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week 1 > intracellular processes > Flashcards

intracellular processes Flashcards

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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
what is a signal peptide
specific sequence on the N-terminal amino acids
26
what two things allows the guidance of the signal peptide
Signal-recognition particle (SRP) SRP receptor
27
what is SRP ?
SRP is in the cytosol and binds to ER signal peptide when it’s exposed on ribosome
28
what is the SRP receptor found ?
embedded on ER membrane
29
explain process of the signal peptide
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
as polypeptide continues to be created what is it threaded through ?
translocon in the ER membrane
31
what happens to the signal Peptide in the ER after peptide targeted to ER
Signal peptide then cleaved by signal peptidase (an ER enzyme)
32
what is the next step after signal protein is cleaved
Protein in the ER lumen is encapsulated into a transport vesicle that ‘buds off’ & is secreted from the ER
33
what organelle is involved after the ER
the golgi apparatus
34
what are proteins carried in the golgi
are carried in vesicles that fuse to become cis cisterna
35
explain the cis maturation model
proteins move through the Golgi stack As they do, they undergo enzymatic modification, which labels them for a specific cell destination
36
transport from er-> golgi -> other compartments is carried out how?
continual budding and fusion of transport vesicles
37
what do vesicles from the ER ultimately fuse with
with the plasma membrane
38
what is m6p ?
, mannose-6-phosphate (M6P)
39
what do proteins labelled with M6p do ?
bind to specific receptor in Golgi membrane arrives at destination of endosome which matures to become lysosomes
40
as proteins are transported along pathways what can happen
undergo modifications
41
what is an example of proteins becoming modified. ie
Adding sugar residues (carbohydrates) such as mannose-6-phosphate
42
proteins that are extensively glycosylated are called what
proteoglycans
43
what are proteins with small sugar component called
glycoproteins
44
what can be a negative side effect of post transitional modification
Hyperphosphorylation of the protein Tau is a hallmark of several neurodegenerative disorders (tauopathies)
45
what is phosphorylation an addition of and function
a phosphate group alters activity of protein
46
what is acetylation a function of and the function
an acetyl group in histones – regulation of gene expression
47
what is Farnesylation an addition of and function
a farnesyl group targets proteins to cytoplasmic face of plasma membrane
48
what is Ubiquitination an addition of
Ubiquitin chain targets protein for degradation
49
what does the plasma membrane do ?
stop translocation
50
how is the mitochondrial import sequence kept unfolded
by binding to ATP-dependent chaperone proteins. Imported via translocases
51
what is the function of protein degradation
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
what are the two mechanisms for protein degradation
Lysosomal degradation Proteasomal degradation
53
what are the components of lysosomal degradation
long half life membrane proteins extracellular proteins
54
what are the components of proteasomal degradation
short half life key metabolic enzymes defective proteins
55
what are examples of lysosomal enzymes
lipases, nucleases, proteases/proteolytic enzymes
56
how are lysosomal enzymes activated
Activated by acidic environment (pH 4.8) inside lysosome
57
what is lysosomal degradation used for
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
where does proteasomal degradation take place
in the cytosol at proteasomes = cylindrical protein complexes
59
in a proteosome what the wall are formed from ?
protease enzymes - the active site is inside cylinder
60
why are there protein stoppers at either end of the proteosome
they are open to allow protein that is going to be degraded to get in ATP-dependent
61
what is proteasomal degradation used for
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
the proteins that need to be removed quickly and are involved in proteasomal degradation have what ?
: PEST, rich in proline (P), glutamic acid (E), serine (S) and threonine (T)
63
what do shuttling proteins do ?
take ubiquitinated protein to proteasome
64
what occurs after ubiquitinated proteins are in proteosome
Tagged proteins recognised, unfolded and translocated Degraded inside proteasome to give peptides
65
what process occurs with the peptides that are formed in the proteosome from degradation
Peptides extruded & digested by cytosolic peptidases

week 1 (6 decks)

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