Protein primary, secondary, tertiary and quaternary structures Flashcards
Primary structure
amino acid in linear sequence
secondary structure
regions of regularly repeating conformations of the peptide chain, such as α-helices and β-strands (local folding)
tertiary structure
describes the shape of the fully folded polypeptide chain
Quaternary structure
arrangement of two or more polypeptide chains into multisubunit molecule
3 ways to represent a protein structure
(a) Space-filling model
(b) Cartoon ribbon model (shows secondary structure)
(c) Substrate-binding site view
factors contributing to protein structure
allowable bond rotations define the possible conformations of the polypeptide chain
weak non-covalent interactions between backbone and sidechain groups (e.g., hydrophobic, H-bonding, electrostatic)
The C—N peptide bond has double bond character (due to resonance) resulting in ?
no bond rotation around C—N bond and
6 atoms all lying in the same plane (= peptide group)
WHich conformation is more favorable - trans or cis and why?
Cis conformation is less favorable than trans due to steric interference of α-carbon side chains
which conformation is more common- trans or cis?
Nearly all peptide groups in proteins are in the trans conformation
what is phi rotation?
rotation about N- C alpha bond
what is psi rotation?
rotation about C alpha-C bond
why is phi rotation in proline restricted?
because of its ring structure
properties of alpha helix in terms of rise and pitch
rise - each
residue
advances by 0.15 nm along the long axis of the helix
pitch - the advance
along the helix long
axis per turn =
0.54 nm
how many amino acids per turn in alpha helix?
3.6
is alpha helix left or right handed?
right handed - backbone turns clockwise when viewed from n terminus
how is the helix stabilised?
by hydrogen bonds which are nearly parallel to long axis of the helix
why are alpha helices ampipathic?
Hydrophobic residues directed inward, hydrophilic outward
what are beta strands and beta sheets?
β Strands - polypeptide chains that are almost fully extended
β Sheets - multiple b strands arranged side-by-side
- stabilized by hydrogen bonds between C=O and -NH on adjacent
types of beta sheets
Parallel β sheets - strands run in the same N- to C- terminal direction
Antiparallel β sheets - strands run in opposite N- to C- terminal directions
what are loops and turns?
Loops and turns connect α helices and β strands and allow a peptide chain to fold back on itself to make a compact structure
Loops - often contain hydrophilic residues and are found on protein surfaces
Turns - loops containing 5 residues or less
how are tertiary structures stabilized?
Protein tertiary structures are stabilised primarily by non-covalent interactions between side chains.
Disulfide bridges can also stabilise tertiary structure
