EXAM II

Question 1

What’s the matter with having a side chain that is non-polar inside of a cell?

Answer 1

the protein is scared of water, it has several ways of hiding:
Hiding in organelles, phospholipid bilayer, and non-polar sides will change shape

Question 2

For the most part , where does a protein get the information from how to fold?

Answer 2

the side chain chemistry (from h-bonds, N-C-C backbone, polarity/ non polarity)

Question 3

How many chaperone proteins would the cell make to ensure other proteins fold correctly in humans?

Answer 3

there are both types; (chaperone and binding) in humans and multiple versions of each type.

Question 4

Does an alpha helix that lives in the plasma membrane always have to be hydrophobic?

Answer 4

No, if lots of aloha helices group together they can make a passageway into the cell with hydrophilic core and hydrophobic outside.

Question 5

What type of chemical reaction might be needed to break a disulfide bond?

Answer 5

Oxidation and Reduction Reaction (you are adding H’s to the reaction to separate the Ss)

Question 6

Why do ligand interactions need to be non-covalent?

Answer 6

to allow them to bind on and off; so you can start and stop a reaction when the cell needs it.

Question 7

In addition to the active site what must a protein have to be regulated?

Answer 7

Has to have regulation site (allosteric site) this site is likely somewhere else other than the active site.

Question 8

Regulation sites are reversible or irreversible?

Answer 8

reversible; nothing in the cell is permanent

Question 9

Does adding a phosphate mean a protein must be active? Turn on or off?

Answer 9

No, just because a phosphate is added does not mean it is on or off, it means a conformational change will occur, the activity depends on the specificity of the protein

Question 10

What small molecule do you know that can be added that carries energy and is likely NOT reversible?

Answer 10

ATP

ATP Hydrolysis; release of ADP +P

Question 11

What is rare in helices?

Answer 11

left-handedness

it can happen, though due to the way the side chain chemistry works out it is usually right-handed

Question 12

Although all protein structures are unique, there common structural building blocks that are referred to as regular secondary structures. Some proteins have helices, some have beta sheet and still other have a combination of both. What makes it possible for proteins to have these common structural elements?

Answer 12

Hydrogen bonds along the protein backbone

Question 13

Which of the following methods would be the most suitable to assess levels of expression of your target protein in different cell types?

Answer 13

western blot analysis

Question 14

Protein folding can be studies using a solution of purified protein and denaturant (urea), a solvent that interfered with non-covalent interaction. Which of the following is observed after the denaturant is removed from the protein solution?

Answer 14

The polypeptide returns to its original conformation

Question 15

Motor proteins use the energy in ATP to transport organelles, rearrange elements of the cytoskeleton during cell migration and move chromosomes during cell division. Which of the following mechanisms is sufficient to ensure the unidirectional movement of a motor protein along its substrate?

Answer 15

A conformational change is linked to ATP hydrolysis.

Question 16

What is true of molecular chaperones?

Answer 16

They assist polypeptide folding by helping the folding process follow the MOST energetically favorable pathway.

Question 17

Which of the statements is true?
-The polypeptide backbone is free to rotate about each peptide bond.
-The sequence of the atoms in the polypeptide backbone varies between different proteins.
Correct!
-Nonpolar amino acids tend to be found in the interior of proteins.
-Peptide bonds are the only covalent bonds that can link together two amino acids in proteins.

Answer 17

Non polar amino acids tend to be found in the interior of proteins

Question 18

The phosphorylation of a protein is typically associated with a change in activity, the assembly of a protein complex, or the triggering of a downstream signaling cascade. The addition of ubiquitin, a small polypeptide, is another type of covalent modification that can affect the protein function. Ubiquitylation often results in

Answer 18

Protein degradation

Question 19

The correct folding od proteins is necessary to maintain healthy cells and tissues. Unfolded proteins are responsible for such neurodegenerative disorders as Alzheimer’s disease, Huntington’s, and Creutzfeldt disease. What is the ultimate fate of these diseases-causeing, unfolded proteins?

Answer 19

The form aggregates (clump together)

Question 20

Which of the following methods would be the most suitable to assess whether your protein exists as a monomer or in a complex?

Answer 20

gel-filtration chromatography

Question 21

Using any of these following methods what ends up in the test tube? 
Sonication 
Ball bearing homogenization
Chemical homogenization 
Shearing homogenization

Answer 21

All parts of the cell

Question 22

In whole cell lysate, where are the proteins after the sample is spun in the centrifuge?

Answer 22

in both the pellet and the supernatant

Question 23

Why would you go through the trouble of serial dilution sequential centrifugation just to get proteins?

Answer 23

you can remove the supernatant and re suspend the pellet to get proteins from a specific area of the cell

Question 24

Why might one choose velocity centrifugation over sequential centrifugation?

Answer 24

You know your protein is in the cytosol

you want to finish faster

Question 25

How would you get the high density protein band out of the tube during equilibrium sedimentation of centrifugation?

Answer 25

pop a hole at the bottom of the tube

Question 26

In column chromatography what does the salt do to the charge interactions that are holding the protein beads?

Answer 26

out-compete ionic interactions

Question 27

Why would an organism make a million antibodies with each one anybody being different?

Answer 27

to ensure the specificity for each antigen

Question 28

Why secrete more antibodies if the antibodies are not attached to a cell?

Answer 28

to try and mark as many antigens as possible