1phi degree rotation of what bond
N-C bond
2psi degree rotation of what bond
C-C bond
3Ramachandran Plot
map displaying polypeptide backbone conformation
4Dark green on Ramachandran Plot
favorable allowed phi and psi
5Light green on Ramchandran plot
allowed but more crowded phi and psi angles
6Proline Ramachandran Plot exception
very restricted due to side chain
7Glycine Ramchandran Plot exception
very flexible, lot more phi and psi angles
8Anfinsen Experiment
4 pairs of disulfide bonds (must be with 2 cys) stabalize small protein
9Primary Structure
sequence of amino acid residues linked together with peptide bonds
10Secondary Structure
Regular structures formed by hydrogen bonds of the carbonyl and amide
groups of amino acid residues
11Tertiary structure
secondary structure elements form 3D structure of polypeptide chain
12Quarternary structure
spatial arrangement of subunit and nature of interactions
13What is alpha helix?
type of backbone; h bond formed btwn -C=O of residue i and -NH of residue i + 4
14alpha helices are
highly restricted
15What aa is NOT compatible with an alpha helix structure? Why?
Proline - phi angle - does not have -NH group
16what aa's are not very compatible with alpha helix?
Ile, Thr, Val, Ser, Asp, Asn, Gly
17Why are Ile, Thr, and val not very compatible with alpha helix? Why is Leucine?
branching. Leucine is compatible because branching occurs on gamma carbon
18Why are ser, asp, and asn not very compatible with alpha helix?
Polar group side chain; competes with main chain for hydrogen binding
19Why is gly not very compatible with alpha helix?
too flexible
20Alpha Helix is often used to cross the ----. How?
lipid bilayer; -hyrdophillic parts form h bonds with interior of helix -protuding nonpolar side chains interact with hyrdophobic parts of lipid bilayer
21Antiparallel beta sheets
- h bonds are not unifromally distrubuted
- VERY STRONG h bonds because they are collinear
22parallel beta sheets
- h bonds are uniformly distributed
- weak h bonds because they are not collinear
23Mixed beta sheets
both parallel and anitparallel
24How are antiparallel beta strands joined?
short loop; beta-haripin motif
25How are parallel beta strands joined?
long loop adopts alpha helical stucture; beta-alpha-beta motif
26Water soluble proteins fold
into compact structure with nonpolar core
27Porin is an exception to water soluble proteins. why?
hyrdophobic residues are on the outside and hydrophillic channel inside
28Domain
any segment in polypeptide that can FOLD INDEPENDANTLY
31four subunits of quarternary structure
tetramer
32X-ray crystallography
- can achieve ATOMIC resolution
- no limit in size
- has to be crystalllized
- majority of structures are obtained through this
33NMR
- can achieve atomic resolution
- limit in size
- doesn't have to be crystallized
34Electron Microscopy (EM)
uses a beam to create images
35Protein Crystallography Steps
1. Purify proteins of protein complex: >2mg (5-30mg/ml)
2. Grow crystals of the protein that diffract well (can take a long time)
3. Obtain X-ray diffraction data
4. Compute electron density maps
5. Fitting/ refinement
36Anfinsen experiment details
- Treated protein with Urea to denature the protein
- Thiol group is a reducing agent, and beta-mercaptoethanol becomes oxidized
- If you remove urea and the beta-mercaptoethanol, the protein will refold back into its
native form
- If you remove beta-mercaptoethanol before the urea, the protein won’t refold correctly