Topic 2 Flashcards

Question

What bonds form the tertiary structure?

Answer 1

R-groups are now involved-2 polypeptide chains-Van der waals, hydrophobic interactions, ionic bonds, & disulfide bonds. Ex.) Myoglobin

Answer 2

2 or more polypeptide chains interacting

Answer 3

Has a heme binding site in the middle, inside is usually very hydrophobic, and the outside very hydrophilic. Ha s a binding site in the center.

Answer 4

They can only successfully interact with substrates that have a structure that matches theirs. Can only recognize certain molecules.

Answer 5

X-ray diffraction and NMR.

Answer 6

Protein must be crystallized, but size does not matter.

Answer 7

Proteins don't have to be crystallized, but the protein must <150 a.a.

Answer 8

Apply x-ray to protein that has been crystalized. Pattern of diffraction is recorded and analyzed to determine the 3D structure.

Answer 9

Protein folding is not random like once believed. It is actually an highly ordered/ controlled process that requires other proteins help and ATP. Ex.) Insulin folding process- Has a signal peptide sequence that helps the protein to the ER and is present at the n-terminal of newly synthesized proteins. It is recognized by signal recognition particles to be brought to ER. Signal recognition particle is cut by signal peptidase in the ER. Other sequences are cut to process insulin. C-terminal, another sequence is cut off. There are 6 cysteine residues in insulin that can form 3 disulfide bonds that allow for hormone function. The 4th and 5th cysteine always form 1st disulfide bond. The 1st and 6th cysteine then for the 2nd disulfide bond. Then the 2nd and 3rd will form the last disulfide bond. This always happens in this order and between these specific cysteine residues. This discovery showed that it is not random, but highly ordered. Does consume energy and require chaperone proteins to help fold it.

Answer 10

E.Coli cells were put into the incubator at what he thought was 37 degrees celsius to crow them. The temperature was changed to a much higher temperature (maybe 50 degree celsius). Researcher came back next day and saw the temperature was too high and that the E.Coli did not grow well, but there were still some colonies that survived in the abnormally high temperature. He extracted the proteins from the cell colonies and grew a new set of E.Coli cells in the 37 degree temp. and extracted proteins from that. He had heat treated colonies and control colonies. The proteins expressed were different. There are 2 major proteins expressed in heat treated protein that aren't expressed in the control. He cloned the colonies, and made mutations. The mutated E.Coli could not survive abnormally high temperatures. This led to the discovery of the two chaperone proteins, initially termed heat shock proteins, GroEL and GroES.

Answer 11

When the environmental condition is higher than ideal temperature, the newly synthesized proteins, can be deposited inside the GroEL and then covered by GroES that makes unique internal environment. This environment can allow the proteins to fold and form normal structures. ATP is also present since it is an ATP-dependent pathway. . The protein is released when it is done folding. These chaperone proteins are present in all eukaryotes and essentially have the same function. (Heat, stress, extreme conditions, etc.)

Answer 12

Heat, UV, 6-10M Urea

Answer 13

Completely destroys protein 3D structure and breaks peptide bonds and no way to renature the proteins.

Answer 14

Completely denatures proteins and damages DNA.

Answer 15

6-10M Urea ideal to study protein folding and renaturation because it can destroy the 3D structure (non-covalent bonds), but doesn't break the peptide bonds. It can then be renatured.

Answer 16

Ubiquitin-mediated protein degradation. Ubiquitin recognizes and tags mis-folded proteins to form a mis-folded protein-ubiquitin complex. It leads the mis-folded protein to a proteasome where proteases can destroy the protein. Ubiquitin will not enter proteasome, but the protein will be dropped of and digested. Ubiquitin is recycled as are amino acid residues.

Answer 17

Contains 2 caps on both ends, 2 alpha subunits close to the caps, and then two beta subunits on the inside.

Answer 18

Ubiquitin sometimes does not recognize mis-folded proteins. There are plaques in the brain that form tangles within the nerve cells that damages them. Tau protein can be highly phosphorylated (has many Tyr, Ser, &/or Thr). When it is highly phosphorylated, it will absorb a lot of water which changes its 3D structure. This can not be recognized by ubiquitin. The tangles/twists may possibly be caused by the tau protein.

Answer 19

Caused by eating undercooked meat contaminated by CNS tissue from a cow that had the disease. Damages brain cells causing spongiform encephalopathy, which are sponge like lesions in the brain tissue that cause a deterioration of brain function. Marked by rapid decrease in brain function, dementia, and death.

Answer 20

Prion-No mutation in the gene, rather it is a rogue/mis-folded protein. No DNA, RNA, or nucleic acid difference. This busted the assumption that infections were all caused by nucleic acids or bacteria.

Answer 21

Infection--> Bacteria, Sickness--> Virus, Fungi, parasites, etc.

Topic 2 Flashcards

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