Session 1 Flashcards
What are amphipathic molecules?
Molecules with polar and non-polar regions.
What is a zwitterion and when does it exist?
An ionised form of amino acid where both the carboxyl and amino group are ionised, found at the isoelectric point (pH) specific to that amino acid.
Which stereoisomer is found in proteins?
L isomer, the D isomer is never found in proteins.
What determines an amino acids behaviour?
R groups.
How can amino acids be classified?
Based on R group:
Non-polar aliphatic/aromatic
Polar charged/uncharged
What state will an amino acid be in if pH is:
- Above pK
- Below pK
- Deprotonated
2. Protonated
How are peptide bonds formed?
By linking 2 amino acids in a condensation reaction (creates a molecule of water).
Why are peptide bonds planar?
Peptide bond C-N has partial double bond characteristics so the bond is rigid and planar.
What is the difference between trans and cis peptide bonds?
There are steric clashes in a cis peptide bond; the R groups are on the same side of the molecule so they clash.
In a trans peptide bond the R groups are on opposite sides of the molecule so there are no steric clashes.
Define the isoelectric point of a protein.
The pH at which there is no overall net charge on a protein.
What is the isoelectric point likely to be for:
- Positively charged amino acids
- Negatively charged amino acids
- Above 7, they are likely to be basic
2. Below 7, they are likely to be acidic
Define primary structure of a protein.
Linear amino acid sequence of a polypeptide chain.
Define secondary structure of a protein.
The local spatial arrangement of the polypeptide backbone.
Define tertiary structure of a protein.
3-D arrangement of all atoms in a polypeptide.
Define quaternary structure of a protein.
3-D arrangement of protein subunits.
What determines the conformation of a protein?
The angles of the covalent bonds, they determine how the protein folds.
What are the properties of an alpha-helix
3.6 amino acids per turn
0.54nm pitch
Right-handed helix
All R-groups are on the outside of the helix so don’t contribute to its secondary structure
Backbone of the -C=O in one residue is H-bonded to the -NH group of the residue 4 amino acids away
Which amino acids are strong helix formers?
Alanine and leucine
Which amino acids are strong helix breakers and why?
Glycine, it has a tiny R-group (-H) so it will readily support other formations.
Proline, rotation around its C-N bond is impossible due to the ring structure.
What are the properties of a beta-strand?
Fully extended conformation
0.35nm between amino acids
R-groups alternate between opposite sides of the chain
Side-by-side arrangement of beta-strands forms a beta-sheet (in anti parallel, parallel or mixed arrangement)
What are the roles of fibrous proteins?
Support, shape and protection.
What are the roles of globular proteins?
Catalysis and regulation.
What are the properties of collagen?
Triple helical arrangement of collagen chains
Contain glycine every third amino acid
Hydrogen bonds stabilise interactions between chains
What is a protein motif?
A folding pattern containing 1 or more elements of secondary structure, e.g. Beta-barrel, beta-alpha-beta loop.
