Protein Protein ChemistryChemistry

Protein ChemistryProtein Chemistry

Proteins are organic compounds Proteins are organic compounds contain alpha amino acids united contain alpha amino acids united by peptide linkages.by peptide linkages.

They are composed of C, H, O and They are composed of C, H, O and NN22..Amino AcidsAmino Acids::

Contain Contain aminoamino group group (NH2)(NH2) and and carboxyliccarboxylic group group (COOH)(COOH)

Chemical ClassificationChemical Classification

Amino Acids

Aliphatic aa Aromatic aa

Neutral aaMono amino-mono carboxylic acid

Acidic aaMono amino-dicarboxylic acid

Basic aaDiamino-monocarboxylic acid

Aliphatic amino acidsAliphatic amino acids (with (with

aliphatic side chains)aliphatic side chains) Contain NO aromatic Contain NO aromatic ring structuresring structures

1. Glycine (Gly; G)

2. Alanine (Ala; A)

3. Valine (Val; V)

4. Leucine (Leu; L)

5. Isoleucine (Ile; I)

1.1. Serine (Ser; S)Serine (Ser; S)

2.2. Threonine (Thr; T)Threonine (Thr; T)

3.3. Tyrosine (Tyr; Y)Tyrosine (Tyr; Y)

Amino acidsAmino acids with side chains with side chains containing hydroxyl group containing hydroxyl group (-OH)(-OH)

1.1. Cysteine (Cys; C)Cysteine (Cys; C)

2.2. Cystine Cystine (2 Cys residues forming (2 Cys residues forming

disulfide bond)disulfide bond)

3.3. Methionine (Met; M)Methionine (Met; M)

Amino acidsAmino acids with side chains with side chains containing Sulfur atoms containing Sulfur atoms (-S-)(-S-)

O |S-CH2-CH-C=O | NH3

O |O=C-CH-CH2-S | NH3

+ +

Amino acidsAmino acids with side chains with side chains containing Acidic group or its containing Acidic group or its amide amide (-COOH / -CONH2)(-COOH / -CONH2)

1.1. Aspartic Acid (Asp; D)Aspartic Acid (Asp; D)

2.2. Asparagine (Asn; N)Asparagine (Asn; N)

3.3. Glutamic Acid (Glu; E)Glutamic Acid (Glu; E)

4.4. Glutamine (Gln; Q)Glutamine (Gln; Q)

Amino acidsAmino acids with side chains with side chains containing Basic groups containing Basic groups (-NH2 / -(-NH2 / -NH)NH)

1.1. Arginine (Arg; R)Arginine (Arg; R)

2.2. Lysine (lys; K)Lysine (lys; K)

3.3. Histidine (His; H)Histidine (His; H)4.4. Proline (Pro; P) Proline (Pro; P) (Pro is a (Pro is a

special case since it’s not an amino acid special case since it’s not an amino acid but it’s imino acid).but it’s imino acid).

Amino acidsAmino acids with side chains with side chains containing Aromatic ringscontaining Aromatic rings

1.1. Phenylalanine (Phe; F)Phenylalanine (Phe; F)

2.2. Tyrosine (Tyr; Y)Tyrosine (Tyr; Y)

3.3. Histidine (His; H)Histidine (His; H)

4.4. Tryptophan (Trp; W)Tryptophan (Trp; W)

Classification based on Classification based on Physical PropertiesPhysical Properties

Amino Acids

Hydrophilic aa Hydrophobic aa

Basic side chain aaArg, Lys, His

Acidic side chain aaAsp, Glu

Polar, uncharged side chain aaSer, Thr, Asn, Gln

Aliphatic Side Chain aaAla, Val, Leu, Ile

Aromatic Side Chain aaPhe, Tyr, Trp

Met

Special aa

Gly, Cys, Pro

Nutritional ClassificationNutritional Classification

Amino Acids PropertiesAmino Acids Properties

All are All are αα-amino acids.-amino acids. Majority are L-amino acids.Majority are L-amino acids. All are optically active All are optically active

(except glycine).(except glycine). Glycine doesn’t contain asymmetric Glycine doesn’t contain asymmetric

carbon atom.carbon atom.

Amino acids’ chargesAmino acids’ charges Amino acids may have positive charges:

R-N+H3 R-NH2 + H+

Amino acids may have negative charges:

R-COOH R-COO- + H+

Amino acids may have ZERO net charge:

H2N-CH(R)-COOH H3+N-CH(R)-COO-

Due to changing of charges of amino acids depending on the pH of the medium, they can be considered as AMPHOTERIC molecules that can act as acids in alkaline solution (carrying negative charges) or as bases in acidic solutions (carrying positive charges).

The effect of pH on the amino acid charge can be seen in the following example: Glutamic acid bears different charges in strong acidic, acidic, near neutral, and strong alkaline solutions.

3+

3+

-

3+

-- --H+ H+ H+

-COOH -COOH -NH2

Strong Acid (pH < 1) Acid (pH around 3) near neutral (pH 6-8) strong alkali (pH > 11)

net charge = +1 net charge = 0 net charge = - 1 net charge = - 2

Amino acids’ charges, cont.Amino acids’ charges, cont.

The pH value at which the chemical group loses a H+ is called its pKa.

Terminal -carboxyl group: pKa ~ 3.0

R-COOH RCOO-

Terminal -amino group: pKa ~ 8.0R-NH3

+ R-NH2

Polar, uncharged amino acid side chains:

Cys (R-S-H) R-S- pKa= 8.3

Tyr (R-ph-O-H) R-ph-O- pKa= 10.6

Acid Base

The pKa values of amino acids with charged side chains (acidic

& basic)

The isoelectric pH of an amino The isoelectric pH of an amino acid (pI).acid (pI).

It is the pH at which the amino acid bears a zero net chargei.e. The number of positive charges is equal to that of negative charges.

At such condition, the amino acid is called di-polar ion OR Zwitterion.

R

33+

-

Levels of Protein Structure:Levels of Protein Structure:

Protein Primary Structure:Protein Primary Structure: The number and order of the amino acid residues

constitute its primary structure. Amino acids are linked together by peptide bonds. The peptide bonds The peptide bonds are formed by linking an -carboxyl

group of one amino acid to an -amino group of a second amino acid followed by a peptide bond between the -carboxyl group of the second and the -amino group of the third and so on, forming what is called peptide backbone.

This means that there will be only one free (not participating in a peptide bond) -amino group and -carboxyl group in each protein. They are called “Amino- or N-” and “Carboxyl- or C-” termini of the protein (Amino acid sequence of a protein is written from left to right, starting with the N-terminal at left and ending with the C-terminal at right).

Amino acids participating in peptide bonds are named as derivatives of the carboxyl terminal amino acid residue

e.g. NH2-lys-leu-tyr-gln-COOH is called lysyl-leucyl-tyrosyl-glutamine.

A prefix that determine the peptide length, e.g. tri-, penta- or octa-peptide represent an oligopeptide that is

3-, 5-, or 8-amino acid residue-long, respectively, NOT 3-, 5-, or 8- peptide bonds.

All proteins are formed from the same building blocks All proteins are formed from the same building blocks (the 20 amino acids) arranged in specific sequences into (the 20 amino acids) arranged in specific sequences into linear chains that perform an incredible array of diverse linear chains that perform an incredible array of diverse tasks.tasks.

The amino acids are bound together by removal of a water The amino acids are bound together by removal of a water molecule (condensation) from an alpha-amino group of molecule (condensation) from an alpha-amino group of an amino acid and an alpha-carboxylic group of another, an amino acid and an alpha-carboxylic group of another, forming what is called “peptide bond”.forming what is called “peptide bond”.

R1

Peptide bond

R2

Amino acid 1 Amino acid 2

Dipeptide

Peptide bond formation:Peptide bond formation:

Proteins: Higher order of Proteins: Higher order of Structure.Structure. Configuration refers to the geometric relationship

between a given set of atoms e.g. L- and D- amino acid configurations. Interconversion between different configurations require breaking the covalent bond(s) that determines the configuration.

Conformation refers to the spatial relationship of every atom in a molecule. Interconversion between different conformations does not require breaking covalent bonds. It typically occurs via rotation about single bond.

Free rotation Free rotation occurs about the -carbon – carbonyl group (C=O) bond and -carbon – nitrogen bond. Presence of double bonds prevent the free rotation and hence forcing certain conformation.

Peptide bond has partial double bond character, oscillating between two formstwo forms.

This double bond nature of the peptide bond requires that the carbon, oxygen and nitrogen atoms to be coplaner, thus restrict free rotation.

Regions of secondary structure arise when series of amino acyl residues adopt certain conformation.

CH |R1

O || CH2N

N |H

R2

|CH

C || O

H |N

N

H

C

O

+N

H

C

O_

+N

H

C

O

The free rotation in protein structure

The double bond nature of the peptide bond

The two most common types of secondary structure are the helix helix and the sheet sheet.

In the helix, the R groups of the amino-acyl residues are facing outward. The stability of the -helix is due primarily to hydrogen bonding between the oxygen of the peptide bond carbonyl group and the hydrogen of the peptide bond amino-group of the 4th residue down the chain (polypeptide chain).

In the sheet, the amino acid residues form a zigzag pattern, in which the R groups of adjacent residues point in opposite directions. The stability of the sheet is driven by hydrogen bonds between carbonyl oxygens and amino- hydrogens of the peptide bonds of adjacent segment of the sheet that is forming an anti-parallel or a parallelan anti-parallel or a parallel patterns, which identify whether the direction of the adjacent segments of the sheet are in opposite or in the same directions.

Proteins: Higher order of Proteins: Higher order of Structure, Secondary structure.Structure, Secondary structure.

The The -helix and the -helix and the -sheet structures-sheet structures

Anti-parallel (A) and parallel (B) patterns of -sheet structures

Proteins: Higher order of Proteins: Higher order of Structure, Tertiary structure.Structure, Tertiary structure. It is the global structure of the protein molecule that is

built from the individual secondary structural units connected together with short segments / connections. This three-dimensional structure is considered to be more conserved than the primary structure since it’s more closely associated with function.

Loops, turns and bends refers to such short segments of amino acids that join two units of secondary structures such as two adjacent strands of an antiparallel sheet. A turn involves 4 amino acyl residues, in which the 1st is hydrogen-bonded to the 4th, resulting in a tight 180° turn.

Loops are regions that contain residues more than the minimum number necessary to connect adjacent segments of secondary structure. They are irregular in conformation but play key roles in biologic functions of proteins such as bridging domainsdomains responsible for substrate binding and catalytic activities of enzymes, e.g. Helix-Loop-Helix motifs represent DNA binding domains of DNA-binding proteins such as transcription factors and enzymes involved in cell replication machinery.

Proteins: Higher order of Proteins: Higher order of Structure, Quaternary Structure, Quaternary structure.structure. Proteins which consist of more than one

polypeptide chain display what is called quaternary structure, in which individual polypeptide chains (subunits) are held together mainly by non-covalent bonds.

Quaternary structure can be as simple as two identical units (e.g. EcoRI; restriction endonuclease enzyme) or as complex as dozens of different subunits (e.g. Hemoglobin A, 2 - and 2 -subunits).

References:References:– Protein Composition and Structure, Chapter 2, Protein Composition and Structure, Chapter 2,

in in Biochemistry, 6Biochemistry, 6thth Ed. Ed., Berg JM, Tymoczko JL , Berg JM, Tymoczko JL and Stryer L. (Eds) (2007). and Stryer L. (Eds) (2007).