peptide bond and proteins

topic 3

the peptide bond

• how amino acids are linked together to form proteins

• peptide bonds are formed when 2 amino acids come together

• Has a partial double bond character on the C-N bond.

• position of the double bond is not fixed over time

general structure of amino acids

• Amino Group (NH₂)

• Hydrogen (H)

• Carboxyl Group (COOH)

• Side Chain (R)

what is the importance of the side chain ( R groups)

Determines the reactivity and characteristics of the amino acid.

Consequences of resonance in the peptide bond - 1

▪ It increases the polarity of the peptide bond
Important for overall proteins

Consequences of resonance in the peptide bond - 2

It restricts movement of the atoms in the bond
Double bonds locked in position; single bonds free to rotate

Mechanism of peptide bond formation-Nucleophilic addition-elimination reaction

Two or more amino acids can condensate via the formation of a peptide
bond (also called an amide bond)

Each amino acid is trans with respect to its neighbours

4 levels of structure

• primary structure

• secondary

• tertiary

• quaternary

level 1- primary structure

• The order of the amino acids in a polypeptide

• The primary structure has direction
  ◦ N-terminal (amino acid group-NH3+ )→ C-terminal (carboxyl group -COO- ) end of the protein

protein sequence flexibility

• Some amino acids can be swapped without affecting the protein’s function.

• Amino acids with similar properties (like non-polar ones) can often replace each other without big changes.

level 2- secondary structure

Local folding of the polypeptide chains into
regular patterns – helix, sheet

2 core secondary structures

• alpha helix

• beta sheet

alpha helix

• Hydrogen bonding between the amide hydrogen of ( residue i+4)

  one AA and the carbonyl oxygen of ( residue i) another AA lead to formation of these structures

• Stabilized by hydrogen bonds

• Provides structural stability to proteins

• Formation of the a-helix leads to
  compaction of the polypeptide

beta pleated sheet

• Beta-Pleated Sheets Structure:

  • Amino acids (AAs) are almost fully extended.

  • Typically contain 5-10 amino acids.

  • R-groups (side chains) alternate, sticking out above and below the plane of the sheet.

• Alignment of Sheets:

  • Sheets can line up next to each other.

  • Hydrogen bonds form between neighboring sheets, stabilizing the structure.

• Types of Beta Sheets:

  • Parallel: The amino acid chains ( N-termini) run in the same direction.

  • Anti-parallel: The amino acid chains run in opposite directions.

beta turns

• Beta turns allow a polypeptide chain to make abrupt turns, essentially making the protein chain fold back on itself.

• essential for the compact and functional folding of proteins.

what are the 2 types of beta turns

• Type I: The third amino acid (AA3) can be any amino acid.

• Type II: The third amino acid (AA3) is glycine which has a small R-group (hydrogen, H), making it more flexible

WHERE A AND B MEET

Super-secondary structures

• more complex

• certain structures found more commonly in protein ex.helix-loop-helix
  ◦ e.g. beta-alpha-beta

  
  

level 3-tertiary structure

• Overall folding of a single polypeptide chain

Disulphide bonds ( level 3)

• Covalent link between two the –SH groups of two cysteine residues

• Important for stabilisation of the overall structure and flexibility

  
  

Tendencies in Tertiary structure

• Charged & polar R-groups on
  the protein surface

• ◦ Interact with water

• Non-polar R-groups tend to be
  buried in the cores of proteins

  
  

Level 4 - Quaternary structure

• More than one polypeptide

• A dimer is the most simple form

• Tetramer

• Hexamer

Change in structure – change in function

summary

❖ Amino acids can bind together to form a peptide bond
❖ This peptide bond can be CIS or TRANS
❖ Resonance: A peptide bond is shifting back and forth between different states and the
average is usually observed.
❖ Proteins have a specific three dimensional conformation, which is essential for their function.
❖ Four levels of structure: Primary – sequence, Secondary – local folding, Tertiary – global
folding and, Quaternary – proteins binding together.
❖ Different interactions for different levels of structure.
❖ Maintaining the correct structure is essential to maintain correct function.