Amino acids Flashcards
Amino acids are grouped into
5
what are the five groups amino acids are grouped into
A. Non polar(aliphatic, hydrophobic)
B. Aromatic
C. Polar
D. Negative at pH 7
E. Positive at pH 7
list the amino acids in the non polar, aliphatic, hydrophobic group
Glycine, Alanine, Valine, Leucine, Isoleucine, Proline, Methionine
Why is the C-N bond rotation constrained
Because it’s a double bond and shorter
Why is the R group in alpha helices in trans
To prevent clashing of R groups
What are the features that disrupt alpha helixes
Electrostatic repulsion
Bulky r groups
Proline amide cannot become planar
Features of the alpha helices
Peptide bond is planar
Hydrogen bonds form between every fourth amino acid
R groups points away from helix to minimize contact
In electrostatic repulsion, at low pH what could you observe with the alpha helices and the R group
At a low pH it had a lot of alpha helices and glutamate was protonated
In electrostatic repulsion, at high pH what could you observe with the alpha helices and r group present
It had less alpha helices and the glutamate was deprotonated causing more electrostatic repulsion which is more destabilized
What can you compare between anti parallel beta sheet and parallel beta sheet
Antiparallel is less compact, longer and more stable whereas parallel is more compact and less stable
What can you say of collagen compared to normal alpha helices
It is five times longer
What is the main stabilizing feature of the tertiary structure
Hydrophobic effect
why is reversibility key in protein ligand interaction
reversibility creates room for flexibility and the ability to adapt to continuous environmental changes
what is allostery
when the binding can also be influenced by the binding of other molecules
what is induced fit
when the binding of the ligand to protein creates structural changes to the protein
