Protein Structure 2 Flashcards
Secondary structure
local regions of proteins characterized by . . .
- similar phi/psi values through phi/psi torsion angles
- backbone hydrogen bonding patterns
Nobel Prize Winner in Chemistry, 1954
Pauling, research in alpha-helix
hydrogen bond
weak bond involving sharing an electron with a hydrogen atom
Strong vs. weak hydrogen bond
this depends on the directionality of the h-bond
strong will be straight
weak will be diaganol
alpha-helix
secondary structure formed by the protein chain folding into a right-handed spiral
traits:
- right-handed helix
- side chains point out and perpendicular with helical axis
- backbone is held together by
hydrogen bonds between the backbone
amides of an i and i+4 amino acids:
C=O (i) and N-H (i+4)
helical axis
imaginary line that runs through the center of a helical structure and follows the path of its spiral twist
Amphipathic helix
type of alpha helix in which the amino acid side chains have a hydrophobic (water-repelling) side and the opposite side is hydrophilic (water-attracting)
found in cell membranes and used in membrane transportation by packing the protein in hydrophobic area and using the hydrophillic part to move through aqueous environments
important for protein packing and function.
alpha helix - #s
- Hydrogen bond pattern: C=O (i) and N-H (i+4)
- Residues per turn: 3.6
- Distance of one complete turn of the helix: 5.4 Å
3 ^10 helix
- Hydrogen bond pattern: C=O (i) and N-H (i+3)
- Residues per turn: 3
- Distance of one complete turn of the helix: 6 Å
pi helix
- Hydrogen bond pattern: C=O (i) and N-H (i+5)
- Residue per turn: 4.4
- Distance of one complete turn of the helix: 4.8 Å
beta sheet aka pleated sheet
beta strands that are connected laterally by hydrogen bonds to form a sheet-like structure
antiparallel beta-sheet
type of beta sheet where the beta strands run in opposite directions
strucuture is stronger bc h-bond is straight instead of diagonal
parallel beta-sheet
type of beta sheet in which the beta strands run in the same direction
structure is weaker bc h-bond is diagonal instead of straight
beta barrel
cylindrical structure formed by beta sheets that are arranged in a circular or barrel-like shape
- beta sheets are (usually) antiparallel and strands are connected by loops which create the barrel structure
twisted beta sheet
beta sheet structure in which the sheet adopts a twisted or helical shape rather than remaining completely flat
- still in progress . . .
beta turn
short, non-regular secondary structural elements in proteins that cause an abrupt change in the direction of the polypeptide chain
- turns 180 degrees
- A hydrogen bond forms between the carbonyl oxygen (from the backbone of one amino acid) and the amide proton (attached to the nitrogen of the peptide bond) of an amino acid that is three residues away in the protein’s sequence. This interaction helps stabilize the turn or bend in the protein structure.
What are common in beta turns?
- Proline in position 2 or glycine in position 3 are common in
b turns
Type I beta turn
beta turn that has a straight hydrogen bond
This type is stronger over the other
Type II beta turn
beta turn that has a diagonal hydrogen bond
This type is weaker over the other
when is amino acid propensity preferred?
conditions align in such a way that certain chemical reactions or processes are more likely to occur
Ramachandran plot (respect to secondary structure)
visual graph presenting backbones in a protein where phi = x and psi = y. range is typically -180 to 180
propensity
tendency or likelihood of a molecule or chemical species to undergo a specific reaction or behave in a certain way under given conditions
why is glycine and proline not preferred in creating proteins?
Glycine is NOT chiral
Proline is chiral but sidechain bonds with backbone
True or False: hydrogen bonds have nothing to do with sidechain R groups in alpha helix
True
