Proteins pt 2 (ppt 2)

primary

linear sequence of amino acids linked by peptide bonds

secondary

C=O is the acceptor

N-H is the donor

• hydrogen bonds forming

• no R groups involved here

tertiary

R groups start to interact here

• folds?

  • H bond, disulfide bridge, hydrophobic interactions, ionic bonds

quaternary

composed of multiple polypeptide chains or subunits

• not all proteins show this level of complexity

beta sheet parallel

angled bonds

beta sheet antiparallel

straight bonds

polypeptide turns and loops

can change directions with reverse turn (aka β turns or hairpin turns) or omega (Ω) loops

exact same sequence but one is alpha helix and the other is a beta sheet?

protein function will differ and might be suited better in one structure vs. the other

hydrogen bonding in alpha helix

whats the pattern? REWATCH VID

motif

• combos of secondary structures

domain

• Independent regions within a polypeptide, connected by a short link

• can have motifs but not the inverse

intrinsically disordered proteins

protein that lacks stability and remains flexible: all organisms have it

• can be the entire protein or a large portion

• p53 →mutated cancer cell

globular protein

compact 3d shape and water soluable

fibrous protein

long fibers with structural roles

keratin

wool and hair

• 2 R handed alpha helices intertwined

• stabilized?
  → Hydrophobic interactions + H bonds

• TRUE alpha helices

collagen

found in skin, bone, tendons, cartilage, teeth

• Gly = tiny → fits in the center → every 3rd position

• Triple coil, not true alpha helices

what interactions stabilize the triple coil structure?

• H bonds between the chains

some amino acids disrupt alpha helix, why?

their unique side chains interfere with the rigid structure

thermodynamics of protein folding

• top of the funnel is the max disorder LEAST STABLE

• middle is where folds begin to form- Trial and error in folding

• bottom is the established folded proteins MOST STABLE