Lecture 11 + 12 Flashcards
Describe alpha-helices their hydrogen bond patterns and general location of the side chains
- alpha helix is a repeating coiled structure stabilized by intra-chain hydrogen bonds between carbonyl O and the amide H of the NH group (i+4)
- N is the donor and O is the acceptor
- character of alpha helix determined by R groups sticking out
Distinguish between a right and left handed helix
- Helices in proteins are almost always right-handed
Amino acids and alpha helices have dipole moments
- a single amino acid has a diploe moment across the peptide bond
- amino acid dipole moments add together to create an overall dipole moment in alpha helices with a partial positive charge on the N terminal and partial negative charge on the C terminal
Distinguish between a parallel and anti-parallel beta-sheets
parallel - beta-strands run in the same direction
- hydrogen bonds connect each amino acid on one strand with 2 different amino acids of the adjacent strand (1 to 2)
- side chains point outward
anti-parallel - beta-strands run in opposite directions
- hydrogen bonds are between NH and CO groups of one amino acid and CO and NH groups on an amino acid of an adjacent strand, connecting and stabilizing the structure (1 to 1)
- side chains point out on either side and alternate from one side to the other
Glycine and Proline in alpha-helices
- found less frequently than other amino acids
- proline residues often serve as “helix breakers” - found at the end of alpha-helices
- proline and glycine residues are often found at the boundaries of alpha-helices and in turns
- no hydrogen on the proline N when it is in a peptide bond
Where on the Ramachandran plot are the phi and si angles for amino acids in alpha-helixes and beta-sheets located
alpha helix - between 0 and -60 on y axis
beta strands - between 180 and 120
- larger area than alpha helices
- more flexible than coiled alpha helix
What is the general structure of amphipathic alpha-helix and distribution of hydrophobic/hydrophilic residues in these structures
Amphipathic = hydrophilic and hydrophobic properties
- these alpha-helices posses hydrophilic (polar) amino acids on one side and hydrophobic (non-polar) residues on the other
- membrane-binding domains of peripheral membrane properties
Describe the structure of an antibody
- made up of beta strands and sheets
- tetramer
- Fc, fragment crystallizable
- Fab, fragment antigen binding
- 2 heavy and 2 light chains
- disulfide bridges between heavy and light chains
What is the general structure of leucine zippers and distribution of hydrophobic/hydrophilic residues in these structures
- 2 separate proteins = dimer
- hydrophobic side chains allow the 2 proteins to zip and bring alpha-helices together
What is the general structure of alpha coiled coils and distribution of hydrophobic/hydrophilic residues in these structures
alpha coiled coils - alpha-keratin
- red line is R groups sticking out, provides stickiness to allow them to coil (strip of hydrophobic amino acids)
- seen in fibrin (blood clots) and myosin and tropomyosin
What is the general structure of non-alpha coiled coils and distribution of hydrophobic/hydrophilic residues in these structures
Non-alpha-helical coiled coils - collagen triple superhelix
- made up of 3 left-handed helical structures twisted together, alpha helix is 3.6 aa per turn
- collagen is the most abundant single protein in vertebrates
- helices held together by H-bonds in strong structure
- every 3rd residue is glycine found in the center of the three stranded collagen superhelix
- repeating peptide unit: Gly-Pro-4-Hyp
- 4-Hyp is modified, hydroxyproline -> can only be made if enough vitamin C
- Scurvy - deprived of vitamin C, defective collagen
What is the general structure of transmembrane alpha-helices and distribution of hydrophobic/hydrophilic residues in these structures
- outside has amino terminus
- inside has carboxyl terminus
What is the general structure of transmembrane beta-barrel proteins and distribution of hydrophobic/hydrophilic residues in these structures
- ex. porin, forms a selective channel in the outer membrane
- hydrophobic side chains line the outer surface to interact with lipid bilayer
- inner channel is lines with hydrophilic amino acids
What are the four structures of a protein and describe them
Primary structure - amino acid sequence
Secondary Structure - alpha-helix
Tertiary structure - folded polypeptide chain
Quaternary structure - assembled subunits
Describe beta-sheets and their hydrogen bond patterns and the general location of the side chains
- unit of a beta-sheet is a beta-strand
- peptide backbone is “extended” as opposed to alpha-helix
- stabilized by hydrogen bonds
- h-bonds form between the CO of one strand and the NH of an adjacent strand
- can be parallel or anti-parallel
- strands and sheets have a bit of a twist
- side chains stick out on either side of the sheet
- because r groups stick out they can give different properties to each face (hydrophobic on one side, hydrophilic on the other)
