ABI 102 Exam 2

neutral drift

random mutations in time that don’t affect function

cytochrome C

peripheral membrane protein with universal function: shuttles electrons between complexes three and four on outer surface of inner membrane

invarient residues

amino acid residues essential to function are conserved

conservatively substituted residues

residue might be replaced and still serve original role

hypervariable

might allow any amino acid replacement (subject to neutral drift/shift)

orthologous proteins

homologous proteins with the same function in different species

paralogous genes

genes evolved independently after a gene duplication event and one gains new function

1º structure

linear sequence of amino acids

2º structure

local spacial arrangement of a polypeptide’s backbone atoms w/o regard for its side chains, general 3D form of local segments of a protein (nothing to do w R-group)

3º structure

3D form of an entire polypeptide, including its side chains (R-groups)

4º structure

spacial arrangement of a proteins subunits

2º structure general

peptide bonds assume trans configuration, planar, rigid structure caused by conformational constraint

regular 2º structure

composed of sequences of residues w/ repeating Φphi and Ψpsi values

Φphi

torsion angle around Ca-N bond

Ψpsi

torsion angle around Ca-C bond

alpha helix

coil, right handed, 3.6 residues per turn, side chains project outwards and down (avoids steric hindrance), Gly and Pro are alpha helix breakers

B sheets

uses H-bonding of polypeptide backbone, H-bonding occurs between neighboring polypeptide chains.

• antiparallel and parallel sheets

antiparallel B sheets

• orientation of backbone causes pleating effect, aka B-pleated sheets

• side chains extend to opposite sides of sheets

parallel B sheets

• usually see 2-22 strands sheets

• parallel sheets believed to be slightly less stable (possible distortion with H-bonds)

situation to avoid with 2º structure

• no charged polar side chains next to each other of same charge

• no bulky a.a like Tyr, Ile, Trp, they constrain structural possibilities

globular proteins

water soluble, characterized by compact and highly folded structure, majority of proteins, contain several types of secondary structure

fibrous proteins

stiff, elongated conformation, forms fibers (keratin and collagen)

keratin

fibrous protein, mechanically durable, relatively unreactive, alpha keratin in mammals, B keratin in birds, alpha keratin resembles alpha helix (3.5 residues per turn)

collagen

fibrous protein, most abundant vertebrate protein, strong, insoluble fibers that are stress-bearing (connective tissue), one collagen molecule consists of three polypeptide chains

How does Proline prevent alpha helix formation

Lacks the backbone N-H to form the intra-helical H-bonds and has a bulky side chain that disrupts regular helical structure.

nonpolar residues- aa spacial distribution

Val, Leu, Ile, Met, Phe occur mostly in the interior of the protein

charged polar residues- aa spacial distribution

Arg, His, Lys, Asp, and Glu are usually on the protein surface in contact w/ aqueous solvent

uncharged polar groups- aa spacial distribution

Ser, Thr, Asn, Gln, Tyr could be either location (interior or exterior), When inside, they are H-bonding with other groups

Domains

globular clusters that give proteins a multi-lobular appearance, 40-200 aa, each domain usually has layers of 2º structure, usually have their own function

Most common domains

form compact and self folding component of the protein, that usually represents a discreet structural and functional unit

• tolerate amino acid deletions, substitutions, and insertions, support essential biological functions

Components of 3º structure

fold (3D arrangement), Motif (supersecondary structure, subcomponent of fold, several motifs comprise a domain), domain