Peptide bonds are delocalized, giving partial charges and the ability to create a resonance structure.

This makes them Rigid (no rotations) and resistant to hydrolysis

C(alpha) is in two different planes

Peptide bonds like to ______ bond because of _____.

Each residue contains ____________ ?

Peptide bonds like to Hydrogen bond because of resonance structure

Each residue contains a H bond donor (amide) & acceptor (carbonyl)

Alpha - Helix

repeats every 3.6 residues. 

The carbonyl O (always pointing down) of each residue is H-bonded to the amino H of the 4th residue.

R groups stick out of helix and can form other interactions.

Beta - Sheet

2+ peptide chains side by side, pleating.  Can stack ontop of one another.

Parallel (causes diagonal H bonds w/ 2 different residues)

Anti-Parallel *STABLE* (causes straight down H bonds w/ only 1 diff residue)

R groups are above & below the plane.

Beta - Turns

Connect the ends of 2 adjacent strands in a B sheet, involves a 180 degree turn. 

C=O of 1st residue forms H bond with NH of 4th residue

Trans: R groups stay apart, no steric strain, common

Cis: Too much steric strain, not common

Measuring Secondary Structure

Best?

2nd Best?

3rd Best?

Increasing # of H bonds = ____ speed

^#H bonds slow speed down

Best = NMR: chemical shifts correlate with phi, psi, and H bonds slow down H-D exchange.

2nd Best = Circular Dichroism (CD): more common, easy, quick, differential absorption of L & R handed polarized light.  Estimates % of Alpha & Beta structure

3rd Best = Infrared Spectroscopy (IR): rarely used, H bond affects oscillation frequency, but H3O absorbs well in IR and gives a huge peak.  Does contain H bonding.

Controversial!!

arrangement of several elements of 2ndary structure and the connections b/w them. 

AKA "motif" and "fold"

Way 2ndary structure comes together to form specific shapes/configurations

Tertiary Structure

Quaternary Structure

Tertiary Structure

overall 3D arrangement of all the atoms in a polypeptide - incl random pieces

Quaternary Structure

In proteins with more than 1 polypeptide chain, it is the 3D arrangement of individual subunits.  Not all have this.

Fibrous: polypeptide chains arranged in LONG strands/sheets.  Repeating structure/pattern, incl super secondary.  Insoluable (hydrophobic inside & outside).  Often provide support, shape, protection.

Globular: polypeptide chain folded into spherical or globular shape, back on themselves.  Typically, multiple secondary structures present.  Often enzymes or regulatory proteins

Alpha-keratin

[image]

Keratin a-helix (x2) forms

2 chain (L handed) coiled coil (x2) forms

Protofilament (x2+) forms

Protofibril

Super twisting amplifies strength

nonpolar amino acids on interface b/w helices

DISULFIDE BONDS b/w cys residues add strength

Ex: hair, nails, claws, hooves, quills

Fibrous Protein

left handed helix forms 3 stranded r handed coil with 3 amino acids per turn

Repeating units: Gly - X (Pro) - Y (4-Hyp)

Only very small Gly can fit in tight spots

Pro & 4Hyp allow sharp twisting and kinks

higher order structures form cartiledge, tendons

psi ~ -60 degrees

B sheets arranged in overlapping layers into microcrystalline structure

Ala, Gly side chains allow close packing of sheets and interlocking arrangement of R groups

Does NOT stretch b/c B-conformation is already highly extended

Does Bend, held together by many weak (VDW) interactions

Globular Proteins

[image]

Have multi types of 2ndary &/or super-2ndary structures

How that stable structure comes together defines Tertiary Structure.  Most stable when B conformation segments individually twisted in R handed sense.

Wants to maximize # backbone groups H bonded; Densely packed!

Bury nonpolar surface ("hydrophobic effect") Primary driving force for tertiary structure

To exclude water from core, need 2+ layers of 2ndary structure

Connections bw elements can NOT cross/form knots.  Larger motifs can be made from smaller ones.

Tertiary Structure and Folding

___ folds observed again & again

___ structure more reliably conserved than ___ structure

Can provide info about _____

High similarities are in same protein ____

____ leads to ____

NINE folds observed again & again

TERTIARY structure more reliably conserved than PRIMARY structure

Can provide info about EVOLUTION

High similarities are in same protein FAMILIES

STRUCTURE leads to FUNCTION