3D Protein Structures (Ch. 4) Flashcards
Protein stability
tendency to maintain a native conformation, stabilized by disulfide (covalent) bonds and, primarily, weak (noncovalent) interactions
Weak interactions
noncovalent. hydrogen bonds, the hydrophobic effect, and ionic interactions.
Hydrophobic effect
A type of weak, noncovalent interaction. Increase in entropy of surrounding water when nonpolar molecules are clustered together.
Peptide bond
rigid, planar
Ramachandran plot
psi vs. phi, which represent dihedral angles and work to define peptide conformation.
Secondary structure
The local spatial arrangement of a segment of a polypeptide chain.
Alpha-helix
2˚ structure. Can be left-handed or right-handed (more common). Stabilized by hydrogen bonds. Alanine shows greatest tendency to form alpha-helices. Proline is not conducive to alpha-helices.
Beta turn
2˚ structure
Beta-conformation
2˚ structure. Backbone of polypeptide chain is in a zigzag structure.
Beta turn
2˚ structure found in globular proteins. Connect the ends of two adjacent segments in antiparallel beta-sheet. Consists of a 180˚ turn in 4 AA’s. There are two types: Type I beta-turn and Type II beta-turn.
Beta-sheet
Several segments in beta-conformation, side by side. Hydrogen bonds hold the sheet together. The polypeptide chains can run parallel or anti-parallel.
Tertiary structure
Overall 3D arrangement of all atoms in a protein.
Quaternary structure
3D arrangement of protein subunits (2+ polypeptide chains).
Fibrous proteins
with polypeptide chains arranged in long strands or sheets. Make up most support structures. The group includes alpha-Keratin, collagen, and silk fibroin.
Fibrous proteins
with polypeptide chains arranged in long strands or sheets. Make up most support structures, since they provide strength and/or flexibility to the structure. The fundamental structural unit is a simple repeating secondary structure. The group includes alpha-Keratin, collagen, and silk fibroin.
Insoluble in water (lots of hydrophobic AA’s). Their strength is enhanced by covalent cross-links between chains.
Globular proteins
with polypeptide chains folded into spherical shape. Make up most enzymes and regulatory proteins, transport proteins and immunoglobulins. More compact shape.
Alpha-Keratin
A fibrous protein. Super strong. Only found in mammals. It is a right-handed alpha-helix. Two parallel strands form a coiled coil. Rich in hydrophobic AA residues. Disulfide bonds stabilize quaternary structure.
Collagen
A fibrous protein. Strong. It is a left-handed helix (not alpha!). A coiled coil made up of three polypeptides called alpha chains.
Collagen
A fibrous protein. Strong. It is a left-handed helix (not alpha!). A coiled coil made up of three polypeptides called alpha chains.
Silk fibroin
A fibrous protein, produced by insects and spiders. It is usually in beta conformation, and then close packing of beta-sheets, due to large amount of Ala and Gly. Structure does not stretch, but it is flexible –> beta conformation is already stretched, and the sheets are held together by weak interactions, not covalent bonds.
Silk fibroin
A fibrous protein, produced by insects and spiders. It is usually in beta conformation, and then close packing of beta-sheets, due to large amount of Ala and Gly. Structure does not stretch, but it is flexible –> beta conformation is already stretched, and the sheets are held together by weak interactions, not covalent bonds.
Myoglobin
Oxygen-binding protein in muscle cells. Stores oxygen and facilitates oxygen diffusion in muscle tissue. Contains a single polypeptide chain and a heme group
Myoglobin
Oxygen-binding protein in muscle cells. Stores oxygen and facilitates oxygen diffusion in muscle tissue. Contains a single polypeptide chain and a heme group. It’s predominantly alpha-helices.
Motif
Aka a fold. A recognizable folding pattern involving 2+ elements of secondary structure and the connection(s) between them.
