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week 1 > intracellular processes > Flashcards

intracellular processes Flashcards

1
Q

what are intracellular processes

A

Processes that take place within a cell
Each cellular process involves 1000s of chemical reactions however many of these are incompatible

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2
Q

what are the two major strategies to segregate molecules

A

multicomponent complexes
compartmentalisation into membrane-bound organelles

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3
Q

what do organelles contain ?

A

Specific proteins in the membrane of the organelle and/or in its interior

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4
Q

what is the movement of proteins in an organelle

A

transferred from cytosol (where they are made) to compartment where they are used (organelle)

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5
Q

what percentage of cell volume is organelles

A

approximately 50% of cell volume

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6
Q

what needs to happen to newly synthesised proteins

A

need to be targetted to the organelles

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7
Q

what is the first process of protein targetting ?

A

1st: protein needs to be synthesised

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8
Q

where does protein synthesis start ?

A

in the cytosol
in particular on ribosomes

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9
Q

what are ribosomes

A

= multicomponent complex of RNA and proteins)

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10
Q

what are ribosomes make up what ?

A

proteins and ribosomal RNA (rRNA)

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11
Q

what is each ribosome composed of ?

A

two subunits
60S + 40S = 80S

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12
Q

what does the s in ribosomes stand for ?

A

Svedberg, a non-linear measurement dependent on mass, density and shape

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13
Q

what is svedberg ?

A

Measures ‘sedimentation rate’ = how quickly it will settle at the bottom after centrifugation.

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14
Q

explain the role of ribosomes in antibiotics

A

antibiotics target either decoding site on small ribosomal subunit (30S

peptidyl-transferase centre on the large subunit (50S)

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15
Q

what does targeting the small ribosomal unit (30S) lead to

A

Prevents tRNA binding or moving through ribosome

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16
Q

what does the antibiotic targeting peptidyl-transferase centre lead to ?

A

Prevents polypeptide chain elongation

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17
Q

what difficulty do hydrophilic proteins have when getting into organelles

A

they are hydrophilic (water loving) but need to get across hydrophobic (water hating) membrane

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18
Q

what are the 3 mechanisms that get bacteria into organelles

A

nuclear pores
protein translocators
transport vesicles

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19
Q

explain nuclear pores

A

selective gates for nuclear proteins

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20
Q

explain protein translocators

A

for proteins moving from cytosol into ER, mitochondria, peroxisomes (all have membranes)

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21
Q

explain transport vesicles

A

for proteins moving from the ER onwards

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22
Q

as well as protein movement what is also important

A

protein sorting -> making sure proteins go to the correct organelles

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23
Q

what is the difference between free ribosomes and those attached to the membrane

A

No difference between ‘free’ ribosomes and those attached to ER membrane, except from the proteins they happen to be making at that time

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24
Q

how do ribosomes know to go to the ER

A

of the ‘signal peptide’ on protein being made

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25
Q

what is a signal peptide

A

specific sequence on the N-terminal amino acids

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26
Q

what two things allows the guidance of the signal peptide

A

Signal-recognition particle (SRP)
SRP receptor

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27
Q

what is SRP ?

A

SRP is in the cytosol and binds to ER signal peptide when it’s exposed on ribosome

28
Q

what is the SRP receptor found ?

A

embedded on ER membrane

29
Q

explain process of the signal peptide

A

signal peptide on polypeptide in the ribosome

signal recognition particle binds to signal peptide in polypeptide

SRP receptor on ER membrane binds to SRP which is in ribosome

30
Q

as polypeptide continues to be created what is it threaded through ?

A

translocon in the ER membrane

31
Q

what happens to the signal Peptide in the ER after peptide targeted to ER

A

Signal peptide then cleaved by signal peptidase (an ER enzyme)

32
Q

what is the next step after signal protein is cleaved

A

Protein in the ER lumen is encapsulated into a transport vesicle that ‘buds off’ & is secreted from the ER

33
Q

what organelle is involved after the ER

A

the golgi apparatus

34
Q

what are proteins carried in the golgi

A

are carried in vesicles that fuse to become cis cisterna

35
Q

explain the cis maturation model

A

proteins move through the Golgi stack
As they do, they undergo enzymatic modification, which labels them for a specific cell destination

36
Q

transport from er-> golgi -> other compartments is carried out how?

A

continual budding and fusion of transport vesicles

37
Q

what do vesicles from the ER ultimately fuse with

A

with the plasma membrane

38
Q

what is m6p ?

A

, mannose-6-phosphate (M6P)

39
Q

what do proteins labelled
with M6p do ?

A

bind to specific receptor in Golgi membrane
arrives at destination of endosome which matures
to become lysosomes

40
Q

as proteins are transported along pathways what can happen

A

undergo modifications

41
Q

what is an example of proteins becoming modified. ie

A

Adding sugar residues (carbohydrates) such as mannose-6-phosphate

42
Q

proteins that are extensively glycosylated are called what

A

proteoglycans

43
Q

what are proteins with small sugar component called

A

glycoproteins

44
Q

what can be a negative side effect of post transitional modification

A

Hyperphosphorylation of the protein Tau is a hallmark ofseveralneurodegenerative disorders (tauopathies)

45
Q

what is phosphorylation an addition of and function

A

a phosphate group

alters activity of protein

46
Q

what is acetylation a function of and the function

A

an acetyl group
in histones – regulation of gene expression

47
Q

what is Farnesylation an addition of and function

A

a farnesyl group

targets proteins to cytoplasmic face of plasma membrane

48
Q

what is Ubiquitination
an addition of

A

Ubiquitin chain
targets protein for degradation

49
Q

what does the plasma membrane do ?

A

stop translocation

50
Q

how is the mitochondrial import sequence kept unfolded

A

by binding to ATP-dependent chaperone proteins. Imported via translocases

51
Q

what is the function of protein degradation

A

Required for proteins that are past their ‘sell by’ date
Proteins that are faulty
Proteins that are foreign to the cell /e.g. from pathogens

52
Q

what are the two mechanisms for protein degradation

A

Lysosomal degradation
Proteasomal degradation

53
Q

what are the components of lysosomal degradation

A

long half life
membrane proteins
extracellular proteins

54
Q

what are the components of proteasomal degradation

A

short half life
key metabolic enzymes
defective proteins

55
Q

what are examples of lysosomal enzymes

A

lipases, nucleases, proteases/proteolytic enzymes

56
Q

how are lysosomal enzymes activated

A

Activated by acidic environment (pH 4.8) inside lysosome

57
Q

what is lysosomal degradation used for

A

Proteins with a long half life (>20 hours) =
autophagy
Membrane proteins brought into the cell via endocytosis

Extracellular proteins brought into the cell via receptor-mediated endocytosis

Pathogenic proteins brought into the cell via phagocytosis

58
Q

where does proteasomal degradation take place

A

in the cytosol at proteasomes = cylindrical protein complexes

59
Q

in a proteosome what the wall are formed from ?

A

protease enzymes - the active site is inside cylinder

60
Q

why are there protein stoppers at either end of the proteosome

A

they are open
to allow protein that is going to be degraded to get in
ATP-dependent

61
Q

what is proteasomal degradation used for

A

Proteins that need to be removed quickly i.e. those with a short half-life (t1/2 = seconds or minutes)

Key metabolic enzymes & defective proteins

Proteins covalently tagged with ubiquitin in a 3-step pathway

62
Q

the proteins that need to be removed quickly and are involved in proteasomal degradation have what ?

A

: PEST, rich in proline (P), glutamic acid (E), serine (S) and threonine (T)

63
Q

what do shuttling proteins do ?

A

take ubiquitinated protein to proteasome

64
Q

what occurs after ubiquitinated proteins are in proteosome

A

Tagged proteins recognised, unfolded and translocated
Degraded inside proteasome to give peptides

65
Q

what process occurs with the peptides that are formed in the proteosome from degradation

A

Peptides extruded & digested by cytosolic peptidases

week 1 (6 decks)

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