Protein Building Blocks

Question 0

Ramachandran map

Answer 0

Of allowed phi and psi angles (only in dark areas) Limited space allows only certain structures to form Glycine has large dark areas because it only has a H for side chain, allowing chain to be more flexible

Question 1

Peptide bond

Answer 1

Is trans and planar due to the partial double bond between C and N Phi and psi dihedral angle combinations determine backbone of protein (180 in almost fully extended beta sheets, 0 in scrunched alpha helical)

Question 2

Hydrophobic side chains

Answer 2

Alanine Valine Leucine Isoleucine Proline (imino, produces kinks and turns) Phenylalanine Tyrosine Tryptophan Methionine Glycine (flexible)

Question 3

pKa

Answer 3

pKa=pH at which 1/2 of ionizing groups are protonated and other half are deprotonated High pKa means bind H+ tightly Low pKa means bind H+ weakly pHpKa means low H+ so draws off H Local environment can change pKa (when asp is near a positively charged amino acid, pKa decreases because it wants to give up H+ more)

Question 4

Polar charged amino acids

Answer 4

Aspartic acid (pKa=4) Glutamic acid (pKa=4) Cysteine (pKa=8.5; thiol group S-S) Histidine (pKa=6.5; imidazole ring, can be used as catalytic residue) Lysine (pKa=10) Argenine (pKa=12)

Question 5

Polar uncharged amino acids

Answer 5

Serine Threonine Asparagine Glutamine

Question 6

Forces that determine protein structure

Answer 6

Primary structure: covalent Secondary, tertiary, quaternary: noncovalent

Question 7

Electrostatics

Answer 7

Opposite charges attract, like charges repel Strong in vacuum but weak in water because water interacts with charges Salt bridges are strongest, usually on protein surface Dipolar interactions are weaker because only difference in electronegativity not net charge

Question 8

Hydrogen bonding

Answer 8

Special case of electrostatic attraction Hydrogens bonded to electronegative (O, N, S) atoms which pull electron density from hydrogen