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Polarity of amino acids, Structure of Polypeptide Chains and Structural Pattern of Secondary and Tertiary Chains.
Typology: Lecture notes
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M.Sc. Zoology (Semester II) CC7- Biochemistry
Unit: 3.
Dr Gajendra Kumar Azad Assistant Professor Post Graduate Department of Zoology Patna University, Patna Email: gajendraazad@outlook.com
Protein are built from a Repertoire of 20 amino acids
Amino-acids are natural compounds composed of amine (-NH2) and carboxylic acids (-COOH) functional groups, linked to the same carbon atom.
The key elements of an amino acid are carbon, hydrogen, oxygen and nitrogen.
Amino acids are the building blocks of proteins. All AA’s have the same basic structure: Chain^ Side
Carbon^ Alpha
Amino Group
Carboxyl Group
Amino acids are the building blocks of proteins.
Amino acids in the solution at Alpha-carbon neutral pH exist predominantly as dipolar ions (also called zwitterions). In the dipolar form, amino group is protonated (-NH3+) and the caroxyl group is deprotonated (-coo-). Figure 1: Basic structure of amino acids 2
Nonpolar Amino Acids
Nonpolar amino acids have nonpolar (hydrophobic) side-chains and their predominant forms have uncharged side-chains at physiological pH.
Figure 2: non-polar amino acids (^4)
Polar Neutral Amino Acids
Polar neutral amino acids have polar (hydrophilic) side-chains and their predominant forms have uncharged side-chains at physiological pH.
Figure 3: Polar neutral amino acids (^5)
arginine lysine histidine
Polar Basic Amino Acids
Polar basic amino acids have polar (hydrophilic) side-chains and, except for histidine , their predominant forms have side-chains with positive formal charge at physiological pH.
This formal charge is from a quaternary ammonium group.
Figure 5: Polar basic amino acids (^7)
Primary structure of polypeptide
Amino acids are linked together by peptide bonds to form polypeptide chains Proteins are linear polymers formed by linking the α- carboxyl of one amino acid to the α- amino group of another amino acid. This type of linkage is called peptide bond (or an amide bond).
Formation of a Peptide Bond
Step 1: The oxygen of first amino acid ( from the carboxylate group) and two hydrogen atoms (from the ammonium group) of second amino acid combines to form a water molecule.
Step 2: A new bond is made between the carbonyl carbon and the nitrogen.
The new bond between the two amino acid residues is called a peptide bond. Figure 6: amino acids are joined by peptide bonds 8
Primary structure of polypeptide
Proteins are composed of a long polypeptide chains.
Chains that are less than 40-50 residues are often referred to as polypeptide chains since they are too small to form a functional domain.
Larger than this size, they are called proteins.
The structure, function and general properties of a protein are all determined by the sequence of amino acids that make up its primary sequence.
Figure 8: Primary structure of polypeptide chain 10
Figure 9: Typical bond length within a peptide unit
Polypeptide chains are flexible yet conformationally restricted
The geometry of protein backbone reveals several important features.
Rotation of bonds in a polypeptide
Peptide conformations is defined by three dihedral angles (also known as torsion angles) called φ (phi), ψ (psi), and ω(omega), reflecting rotation about each of the three repeating bonds in the polypeptide backbone.
Within the peptide bond, the bond between the amino group and the α-carbon atom and between the α-carbon atom and the carbonyl group are pure single bonds.
The two adjacent rigid peptide unit s may rotate about these bonds, taking various orientations.
The angle of rotation between the nitrogen and the α-carbon atom is called φ.
The angle of rotation between the α-carbon atom and the carbonyl group is called ψ.
Ω is not often considered. It involves the carbon and nitrogen atom of peptide bond, where rotation is constrained. (^) Figure 11: dihedral angles in peptide backbone 13
Three- quarters of the possible (φ and ψ ) combinations are excluded simply by local steric clashes based on calculations using known van der Waals radii and dihedral angles.
The area shaded dark blue represents conformations that involves no steric overlap. Medium blue represents conformations allowed at the extreme limits for unfavourable atomic contacts. Lightest blue represents conformations that are permissible if a little flexibility is allowed in the dihedral angle. Yellow region are conformation that are not allowed.
Ramachandran Plot
In principle, the φ and ψ can have any value between - 180 ° to +180°, but many values are prohibited by steric interference between atoms in the polypeptide backbone and amino acid side chains (glycine is an exception).
(degrees)
φ (degrees)
Figure 12: Ramachandran plot for l-Alanine residues
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Secondary structure: α helices
The α helix is the most common secondary structure.
They are regular structures that repeats every 5.4 Å.
The poly peptide backbone is tightly wound around an imaginary axis down longitudinally through the middle of the helix, and the R-group of amino acid residues protrude outward from the helical backbone.
The amino acid residues in the α helix have conformations with φ= - 57 ° and ψ= - 47 °, and each helical turn includes 3.6 amino acid residues.) angles.
Linus Pauling and Corey were pioneer in proposing α helix structure and build model in 1951.
Helical twist of the α helix found in all protein is right handed
Figure 13: alpha helix structure 16
Secondary structure: α helices
The α helix is stabilised by hydrogen bonds.
The hydrogen bonds are formed between hydrogen attached to electronegative nitrogen atom of the peptide linkage and the electronegative carbonyl oxygen atom of the fourth amino acid on the amino terminal side of the peptide bond.
Within the α helix every peptide bond participates in hydrogen bonding
All hydrogen bonds together provide the stability to the α helix
Figure 14: Hydrogen bonding pattern in alpha helix
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Secondary structure: β sheets
The β conformations organises polypeptide chains into sheets. The β conformations is an extended form of polypeptide. The backbone of the zigzag rather than helical structures.
The zigzag polypeptide chains can be arranged side by side to form a structure resembling a series of pleats called β sheets.
β sheets are composed of two or more polypeptide chains called β strands.
The structure is stabilized by hydrogen bonds. The H-bond is formed between the adjacent segments of the chains.
The R-groups of adjacent amino acids protrude from the zigzag structure in opposite directions creating the alternating patterns.
The adjacent polypeptide chain in a β sheet can be either parallel or antiparallel (having the same or opposite amino-to-carboxyl orientations, respectively).
The idealized structures corresponds to φ= - 119 ° and ψ= +113 (parallel) and φ=-139, ψ=+135 (antiparallel); these values vary somewhat in real proteins, resulting into some structural variations. (^19)
Secondary structure: β sheets
Two types of β conformations organises polypeptide chains into sheets.
a) anti-parallel β sheets
b) Parallel β sheets
Figure 16: Ramachandran diagram for β strands.
The red areas show the sterically allowed conformations of extended, β strand-like structures
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