1 - Intro to protein structure Flashcards
What amino acids have non-polar side chains (hydrophobic)?
Glycine Alanine Proline Valine Leucine Isoleucine Methionine Trytophan Phenylalanine
Which amino acids have polar side chains (are hydrophilic)?
Serine Threonine Tyrosine Asparagine Glutamine Cysteine
What bond joins amino acids?
peptide binds
What are the strongest binds within the protein?
covalent bonds
NOTE: can exist as disulphide bonds - when cysteine side chains within a protein are oxidised resulting in a covalent bond forming between the 2 amino acids
What other forces are there within the protein?
Hydrogen bonds (stabilise the helices and the sheets) Ionic bonds (electrostatic attraction) Van der Waals Hydrophobic interactions
Why is glycine not chiral?
The variable group is just a hydrogen
What are the properties of arginine and lysine?
- positively charged
- basic (protonated at physiological pH)
What are the properties of histidine?
- positive charged
- protonated below pH 6
What are the properties of glutamate and aspartate?
- negatively charged
- acidic at physiological pH
What form (in terms of chirality) are amino acids found in?
L-form
What is the binding in the secondary structure?
hydrogen
ALPHA HELICES:
Are right handed or left handed helices usually favoured?
right handed
ALPHA HELICES:
why is proline a ‘kinky’ amino acid?
when proline is joined to the polypeptide chain, the NH group is lost
this means that the side chains cannot (hydrogen) bond to the C=O group or other amino acids/residues
this distorts the helical formation and puts a kink in it
ALPHA HELICES:
there are hydrogen bonds between C=O and N-H every ___ amino acids
4
What is the name of the conformation that proteins fall into?
This can be spontaneous or be caused by _____
single conformation of lowest energy
chaperones
