Protein Structure Flashcards
What is the primary structure?
It is the order of the amino acids
What is secondary structure mainly based on?
Main chain amide-amide hydrogen bonds.
The interactions in the secondary structure are due to the main chain of hydrogen bonds.
What makes NH a good hydrogen bond donor?
IDK
What amino acids favour alpha helix conformation?
Met, Ala, Leu, Glu & Lys.
What amino acids disfavour alpha helix conformation?
Gly, Pro because they are too bulky.
What is the alpha helix held together by?
It’s a right-handed helix held together by hydrogen bonds between the amide nitrogen & hydrogens and oxygens on the carbonyls.
How are the angles arranged for the beta-sheet?
Fairly linear
How are the side chains and main chain arranged in the beta sheet?
The side changes alternatively stick out from either side to keep them out of the way of the main chain and the main molecule is arranged in a zigzag way.
The carbonyls point in the same place and the hydrogens point in the same plane.
Why do beta strands form beta sheets?
The NHs on the carbonyls line up with another strand as there is a hydrogen bond donor and a hydrogen bond acceptor facing each other.
They have really nice hydrogen bond complementarity.
L4 protein structure (rewatch)
What is an anti-parallel beta-sheet?
When the N terminus alternates down the sheet.
What amino acids favour the beta-sheet conformation?
Bulky amino acids favour this conformation because of their bulky side chains. A beta sheet gives them more space than they get in the alpha helix and they’re freer.
Tyrosine, Phenylalanine, Tryptophan, Threonine, Valine and Isoleucine.
What is tertiary structure and what determines it?
This is where the secondary structure comes together and it is dominated by side chains and how they react.
How can you break disulfide bonds?
By introducing reducing agents or by scrabbling it by introducing more sulfides which can displace the other sulfide.
When the displacement occurs it ruins the tertiary structure.
What are disulfide bonds?
Covalent bonds between Sulfur
What structure does lysosome have and why?
It has a beta-sheet and random coils.
It needs the random coils so the molecule can chain together correctly.
What does ribbon structure tell us?
It tells us the general size and shape of the protein and how it’s related to other proteins.
What are coiled coils?
Two alpha helices wrapped around each other.
What interactions do coiled coils have?
It has a hydrophobic line going across it and salt bridges which give it strong ionic interactions and provide protection to the hydrophobic residues.
Why do coils occur?
They occur due to a 7 fold repeat of amino acids.
It takes 7 times to get round to the same place.
Why do coils occur?
They occur due to a 7 fold repeat of amino acids.
It takes 7 times to get around to the same place.
What forces drive quaternary and & tertiary structures?
Side chains and how they react…?
How can gel electrophoresis be used to analyse a charged molecule?
- If you have a charged molecule in solution and you put it under a voltage it will move towards the electrode with the opposite charge.
- Positively charged molecules move towards the cathode
In gel electrophoresis what electrode will negatively charged molecules move towards?
Anode
In gel electrophoresis what electrode will positively charged molecules move towards?
Cathode
In electrophoresis what does the moving force depend on?
How heavy the molecule is.
What conditions is gel electrophoresis done under?
Native conditions
What can you calculate from gel electrophoresis?
The mass/charge ratio
What methods can be used to determine structure?
- XRD
- NMR
- Cryo-EM
- Computation
What are the benefits of NMR in terms of structure determination?
- It happens in solution so you don’t need to crystalise the sample.
- You can replicate conditions similar to nature due to it being in solution.
- You can create a 3D structure
What are the drawbacks of NMR in terms of structure determination?
- Less precision over what you can measure
- Less automated
What are the drawbacks of cryo-EM in terms of structure determination?
- Lower resolution, although now it’s improved.
- Relies on previous models
- Doesn’t provide much detail.
What are the advantages of cryo-EM in terms of structure determination?
- More native conditions
- No need for crystallisation
What happens in secondary structure?
Partial double bond character
The partial double bond character between nitrogen and carbon at the bottom of the carbonyl, because of that there is no rotation around the bond of the nitrogen and carbon so It’s a fixed and always a flat structure
How do you determine structure using Cryo-EM?
Electron Microscope
You get a solution of protein and freeze it really quickly in a thin film on a tiny grid which then goes into the electron microscope and then you shine light through it and you’ll see features of the structure.
Disulfides form…
Disulfides form reversible covalent links in tertiary structure
Glycine has an amine with…
Electrostatic
Glycine has an amine with pka of 10 and has a strong electrostatic interaction with the oxygens and another molecule
What is a thiol?
-SH
Cysteine can form…
- Cysteine can form disulphide bonds or “bridges” in a protein
- These bring two peptide fragments together.
- It will do this whenever it has the chance to.
Sulfur can…
Sulfur can easily be oxidised or reduced
What happens to thiols under oxidative conditions?
- When you have two thiols under oxidising conditions, the hydrogen gets taken away and they will form a covalent bond between them.
- This makes quite a strong link as it brings together two parts of the polypeptide chain
