Protiens 3

Question 1

How many residues does myoglobin have?

How would you find the angstroms of myoglobin from this

Answer 1

153 AA residues

153 res x 1.5ang/res

229.5 A

Question 2

What role do myoglobin have and how does it do this

Answer 2

It binds oxygen through the use of the iron atom in the heme group

Question 3

What is the heme group in myoglobin

Answer 3

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

Question 4

What is myoglobin

Answer 4

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

Question 5

What are supersecondary motifs

Give an example

Answer 5

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

Question 6

What is a another example of a supersecondary motif

Answer 6

The beta hairpin

The beta strand in the secondary structure loops back and forms a hairpin

Creating the tertiary structure

Question 7

What is a domain in tertiary structure

Answer 7

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

Question 8

How many domains does CD4 have

What type of protien is it

Answer 8

4 domains

Cell surface protien

Question 9

What is the quaternary structure of protiens

Answer 9

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

Question 10

What is cro

Answer 10

A dimer (quaternary made of two protiens)

A dna binding protien
But doesn’t have a helix turn helix LOOK IN TEXTBOOK

Question 11

Do the polypeptide chains in quaternary structure protiens have to be the same

Give example of protien that has diff subunits

Answer 11

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)

Question 12

Describes the aim of the “AA sequence determines 3D structure of protien” experiment

Answer 12

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

Question 13

Describes generally what you need for the sequence determines 3D structure of protien experiment

Answer 13

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

Question 14

How do we know if the protein is in the folded conformation for the experiment

Answer 14

Analyze the enzymatic activity

Question 15

How many aA residues in ribonuclease

Answer 15

124

Question 16

What is urea

Answer 16

Nh2 C=O nH2

A small molecule that can donate and accept h bonds

It disrupts the h bonds in the protiens

Chaotropic agent

Question 17

What happens when and excess of 2-mercaptoethanol is introduced to the protien

Answer 17

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

Question 18

What were the results when the 2-mercaptoethanol and the 8M urea were introduced to the protien ribonuclease

Answer 18

The protein became denatured (disulfide bonds broke and h bonds also broke)

Unraveled

Question 19

What is the role of the dialysis bag

Answer 19

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.

Question 20

What happens to the ribonuclease after the urea and 2-me were departed from it via dialysis

Answer 20

The unraveled ribonucleases left in the bag slowly regained activity

Meaning it transformed back to its native (folded) conformation

Question 21

What is the conclusion of the AA determines function experiment

Answer 21

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

Question 22

If you have a protien with 100 residues and each residue can have 3 conformations how many possible conformations are there

Answer 22

3^100

Question 23

What is levinthals paradox

Answer 23

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

Question 24

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

Answer 24

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

Question 25

Describe the folding funnel visualization of folding protiens

Answer 25

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

Question 26

What does the native structure or protiens mean

Answer 26

100% of the AA residues are folded in the correct conformation

Question 27

What are intrinsically disordered protiens

Answer 27

They don’t adopt one single fixed conformation, only when they find a binding partner do we see the conformation

Question 28

What is an example of a disease caused by protien misfolding

What does it do

Answer 28

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