Lecture 5 - Amino Acids Flashcards
Describe the different structures
Primary: amino acid sequence
Secondary: local conformation
Tertiary: 3D structure
Quaternary: association of protein subunits
Which aa is not chiral?
Glycine
What is the L isomer
L: levorotary, D: dextrorotary
When R is facing you, H on top, amine group to left, carboxyl group to right
What is the zwitterion
At physiological pH, when there is no net charge, but both ionizable groups on the main chain are ionized
Why does glycine impart flexibility?
Doesn’t contain an R-group, so no steric hindrance
Which aa has an additional chiral center
Isoleucine
Why are tyrosine and tryptophan only moderately hydrophobic?
Aromatic ring contributes to hydrophobicity, but presence of electronegative atoms moderates this
What are the basic amino acids?
Lysine, Arginine, Histidine
Lysine has amine group, arginine has guanidinium group, histidine has imidazole group
How is a disulfide bond formed?
Hydrogens at top of cysteine R-group lost, covalent bond forms between S-S
Which aromatic acids can be used to measure protein concentration using UV absorbance at 280nm?
Tryptophan, tyrosine, phenylalanine
What is the minimum number of ionizable groups
2 –> carboxyl and amine group FOR FREE AMINO ACIDS
What are the pKas of the basic and acidic aa
Glutamate --> 4.1 Aspartate --> 4.1 Arginine -->12.5 Lysine --> 10.8 Tyrosine -->10.9 Cysteine --> 8.3 Histidine --> 6 N-terminus --> 8 C-terminus --> 3
Which order is the hydrogens lost in a histidine
c-terminus, off of Nitrogen in R-group, N-terminus
Describe a Ramachandran plot
Phi bond angle is on the x-axis, psi bond angle is on the y-axis. top left quadrant=beta sheets, top right quadrant=left-handed helices, bottom left quadrant=right handed helices
