test 1 part 3

Primary Structure

sequence of amino acids covalently linked to form a polypeptide chain. It is NOT the folding of a protein, but the sequence that determines the fold.

seconadry structure

Local folding held together by hydrogen bonds

tertiary structure

folding of the secondary structure elements into a compact, 3d structure. Often this folding creates domains of folded protein

quarteary strcutre

association of 2 or more folded proteins into a multisubunit complex. These may be identical or different subunits

to further define protein secondary strcutre we use

torsion angles

N to alpha carbon is

φ

alpha carbon to CO is

ψ

carbon to nitrogen is

ω

ideal φ torional angle in alpha helix

-57 degrees

ideal ψ torsional angle in aplha helix

-47 degrees

the alpha helix backbone atoms pack closely together making

favorable van der waals contacts

H bonding occurs in the alpha helix between the C=O residue and the

NH of residue i+4

the H bonds within an alpha helix are

near linear and almost parallel to the helix axis

the overall dipole effect on the alpha helix is a

partial net positive charge on the amino end and a negative charge on the carboxyl end

the dipole arrow of an alpha helix points

towards the carboxyl end

the antiparallel b sheet is the

most stable with reuglar hydrogen bonding pattern and side chains that alternate above and below the sheet

ideal φ and ψ torsional for antip sheet

φ= -139 degree

ψ = 135 degrees

parallel b sheet

more staggered hydrogen bonding pattern, not as regular

pleat rolls a bit more

side chains go up and down

h-bonds not at right angles

ideal φ and ψ torsional for p sheet

φ = -119

ψ = 113

regiosn inside membranes are frequently

alpha helixes whose surfaces are covered in hydrophobic side chains

a coiled coil is a

strucutral motif in proteins in which two alpha proteins are coiled together

amphipathic

one side of the helix is hydrophobic and the other side is hydrophilic

amino acids seperated by 3-4 amino acids are

on the same face of a helix

A/B structures are the most

observed domains and contain a mixed b sheet surroudned by alpha helixes

all the glycotic enzymes and proteins that beind and transport metabilosites are

a/b structures

in A/B proteins

binding crevices are formed by loop regions

what are the three main classes of a/b structures

1. closed barrel

2. open twisted sheet

3. horseshoe

Closed Barrel a/b structure

contains a core of twisted parallel b-strands

Antiparallel b-structures comprise the

second large group of protein structures

what group of structures is the most diverse for proteins

beta structures

beta sheets have an unusual twist which creates a

barrel-like structure

barrel's have three key strucutures

1. up-and-down barrels

2. greek keys

3. jelly roll barrels

All-beta-sheet proteins

immunoglobulin fold

an antibod