Peptide bond and friends Flashcards
How is the peptide bond formed?
Produced by a condensation reaction between amino acids
Typically occurs in the ribosome during translation (though a small number of specialized peptides are produced by non-ribosomal peptide synthesis)
What are the chemical properties of the peptide bond?
The bond is planar, with a partially double bonded nature due to electrical resonance between carbonyl carbon and the nitrogen
It is almost always in the trans conformation as the cis conformation results in greater steric interference
What is unique about the peptide bond in prolines?
As proline has a tendency to form a cyclic compound it is more commonly found in the cis formation (3:1), allowing proline and glycine to form tight turns
What are rotamers and their role in protein structure?
Rotamers are rotational isomers, which each have energy forms, the lowest energy form is the most common seen in proteins
What are the angles around the peptide backbone?
Omega which is either 0 (cis) or 180 (trans)
Phi which is the angle around the bond between the chiral carbon and the Nitrogen
Psi which is the angle between the chiral carbon and carbonyl carbon
Phi and Psi are freely rotatable
What is the purpose of the Ramachandran plot?
Although Psi and Phi are freely rotatable due to steric collisions only certain combinations are possible and favourable
The Ramachandran plot is a graphical representation of what angles are likely to occur for the all the amino acids in a protein resulting in certain regions having high density allowing a structure to be determined
What are the non-peptide bonds in proteins?
Disulphide Bonds
Ionic Bonds
Hydrogen Bonds
Hydrophobic interactions/ Vanderwaals interactions
What is the role of disulphide bonds in protein structure?
Play a key role in extracellular proteins as they stabilise proteins and make them less susceptible to degradation
They can also be used to connect two polypeptides as in Ig or Insulin
How are disulphide bonds formed and why are they unlikely to be formed in intracellular proteins?
The disulphide bond is formed through a redox reaction between two cysteine residues
Inside of cells is a reduced environment maintained through buffers such as glutathione (glutamate-cysteine- glycine) which is a reducing agent which both keeps cysteines in proteins reduced (preventing disulphide bond formation) as well as detoxifying reactive oxygen species
What is the role of ionic bonds in protein structure?
Strong Ionic bonds can be formed between positive (lysine, Arginine, histidine) and negative (glutamate, aspartate)
these charged amino acids are usually at the surface of proteins, if they are in the core they will most likely be paired up as otherwise they will be extremely disruptive and energetically unfavourable in the hydrophobic environment
What is the role of hydrogen bonds in protein structure?
Hydrogen bonds are made when two relatively electronegative atoms share a hydrogen atom, as thus causes a strong dipole to form which can be up to 10% as strong as a covalent bond (but frequently are less than this)
What role do hydrophobic interactions play in protein structure?
Hydrophobic sidechains are typically buried in the core of the protein, due to solvent shielding (although vanderwaals interactions also plays a minor role) as these sidechains want to avoid the polar, aqueous cellular environment. This is the major driving force between protein folding
