Module 2: V5 - V9 Flashcards
Why are phi and psi so important?
because all conformational freedom in the backbone of a polypeptide is due to these two rotations
everything else is fixed
What is a Ramachandran plot and what does it show?
describes the backbone conformation of a protein in terms of the phi and psi values
shows the distribution of phi and psi dihedral angles that are found in a protein (shows common secondary structure elements and reveals the presence of unusual backbone structures)
Why are all phi/psi pairings not equally probable?
because Ramachandran plots are never filled with data points evenly
What determines the favorability of phi and psi combinations?
steric crowding of backbone atoms with other atoms in the backbone or side chains and because of the chance to form favourable H-bonding interactions along the backbone
What are the regions of a Ramachandran plot?
alpha (bottom left), beta (top left), left-handed turn (top right) and disallowed (bottom right)
What does ‘disallowed’ mean in the case of the Ramachandran plot?
means unfavourable or uncommon, but not impossible
What does secondary structure refer to?
a local spatial arrangement of the polypeptide backbone
What are two common regular arrangements?
the ɑ helix (stabilised by hydrogen bonds between residues nearby in the sequence) and the β sheet (stabilised by hydrogen bonds between adjacent segments that may not be nearby in the sequence)
What is a random coil?
irregular arrangement of the polypeptide chain
What must any polar group buried in a protein do?
form a hydrogen bond
Why do hydrogen bonds increase the compactness and stability of a protein?
this is because the atoms of a hydrogen bond can approach much closer than a VDW interaction (2.7 A compared to 1.9 A) due to covalent character of the hydrogen bond
What type of interactions occur within a protein?
backbone-backbone interactions, backbone-side chain interactions and side chain-side chain interactions
Do side chains project outwards or inwards from alpha helix axis?
outwards
Which type of interactions are occurring in an alpha helix?
NH (residue i) hydrogen bonding to C=O (residue i-4)
peptide bond dipoles which add together to give a macrodipole
Are alpha helices left or right handed?
right handed
What does amphipathic mean in a protein?
having both hydrophilic and hydrophobic character but separated onto different faces of the helix
What is the inner diameter of the alpha helix? Can anything fit into this hole?
4-5 A
no, not even water molecules are able to fit inside an alpha helix
What is a heptad repeat?
a repeating pattern of amino acid residues that corresponds to an alpha helix with hydrophobics all on one face
What amino acid residues are strong helix formers?
small hydrophobic residues such as Ala and Leu
Which amino acid residues act as helix breakers?
Pro because it lacks the NH hydrogen bond donor and Gly because the tiny R group doesn’t contribute to the stability of the helix
How are alpha helices stabilised?
by attractive or repulsive interactions between side chains 3 to 4 amino acids apart (e.g. stabilised by oppositely charged residues 3-4 away in sequence)
What creates a pleated sheet-like structure?
the planarity of the peptide bond and tetrahedral geometry of the ɑ carbon (held together by hydrogen bonds between the backbone amides in different strands)
How do side chains protrude from β strand?
in an alternating up-and-down direction
What forms a β sheet?
multiple parallel/antiparallel strands which undergo hydrogen bonding
Are parallel or antiparallel β sheets more stable? Why?
antiparallel β sheets because the H-bonded strands run in opposite directions resulting in less of an angle between neighbouring N-H and C=O groups allowing for stronger hydrogen bonding
What are reverse turns (β turns)?
a turn which frequently occurs when strands in β sheets change direction
How are reverse turns stabilised?
by a hydrogen bond from a carbonyl oxygen of position 1 to amide hydrogen of position 4 in the turn (i and i+3)
What is common in reverse turns?
proline in position 2 (i+1) or glycine in position 3 (i+2)
What is the difference between a type-1 turn and a type-2 turn?
the oxygen atom on the carbonyl of residue 2 in a type-1 turn points away from us into the page and the oxygen atom on the carbonyl of residue 2 in a type-2 turn points towards us out of the page (dictated by phi and psi values)
What are supersecondary structural elements?
simple ways of arranging secondary structures
more than half of all of protein structure is composed of three very simple arrangements of structural elements (ɑɑ-hairpin, ββ-hairpin and βɑβ)
What would the Ramachandran plot look like for a planet where the naturally occurring amino acids are D-amino acids?
since d-amino acids differ from l-amino acids by 180˚ the Ramachandran plot of a d-amino acid will be the inverse of an l-amino acid plot
