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BIOCHEM 2 > Protein Regulation > Flashcards

Protein Regulation Flashcards

1
Q

What is the lac operon?

A

The lac operon ensures that the genes to metabolize lactose are only present when lactose is abundant.

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2
Q

What is lactose metabolized to?

A

glucose and galactose.

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3
Q

What are two systems in which the lac operon is regulated?

A
  1. High concentration of lactose needs to be present.
  2. Glucose cannot be present.
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4
Q

What happens when there is no lactose present?

A

When there is no lactose present, the lac repressor binds to the operator and this inhibits the RNA polymerase from transcribing the lac operon.

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5
Q

What happens when there is lactose?

A

Some of the lactose is converted to allolactose by beta galactosidase. The allolactose will bind to the operator causing the repressor to dissociate from the operator. This allows RNA Polymerase to transcribe the genes.

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6
Q

How does the lac repressor ensure that the operon is only transcribed when lactose is present?

A

Avidity, each repressor can bind to two operator sites. This increases the avidity because the two copies of the dimeric protein each bind to the DNA.

Since the repressor binds to the DNA twice this ensures that the lac operon is not transcribed when there is no lactose.

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7
Q

What happens to the regulation of the lac operon when glucose is present?

A

When glucose is present, it will not phosphorylate the enzymes beta galactosidase and lac permease.

As a result, the enzymes will bind to the adenylate cyclase and inhibit its activity.

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8
Q

Which reaction does adenylate cyclase catalyze?

A

ATP —-> cAMP

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9
Q

What happens to the regulation of the lac operon when glucose is not present?

A

When glucose is not present, the enzymes (beta galactosidase and lac permease) will be phosphorylated. The adenylate cyclase enzymes will be released and begin to convert ATP to cAMP.

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10
Q

What is the significance of cAMP in the regulation of lac operon?

A

when cAMP is present it will bind to and activate the CR/AP (catabolite repressor/activator protein) which increases the affinity of RNA polymerase for the promoter and increases the level of gene transcription.

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11
Q

Why is CR/AP needed?

A

The RNA polymerase generally has weak affinity for the promoter. CR/AP is needed to increase the affinity.

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12
Q

What is the key take away for the lac operon?

A

The lac operon is only transcribed when there is a lot of lactose and when lactose is the preferred fuel source.

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13
Q

What happens when glucose is high, lactose is low?

A

The lac operon will be off. Lac repressor will be bound to operator. No CR/AP is bound to the DNA.

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14
Q

What happens when glucose low, lactose low?

A

The lac operon will be off, lac repressor will be bound to operator.

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15
Q

What happens when glucose low, lactose high?

A

The lac operon will be on, because the adenylate cyclase will not be inhibited, cAMP will be produced and CR/AP will be activated and bound to DNA. Also the allolactose will be bound to the operator dissociating the repressor from operator.

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16
Q

What happens when glucose high, lactose high?

A

The lac operon will be off, because adenylate cycle will be inhibited, no cAMP, CR/AP not activated and will not bind to DNA.

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17
Q

What is Trp operon?

A

The Trp operon ensures that the genes for the synthesis of tryptophan from chorismate is only present when there is a low concentration of Tryptophan.

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18
Q

What happens when there is no tryptophan?

A

The tryptophan repressor cannot bind to operator, RNA Polymerase can transcribe five structural genes that are needed to synthesize tryptophan from the chorismate intermediate.

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19
Q

What happens when there is tryptophan?

A

Tryptophan binds to the repressor, causes conformation change in the TRP protein. Allows repressor to bind to the operator, blocking the polymerase.

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20
Q

What is attenuation in the regulation of the Trp operon?

A

avoids synthesis of five structural genes even when there is sufficient tryptophan in the cell.
Gives a second set of regulation for the Trp operon.

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21
Q

What is the leader peptide?

A

codes for two Trp in a row.

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22
Q

What is the leader sequence?

A

4 sequences that are self complementary and can form a hairpin. Makes the leader peptide.

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23
Q

What happens to the attenuation mechanism when there is no Trp?

A

When there is no Trp the leader peptide is not synthesized completely because it stops when it reaches a codon that codes for Trp because there is not enough tRNA loaded with Trp in the cellular environment.

Region 3 forms hairpin with region 2. Region 4 cannot form a hairpin. There is no termination sequence. Remainder of operon is transcribed into RNA.

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24
Q

What happens to the attenuation mechanism when there is Trp?

A

When there is sufficient Trp, the leader peptide is complete. The ribosome blocks region 1 and 2. Region 3 and region 4 form a hairpin. 3-4 hairpin followed by many Us acts as a termination sequence.

Rest of RNA does not get made.

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25
Q

Why does region 2 and region 3 form a hairpin when there is no tryptophan?

A

while the ribosome is waiting for a Trp loaded tRNA to arrive it blocks region 1 but not region 2. This causes region 2 to form a hairpin with region 3.

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26
Q

What form of regulation is the Trp operon?

A

Negative regulation, presence of Trp repressor protein inhibits transcription of the operon.

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27
Q

What form of regulation is the lac operon?

A

positive regulation because presence of lactose positive regulation by the catabolite activator protein.

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28
Q

Why do we need regulation of ribosome synthesis?

A

have to maintain the appropriate number of ribosomes found in a bacterial cell.

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29
Q

How is the synthesis of ribosomes regulated?

A

r proteins

30
Q

Which of the r-proteins is a dual function protein?

A

L4

31
Q

Ribosome regulation

A

L4 binds tightly to the r-RNA in the process of ribosome synthesis.

When the amount of L4 exceeds the amount needed to bind the r-RNA, L4 binds to mRNA. mRNA bound to L4 cannot be translated. Production of ribosomal protein ends.

32
Q

What happens when we run out of r-RNA?

A

we need a repressor to repress this operon, the repressor is the ribsomal protein.

33
Q

Who is the repressor for the ribosomal synthesis operon?

A

Ribosomal protein acts as its own repressor.

34
Q

What is the preferred binding site for the ribosomal protein?

A

Preferred binding site is on rRNA.

35
Q

The regulatory mechanisms we have discussed so far for lac operon, trp operon, and ribosomal synthesis operon are for prokaryotic or eukaryotic?

A

Regulatory mechanism of prokaryotic genomes.

36
Q

Translational Riboswitch

A

in the presence of ligand mRNA forms a hairpin that blocks the ribosome binding site which prevents translation.

37
Q

What are the similarities of translational and transcriptional riboswitch?

A

binding results in the change in the structure of mRNA.

both bind to a specific metabolite related to the path they are regulating.

38
Q

What are the differences of translational and transcriptional riboswitch?

A

translational riboswitch, the structural change results in the formation of an mRNA secondary structure (hairpin)

39
Q

What is the significance of eIF2 phosphorylation?

A

When eIF2 is phosphorylated it binds to the eIF2B tightly, the eIF2B is needed to recycle eIF2. However, once eIF2 is bound to eIF2B the binding is irreversible and eIF2B cannot function in translation.

40
Q

How does eIF2B cause the recycling of eIF2?

A

eIF2B binds to eIF2-GDP, kicks off GDP and allows it to be replaced with a GTP, allowing another cycle of translation to begin.

41
Q

What is hemoglobin regulation?

A

we want to have the right amount of heme for the right amount of globin chains.

42
Q

What happens when there is free heme?

A

When there is free heme the Heme Receptor kinase is turned off, therefore, eIF2 is not phosphorylated and polypeptide synthesis continues.

43
Q

What does it mean that heme Responsive kinase is allosterically inhibited by free heme.

A

only in the presence of free heme does protein synthesis occur.

44
Q

What happens when there is no free heme?

A

Heme Responsive kinase turned on, eIF2 phosphorylated, synthesis of polypeptide comes to a stop.

45
Q

How does RNA secondary structures and allosteric regulation of protein conformation regulate the synthesis of iron storage and transport proteins to obtain iron homeostasis?

A

The IREs form stem loop structures that are recognized by iron regulatory proteins (IRPs).

46
Q

What is ferritin?

A

protein complex that binds and stores excess iron in cells.

47
Q

What is transferrin?

A

protein that binds iron in the blood and transports it to cells.

48
Q

When is ferritin produced?

A

Ferritin is only produced when there is sufficient iron available for storage.

49
Q

What happens when iron is present in IRE in the 3’-UTR of the transport protein transferrin and 5’ region of the transferrin receptor gene?

A

3’ UTR: Fe-S cluster can form, and protein dissociates from the stem loop. No transferrin receptor gets made.

5’ region: the iron will form an Fe-S cluster causing the protein to lose its affinity for the stem loop. Translation of the mRNA can occur.

50
Q

What happens when the iron is absent in IRE in the 3’ UTR of the transport protein transferrin and 5’ region of the transferrin receptor gene.

A

3’ UTR- the IRP can bind to the stem loop structure. This allows for translation to occur.

5’ region - the IRP can bind to the stem loop structure; this effectively blocks translation of the ferritin mRNA and no protein is made.

51
Q

What is the significance of poly A tail and 5’ cap other than protecting from degradation?

A

The poly A tail and 5’ cap are needed to circularize mRNA. The eukaryotic ribosome will only take mRNA that have been circularized.

52
Q

Describe the most common forms of post-translational modifications and how they impact protein structure.

A

phosphorylation, methylation. Post translational modifications are critical for folding, protein localization, and function.

53
Q

For what protein is blocking the covalent addition of a lipid a potential anti-cancer therapeutic strategy and why?

A

G-protein Ras, because when farnesylation of this protein is blocked the protein is effectively non-functional.

Ras is overactive in many cancers.

54
Q

Anterograde transport

A

movement of particles from cell body to cell membrane

55
Q

What are ER signal sequences?

A

sequences that direct a protein to the ER.

56
Q

What is a retention sequence?

A

sequences that cause a protein to be retained in a cellular compartment.

57
Q

What are the common properties of ER signal sequences?

A
  1. 10-15 continuous hydrophobic amino acids.
  2. end there are few polar small amino acids such as alanine/serine.
58
Q

What is the signal recognition particle?

A

a complex of 300 nt RNA and six different proteins.

59
Q

Describe the process by which proteins are translocated into the ER?

A
  1. binding of mRNA to ribosome.
  2. amino terminal signal sequence is synthesized.
  3. sequence is bound by the signal recognition particle.
  4. SRP binds to GTP terminating polypeptide synthesis.
  5. GTP-SRP-Ribosome binds to receptor on cytoplasm side of ER.
  6. This entire complex is then directed to peptide translocation complex.
  7. The SRP dissociates and GDP is hydrolyzed and polypeptide synthesis is resumed.
  8. Translocation of the polypeptide through the protein channel, process requires ATP hydrolysis.
  9. Once polypeptide is inserted the signal sequence is cleaved by a protease.
  10. Ribosome dissociates from the ER.
60
Q

Where does most disulfide bond formation take place?

A

interior of the ER

61
Q

If a protein has a disulfide bond, is it more likely to be a cytosolic protein or a secreted protein?

A

secreted protein

62
Q

What is the function of GTP in protein translocation to ER?

A

GTP provides energy for the movement of the nascent polypeptide chain through the translocon.

63
Q

What is ubiquitin?

A

is a small highly conserved protein that regulates the process of protein degradation.

64
Q

What is ubiquitination?

A

tags proteins for degradation.

65
Q

What is E1?

A

E1 (ubiquitin-activating enzyme)
C-terminal glycine of ubiquitin is linked to E1 enzyme through thioester bond.

ATP dependent process

66
Q

What is E2?

A

E2 (Ubiquitin-Conjugating Enzyme) activated ubiquitin is moved to the E2 enzyme also through thioester bond.

67
Q

Why is ATP needed in ubiquitination?

A

energy needed to unfold the substrate and guide it inside of the protease complex.

68
Q

What is E3?

A

E3 (Ubiquitin- Ligase Enzyme)
C-terminus is attached to target protein through a side chain amino group on a lysine present on the target protein.

69
Q

What is a proteasome?

A

is a large multi subunit complex responsible for the degradation of proteins.

70
Q

How does the target protein enter proteasome?

A

Target protein will be recognized by regulatory cap on proteasome and the protein will be pushed into the proteasome. Proteasome will degrade protein.

71
Q

What is the significance of ATP in the ubiquitination process?

A

activating the ubiquitin molecule prior to its attachment to the substrate protein. If the C-terminal glycine of ubiquitin and SH of E1 form a reaction, there will be no available leaving group.

However, if the OH of C-terminal glycine of ubiquitin attacks the phosphate of ATP first, the ubiquitin is activated, because when SH of E1 attacks then there will be an available leaving group which is AMP. The release of AMP will drive the reaction forward.

BIOCHEM 2 (17 decks)

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