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Lecture 5. Proteins-I

This document discusses the four main types of biomacromolecules - proteins, nucleic acids, lipids, and carbohydrates. It focuses on proteins, describing how they are made up of amino acids linked together through peptide bonds. The document discusses common protein secondary structures like alpha helices and beta sheets that are formed based on restrictions on the dihedral angles between amino acids. It notes how proline and glycine can affect secondary structure formation due to their unique properties.

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Saksham Jain
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32 views

Lecture 5. Proteins-I

This document discusses the four main types of biomacromolecules - proteins, nucleic acids, lipids, and carbohydrates. It focuses on proteins, describing how they are made up of amino acids linked together through peptide bonds. The document discusses common protein secondary structures like alpha helices and beta sheets that are formed based on restrictions on the dihedral angles between amino acids. It notes how proline and glycine can affect secondary structure formation due to their unique properties.

Uploaded by

Saksham Jain
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
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Biomacromolecules

Biomacromolecules

 Proteins

 Nucleic acids: DNA and RNA

 Lipids: Storage and structural

 Carbohydrates: Storage and structural


Proteins
Amino acids

 Proteins are unbranched polymers of amino acids

 There are 20 different amino acids present in proteins

Side-chain
R
Carboxylic
Amino group NH3+ C COO‒ acid group

H
Amino acid chirality

 Proteins are made up of L-α-amino acid

 There are 20 of them


pKa

 The pH at which an acid is 50% ionized.

pKa ~2

pKa ~9-10

 Assuming “R” to be a non-ionizable group, what will be the


ionization status of an amino acid at physiological pH of ~7.4?

 The pH at which there is not net charge on the amino acid is called
the isoelectric point, pI.

𝐩𝐊 𝐚 𝟏 + 𝐩𝐊 𝐚 𝟐
𝐩𝐈 =
𝟐
Amino acid titration
Peptide bond

 The bond between amino acids is also known as peptide bond.

 A dipeptide means a peptide with two amino acids, not three.

 Peptide bond imparts planarity in the protein backbone.


C H

C N
O C
Planarity of peptide bond puts restrictions on
backbone conformation
Protein dihedral/torsion angles
Peptide bond: planarity & trans-configuration

Trans Cis

Planar peptide bond


Trans-configuration Trans Cis

Proline is an exceptional amino acid residue in that the cis-trans equilibrium


only slightly favors the trans form in peptidyl-proline bonds.
Are all dihedral angles allowed?
Some combinations of dihedral angles are more
probable than others

Ramachandran plot
Ball-and-stick models provide some insight on
infrequency of >0
Conformational restrictions for the different amino acids
Glycine does adopt positive  values

Less steric hindrance because


side chain (green) is very small
Proline’s  value is (somewhat) fixed by its side chain’s
bond to the backbone

This side chain can clash


sterically with the preceding
amino acid, so the “pre-proline”
Ramachandran plot is also unique
Pre-Proline Ramachnadran plot
Trend for consecutive amino acids: correlation in position

What do we get if
we repeat the
same torsion
angles many times
Amino acid n in a row?

Amino acid n+1


A helical backbone conformation: α-helix
α-helix

 H-bonding between –C=O of residue “i” and –NH of “i+4” residue

 3.6 residues per turn

 Pitch = 5.4 nm
Extended structure: -strand
-sheets

These amino acids are


part of beta sheets
Parallel -sheets
Antiparallel -sheets
Left-handed helix

These amino acids


participate in the less
common, left-handed
forms of helices
Turns
 Beta-turns (4-residue turns) are the most prevalent turns.

 Often connect the two strands of an antiparallel -sheets.

Turn-type φi+1 ψi+1 φi+2 ψi+1


I –60 –30 –90 0
I′ 60 30 90 0
II –60 120 80 0
II′ 60 –120 –80 0
Protein secondary structure conclusion
Structural implications of having Pro and Gly

 Proline is considered a helix-breaker due to


its conformational rigidity.

 Glycine is considered a helix-breaker due to


its conformational flexibility
Proline and Glycine support turn formation

Turn-type φi+1 ψi+1 φi+2 ψi+1


I –60 –30 –90 0
I′ 60 30 90 0
II –60 120 80 0
II′ 60 –120 –80 0

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