Ribosomes, translation & the Endoplasmic Reticulum (ER)- week 2

Question 1

what is the composition of a ribosome (approx size and subunits, proportion and location of rRNA and protein)

Answer 1

made up of 2 subunits:
60s and 40s, there are 3 rRNA that make up the 60s and 1 rRNA that make up the 40s (roughly 2/3 rRNA and 1/3 protein)
-the rRNAs are in the nucleolus apart from 5s

Question 2

Describe the processes that occur during ribosome production/synthesis, the 3 stages

Answer 2

➢rRNA – synthesis & processing
➢Ribosomal proteins – transcription, translation
➢Ribosomal subunits – assembly

Question 3

in rRNA synthesis what happens to parts of the chromosomes in which code to ribosome called

Answer 3

Nucleolar organizers - happens in a dark patch within the nucleolus and forms around parts of chromosomes where the ribosomal RNA is coded (so 10 chromosomes that are in the nucleus will form around only the bits that encode the ribosomal RNA- lots of active transcription happens here)

Question 4

where does rRNA synthesis occur

Answer 4

dark patch in the nucleus called the nucleolus

Question 5

what is the difference between RNA polymerase and RNA polymerase II and RNA polymerase III

Answer 5

RNA Polymerase I is an enzyme that transcribes ribosomal RNAs (apart from 5s rRNA)
RNA Polymerase II is an enzyme that transcribes precursors of mRNAs.
RNA Polymerase III is an enzyme that transcribes tRNAs, rRNA (this would include the 5S rRNA), and other small RNAs

Question 6

what are the properties of the nucleosome that make it suited for ribosomal subunit synthesis

Answer 6

-10^6 ribosomes in each cell (used for protein synthesis)
-10^6 copies of each ribosomal RNA
-multiple copies of rRNA genes to produce rRNA (so that the process of making ribosomes is sped up- can make multiple at a time)

Question 7

what enzyme transcribes rRNA

Answer 7

RNA polymerase I

Question 8

what is the process of processing rRNA precursor RNA, (give the numbers of the rRNA’s that make the large and small subunit of the ribosome)

Answer 8

-the chain of nucleotides go through chemical modification- where the binding of ribosome RNA proteins to the precursor rRNA
-this then signals for the cleavage of the molecule into 3 different independent rRNA’s- (its the cutting of the spacer DNA that doesn’t code for anything, so whats left is single sections of rRNA which code for something)
- so 2 of the rRNAs: 5.8S & 28S rRNA’s go toward the large ribosomal subunit and the third one the 5S rRNA comes from else where in the nucleus (not in the nucleolus) to join whilst the 18S rRNA is incorporated into the small ribosomal subunit

Question 9

what enzyme transcribes the large subunit of a ribosome

Answer 9

RNA polymerase III

Question 10

What is the large subunit of a ribosome made from (give numbers of each)

Answer 10

2000 5S rRNA genes in 1 cluster on a chromosome not part of nucleolus organiser-& from 5.8S and 28S rRNA

Question 11

how many structural proteins are there

Answer 11

55

Question 12

where are the subunits exported to ready for their role in translation

Answer 12

cytoplasm

Question 13

what are the sites on a ribosome and what are they called

Answer 13

E site= exit site
P site= peptide site
A site= arrival site

Question 14

how does the initiation of translation occur (3 points)

Answer 14

• small subunit with tRNA bind to DNA
  -scans for the first AUG
  -signals for the large subunit to bind
  translation begins

Question 15

what acts as a hydrogen acceptor during the peptide bond formation

Answer 15

adenine in the small subunit rRNA- 28s

Question 16

how does translation terminate

Answer 16

• A Release Factor binds to A site- has no amino acid attached to it
  -Last tRNA molecule moves to the E site and Releases Factor occupies the P site
  -that moves the last codon out/exits & at that point the Release Factor causes the DISSOCIATION of the large subunit from the small subunit and mRNA

Question 17

how is protein degradation controlled

Answer 17

• UBIQUITIN is a short peptide
  -its ACTIVATED by binding to UBIQUITIN Activating Enzyme (E1)
  -this then transfers it to Ubiquitin Ligase (E2/E3 complex)
  -E2/E3 recognises the protein targeted for degradation
  -then transfers Ubiquitin to it
  -FURTHER ubiquitin molecules added by E2
  -multiple ubiquitin chains are the signal for degradation by proteasome

Question 18

what is ubiquitin

Answer 18

its a short peptide which can be attached to the NH2 side chains of LYSINE (the triplet codon that codes for 1 single amino acid which is lysine) it residues in proteins- gives the signal for degradation

Question 19

what are the diseases caused by failure of protein degradation (name 3)

Answer 19

Parkinson, Huntington, and Alzheimer diseases

Question 20

how can protein turnover be controlled

Answer 20

-controlling of regulatory proteins - some key regulatory proteins are maintained at low levels, gets used for a period of time then gets degraded (e.g cyclin which are degraded at the end of mitosis)
-removal of misfolded proteins

Question 21

what is the role of the ribosome in translation by catalysing peptide bond formation

Answer 21

it is said that the ribosome acts as a enzyme and is called a ribozyme

Question 22

what is the role of the ribosome in translation by getting the mRNA and amino acid tRNAs together

Answer 22

the adenine in the rRNA acts as a temporary hydrogen acceptor to allow the peptide bond happen between the carboxyl group of and the NH2 group

Question 23

Describe the differences between the Rough endoplasmic reticulum
(RER) and smooth endoplasmic reticulum (SER) with regard to its
structure.

Answer 23

> RER its membrane arranged in flattened sheets where SER is tubular with many branches.
RER has ribosomes attached to it whereas SER doesn’t.

Question 24

Describe what the ER is made up of

Answer 24

-contiguous tubules and sacs
-ER lumen bounded by ER membrane
ER membrane is contiguous with outer nuclear membrane
-membranous labyrinth (maze of tubes)

Question 25

What is the relevance of the nucleolar organiser?

Answer 25

Lots of RNA polymerase are in one place, where multiple
copies of the rRNA genes are brought together

Question 26

Is meant by RNA processing?

Answer 26

One original RNA template from one gene, which is then chopped up into the
3 rRNAs

Question 27

What is the point of RNA processing? (Why don’t we just have multiple genes?)

Answer 27

In one place the polymerase doesn’t need to find 3 promoters, just hops on
and does it all in one go. Enables many more polymerases to be on the same
gene (overall more efficient)

Question 28

state the 4 stages of how the ER enables protein synthesis

Answer 28

-recognition
-targeting
-release of ribosome
-recycling

Question 29

How does the ER enables protein synthesis for proteins that are meant to be in the membrane of the ER (6 points)

Answer 29

-Signal Peptide binds to Signal Recognition Particle (SRP) which PAUSES translation
-when the SRP binds to the SPR receptor in the ER membrane it causes a change in shape which allows translation
-the signal peptide (the hydrophobic bit) is fed into the PROTEIN TRANSLOCATER, once that happens it stays within the membrane
-translation and passage through protein translocator in ER membrane
-the ribosome disengages and releases
-the SRP receptor sits there waiting for the next SRP loaded with a ribosome to come along to bind to it

Question 30

How does the ER enables protein synthesis for proteins that are NOT meant to be in the membrane of the ER

Answer 30

the protein will be cleaved and you get that release of the protein from the protein translocator in the membrane, if not it will get left in the membrane. when released it can fold up into the protein it was made for in the ER lumen

Question 31

what happens to the fate of membrane bound proteins within the RER

Answer 31

-the protein translocator in the ER membrane will recognise the signal peptide and will only feed the polypeptide chain part along the way
-the Signal Recognition Particle (SRP) recognises the signal peptide and will start to feed the chain in
-when it reaches the stop sequence it will then become embedded in the membrane with some of the protein inside of the ER and the other outside the ER

Question 32

how how we identify which proteins are meant to stay withing the ER membrane i.e transmembrane proteins

Answer 32

we get N-LINKED GLYCOSILATION in ER
-almost all proteins synthesised into the RER are glycosylated (means there is a transport of roughly 14 sugar modification which is added to the sequence, Asn,Ser,Thr- one of theses has to be present for it to happen
-the oligosaccharide is assembled onto Phosphodolichol (a lipid molecule) found in the ER membrane
- A membrane bound oligosaccharide Transferase transfers the phosphodolichol a asparagine
-

Question 33

Describe the differences between the Rough endoplasmic reticulum
(RER) and smooth endoplasmic reticulum (SER) with regard to its function

Answer 33

> RER serves to collect the proteins synthesized by its attached ribosomes and allow them to be transported within the cell, and as they collect, the ER pinches off creating a vesicle filled with protein.
SER synthesizes steroids and, in the liver, breaks down toxins and converts glycogen to glucose & in muscle it stores calcium ions

Question 34

Name two types of protein which are sythesised into the endoplasmic reticulum.

Answer 34

(ER, /secretory/, /transmembranous/, Endoplasmic Reticulum, /Golgi/, /lysosomal/, secreted, transmembrane, lysosome)

Question 35

Amino acids in the signal peptide that sends a protein into the endoplasmic reticulum and typically:
hydrophobic
hydrophilic

Answer 35

hydrophobic

Question 36

True or false: Co-translational translocation into the ER lumen requires no more energy than translation in the cytoplasm?

Answer 36

true
Once the ribosome has docked with the protein translocator the only path open is through the pore and into the ER lumen. As the protein is synthesised and pushed out of the ribosome passes into the lumen without requiring any extra energy.

Question 37

Name the enzyme which removes the signal peptide from a soluble secretory protein. ________
Why is this necessary?
The ________ signal peptide is retained within the membrane.

Answer 37

(signal peptidase)
(hydrophobic, lipophilic)

Question 38

Where does the majority of new membrane synthesis occur?

Answer 38

endoplasmic reticulum/, ER

Question 39

Where are the majority of rRNAs synthesised?

Answer 39

(Nucleolus)

Question 40

1)Where are the ribosomal proteins transcribed?
2)Where are the ribosomal subunits assembled?

Answer 40

1) nucleus
2)Nucleolus

Question 41

The majority of Ribosomal RNAs are produced in the nucleolus from multiple genes found in clusters on _______chromosomes. The regions containing these clusters are known as ___

Answer 41

(ten, 10)
(nucleolar organisers)

Question 42

In what direction is mRNA read during translation?

Answer 42

(5’ to 3’, 5 to 3)

Question 43

What is a catalytic RNA called? ___
Give one example. ________

Answer 43

1) ribozyme
2) ribosome, 28S ribosomal RNA, spliceosome, self splicing introns, 28S rRNA

Question 44

what is the start codon and what amino acid does it encode for

Answer 44

AUG - methionine, Met, M

Question 45

how many stop codons are in eukaryotic cells give a example

Answer 45

3 stop codons: TAG ,TAA, TGA

Question 46

What is the name of the eukaryotic protein degradation machinery?

What is its structure? ___

What allows selective access into this structure?

Answer 46

proteasome
hollow tube, tube
cap, caps
*Cap structures at either end act as selective gateways into the proteasome.

Question 47

Name two types of protein which are sythesised into the endoplasmic reticulum.

Answer 47

ER, /secretory/, /transmembranous/, Endoplasmic Reticulum, /Golgi/, /lysosomal/, secreted, transmembrane, lysosome