BCH4024 Lecture 4

proteins are stabilized by ___ interactions

noncovalent

function is based on the ____ structure

tertiary or 3D

native

functional, stabilized by weak interactions but with decent stability

H bonds, Hphobic effect, ionic interactions

disulfide bonds rare but important

solvation layer

shell of H2O structure around Hphobic molecule

decreases with np clusters, causes increase in entropy

repeating units optimize ____

H bonding and salt bridges

R groups are (in/out) of the plane of a peptide group

out

alpha helix

simplest, common, maximizes H bonds

each helical turns 3.6 residues or 5.4A

1 pitch per helix

proline

introduces destabilizing kink

glycine

has high conformational flex and takes up coiled structures

right-handed

R groups protrude away

most common;

backside arrow faces right

extended left-handed heliz

theoretical but not stable enough;

backside arrow faces left

beta conformation

backbone extends into zigzag, organizes into sheets

strand = single protein segment

sheet = several strands

anitparallel beta sheet

more frequent, H bonds are linear = stronger, upside down next to right side up

parallel

copy paste, go same direction, less stable

beta turns

connect ends of 2 antiparallel sheets;

4 residues and 180 turn

often involves Pro and Gly

Ramachandran plots

visualize phi and psi angles to test quality of structure

!!ci

circular dichroism (cd) spec

measures diff in molar absorption of left v right handed light

delta epsilon = epison L - epsilon Rch

chromophore

peptide bond, can absorb light

membrane proteins

embedded in Hphobic lipid membranes

intrinsically disordered proteins

lack stable tertiary structures;

lack Hphobic core;

lots of charged residues which helps multiple binding partners;

can change structure

fibrous protein

long strand or sheets;

give strength and flex;

simple repeating element, H2O insol

alpha helix crosslinked by disulfide bonds (fibrous proteins)

tough, insol, protection, hardness, flex;

keratin

beta conformation (fibrous proteins)

soft, flex filaments;

silk fibron

collagen triple helix (fibrous proteins)

high tensile strength, no stretch;

tendon collagen, bone matrix

alpha keratin in hair

right hand alpha heliz;

2 strands of alpha keratin parallel and supertwisted to the left bc of their Hphobic side chains;

rich in Hphobic residues ala, val, leu, ile, met, phe;

cross link stabilized by disulfide

collagen in connective tissue

left handed tripeptide Gly-Pro-Hyp;

right trwisting of 3 poly;

fibrils cross linked by covalent bonds with Lys or His

scurvy

lack of vitamin C

degeneration of connective tissue

vit c required for hydroxylation of proline and lysine in collagen

globular proteins

folded into spherical or globular shape;

fold back onto each other to be super compact

enzymes, transport, motor, regulation, immunoglobulins

myoglobin

alpha helical regions, binding pocket, and Hphobic R chains

motif

fold with 2+ elements of secondary structure

beta-alpha-beta loop or beta barrel

domain

polypeptide chain part that is independently stable

protein folding rules

bury Hphobic R groups with 2+ layers of secondary

a helix and b sheets are in diff. layers

beta conformation best with right hand connections

alpha-beta barrel

series of alpha-beta-alpha loops so B forms barrel

!

topology diagram

!

families

same primary functions and or tertiary structure

superfamily

2+ families with similar structural motif and function but not sequence

oligomer

multimer = multi-subunit protein