Proteins Flashcards
How does a hydrogen bond compare to a covalent bond? 2 ways
What is the length & angle of the entire hydrogen bond? (including donor, bond, acceptor)
Weaker, longer (2A rather than 1A)
3A, 180 degrees
Briefly describe the dipole in the a-helix
How are the hydrogen bonds orientated? In what pattern do they form between the residues?
Are the side chains projected inwards or outwards? Why?
What is the distance between 2 residues?
What is the residues per tern & what is this distance? (aka what is the pitch)
Is it right or left handed?
Goes from +ve to -ve (N at top C at bottom)
Orientated parallel & x and x+4
Outwards- minimise steric hinderance
- 5A
- 6 residues per turn- so 5.4A
right handed
What is the orientation of the 2 polypeptide chains?
Hydrogen bonds form between the 2 strands- in what residues do they occur?
In what direction do the side chains of adjacent amino acids point?
What is the distance between 2 residues? What does this mean about the sheet?
How strong are the hydrogen bonds?
Run parallel next to eachother from N->C
x and x+2 - polar residues
opposite
3.5A - fully extended
Weak
What is the orientation of the 2 polypeptide chains?
Hydrogen bonds form between the 2 strands- in what residues do they occur?
In what direction do the side chains of adjacent amino acids point?
What is the distance between 2 residues? What does this mean about the sheet?
Is this structure stronger than the parallel B sheet? Why?
One is N->C and the other is C->N
x (2 bonds form within the same residue)
opposite
hydrogen bonds are perpendicular to the polypeptides- more stable
Where are the hydrogen bonds?
For both types, what are the following angles for: Phi x + 1 Psi x + 1 Phi x + 2 Psi x + 2
What is a secondary structure propensity score?
What amino acids have the higher propensity scores for:
alpha helix
beta sheets
beta turn
what residues are the helix breakers? why?
x and x+3
type I: -60, -30, -90, 0
type II: -60, 120, 90, 0
amino acid residues that appear most frequently in a specific secondary structure
Glutamate, methionine, alanine
valine, isoleucine, tyrosine
glycine, asparagine, proline
proline- steric hinderance causing kink in backbone & NH instead of NH2 means can’t provide hydrogen bonding with residues
glycine- lots of conformational freedom so prefers unfolded forms
What happens when 2 hydrophobic molecules enter water?
What does this effect do?
In the hydration shell around the hydrophobic molecule, what 2 positions can the water molecules take?
What is the strongest force in a tertiary structure?
2nd strongest?
Hydrogen bonding is the 3rd strongest. What 3 different types of hydrogen bonding can occur in a tertiary structure?
What are the weakest forces?
Water molecules order around them & molecules join together releasing water & increasing entropy
Increase in entropy drives folding into proteins
Surface & buried
Disulfide bridges between 2 Cys groups
Salt bridges between residues of opposite charge
Between side chains
Side chain & peptide group
2 peptide groups
Hydrophobic interactions driven by hydrophobic effect: Van der Waals (instantaneous dipole) between non-polar residues
How do metal ions/ligands alter the tertiary structure?
What is a zinc finger motif made up of?
What residues can the ion be coordinated by?
Describe the palmitic acid ligand
In topology diagrams, what do these mean:
arrows? - one up and one down
rectangles
what colours are the N and C terminus?
how large is a domain? where are they most likely seen? what are some of their characteristics & what are they separated by?
Stabilise it
Antiparallel beta sheet & alpha helix & zinc ion
His, cys or glu residues
fatty acid with hydrophobic part inside & polar/hydrophilic part outside
arrows = beta sheet- one up & one down = antiparallel beta sheet rectangle = a helix
N = blue C = red
100-200AA so seen in large proteins >200AA. very stable & independently folded units & separated by linker regions
What is the difference between a heteromultimer & a homomultimer?
protein dynamics
what are the different scales for:
covalent bond vibrations side chain rotation backbone movements movement of protein loops movements when ligands bind whole domains move
when a substrate binds to an enzyme/protein, what happens to the protein loops & domains?
Heteromultimer = protein with different subunits Homomultimer = protein made of identical subunits
Heterotetramer (different 4 subunits)
femtoscale pico scale pico-nano scale nano-micro scale micro-milli scale milli scale
loops go from open to close
upper domain moves to cover the substrate
what is an intrinsically disordered protein?
what is their main characteristic?
what are they involved in and how common are they?
protein without a define structure
very flexible- easily interact with other proteins
diseases- 30% of proteome in eukaryotes
What does the graph have on the x and y axis of Levinthal’s paradox?
If the graph in Levinthal’s paradox is the golf course landscape: what does the graph look like & what does it explain?
What does the graph in Levinthal’s paradox of the predetermined pathway look like & describe?
What axis does the folding funnel have?
What does the folding funnel model explain?
What does the molten globule stage represent?
What is the slowest part of the folding process according to the folding funnel model? Why?
x = extent of folding y = free energy
Graph is flat with 1 minimum. Random folding to find perfect structure- will never be found this way. Goes from high to low energy structure.
Downwards bumpy gradient- free energy surface isn’t flat so the forces that stabilise the folded state will also stabilise near folded states
x = entropy y = energy
there are multiple pathways & intermediates. goes from high energy/unfolded to molten globule to transition state & then to folded (lower energy and higher entropy)
ensemble of conformations with many different secondary structures present in their native structures but not correctly packed together yet
Molten globule -> Folded. have to pass the higher energy transition state
What do chaperones do?
How do they do this?
How do the following denature proteins:
temperature
chaotrophic agents (urea & guanidinium chloride)
deterrgents
pH
reducing agents (ß-mercaptoethanol & dithiothreitol)
mechanical stress
Help unfolded/misfolded proteins correctly fold
remove aggregates & transport them with unfolded proteins for degradation by proteases
- vibrations break H bonds
- break hydrophobic contacts
- hydrophobic (& hydrophilic) parts break hydrophobic interactions of protein
- change protonation states of amino acid side chains- breaks salt bridges
- break disulfide bridges
- mechanically breaks bonds
What does Anfinsen’s Dogma hypothesise?
How would you prepare the protein in the experiment?
what happens when you take away ßME but leave urea?
what % of sequences go back into their native protein state?
why is this?
The native structure of a protein is determined by its amino acid sequence
add ß-mercaptoethanol & urea in order to break disulfide bridges & unfold it
remain unfolded but try to reform disulfide bridges between the cys residues
1%
weak forces (hydrophobic interactions & H bonds) determined by the primary structure & are needed for the native structure- not often present after as they need a position protein
Where is Tm on the graph & what does it show?
Melting temperature- when 50% of the protein is unfolded (& 50% folded) so Kd/Keq = 1 and G = 0
What forms when a receptor and ligand bind? (with specific affinity)
What is Kon and Koff in this equilibrium?
What happens when Kon and Koff are in equilibrium?
so what is the equilibrium dissociation constant Kd (M)?
so what is the equilibrium ASSOCIATION constant Ka (M-1)?
What does Kd tell you about affinity?
Receptor-ligand complex bound by non-covalent interactions [RL]
Kon = forward rate constant of binding Koff = reverse rate constant of dissociation
[R] [L] and [RL] are constant but there is flux in each direction
Kon[R][L] = Koff [RL]
Kd = Koff/Kon = [R][L]/[RL]
1/Kd
High Kd = low affinity & vice versa
