intracellular processes Flashcards
what are intracellular processes
Processes that take place within a cell
Each cellular process involves 1000s of chemical reactions however many of these are incompatible
what are the two major strategies to segregate molecules
multicomponent complexes
compartmentalisation into membrane-bound organelles
what do organelles contain ?
Specific proteins in the membrane of the organelle and/or in its interior
what is the movement of proteins in an organelle
transferred from cytosol (where they are made) to compartment where they are used (organelle)
what percentage of cell volume is organelles
approximately 50% of cell volume
what needs to happen to newly synthesised proteins
need to be targetted to the organelles
what is the first process of protein targetting ?
1st: protein needs to be synthesised
where does protein synthesis start ?
in the cytosol
in particular on ribosomes
what are ribosomes
= multicomponent complex of RNA and proteins)
what are ribosomes make up what ?
proteins and ribosomal RNA (rRNA)
what is each ribosome composed of ?
two subunits
60S + 40S = 80S
what does the s in ribosomes stand for ?
Svedberg, a non-linear measurement dependent on mass, density and shape
what is svedberg ?
Measures ‘sedimentation rate’ = how quickly it will settle at the bottom after centrifugation.
explain the role of ribosomes in antibiotics
antibiotics target either decoding site on small ribosomal subunit (30S
peptidyl-transferase centre on the large subunit (50S)
what does targeting the small ribosomal unit (30S) lead to
Prevents tRNA binding or moving through ribosome
what does the antibiotic targeting peptidyl-transferase centre lead to ?
Prevents polypeptide chain elongation
what difficulty do hydrophilic proteins have when getting into organelles
they are hydrophilic (water loving) but need to get across hydrophobic (water hating) membrane
what are the 3 mechanisms that get bacteria into organelles
nuclear pores
protein translocators
transport vesicles
explain nuclear pores
selective gates for nuclear proteins
explain protein translocators
for proteins moving from cytosol into ER, mitochondria, peroxisomes (all have membranes)
explain transport vesicles
for proteins moving from the ER onwards
as well as protein movement what is also important
protein sorting -> making sure proteins go to the correct organelles
what is the difference between free ribosomes and those attached to the membrane
No difference between ‘free’ ribosomes and those attached to ER membrane, except from the proteins they happen to be making at that time
how do ribosomes know to go to the ER
of the ‘signal peptide’ on protein being made
what is a signal peptide
specific sequence on the N-terminal amino acids
what two things allows the guidance of the signal peptide
Signal-recognition particle (SRP)
SRP receptor
what is SRP ?
SRP is in the cytosol and binds to ER signal peptide when it’s exposed on ribosome
what is the SRP receptor found ?
embedded on ER membrane
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
as polypeptide continues to be created what is it threaded through ?
translocon in the ER membrane
what happens to the signal Peptide in the ER after peptide targeted to ER
Signal peptide then cleaved by signal peptidase (an ER enzyme)
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
what organelle is involved after the ER
the golgi apparatus
what are proteins carried in the golgi
are carried in vesicles that fuse to become cis cisterna
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
transport from er-> golgi -> other compartments is carried out how?
continual budding and fusion of transport vesicles
what do vesicles from the ER ultimately fuse with
with the plasma membrane
what is m6p ?
, mannose-6-phosphate (M6P)
what do proteins labelled
with M6p do ?
bind to specific receptor in Golgi membrane
arrives at destination of endosome which matures
to become lysosomes
as proteins are transported along pathways what can happen
undergo modifications
what is an example of proteins becoming modified. ie
Adding sugar residues (carbohydrates) such as mannose-6-phosphate
proteins that are extensively glycosylated are called what
proteoglycans
what are proteins with small sugar component called
glycoproteins
what can be a negative side effect of post transitional modification
Hyperphosphorylation of the protein Tau is a hallmark ofseveralneurodegenerative disorders (tauopathies)
what is phosphorylation an addition of and function
a phosphate group
alters activity of protein
what is acetylation a function of and the function
an acetyl group
in histones – regulation of gene expression
what is Farnesylation an addition of and function
a farnesyl group
targets proteins to cytoplasmic face of plasma membrane
what is Ubiquitination
an addition of
Ubiquitin chain
targets protein for degradation
what does the plasma membrane do ?
stop translocation
how is the mitochondrial import sequence kept unfolded
by binding to ATP-dependent chaperone proteins. Imported via translocases
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
what are the two mechanisms for protein degradation
Lysosomal degradation
Proteasomal degradation
what are the components of lysosomal degradation
long half life
membrane proteins
extracellular proteins
what are the components of proteasomal degradation
short half life
key metabolic enzymes
defective proteins
what are examples of lysosomal enzymes
lipases, nucleases, proteases/proteolytic enzymes
how are lysosomal enzymes activated
Activated by acidic environment (pH 4.8) inside lysosome
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
where does proteasomal degradation take place
in the cytosol at proteasomes = cylindrical protein complexes
in a proteosome what the wall are formed from ?
protease enzymes - the active site is inside cylinder
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
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
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)
what do shuttling proteins do ?
take ubiquitinated protein to proteasome
what occurs after ubiquitinated proteins are in proteosome
Tagged proteins recognised, unfolded and translocated
Degraded inside proteasome to give peptides
what process occurs with the peptides that are formed in the proteosome from degradation
Peptides extruded & digested by cytosolic peptidases
