Organic Chemistry

Module 6. Proteins

Lesson 18A
A PRIMARY, SECONDARY, TERTIARY AND QUATERNARY STRUCTURE OF PROTEINS

18.A.1 Introduction

Four basic structural levels of organization in proteins – primary, secondary, tertiary and quaternary.
1. Primary structure: H₂N-----------------------COOH

• Refers to combination of amino acids in a proper sequence via peptide bonds (a covalent bond)
• A linear sequence of amino acid residues making a polypeptide chain

2. Secondary structure

• Refers to the regular reoccurring arrangement of polypeptide chain in one direction
• A helical spiral of polypeptide is formed, which is stabilized by hydrogen bonding

3. Tertiary structure

• Refers to bending or folding of polypeptide chain in three dimensional space.
• Stabilize by disulphide linkage, salt linkage, hydrophobic bond, dipole-dipole interaction, phosphodiester linkage etc.

4. Quaternary structure

• Refers to how the individual polypeptide chains in the protein are arranged relative to each other- arrangement and interrelationship of the polypeptide chains
• Most of the high mol.wt. proteins consist of two or more polypeptide chains- known as oligomer proteins
• Stabilized by any one or all types of forces which can exist between amino acids side chain, except covalent bond.

18. A. 2 Primary Structure

• Refers to the linear sequence in which the constituent amino acids are covalently linked through peptide (amide) bonds - results from condensation of α-COOH group of one amino acid and α-NH₂ group of another amino acid
• All the amino acids are in L-configuration
• Protein with n amino acid residues contains n-1 peptide linkages
• In a given protein

• Type of amino acids
• Number of amino acids ( n ) and
• Sequence in which the amino acids are linked

• Determine the physical, chemical, biological, functional and structural properties of the protein

• The peptide bond is represented as a single covalent bonds . However in reality it has a partial double bond character- because of resonance structure caused by delocalization of electrons

Fig. 18.1 Resonating structure

• This has several important structural implications in proteins

1. The resonance structure includes protonation of peptide group
2. The partial double bond character, the rotation of peptide bond is restricted to a max. of 6⁰, known as ‘w’ angle - restricted rotational freedom drastically reduces backbone flexibility. Only N-Cα and Cα-C bonds have rotational freedom – termed as φ (phi) and ψ (psi) dihedral angles respectively.
3. Delocalization of electrons impart partial : positive charge to hydrogen atom of the group and negative charge to oxygen atom of the group. - because this hydrogen bonding between and groups of the peptide backbone is possible under appropriate conditions
4. Four atoms attached to the peptide bond can exist either in cis or trans form

Fig. 18.2 Geometrical isomerism in peptide linkage

• However, almost all protein peptide bonds exists in trans configuration - because grater thermodynamic stability
• Since trans-cis transformation increases free energy of the peptide bond by 34.8 kJ/mol, such isomerization does not occur in protein.

18. A.3 Secondary Structure

• Refers to periodic spatial arrangement of amino acid residues
• The periodic (regular) structures – two forms

• Helical structure
• Extended sheet-like structure

18.A.3.1 Helical structure

• Three types – α-helix, ³10- helix and π-helix
• However, α-helix is the major form found in proteins and it is the most stable form among the three forms
• The α-helixes are stabilized by hydrogen bonding
• Each backbone group is hydrogen bonded to the >C=O group of the fourth preceding residue
• The pitch of the helix (axial length occupied per rotation) – 5.4°A
• Each amino acid residue extends the axial length by 1.5°A
• Each helical rotation involves 3.6 amino acid residues
• Thirteen backbone atoms are in the hydrogen bonded loop- therefore α-helix is sometimes also called 3.6₁₃ helix
• H bonds are oriented parallel to the helix axis
• N,H, and O atoms at the H bond lie almost in a straight line - therefore H bond angle is almost zero
• H bond length is about 2.9 °A
• Strength of H bond is about 18.8 kJ/mole
• The α-helix can exist in either a right or left handed orientation
• However, the right handed orientation is more stable
• In proline and hydroxy proline residues

Fig. 18.3 Proline and hyroxyproline

1. One N of the N-H group is involved in ring structure- rigid - therefore rotation of the N-Cα bond is not possible, therefore φ angle has a fixed value of 70°
2. H of the N-H involves in peptide bond formation- therefore no free H atom remains available to form hydrogen, therefore it can not form H bond

• Because of these two attributes segment containing high amount of proline or hydroxyproline residues and their uniform distribution can not form α-helices- therefore these amino acid residues are considered to be an α-helix breakage.
• e.g. In β-casein proline residues constitute 17% of the total amino acids and 8.5% in α_s1 casein - therefore α-helices are not present in these proteins , therefore these proteins have random structure

18.A.3.2 β-sheet structure: (Extended structure)

• The and groups are oriented perpendicular to direction of the chain- therefore hydrogen bonding is possible only between segments (i.e. intersegments) and not within a segment (i.e. intersegment)
• The β-strands are usually about 5-15 amino acid residues long
• In proteins, two β-strands of the same molecule interact via hydrogen bonds, forming a sheet-like structure - known as β-pleated sheet
• In this structure, the side chains of amino acid are oriented perpendicular (above and below) to the plane of the sheet
• Depending on the N→C directional orientation of the strands - two types of β-sheet structures can form: parallel sheet and antiparallel sheet
• In parallel β-sheet the direction of the β-strands run parallel to each other
• In antiparallel β-sheet the direction of the β-strands run antiparallel (opposite) to each other (Fig. 18.4)

• These differences in chain directions affect the geometry of H bonds.

• In antiparallel β-sheets N-H-----O-C atoms lie in a straight line- zero H-bond angle, which enhances the stability of this bond
• In parallel β-sheets the atoms lie at an angle, which reduces stability of the H bonds

Therefore antiparallel β-sheets are more stable than parallel β-sheets

• Polypeptide segments containing alternating polar and nonpolar residues have a high propensity to form β-sheet structure
• Segment rich in bulky hydrophobic side chains (e.g. Val and Ile) also have tendency to form β-sheet structure

18.A.4 Forces Involved In Structural Organization of Proteins

1. Peptide bond: (Amide linkage)

• Back bone of protein structure and covalent in nature
• Formed by reaction of α-NH₂ group of one amino acid with α-COOH of another amino acid. (Fig. 18.5)

2. Hydrogen Bond

• A weak electrostatic interaction between two strongly electronegative atoms (e.g. O and N) via hydrogen atom in Fig. 18.6.
• In protein hydrogen bond is formed between oxygen of carbonyl group (-C-O-) and nitrogen of imino group (-N-H-)

Fig. 18.6 Formation of hydrogen bond (>C=O ------H------N)

3. Disulfide linkage

• Formed by reaction of two sulfhydryl groups of cystein

Fig. 18.7 Disulfide linkage

4. Hydrophobic bond

• Formed when two long chains of hydrocarbon or aromatic rings come nearer to each other
• They have tendency to repel the water

Fig. 18.8 Hydrophobic bond

5. Ionic bond

• Formed by interaction between two opposity charged ions or groups—e.g. positively charged group of basic amino acid (lysine) and negatively charged group of acidic amino acid (glutamic or aspartic acid)

Fig. 18.9 Ionic bond

6. Salt bridge

• Formed by interaction between two negatively charged groups of acidic amino acids with divalent cation.

Fig. 18.10 Salt bridge

7. Dipole-dipole interaction

• Formed by interaction between two hydroxyl groups of hydroxy amino acids (serine and threonine)

Fig. 18.11 Dipole-dipole interaction

8. Phosphodiester linkage

• Formed by interaction of two hydroxyl groups of hydroxy amino acids with a phosphoric acid molecule

Fig. 18.12 Phosphodiester linkage

18.5 Schematic Representation of Different Types of Forces Or Interactions In Protein Molecule (Fig. 18.13)

18.5.1 Terminals of proteins

H₂N---------------------------------------------------------------------COOH

N-terminal C-terminal

• Information of peptide chain
• At one end –NH₂ group remains free – N- terminal- L.H.S.
• At other end –COOH group remains free- C- terminal- R.H.S.