Proteins 3 Flashcards
primary protein structure
sequence of a chain of amino acids
secondary protein structure
regular, local arrangement of polypeptide chain
tertiary protein structure
complete folding of a single chain
quaternary protein structure
association of multiple chains into multi-subunit structures
residue
an amino acid in a polypeptide chain
no. of peptide bonds in a polypeptide chain
no. of residues - 1
features of polypeptides in 3D
- flexible yet conformationally restricted
- peptide bond is essentially planar
- peptide bond is uncharged
2 configurations for a planar peptide bond
Trans, Cis
Cis causes steric clashes to arise, so Trans is strongly favoured
Alpha helix
This conformation is formed when the polypeptide chain is twisted by the same amount about phi and psi rotation
a helix may be characterized by the number, n, of peptide units per helical turn, by its pitch, p, the distance the helix rises along its axis per turn and by helical rise per repeating unit, d=p/n
define a repeat unit
a single turn of the helix
what is an alpha helix stabilised by?
hydrogen bonds between the NH and CO groups of the main chain
if the helix has a positive value for n
Right-handed helix, anticlockwise
if the helix has a negative value for n
Left-handed helix, clockwise
helical structures
only one helical polypeptide conformation has simultaneously allowed conformation angles and a favourable hydrogen bonding patter –> the alpha helix
the polypeptide made from L-alpha amino acid residues is …
right handed
torsion angles (phi)= -57 (psi) = -47 n=3.6 residues per turn p=5.4 Å d=1.5 Å
the polypeptide made from D-alpha amino acids residues is …
left handed
torsion angles phi = 57 psi = 47 n= -3.6 residues per turn p=5.4 Å d=1.5 Å
are essentially all alpha helices in proteins right or left-handed?
right handed
are alpha helices common in fibrous or globular proteins?
both
the combination of multiple alpha helices by loop and turn can construct large proteins such as Ferrin
Beta pleated sheet
composed of two or more polypeptide chains called β strands.
- common structural motifs in proteins
- β strand is almost fully extended. A range of extended structures are sterically allowed
antiparallel β sheet
neighbouring hydrogen bonded polypeptide chains run in opposite directions
parallel β sheet
hydrogen bonded chains extend in the same direction
how do β sheets compare with alpha helices
β sheets are structurally diverse more than α helices
what is a dipole moment
the product of magnitude of electronic charge of the molecule and the internuclear distance between the atoms in a molecule
which type of secondary structure has dipole moments?
alpha helices have a dipole moment, beta sheets have no dipole moment
Types of β turns
two types of β turn:
- Type 1 contains proline residues, occurs more frequently
- Type 2 always have Glycine as 3rd residues
features of loops and turns
connect segments of an alpha helix and beta strands
loop structures are often rigid and well-defined
Turns and loops invariably lie on the surfaces of proteins and often participate in interactions between proteins and other molecules
techniques used for tertiary structure analysis
- X-ray crystallography
- nuclear magnetic resonance
- cryo-electron microscopic studies
how does the properties of amino acids affect where they are found in the tertiary structures if proteins?
hydrophobic amino acids are found on the inside of the the structure
charged (polar) amino acids are found on the protein surface
how does the structure of globular proteins compare to fibrous proteins?
Insoluble fibrous proteins, such as those that make up keratin, collagen, and silk, have simple repeating elements of secondary structure
Globular proteins have more complicated tertiary structures, often containing several types of secondary structure in the same polypeptide chain
what is the ramachandran plot
a map of sterically allowed values of phi and psi rotations - only 3 regions are physically accessible to a polypeptide chain due to local steric clashes
C-N bond
Phi
C-C bond
Psi
