Download MBBS Biochemistry PPT 81 Roperties Of Amino Acids Lecture Notes

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Properties of Amino Acids

Specific learning objectives

? Properties of amino acids.
? Structure organization of the Proteins:
1) Primary structure
2) Secondary Structure
3) Tertiary Structure
4) Quaternary Structure
Properties of Amino Acids

Amino Acids have an Asymmetric Center

? Optically active molecules have an asymmetry such that they are not

superimposable on their mirror image.

? C atoms of all aa are asymmetric centers and optically active except glycine, in

which R=H two of the four substituents on the -carbon atoms are hydrogen.

? C is a chiral center, this carbon atom is attached to four different groups.
Absolute Configuration of Amino Acids

? All -amino acids (aa) derived from

proteins have the L-stereochemical

configuration.

? They all have the same relative

configuration about their C atoms.

? If the NH +

3 projected to the left, the aa

has L (Levo) absolute configuration.

? NH +

3 projected to the right, the aa has

Fig. 2.7. Textbook of Biochemistry with Clinical Correlations, 4th edition by

Thomas M Devlin

D (Dextro) absolute configuration.

Acid-Base Properties of Amino Acids
? Amino acids in aqueous solution, contain weakly acidic -carboxyl groups and

weakly basic -amino groups.

? Charged and uncharged form of the ionizable weak acid groups ?COOH and -NH +

3

exist in protonic equilibrium:

R-COOH

R-COO- + H+

R- NH3+

R- NH2+ + H+

? Both R-COOH and R-NH + are weak acids. R-COOH are stronger acid than R-NH +

3

3

? At physiological pH, carboxyl group exists as R-COO- and amino group as R-NH3+

Henderson-Hasselbalch equation: Quantitative relationship between pH and

concentration of a weak acid (HA) and its conjugate base (A-).

Derivation of Henderson-Hasselbalch equation: Consider the release of a proton

by a weak acid represented by HA:

The "salt" or conjugate base (A?) is the ionized form of a weak acid.
? Dissociation constant of the acid, Ka, is:

OR

? By taking the negative logarithm of both sides:

? Substituting pH = -log[H+] and pK a = -log K a obtain Henderson-Hasselbalch

equation:

Cont--

? Larger the K a, the stronger the acid, because most of the HA has dissociated into

H+ and A?.

? Conversely, the smaller the K a, the less acid has dissociated and, therefore, the

weaker the acid.

? pKa values for a particular molecule are determined by titration.
Titration of an Amino Acids

Dissociation of the carboxyl group of

Alanine:

Ionic forms of alanine in acidic, neutral, and basic solutions

? At a low (acidic) pH, both of

ionizable -carboxyl and -amino

group are protonated.

? As pH of solution raised, ? COOH

group of form I can dissociate by

donating a proton to the medium.

? Release of a proton results in the

formation of carboxylate group, ?

Fig. 1.10: Lippincott's il ustrated reviews- Biochemistry 6th edition

COO? of form I , which is the dipolar

form of the Alanine.

Cont--

Dissociation of the amino group:

? Second titratable group of alanine is amino (? NH3+) group.

? This is a much weaker acid than the ? COOH group and, i.e, has a much smaller

dissociation constant, K 2.

? Release of a proton from protonated amino group of form I results in fully

deprotonated form of alanine, form I I.
Titration Curve of Alanine

? pKa for acidic group (?COOH) is pK 1 is 2.35,

whereas pKa for next acidic group (? NH3+)

is pK 2 is 9.69.

? Isoelectric pH (pI) of Alanine is:

Fig. 1.11: Lippincott's il ustrated reviews- Biochemistry 6th edition

Cont--

? In clinical laboratory, knowledge of the isoelectric pH guides, selection of

conditions for electrophoretic separations.

? For example, two simple aa (with one COOH and one NH3+ group) separated by

electrophoresis either at an acidic or basic pH that exploits subtle differences in

net charge based on subtle differences in pK 1 or pK 2 values.
Ultraviolet Spectra of Ty r, Phe andTrp

? Amino acids do not absorb visible light.

? Ty r, Phe, and Trp absorb high-wavelength

(250-290nm) UV light.

? Absorption of light at 280nm used to

estimate the concentration of a protein in

solution, if the number of Trp and Ty r

residues in the protein is known.

Fig.3.7. Harper's Il ustrated Biochemistry 30th edition

Structural organization of Proteins

Fig.3.16. Lehninger Principles of Biochemistry
Primary Structure of Proteins

Primary Structure

? Amino acids are linked by peptide bonds to form polypeptide chains.

? Ordered sequence of aa in a polypeptide chains is the primary structure of the

protein.

? It is the unique primary structure that enables a polypeptide chain to fold into a

specific 3-D structure that gives the protein its chemical and physiological

properties.
Amino Acids are Polymerized into Peptides and Proteins

? -carboxyl group of an aa with side chain R1

forms a covalent peptide bond with -amino

group of the aa with side chain R2 by elimination

of a molecule of H 2O.

? Dipeptide (contain two aa bonded to each other

via a single peptide bond).

Fig. 2.8. Peptide bond formation:

Textbook of Biochemistry with Clinical Correlations

4th edition by Thomas M Devlin

Cont--

? Tripeptides (contains three aa) form a second peptide bond through its terminal

carboxylic acid group and the a amino of a third amino acid (R3).

? Repetition of this process form a polypeptide or protein of specific aa sequence

(R1R,2R,3R4 Rn).
Components of a Polypeptide Chain

? It consists of a repeating part, backbone, and a

variable part, comprising the distinctive side

chains.

? Polypeptide backbone is rich in hydrogen-

bonding potential. Each residue contains a

carbonyl group, and, with the exception of

proline, an NH group.

? Mass of a protein expressed in units of

daltons; one Dalton (Da) is equal to one

Fig.2.15: Components of a polypeptide chain: Biochemistry 7th edition by Berg,

atomic mass unit.

Tymoczko and Stryer

Peptide Bond has Partial Double-Bond Character

? Single bond linked the -carboxyl and -nitrogen

atoms, this peptide bond exhibits partial double-

bond character.

? Bond that connects a carbonyl carbon to an -

nitrogen cannot rotate and thus conformation of

the peptide backbone is constrained.

? Almost all peptide bonds in proteins are trans.

Fig.2.18: Peptide bonds are planar: Biochemistry 7th edition by Berg, Tymoczko

and Stryer

? The O, C, N, and H atoms of a peptide bond are

coplanar.
Rotation about Bonds in a Polypeptide

? Structure of each aa in a polypeptide adjusted by

rotation about two single bonds.

? Phi () is angle of rotation about bond between

N-C bond.

? psi () is angle of rotation about bond between

C -C

bond.

? Freedom of rotation about two bonds of each aa

Fig.2.22: Biochemistry 7th edition by Berg, Tymoczko and Stryer

allows proteins to fold in many ways.

Ramachandran Plot

? In principle, values of and bet. -180?

and +180?, but many values are prohibited

by steric interference between atoms in

the polypeptide backbone and aa side

chains

? Allowed/favorable regions with no steric

overlap are shown in dark green;

borderline regions are shown in light

green.

? In peptides, for aa other than glycine, most

combinations of and angles are

Fig.2.23: Biochemistry 7th edition by Berg, Tymoczko and Stryer

disallowed because of steric hindrance.
Amino Acid Sequences have Direction

? A polypeptide chain has polarity because its

ends are different: an -amino group is

present at one end and an -carboxyl group

at the other.

? Amino end is taken to be the beginning of a

polypeptide chain, and so the sequence of aa

in a polypeptide chain is written starting with

the amino-terminal residue.

Fig.2.14: Amino acid sequences have direction: Biochemistry 7th edition by

Berg, Tymoczko and Stryer

Cross-Links: Formation of a Disulfide Bond

? In some proteins, the linear polypeptide

chain is cross-linked.

? The most common cross-links are disulfide

bonds, formed by the oxidation of a pair of

cysteine residues.

? The resulting unit of two linked cysteines is

called cystine.

Fig.2.16: Cross-links: Biochemistry 7th edition by Berg, Tymoczko and Stryer
Cont--

? Extracellular proteins often have several disulfide bonds, whereas

intracel ular proteins lack them.

? For ex., collagen fibers in connective tissue and fibrin blood clots.

Summary

? All aa possess at least two weakly acidic functional groups, R-NH3+ and R-COOH.

? Many also possess additional weakly acidic functional groups such as phenolic -

OH, -SH, guanidino, or imidazole moieties.

? The pKa values of all functional groups of an aa or of a peptide dictate its net

charge at a given pH.

? pI, the isoelectric pH, is the pH at which an aa bears no net charge, and does not

move in a direct current electrical field.
Cont--

? The most important element of primary structure is the sequence of amino acid

residues.

? Nature of the covalent bonds in the polypeptide backbone places constraints on

structure.

? Peptide bond has a partial double bond character that keeps the entire peptide

group in a rigid planar configuration.

? The N-C and C -C

bonds can rotate to assume bond angles of and ,

respectively.

Group Discussion

? Subtopics of previous class discussed in groups.
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