summary

? Functions of Proteins: transport, defense, movement, storage, signaling etc.

? Both -amino acids and non--amino acids occur in nature, but proteins are

synthesized using only L--amino acids.

? The R groups of amino acids determine their unique biochemical functions.

? 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

? Distributed subtopics of class to students to participate in group

discussion in next class.

Reference Books

1) Harper 's Il ustrated Biochemistry-30th edition
2) Textbook of Biochemistry with Clinical Correlations. 4th edition. Thomas M.

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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This post was last modified on 05 April 2022