h bonding

vander waals 

electrostatic 

hydrophobic interaction

H bonds tend to form wherever possible within a protein structure,but usually component of atoms of peptide backbone 

also hb form around protein surface with water solvent or surface residues 

ionic interactions usually occur where on proteins

and why?

vander waals interactions are ubiquitous 

what function do they in protein

6.3 *** exam

All protein structures is based on what?

rotation at 

φ = 0°, ψ = 180° 

unfavorable because of overlap between the carbonyl carbons.

φ = 180°, ψ = 0

unfavorable because of overlap of the N-H hydrogens

φ = 0°, ψ = 0°

φ = 0°, ψ = 0° is unfavorable

Structure                f      y

Fully extended             -180  +180

Antiparallelb -Sheet  -139  +135

Parallel b-Sheet  -119  +113

Right Handed a-Helix  -57  -47

Left Handed a -Helix  +60  +60

310 Helix              -49  -26

a -Helix              -57  -70

what residues cannot form a ull complement of intra-helical H-bonds.

alpha helics: section what are the elements etc...

1st and last 4 residues cannot form full complement of intra helical HBONDS

=therefore acquire HB to solvent molecules

What do alpha helix have that is caused by carboxy C end and nitro N end? 

beta sheets 

describe the bonding characteristics of beta sheet

1. parallel Beta sheets-

2. antiparallel beta sheets

parallel beta sheets

Beta sheets have

extended residues _____ A apart. 

The entire structures is somewhat pleaded due to the ____ of the polypeptide bond

3.5 A

geometry 

beta sheet

[image]

alpha helix

[image]

beta bend

composed of how many residues 

special characteristic of beta bend

how many types of beta bend are there?

C comes before N in beta bend, C reacts with H of N 3 residues away

composed of four residues

carbonyl of first residue is HB to NH of the reside 3 amino acids away (rather than 4) 

allows the peptide to turn back on itself through 180 degrees 

***2 types of beta bend : type 1 type 2

only POSSIBLE with glycine bc/ of third residue 

function of fibrous proteins ** on exam 

characteristic 

structural role 

mechanically strong

resisitent to solubilization in water 

dilute salt solutions 

1. alpha keratin

2. beta keratin

3. collagen 

claws fingernails 

hair

and horns in mammals 

think alpha dog- has nails and horns!!!

C-----4----->NH

C comes before N- 4 residues away rather then 3 in (beta bend)

The core, rod like structure comprised of the tightly coiled polypeptide.

-each carbonyl forms a hydrogen bond with the amino group of the  4th residue ahead in the sequence.

-Each residue is separated by 1.5 Åtranslationally and each is 100 degrees from the next. Thus we have 3.6 amino acids per turn.

beta keratin characteristics 

NOT IMPORTANT 

only alpha and collagen are

basic unit of collagen

3 interwined polypeptide chains MW: 285,000

1. lg number of folded structures that polypeptide chains can adopt

2. chemistry of the side chains- providing multiple reactivity opportunities 

Why does the globular protein core consist primarily of α–helices and β–sheets?

Protein ______ are nature’s modular strategy for protein design

are structure and function are always the linked

same domains = same function and sturcture?

NOO false.

they are not linked

sequence (see Figure 6.23 ie; TonEBP

continuous portion of the protein

sequence (see Figure 6.23 ie; TonEBP

separate folded monomeric protein subunits associate to form the oligomeric protein

independent monomeric protein aggregations that fold onto one angother forming oligmeric protein better known as quarter structures

nvolve nonidentical interfaces. These surfaces must be complementary, but they are generally

not symmetric.

similar to puzzles. Although the pieces fit together (complementary) , they are not alike. therefore they are NOT symetric either!

Many multimeric proteins are symmetric arrangements of asymmetric objects. All of the polypeptide’s a-carbons are asymmetric and the polypeptide nearly always folds to form low-symmetry structures.

Thus protein subunits do not have mirror reflection planes, points, or axes of inversion

structure of alpha helix

residue

what is bonded to what?

how many angstroms and residues apart are each

The core of the alpha-helix is a rod like structure comprised of the tightly coiled polypeptide. The side chains of the amino acids form a helical array out from the helix

-The helix forms spontaneously as a consequence of each carbonyl forming a hydrogen bond with the amino group of the  4th residue ahead in the sequence.

-Each residue is separated by 1.5 Åtranslationally and each is 100 degrees from the next. Thus we have 3.6 amino acids per turn.

Pairs of right handed a-helices

wrap around each other to form a

left-twisted coiled coil.

Primary structure of helical rods consists

of 7-residue repeats: (a-b-c-d-e-f-g)n,

where a and d are nonpolar.

This structure promotes association of

helices to form coiled coils

identical subunits

non-identical subunits

isologous- interacting surfaces are identical- structure is "dimeric" and close with 2 fold axis of symetry

heterologous- nonidentical interfaces- complementary but NOT symmetric like isologous

how are alpha keratin fibrous proteins formed through alpha helics??

which resides are nonpolar?

Pairs of right handed a-helices

wrap around each other to form a

left-twisted coiled coil.

Primary structure of helical rods consists

of 7-residue repeats: (a-b-c-d-e-f-g)n,

where a and d are nonpolar. 

Individual strands in the beta-sheet tend to comprise 5-10 residues.