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Cell biology > Ribosomes & Protein synthesis > Flashcards

Ribosomes & Protein synthesis Flashcards

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1
Q

what is the small subunit in ribosomes used for?

A

Used in transcription. mRNA binding site and has large subunit attached to it, decodes genetic information from mRNA

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2
Q

What is the large subunit in ribosomes used for?

A

Used in translation. Catalyses formation of protein bonds between aa to form polypeptide chain

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3
Q

Are the subunits always separate?

A

When not actively synthesising proteins they are separate but when mRNA binds, they join together (that’s when protein synthesis starts)

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4
Q

When does the protein construction process stop?

A

mRNA is pulled through three nucleotides at a time until a stop codon is reached. This is when the process stops.

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5
Q

What are the three binding sites of a ribosome and how is the mRNA held on them?

A

A(arrival site), P(peptide bond site) and E(exit site)
The mRNA is held tightly at A and P but only if the anticodons form base pairs with complimentary codons on the mRNA. The E site is the final stage of the fit process.

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6
Q

Where does translation happen?

A

Cytosol

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7
Q

What happens when tRNA comes in with an anticodon?

A

It binds to the small subunit and translation starts at the start code recognised by the initiator tRNA

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8
Q

What does translation use for energy source?

A

GTP hydrolysis

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9
Q

What are the three classes of mRNA and their roles?

A

-Messenger RNA=> carries cooding sequences for protein synthesis from DNA to cytoplasm.
-Ribosomal RNA =>forms the core of a cell’s ribosomes.
-Transfer RNA =>carry aa to the ribosomes during protein synthesis.

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10
Q

What needs to happen at the end of transcription?

A

RNA needs to peel away from the DNA template so a nucleotide(N7-methylated guanosine) is added to the 5’ end which is called capping.

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11
Q

What are introns?

A

non-coding nucleotide sequences which are removed from the mRNA strand by splicing, catalysed by endonuclease.

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12
Q

What is an important signal that tells the cells that the mRNA is ready to leave the nucleus and enter the cytoplasm?

A

poly-A-tail- a sequence of nucleotides that is added to the 3’ end of mRNA molecule

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13
Q

What are the functions of RNA polymerase I, II and III?

A

RNA polymerase I produces rRNA.
RNA polymerase II synthesis mRNA and needs transcription factors to initiate transcription.
RNA polymerase III synthesis tRNA.

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14
Q

What are the three steps in regulating transcription?

A

Initiation
Elongation
Termination

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15
Q

What happens at the initiation stage in transcription?

A

RNA polymerase binds to the DNA strand at the promoter region which usually includes a specialised nucleotide sequence -TATAA (the TATA box)

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16
Q

What happens at the elongation stage in transcription?

A

RNA polymerase moves down the template strand adding complementary nucleotides in the 3’ to 5’ direction. (Antiparallel)

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17
Q

What happens at the termination stage in transcription?

A

reach stop codon or sometimes termination factor(protein) is needed.

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18
Q

What is the role of tRNA?

A

Translates the mRNA into protein. The tRNA matches aa with appropriate codons in the mRNA. The tRNA molecule has two ends- one binds to specific aa and the other binds to the corresponding mRNA codon.

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19
Q

Which enzyme is important for pairing tRNA with aa?

A

aminoacyl-tRNA syntheses

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20
Q

What is redundancy?

A

some aa have more than one tRNA so they have more than one coding sequence.
Some tRNAs only need accurate base pairing at the first two positions of the two codons and can tolerate a mismatch(wobble) at the third position. The wobble pairing indicates why so many of the alternative codons for an aa differ only in the third nucleotide.

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21
Q

Trimming and splicing in the tRNA requires what?

A

Requires the tRNA to be correctly folded in a clover leaf way- quality control process so that the tRNA fits into the ribosome. Those that fail test are degraded by nuclear exosome.

22
Q

If there is a mismatch between aa and codon, they go to the editing site. What mechanisms happen here?

A

-Favourable binding= correct aa has highest affinity for active side pocket of synthetase
-Hydrolytic editing= when tRNA binds, synthetase forces aa into second editing pocket and aa is removed from the AMP by hydrolysis.

23
Q

What is the start codon attached to?

A

AUG(formylmethionine)

24
Q

What happens at each of the three sites?

A

tRNA comes into the A site, moves to the P site once the aa is stuck onto it. Then the new tRNA will arrive and there will be a transfer between a peptide bond formation between 3 and 4> bond transfers to 4 and 3 moves to exit site and 4 moves to p site.
Supported by eukaryotic initiation factors.

25
Q

What are the three possible stop codons?

A

UAA, UAG OR UGA

26
Q

When does the translation process stop?

A

Release factors bind with a stop codon at the A site- forcing the addition of water instead of an aa using peptide transferase enzyme. This frees the carboxyl end of the polypeptide chain and the chain is released into the cytoplasm. The ribosome releases bound mRNA molecule and separates into subunits.

27
Q

How is cellular rubbish removed from the cell?

A

By the proteasome- a central hollow tube which contains a subunit protein ring which proteins go through, has caps to allow selective access.

28
Q

What are chaperones?

A

binds to proteins allowing them to fold properly. Many chaperones are heat shock proteins-made in increased amounts when cells are exposed to higher temps.

29
Q

What are the major families of Hsp and how do they work?

A

Hsp 60 and Hsp 70(usually first in protein folding)
The protein is crammed in and lid is shut to get properly folded protein in the end. Lid removed at the end.

30
Q

What is the function of the golgi?

A

Builds and attaches oligosaccaride chains(can act as tags for transport to endosomes) to the proteins and lipids that the ER sends to it.

31
Q

What are some features of the Smooth ER?

A

-proteins and lipids bud off for transport to Golgi
-are prominent in cells that make steroid hormones
-used in detoxification of drugs
-transition between RER and Golgi

32
Q

what is attached to ribosomes recruited to the ER membrane?

A

lipophilic sequence

33
Q

How are steroid hormones synthesised in the SER?

A

The SER is expanded to accommodate the enzymes which make and modify cholesterol.
E.g, Testosterone is made from cholesterol in the SER of the Leydig cells of the testis.

34
Q

Where and how does detoxification of drugs take place?

A

-Occurs in the SER of the hepatocytes in the liover
-Lipophilic drugs(dissolve in fats) are modified to increase water solubility
-Further modification in the cytosol, before excretion from the body in bile or urine(needs to be water soluble)
-Hepatocytes are major producers of lipoproteins
Cellular adaptation is to expand SER membrane to enable cells to carry out functions.
Key enzyme is cytochrome p450

35
Q

What are the features of the Sarcoplasmic Reticulum?

A

-Acts as a calcium store in the muscles
-Not continuous with external membrane
-Voltage-sensitive channels release Ca2+
-Resting: High Ca2+ concentration

36
Q

Where are new phospholipids arranged on the ER membrane?

A

On the outer surface because thats where the enzymes needed for that construction are.

37
Q

What is a key enzyme in membrane synthesis and what does it do?

A

Scramblase- phospholipid translocator which causes equilibration of the two leaflets of the ER. Once equilibrated, we can get movement to the golgi.

38
Q

What does the signal sequence do and when is it removed?

A

It directs protein to where it needs to go and is removed during the transport process or after the protein reaches its final destination.

39
Q

One class of signal sequences is recognised by what particle and what does it do?

A

Signal Recognition particle(SRP) which binds to the signal sequence when its on the ribosome and transfers the ribosome and incomplete polypeptide to the ER.

40
Q

What are some features of the Golgi?

A

-made up of cisternae and sheets
generates lots of vesicles and lysosomes
-there’s modification and packaging of proteins and lipids for exocytosis

41
Q

Describe the structure of the golgi

A

At the top, there is ER and there are some Golgi vesiccles moving in both directions across here. Below the vesicles, there is the vesicular tubular cluster(lots of vesicles joined together). The next below is the cis Golgi network which is the nearest thing to the ER, the site at which vesicles start to form, we start to see a change in pH. Below this are the cisternae which are close together: cis, medial, and trans which is closest to the trans-Golgi network. As you move through the cistern, there are enzymes for trimming. trans-Golgi network is the site for the vesicles to go to their different locations.

42
Q

What are the functions of the golgi?

A

It is also a major site of carbohydrate synthesis in the form of glycoproteins and proteoglycans so the Golgi is prominent in secretory cells like this intestinal goblet cell

43
Q

How does dispatch from the Endoplasmic Reticulum to the Golgi occur?

A

During the initial phases of folding 2 of the 3 terminal glucose molecules are removed to leave one. Calnexin is a chaperone which recognises the single glucose of incompletely folded proteins and prevents their export to Golgi
The final glucose is removed then:
1. If partially folded glucosyl transferase adds
another glucose and it tries again
2. Misfolded proteins are chaperoned back to the ER protein translocator and are sent to
the cytoplasm for degradation
3. Correctly folded proteins go on to be exported to the Golgi

44
Q

Fully folded proteins are targeted to ER exit sites

A

For soluble proteins this involves interactions with transmembrane receptors/cargo receptors

  • Proteins need “exit” signals for efficient export: non-cargos are packaged at a much lower rate
  • The coat protein COPII interacts with the cytosolic tail of the receptor (part of the receptor in the cytoplasm) causing a vesicle to bud off
45
Q

Movement of the transport vesicles

A
  • Once COPII coated vesicles bud from the ER they lose their coat
  • They undergo homotypic fusion – like joining with like and make larger and larger vesicles. eventually become vesticular tubular cluster
  • The resulting vesicular tubular cluster (VTC) moves along microtubules
  • Once the cargo reaches the Golgi it is released from its receptor

…. Mediated by a decrease in pH

46
Q

Why might the change in pH cause the cargo to be released from its receptor?

A

Decreasing pH means it becomes more acidic in the vesicle.
More H+ ions means there is a shift in the form of some aa E.g. a lower pKa is a stronger acid and its more likely to become dissociated.
Changes in the shape of the aa(cargo) means its no lopnger complementary to the receptor so they break apart.

47
Q

What happens to receptors and non cargo after they reach the golgi?

A

They enter vesicles and are recycled. Because they are sent back in the other direction, they need a different coat protein- COPI
Normally have two lysine and two other aa that tell COPI to bind.

48
Q

The oligosaccaride is trimmed through the cistern, what happens at each layer?

A

N-linked glycosylation(happwns in ER on asparagine at N terminus of protein)
Folding and glucose trimming
Mannose trimmed
N-acetyl glucosamine added
Addition of galactose and
N-acetylneuraminic acid

49
Q

What other modifications happen to oligosaccharides within the golgi?

A
  • O-linked glycosylation (in the cisternae)
  • the addition of sugars to the -OH group of Ser, Thr or hydroxylysine - catalysed by glycosyl transferases
  • usually N-acetyl galactosamine is added first
  • additional residues ranging from a few to over 10 are then added
  • Phosphorylation(usually at a lycine) of oligosaccharides on lysosomal proteins (in the CGN) (tells Golgi they go in the lysosome due to phosphate)
  • Sulphation of tyrosine and carbohydrates (in the TGN)
  • increases their negative charge
50
Q

What is the point of glycosylation?

A
  • As a protein marker
  • for complete folding
  • for targeting transport between the ER and Golgi - for sorting within the Golgi
  • As a protector
  • relatively inflexible oligosaccharides prevent proteases from approaching and digesting extracellular proteins
  • As a cellular marker
  • Regulatory Roles (make sure proteins arent stuck together)
  • Cell surface signalling receptors may be glycosylated and alterations to their glycosylation pattern may affect their activity in different cell types

Cell biology (1 decks)

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