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HNC Applied Science in Biology and Chemistry > Cell Biology - Outcome 2 > Flashcards

Cell Biology - Outcome 2 Flashcards

Protein Processing and Degradation

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1
Q

where do all protein begin synthesis?

A

on free ribosomes

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2
Q

what does the signal peptide sequence determine?

A

the fate of this protein being synthesised at the ribosome

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3
Q

what is the signal peptide sequence composed of?

A

approximately 20 amino acids and its location within the growing polypeptide

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4
Q

what are the two terminals on a polypeptide chain and what are they composed of?

A

amino acid terminal (n-terminal)
- NH3+

carbonyl terminal (c-terminal)
-COO-

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5
Q

what is another determining factor of the fate of the protein?

A

whether the protein is being synthesised on a free ribosome or on a ribosome attached to the ER (‘bound’ ribosome)

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6
Q

what determines whether or not the ribosome will dock at the ER membrane and become a ‘bound’ ribosome

A

the protein that the ribosome is synthesising

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7
Q

what happens if no signal peptide is detected on the protein?

A

the free ribosome completes the synthesis and the protein is released into the cytoplasm

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8
Q

what happens if the protein has an organelle specific signal sequence?

A

it will be targeted to the organelle for import

eg. the nucleus, mitochondria, chloroplasts and peroxisomes

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9
Q

what pathway is entered if the ribosome synthesising the protein becomes a ‘bound’ ribosome and attaches to the the RER?

A

the secretory pathway

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10
Q

what happens if the protein being synthesised has a signal peptide at the n-terminal?

A
  • protein synthesis will be halted
  • ribosome synthesising the protein will be moved to the membrane of the RER by the signal recognition particle (SRP)
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11
Q

what is the function of the signal recognition particle (SRP)?

A
  • scans the cytoplasm and looks for an ER n-terminal signal sequence
  • binds to signal sequence and then pulls protein (and ribosome its attached to) to membrane of RER and ‘docks’ the ribosome to membrane of the RER
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12
Q

what is the transmembrane channel that SRP brings the protein to and what happens?

A

brings protein to a translocon and protein synthesis continues

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13
Q

what happens to the synthesising protein if it is hydrophilic in nature?

A

the protein will enter the lumen of the ER

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14
Q

what happens once the protein is inside the lumen of the RER?

A
  • the signal sequence is cleaved off by an enzyme called signal peptidase
  • the protein will then be folded into its functional conformation, and may also get post-translationally modified
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15
Q

what happens to a protein that is destined to be an ER protein and it requires no further modifications?

A

it will remain in the lumen of the ER

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16
Q

what happens to the protein if it does require further modifications?

A

it will proceed to the Golgi apparatus via a RER vesicle

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17
Q

where do proteins that have a highly hydrophobic. central region remain/ where do they go and what are they capable of?

A
  • in the bilayer of the ER membrane or be sent to another organelle membrane via RER or Golgi vesicle
  • capable of diffusing laterally along the ER membrane.
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18
Q

what is the fate of newly synthesised proteins that have hydrophobic central regions?

A

to be transmembrane proteins which serve as:
- channels
- pumps
- enzymes
- receptors
in the cell membrane and in organelle membranes

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19
Q

where may hydrophobic proteins be sent to?

A
  • a lysosome
  • to be secreted out of the cell, out into surrounding extracellular fluid, picked up by bloodstream and transported to its target tissue
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20
Q

what does it mean for a protein to be GLYCOSYLATED?

A

a sugar group will be added (aids cellular location)

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21
Q

what does it mean for a protein to be CLEAVED?

A

parts of the protein will be cut off/ bonds in the protein will be broken
(may activate protein to become functional)

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22
Q

what does it mean for a protein to be PHOSHORYLATED?

A

a phosphate group will be added (may activate protein)

23
Q

what happens if a protein is destined to be a membrane protein?

A

the vesicle will fuse with the cell membrane and the protein will insert

24
Q

what happens if a protein is destined to be a protein in another part of the body?

A
  • the vesicle will use with the membrane and be secreted out into the surrounding extracellular fluid
  • picked up by bloodstream and transported to its target tissue
25
Q

what happens if a protein is destined to be a protein in an organelle?

A

the vesicle will fuse with the specific organelle membrane and the protein will insert

26
Q

what happens if a protein is destined to be used by a lysosome/needs to be degraded?

A

vesicle will fuse with the lysosomal cell membrane and the protein will insert

27
Q

why may a protein only be short-lived in a cell due to regulatory processes?

A

to allow control of a signalling/metabolic pathway

28
Q

what happens to newly synthesised proteins in the lumen of the RER?

A

a quality control check is carried out on them

29
Q

what type of proteins are rejected when being checked in the lumen of the RER?

A

any proteins that are found to be incorrectly formed or incorrectly folded

30
Q

what are abnormal proteins targeted for?

A

degradation

31
Q

what are the 3 processes of degradation and removal of proteins?

A
  • ubiquitination
  • lysosomes
  • autophagy
32
Q

what is involved in the ubiquitination process?

A
  • it uses a molecule of ubiquitin to ‘tag’ obsolete proteins for destruction

it involves 3 main enzymes:
- ubiquitin activating enzyme (E1)
- ubiquitin conjugating enzyme (E2)
- ubiquitin ligase (E3)

33
Q

what does the ubiquitin activating enzyme (E1) do?

A

activates the ubiquitin molecule in the presence of ATP

34
Q

what does the ubiquitin conjugating enzyme (E2) do?

A

it covalently links the ubiquitin molecule to itself (E2)

35
Q

what does ubiquitin ligase (E3) do?

A

it ligates the ubiquitin molecule to the target molecule (ie. protein)

36
Q

what is monoubiquitination?

A

where a tag of only one ubiquitin molecule is sufficient to tag the protein and completes one cycle of the tagging process

37
Q

what is polyubiquitination?

A

where a protein is tagged with many ubiquitin molecules hence multiple cycles of the process occurs adding a ubiquitin molecule during each cycle

38
Q

how many of E1, E2 and E3 enzymes do mammalian genomes encode approximately?

A
  • 12 E1 enzymes
  • 30-40 E2 enzymes
  • hundreds of E3 enzymes
39
Q

what does the variation of enzymes (E1, E2 and E3) suggest?

A

a wide variety of protein targets with different regulatory mechanisms for each one

40
Q

what do lysosomes account for cellular protein degradation?

A

10-20%

41
Q

what does the ubiquitination process account for all cellular protein degradation?

A

80-90%

42
Q

what are lysosomes?

A

special vesicles derived from the Golgi apparatus

43
Q

what is the function of lysosomes?

A

to degrade damaged or unwanted macromolecules back down to macromolecules

44
Q

what are macromolecules?

A
  • proteins
  • nucleic acids
  • lipids
  • complex carbohydrates
45
Q

what are micromolecules?

A
  • amino acids
  • simple sugars
46
Q

describe the full process for when macromolecules are targeted for degradation.

A
  • macromolecules that are targeted for degradation are packaged into vesicles by the Golgi.
  • Golgi then fuses with the lysosome and delivers its contents (macromolecules) into interior of lysosome.
  • hydrolytic enzymes (eg. lipases, proteases, nucleases) and an acidic environment (pH 2) inside the lysosome degrade the macromolecules to micromolecules
  • lysosome then transports micromolecules out into the cytosol for re-use.
47
Q

what is autophagy?

A

a self-destruction process where the cell removes dysfunctional organelles

48
Q

what are the 4 stages of autophagy?

A
  • induction
  • formation
  • docking and fusion
  • breakdown
49
Q

describe what happens during induction

A

double membrane starts to ‘cup’ around organelle

50
Q

describe what happens during formation

A

organelle completely surrounded. autophagosome is formed

51
Q

describe what happens during docking and fusion

A

autophagosome fuses with lysosome

52
Q

describe what happens during breakdown

A

organelle and phagosome membrane are digested by the lysosome

53
Q

when may autophagy occur and give an example

A
  • may occur at times of cellular stress and low energy states
  • during starvation molecules are broken down to be put back into the cycle to generate energy for proteins for survival

HNC Applied Science in Biology and Chemistry (6 decks)

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