Module 2 Flashcards
protein structures
What forces drive protein folding
Electrostatic forces, van der Walls interactions, hydrogen bonds, hydrophobic interactions
How do you help protein refold properly
adding a trace of beta ME. beta-mercaptoethanol to reduce srcambled disulfides
Does disulfide bonds direct folding
No, folding directs disulphide bond formation
What do disulfide bonds do
increase relative stability of the folded state over the unfolded states
Why does the condition in the call make the folding slow or impossible
Molecular crowding
What does chaperones do
they help to avoid misfolding but does not fold proteins
what does Ionic interactions between oppositely charged groups in proteins are called
salt bridges, Charges tend to be distributed over several atoms, component due to electrostatic interactions and hydrgen bonding
Arrange N,C,S,H,O from most electronegative to leave electronegative
O>N>C>S>H
What is the optimal distance between two particle
~3 angstrom
What is the distance for 1 Å
0.1 nm
What drives protein folding
Negative gibbs free energy, G = H-TS
Why are some phi and psi combination unfavourable
steric crowding
Why are some phi and psi combination favourable
because of the chance to form favorable H-bonding interactions along the backbone
what are the region of the ramachandran plot
beta L
alpha D
What are the distance for VDW and hydrogen bonding
2.7 angstrom and 1.9 angstrom
Beta sheets hydrogen bonding sequence
NH residue i to C=O residue j
alpha-helix hydrogen bonding sequence and its angle
NH residue i to C=O residue i-4 (phi, psi, -57, -47
Reverse turns hydrogen bonding sequence
NH residue i+3 to C=O residue i
Where are the non-polar aa placed in a alpha helix
heptad repeat, 1st - 4th, a-d
Which hydrophobic residues are strong helix formers
Ala and Leu
Which aa are helix breakers and why?
Pro because it lacks NH hydrogen bond donor, Gly because the tiny R group don’t contribute to stability of helix
phi and psi angles of beta sheets
-130, +130
What are the reverse turns position for proline and glycine
Pro in position 2(i+1), Gly in position 3(i+2)
what are tertiary structures
Fold, modules, domains and arrangement of domains(in a single subunit)
What are quarternary structures?
arrangement of two or more protein subunits
What is a domain
an existence independant of the rest of the protein( fold independantly)
`What is a fold?
arrangement of secondary stucture elements relative to each other in space
What is a module?
Have one or more repeating fold within the overall structure
What is intragenic mutation
point mutations, insertions and deletions
What is gene duplication
whole or part of a genome is duplicated
what is DNA segment shuffle
two or more existing genes can be broken and recombined
What is gene lateral transfer
one organism acquires parts of the genome of another
Why are domain defined as an evolutionary unit
New proteins are evolved by gene duplication annd domain shuffing, no new domains are created
What does identical mean
exactly the same residue
What does similar mean
residues with similar physical chemical properties
What are honologues
2 sequence that shows >25% identity
What are orthologue
Homologous proteins that perform the same function in different species
What are paralogue
Homologous protein that perform different but related functions within one organism (eg. human trypsin, compared with human thrombin)
Does structure change slower than sequence?
yes
Does different parts of the protein mutate at different rates
yes
What are chymotrypsin(digestion) and thrombin(blood clotting)?
Paralogues
