Protein Structure and Function 1 (L3) Flashcards
what is the bond between amino acids in a protein?
peptide bond (amide bond)
how is a peptide bond formed?
condensation/dehydration reaction
hydrophobic amino acids
A, V, I, L, M, F, Y, W (not charged)
hydrophilic amino acids
either polar or carry net charge:
Basic - K, R, H (positive charge)
Acidic - D, E (negative charge)
Polar uncharged - S and T (hydroxyl), and N and Q (amide group)
what functional group does the side chain of His contain?
imidazole ring (ring w/ 2 N’s)
special amino acids
P: structural rigidity
G: neutral, very small
C: sulfhydryl group that can form -S-S- bonds - relatively permanent covalent bond (adds rigidity)
what are the 5 amino acid modifications?
- acetylation
- phosphorylation
- hydroxylation
- methylation
- carboxylation
what two amino acid modifications are important for control of gene expression?
acetylation and methylation
what does the hydroxylation of tyrosine initiate?
catecholamine biosynthesis
what is one implication of phosphorylation?
activates/inactivates proteins as part of signal transduction - can get uncontrolled growth if a protein is always on (cancer)
what is the charge on an amino acid a function of?
pH
what is a buffer?
substance that resists changes in pH
Ka
acid dissociation constant
relationship b/w acid strength and Ka
higher Ka = stronger acid
lower Ka = weaker acid
H-H equation
pH = pKa + log ([A-] / [HA])
pKa
pH where [HA] = [A-]
when do buffers work best?
b/w pKa+1 and pKa-1 (best when pH = pKa)
primary structure of a protein
linear sequence of aa’s - N terminal and C terminal
how are proteins built?
from N-terminal to C-terminal
why do peptide bonds have planar properties and what does this cause in the arrangement of the polypeptide?
partial db character that prevents free rotation -> planar;
causes R groups to come off opposite of one another in an alternating manner
secondary structure - 4 types of side chain interactions
- electrostatic
- H-bond
- hydrophobic interactions
- covalent bond (disulfide)
alpha helix
side chain 1 interacts with side chain 4 aa away; side chains point to outside
beta sheet
antiparallel manner; side chains point perpendicular to plane of backbone; pleat due to permanent fold b/c of peptide bond rigidity
supersecondary structure - 3 motifs
- coiled-coil motif
- EFhand/helix-loop-helix motif
- zinc-finger motif
