Peptide Bonds Flashcards
What is the shape of a peptide bond?
Planar
Is the peptide bond delocalised?
Yes
What type of reaction forms a peptide bond?
Condensation
How are polypeptides chemically synthesised?
- Selective acylation of a single free amine
- Protective groups must be reversibly added
Why are protective groups temporarily added to amino acids?
All avaliable amines can potentially react with all carboxyl groups, so this temporarily protects amino acids from nucleophilic attack
Give 2 typical blocking groups in peptide synthesis
- BOC
- FMOC
How does solid phase peptide synthesis work?
- A column with a solid support (powder) is used
- The first aa is bound to the solid support
- This is then washed with a buffer which contains blocking compounds
- Then active aa substrates added
What are is the orbital structure of a peptide bond?
sp2
What does the delocalised nature of a peptide bond mean about the structure if a protein as a whole?
It has a relatively rigid structure
What do phi and psi angles refer to?
The angles of groups either side of the alpha carbon
Are most peptide bonds in the cis or trans configuration?
Trans
Which amino acid is the exception and has a significant proportion of peptide bonds in the cis configuration?
Proline
Which enzyme changes proline from cis to trans?
Prolyl isomerase
What is the effect on structure of adding a cis proline?
Adds a turn in the protein
What mechanism does HIV protease use to break peptide bonds?
Aspartic acid
How is specificity of HIV protease derived?
From the fit of the surrounding amino acid side chains within the hydrophobic binding pocket
What is the effect of water on the aspartic acids in HIV protease?
- Acts as a nucleophile
- Distorts the local environment
- Causes a change in pKa of aspartic acids, causing one to be protonated and one to be deprotonated
How many main genes does the HIV virus have?
3
How does HIV produce so many proteins using only 3 genes?
It produces many polyproteins (many proteins in one string)
How do many HIV drugs work?
- Inhibit HIV protease by mimicking cleavable peptide bonds
- Acts as a competitive inhibitor
- Prevents polyproteins from being cleaved
How does UV region absorbance usually arise?
From elevation of electrons from bonding to anti-bonding orbitals (which are higher energy)
