Protiens 3 Flashcards
How many residues does myoglobin have?
How would you find the angstroms of myoglobin from this
153 AA residues
153 res x 1.5ang/res
229.5 A
What role do myoglobin have and how does it do this
It binds oxygen through the use of the iron atom in the heme group
What is the heme group in myoglobin
A group in the hydrophobic region of myoglobin, the 3D structure of myoglobin allow it to surround the heme group
It’s a prosthetic group (essential for the function of the protien, not a peptide itself
What is myoglobin
Compact soluble protien that’s folded into a 3d shape
The alpha helices that are far apart in the secondary structure pack together in the folded protien
Hydrophobic region on inside with two histidine residues that bind the heme iron to oxygen
hydrophilic and phobic on outside
Hydrophobic effect
What are supersecondary motifs
Give an example
When elements of the secondary (alpha helix) structure come together to form the motif
The helix turn helix motif is where the alpha helix in a secondary structure turns direction and overlap the other alpha helix
This is a dna binding motif, can bind to the dna
What is a another example of a supersecondary motif
The beta hairpin
The beta strand in the secondary structure loops back and forms a hairpin
Creating the tertiary structure
What is a domain in tertiary structure
When amino acid residues in one region of the protien interact with each other more than the rest of the protien
Concentrated regions of AA interactions
This forms domains
How many domains does CD4 have
What type of protien is it
4 domains
Cell surface protien
What is the quaternary structure of protiens
When there’s more than one polypeptide chain that each form a subunit of the whole protein
Diff polypeptides chains, still one protien, have each their own N and C terminus
Made by h, ionic or van der wall
What is cro
A dimer (quaternary made of two protiens)
A dna binding protien
But doesn’t have a helix turn helix LOOK IN TEXTBOOK
Do the polypeptide chains in quaternary structure protiens have to be the same
Give example of protien that has diff subunits
No
Hemoglobin has two different types of subunits (alpha and beta chains) and two copies of each
It’s a alpha 2 beta 2 tetramer
Has a heme in each chain (4 heme)
Describes the aim of the “AA sequence determines 3D structure of protien” experiment
Christian’s anfinsen in the 1950s did this to
Destroy the 3D structure of a protien
Then determine the conditions to restore the tertiairy structure
Describes generally what you need for the sequence determines 3D structure of protien experiment
Need the protien: enzyme ribonuclease
Need a chaotropic agent to disrupt the non covalent (h bond, vanderwal, ionic) interaction in the protein: urea
Need sulfhydryl reagent to break disulfide bonds:
2 (or beta)-mercaptoethanol
How do we know if the protein is in the folded conformation for the experiment
Analyze the enzymatic activity
How many aA residues in ribonuclease
124
What is urea
Nh2 C=O nH2
A small molecule that can donate and accept h bonds
It disrupts the h bonds in the protiens
Chaotropic agent
What happens when and excess of 2-mercaptoethanol is introduced to the protien
The disulphide bond in the protiens (ribonuclease) are cleaved and have H added to them
Instead S-S it’s S-H S-H it’s reduced (protien)
2-mercaptoethanol is oxidized
What were the results when the 2-mercaptoethanol and the 8M urea were introduced to the protien ribonuclease
The protein became denatured (disulfide bonds broke and h bonds also broke)
Unraveled
What is the role of the dialysis bag
It’s a way to retain the protiens and get rid of the urea and 2-ME after treating it
The bag is a semipermeable membrane so the smaller molecules (2-ME and urea) diffuse out of the bag into the buffer while the unravelled large protien stays in the bag.
What happens to the ribonuclease after the urea and 2-me were departed from it via dialysis
The unraveled ribonucleases left in the bag slowly regained activity
Meaning it transformed back to its native (folded) conformation
What is the conclusion of the AA determines function experiment
The info needed to specify the 3D conformation of ribonuclease is held in the amino acid sequence
The sequence specifies the conformation and the confirmation determines the function of the protein
If you have a protien with 100 residues and each residue can have 3 conformations how many possible conformations are there
3^100
What is levinthals paradox
There are many different combinations of aA residue conformations the the protiens can take before getting to the native conformation
This would take year to find the correct confirmation but somehow the protien in able to get the correct conformation in just a few seconds
This is the paradox, we don’t know how it takes on that conformation so fast when the possibilities are endless
What is the energy difference between between the folded and unfolded state of a 100 residue protien
How much energy does the AA residues in this protien give to keep its folded state
What does this mean
42kJ/mol
Small energy difference between folded and unfolded state
Each AA residue contributes 0.42kJ/mol of energy to keep its folded state
Means that even if the residues adopted the right folded conformation, they could easily move away from this conformation
Describe the folding funnel visualization of folding protiens
At the top of the funnel the entropy and energy is the highest , the protiens are unfolded and are capable of taking on manny diff conformations
As the AA residues in the protiens fold they get lower in energy (further down the funnel)
Some conformations of AA residues make the protien get stuck in that conformation, it then needs certain amount of higher energy added to refold into the native conformation
It reaches the molten globule state when the protien has the hydrophobic effect happening and is more or less compact and stable (not fully folded but not fully unraveled)
It then reached the native conformation which is lowest in energy
What does the native structure or protiens mean
100% of the AA residues are folded in the correct conformation
What are intrinsically disordered protiens
They don’t adopt one single fixed conformation, only when they find a binding partner do we see the conformation
What is an example of a disease caused by protien misfolding
What does it do
Prion diseases
The prion protiens is misfolded into a beta sheet conformation
This induced the prion protiens with normal structure to misfold and cause all to be misfolded into beta sheets.
It is infectious
