Lecture 3 - Proteins Flashcards
What is the major driving force of protein folding?
The hydrophobic effect. Polar amino acids are at surface, non-polar amino acids are in middle
What are the features of the peptide bond?
Thermodynamically unfavorable to form, but kinetically stable due to resonance.
Low reactivity, rigid, and nearly planar
Large dipole moment in trans configuration (partial negative towards oxygen, partial positive towards nitrogen)
What are phi and psi?
Rotation around main chain bonds connected to alpha carbons is permitted.
Phi: Angle between alpha carbon and amide nitrogen
Psi: Angle between alpha carbon and carbonyl carbon
What is a Ramachandron plot and what dictates it?
A plot that uses steric hindrance to assess the probability of certain phi and psi combinations which will yield different motifs in proteins.
What defines protein secondary structure?
alpha helices, beta sheets, and beta turns / loops formed by H bonding between atoms of peptide bonds only (not side chains)
What is the orientation of amino acids in alpha helicies?
Backbone atoms point inward, side chains of amino acids point outward. CO carbonyl group accepts a hydrogen bond from amide group of another amino acid looked 4 positions down towards the C terminus. The screw direction follows the right hand rule
What is the spatial distribution of alpha helices?
1.5 Angstrom rise per amino acid, and a rotation of 100 degrees. 3.6 amino acids are thus needed per turn.
What is a beta sheet vs beta turn / loop?
Beta sheet - secondary structure formed by amino acids that are far away interacting via hydrogen bonds. They are strands oriented parallel / antiparallel.
Beta turn / loop - link successive runs of helices or strands together, and have a directional change
What defines a beta turn? What amino acids are typical?
4 amino acids in which that alpha nitrogen of amino acid 1 and the carbonly oxygen of amino acid 4 are H-bonded.
Glycine and Proline are typical
What defines a beta loop?
They are well ordered structures that are between motifs, and contribute important functionality to many proteins.
What is a helix forming vs sheet-forming amino acid?
Helix forming: long-ish / straight. All are, with the exception of alanine (not really that long)
Sheet forming: Shortish / stubby, includes all aromatic rungs, as well as isoleucine
What are two helix breakers and why?
Proline - rotation around phi angle is impossible since it’s R group is bound to the amine.
Glycine - too many confirmations are possible with such a small R group, making helix unfavorable.
What defines protein tertiary structure?
Dependent on amino acid side chains, often very far apart. Disulfide bonds, hydrogen bonds, ionic bonds, van der Waals bonds after hydrophobic effect, etc.
What is the most common type of membrane transporter tertiary structural motif, and what is an exception?
Most cross via helix bundles -> bundles of alpha helices
Porins of outer mitochondrial membrane use transmembrane Beta-barrel motif, which has beta strands arranged in a circular loop.
What are the two classes of protein tertiary structures and what defines them?
Fibrous - insoluble, extended wire-like rods. Often with disulfide bonds. Hair, connective tissue, muscle fibers
Globular - compact, globe-like structures. Hydrophilic will be soluble, hydrophobic will be insoluble except in lipids
