Ch 4- 3D structures of Proteins

BIOL 4087

Spatial arrangement of atoms in a protein

Conformation

A protein in its active form (usually its most stable form)

Native Conformation

1. Hydrophobic AA’s are in the interior of the protein
2. Proteins will maximize H-bonding and electrostatic interactions
3. Peptide bonds are PLANAR

Proteins fold in a way that: (3)

Alpha Helix and Beta Sheet

2 types of secondary structure of proteins…

* Right-handed helix
* 3.6 AAs per turn (condensed in comparison to sheet)
* R-groups “stick out“ away from axis

Alpha helix

Proline

Which AA cannot be in an Alpha helix structure?

* 3.5 AAs per sheet (stretched out in comp to helix)
* R groups stick out above and below plane of sheet
* Antiparallel and parallel
* H bonded to nearby sheets (not close in primary)

Beta Sheet

Proline & glycine

Beta turns are usually composed of what AA?

transmissible spongiform encephalopathy

Importance of 2nd structure (disease gen. name) can cause…

3D structure of a single peptide

Tertiary structure

x-ray crystallography

How can you determine a peptide’s tertiary structure? (NOT NMR (solution structure))

a metal ion/organic molecule covalently bound to a protein that is required for protein activity

prosthetic group

made up of 2 or more elements of a secondary structure

motif/supersecondary structure/fold

the same thing!

A motif, supersecondary structure, & a fold are…

Globular part of a peptide with a distinct function.

Domain

1 exon

Domains may be coded by…

Makes gene expression easier for evolution

Why is it significant that domains are coded by 1 exon?

Interactions of subunits in a multi-unit protein

Quaternary structure