Week 1 - Intracellular Processes

Question 1

What are ribosomes composed of

Answer 1

Protein and rRNA

Question 2

In what 2 ways does the cell act to segregate molecules

Answer 2

Through multicomponent complexes (such as the two subunits of the ribosome)
Through compartmentalisation into membrane-bound organelles

Question 3

What do the membranes around organelles provide

Answer 3

A closed compartment in which sets of enzymes can operate without interference

Question 4

Proteins in the membrane of organelles need to be what?

Answer 4

Replenished and maintained
Through production in cytosol where they are made and then to the organelle where they are used

Question 5

Name the process by which synthesised proteins target their eventual location

Answer 5

Protein sorting

Question 6

Where are proteins initially synthesised

Answer 6

Ribosomes in the cytosol

Question 7

Where is the information that tells a protein where to end up

Answer 7

Specific signal peptides ‘address labels’ contained in the amino acid sequence

Question 8

The ribosome is made up of how many subunits

Answer 8

2

Question 9

Clinically used antibiotics target which sites on the ribosome?

Answer 9

Decoding site (small subunit)

Peptidyl-transferase centre (large subunit)

Question 10

Name 3 ways in which proteins can get into organelles and give an example of when this happens

Answer 10

Nuclear pores
(proteins going into nucleus)
Protein translocators
(proteins moving from cytosol into ER)
Transport vesicles
(proteins moving from the ER onwards)

Question 11

Why do some ribosomes know to go to the ER

Answer 11

The presence of a signal peptide on the protein being made (called the N-terminal amino acids at the start of the protein)

Question 12

What is the C-terminal of the protein

Answer 12

The end of the protein

Question 13

The signal peptide is guided to the ER by what?

Answer 13

The signal-recognition particle ( which detects the presence of signal peptide) and the SRP receptor (which is on the ER membrane

Question 14

What is the name of the protein channel in the ER membrane

Answer 14

The translocon

Question 15

Which enzyme cleaves the signal peptide once the protein is within the ER

Answer 15

Peptidase

Question 16

What happens after the signal peptide has been cleaved by peptidase

Answer 16

The protein in the ER lumen is encapsulated into a transport vesicle that buds off and is secreted from the ER

Question 17

Analogy of signalling to the ER FIX THIS WHEN SOBER

Answer 17

New protein = letter
Signal peptide = address label
Signal recognition particle = postman
SRP receptor in ER membrane = Postman
SRP receptor in ER membrane = Name-plate on door
Translocon (pore/channel in ER) = Letterbox

Question 18

Once proteins are transported by vesicles to the Golgi apparatus, what is this called?

Answer 18

The cis cisterna

Question 19

What happens as the proteins move through the Golgi stack

Answer 19

The proteins undergo enzymatic modification which labels them for a specific cell destination

Question 20

What allows the transport from ER to Golgi apparatus and Golgi apparatus to other compartments

Answer 20

The continual budding and fusion of transport vesicles

Question 21

Which side of the golgi apparatus is closest to the ER

Answer 21

Cis

Question 22

Which side of the Golgi apparatus is furthest away from the ER

Answer 22

Trans

Question 23

What happens at the trans end of the Golgi apparatus

Answer 23

Proteins are sorted into groups with the same target sequence as these are destined for the same location

Question 24

What happens once proteins have been sorted into groups at the trans side of the golgi apparatus

Answer 24

The proteins migrate via vesicles to their eventual location

Question 25

What directs proteins to the lysosome instead of the plasma membrane

Question 26

What are the two processes that can occur after the golgi apparatus

Answer 26

Exocytosis Endocytosis

Question 27

Which signal ensures that the protein takes the exocytosis pathway

Answer 27

The stop translocation signal

Question 28

What causes a protein to take the alternative pathway towards the lysosome

Answer 28

An 'address label' added in the Golgi apparatus such as the side chain 'mannose-6-phosphate' (M6P)

Question 29

What happens to a protein that is labelled with M6P

Answer 29

It binds to a specific receptor in the golgi membrane Protein will then bind with an endosome via vesicle transport which matures to become a lysosome

Question 30

What do endosomes often contain

Answer 30

A pathogen which has been endocytosed by the cell previously for it to be destroyed by the protein has been targeted in the first place (example hydrolase)

Question 31

Names of different sides of golgi apparatus

Answer 31

Cis cisterna (first side reached Trans Golgi Cisternae

Question 32

What is glycosylation

Answer 32

Addition of sugar (such as M6P) to protein (happens in Golgi apparatus(

Question 33

What are proteins called that are extensively glycosylated

Answer 33

Proteoglycans

Question 34

What are proteins that are composed of little sugar content

Answer 34

Glycoproteins

Question 35

What is a hallmark of several neurodegenerative disorders

Answer 35

Hyperphosphorylation of the protein Tau

Question 36

Describe phosphorylation

Answer 36

Addition of a phosphate group which alters the activity of a protein

Question 37

Describe acetylation

Answer 37

Addition of an acetyl group which in histones regulates gene expression

Question 38

Describe Farnesylation

Answer 38

Addition of a farnesyl group which targets proteins to the cytoplasmic face of the plasma membrane

Question 39

Describe Ubiquitination

Answer 39

Addition of a ubiquitin chain which targets proteins for degradation

Question 40

What causes a protein to move to the ER and subsequently the Golgi

Answer 40

The presence of a signal peptide

Question 41

By default what will happen to the protein if there exists nothing other than a signal peptide

Answer 41

It will be secreted out of the cell

Question 42

What happens to protein that has the 'stop translocation' peptide

Answer 42

It will end up in the plasma membrane

Question 43

What will happen to a protein that has had a M6P sugar side chain added in the golgi apparatus

Answer 43

It will end up in the lysosomes

Question 44

What happens to a protein that lacks a signal protein

Answer 44

It will remain in the cytosol

Question 45

What happens to a protein that has a nuclear localisation signal in the protein sequence

Answer 45

It will end up in the nucleus

Question 46

What will happen to a protein that has a mitochondrial import sequence

Answer 46

It will end up in the mitochondira

Question 47

What will happen to proteins that have a c-terminal tripeptide?

Answer 47

They will end up in the peroxisomes

Question 48

What is protein degradation required for (3)

Answer 48

Proteins that have passed their 'sell by' date Proteins that are faulty Proteins that are foreign to the cell i.e pathogens

Question 49

What are the two mechanisms that can cause degradation

Answer 49

Lysosomal degradation Proteasomal degradation

Question 50

Name 3 lysosomal enzymes

Answer 50

Lipases, nucleases and proteases/proteolytic enzymes

Question 51

How are lysosomal enzymes activated

Answer 51

By the acidic environment (pH 4.8) inside the lysosome

Question 52

Which types of proteins is lysosomal degradation used for (4)

Answer 52

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

Question 53

Where does proteasomal degradation occur

Answer 53

At the proteasomes

Question 54

Describe the structure of proteasomes

Answer 54

Cylindrical protein complexes which consist of protease enzymes (the active site is inside the cylinder)

Question 55

What controls the entry of proteins about to be degraded into the proteasome

Answer 55

Protein 'stoppers'

Question 56

What are proteosomes dependant on for their function

Answer 56

ATP

Question 57

What is proteasomal degradation used for

Answer 57

Proteins that have a short half life and hence need to be removed quickly (seconds or minutes)

Question 58

Proteins with a short half life generally are rich in which specific sequence Key metabolic enzymes and proteins that need to gotten rid of Proteins that have been covalently tagged with ubiquitin

Answer 58

PEST (P) proline, (E) glutamic acid (S) Serine and (T) threonine

Question 59

Describe the 4 steps relating to proteasomal degradation of proteins that have been covalently tagged with ubiquitin

Answer 59

Shuttling proteins take ubiquitinated protein to proteasome Tagged proteins are recognised, unfolded and translocated Ubiquitinated proteins are degraded inside proteasome to give peptides Peptides are extruded and digested by cytosolic peptidases