3D Protein Structure Flashcards
Describe peptide bond formation
OH from carboxyl group leaves and binds with H from amine group of neighboring amino acid to form water will amide bond forms between remaining C and N
Secondary structure
Think local folds
alpha helix, beta sheets, beta turns
Important about peptide bond in protein structure
resonance form puts 6 atoms in a plane
Phi and psi
Rotation angles around alpha carbons
Favors trans configuration
3 forms of secondary structures
Alpha helix - densely packed, R groups are sticking out & are not involved so can be formed regardless of sequence, can be amphipathic to interact with different molecules
Beta sheet - loosely packed, antiparallel, R groups alternate & are not involved so can be formed regardless of sequence, can be amphipathic to interact with different molecules
Beta turn - held by H-bonds, 4 carbons make the turn, R-groups not very involved so can be formed regardless of sequence
What secondary structures are amphipathic
Beta sheet & alpha helix
Name the biggest force holding together the proteins in an aqueous solution. Where could this present as an example?
Hydrophobic, makes sense since it is aqueous
In the cytoplasm of a cell because it is watery
Name all forces at work in protein structure
Hydrophobic interactions
Electrostatic interactions
H-bonds
Disulfide bonds
What are some common parallel beta-sheet folds?
Saddle sheets - twisted, saddle shape
Barrel sheets - fold and twist into a round barrel shape
These are common folds in different major types of proteins and are not indicative of protein chemical make-up per se
What are lipid proteins primarily driven by when folding?
Hydrophobic interaction (ex. bacteriorhodopsin)
EXAMPLE OF LIPID PROTEIN:
Describe porin
Lipid protein that acts as a pore by having a hydrophobic exterior and a hydrophilic pore on the interior
EXAMPLE OF LIPID PROTEIN:
How can an alpha helix be inserted into a hydrophobic lipid membrane?
By its hydrophobic amino acid side chains (ex. prostaglandin H2 synthase)
Where do membrane anchors come from?
Give examples
Post-translational modifications Phosphorylation Glycosylation Acetylation Methylation
What is significant about post-translational modifications in lipids?
They provide anchoring for the protein into the lipid membrane
What is an important characteristic of proteins? Explain
They are dynamic:
Polypeptide flexibility Alternative conformations (Hb) Intrinsically unstructured - disordered to some extent
Describe the folding pathway
Classes of helpers
There are a variety of enzymes and other mechanisms to assist in correct folding
disuflide isomerases, peptidyl isomerases chaperonins, chaperones
Describe the protein problem in patients with cystic fibrosis
Disease of protein folding kinetics: folding happens too slowly and so checkpoint enzymes think that these proteins are messed up and begin to degrade them
Describe the protein problem in patients with sickle cell disease
Disease of protein aggregation: One mutation causes lack of O2 binding and thus a hydrophobic patch to be exposed. Protein consequently wants to get out of aqueous environment. It panics and quickly binds to another protein. When many do this a sickle-cell forms
Describe the protein problem with Hungtington’s disease
Disease of abnormal protein-protein interaction: protein that encodes has a lot of glutamines in a row, but when the run of glutamines gets above 39 (normal is 6-39), Huntington’s start to set in
What other disease is thought to develop from abnormal protein-protein interactions?
Alzheimer’s
What are examples of quaternary proteins?
Hemoglobin and myoglobin
What is heme?
A tightly-bound (prosthetic group) cofactor in hemoglobin and in myoglobin that binds O2
