Wolberger_proteins Flashcards
T/F: proteins constitute majority of cells dry mass
True
components of a protein (4)
N-terminus (NH2, amino), side chains, polypeptide backbone, and C-terminus (COO-, carboxyl)
polar amino acids with uncharged side chain (5)
Asparagine, glutamine, serine, threonine, tyrosine - “All good souls thank tyra” - STTAG
polar amino acids with positive side chain (3)
Arginine, lysine, histidine - HAL
polar amino acids with negative side chain (2)
Aspartic acid, glutamic acid
hydrophobic amino acids (10)
FAMILY WV - phenylalanine (F), alanine (A), methionine (M), isoleucine (I), leucine (L), cysteine (Y), tryptophan (W), valine (V)
four weak forces shaping protein structure
hydrophobic force, ionic bonds, hydrogen bonds and van der waals attractions
At pH=7 the amino and carboxyl groups are -
ionized
Proteins consist exclusively of L or D-amino acids?
L
basic amino acids (3)
same as amino acids with positive side chain - arginine, lysine, and histidine
size range of majority of proteins
50-2000AA
why are alpha helices and beta sheets so prevalent?
because they result from hydrogen bonding between N-H and C=O groups in polypeptide backbone, meaning they are largely agnostic to amino acid side chain composition and can adopt a regular, repeated conformation despite AA seq (mosttly)
coiled-coil
secondary structure formed of alpha helices wrapped around each other (largely 2, sometimes 3 or 4), such that the nonpolar side chains are protected from aqueous environment
protein domain
substructure of a protein that can fold independently of the rest of the protein into a compact, stable structure
two types of b sheet structures
antiparallel (polypeptide backbone folds back and forth upon itself, with each section of the chain running in the direction opposite to its immediate neighbors), parallel (sheets form from neighboring segments of the polypeptide backbone that run in the same orientation)
how many domains can proteins have
1 to several dozen, connnected by short, relatively unstructured lengths of polypeptide chain
some advantages to intrinsically unstructured regions (5)
1] allow for movement and flexibility, ie elastin - 2/3] binding/signaling - form binding sites for other proteins that are of high specificity, yet readily altered by posttranslational mods , ie RNA pol, 4] tethering - can hold two protein domains in close proximity to bolster their interactions, ie scaffold proteins 5] diffusion barrier - clumps of disordered protein chains can create micro-regions of gel-like consistency in the cell that restrict diffusion
most common cross-linkage?
disulfide bonds
advantages to smaller subunits for the assembly of larger structures (3)
1] start-up cost - less genetic information needed, 2] errors not as big of a deal, 3] regulation - assembly and disassembly can be readily controlled through reversible processes
most conformationally flexible side chain
glycine, can adopt any phi/psi angle
most rigid side chain
proline, covalently linked to peptide NH, favorable at N-terminus of alpha helix
why does hydrophobic effect happen?
entropy of water increased when waters previously orientated at hydrophobic surfaces are released upon interactions of nonpolar molecules
Five organizing principles of proteins
hydrophobic effect, sequence, h-bonding, backbone restriction, packing
what is backbone restriction
a limitation of the phi/psi angles at which side chains can rotate due to steric clashes between atoms
