Ribosome + Protein Synthesis

Question 1

What is the structure of a ribosome

Answer 1

1. Small subunit - decodes genetic information from mRNA
2. Large subunit - catalyses formation of peptide bonds between amino acids to form a polypeptide chain
   - 4 binding sites = one for mRNA and three (A,P,E) for tRNA

Question 2

What do rRNA molecules do in a ribosome

Answer 2

Direct the catalytic steps of protein synthesis

Question 3

What are ribosomes made out of

Answer 3

1. Proteins
2. rRNA

Question 4

What are tRNA molecules used for

Answer 4

Adaptors to add each amino acid in the correct sequence

Question 5

What is protein synthesis driven by

Answer 5

Elongation factors, using GTP hydrolysis

Question 6

What happens after a ribosome reaches a stop codon during translation

Answer 6

1. Release factor binds to the ribosome - terminating translation and the polypeptide is released
2. The folding of the newly synthesized proteins is assisted by chaperones
3. Control mechanisms destroy any incorrectly folded proteins

Question 7

Do all genes code for proteins?

Answer 7

• No
• For minority of genes, final product is the RNA molecule itself

Question 8

Can genes code for more than one copy of a protein

Answer 8

• Yes
• Many identical RNA copies can be made from the same gene
• Genes can be transcribed and translated with different amounts of proteins

Question 9

What are the 3 RNA types and what do they do

Answer 9

1. mRNA - carry the coding sequences for protein synthesis called transcripts - goes from DNA to cytoplasm
2. rRNA - forms the core of cell’s ribosomes
3. tRNA - carry amino acids to the ribosomes during protein synthesis
   - Each class of RNA has its own polymerase - polymerase I, II, and III

Question 10

What happens to mRNA when translation is complete

Answer 10

1. G-capis added to 5’ end
2. Poly-A tail added to 3’ end called polyadenylation
3. Introns spliced

Question 11

What does the G-cap do for mRNA

Answer 11

1. Protects RNA from degradation
2. Recruits complexes involved in RNA processing, export and translation initiation
3. Marks cellular mRNA as “self” - avoid recognition by innate immune system

Question 12

What does transcriptome mean

Answer 12

• Spectrum of mRNA molecules in a cell
• Each cell carries same DNA but transcriptome varies according to cell type and function

Question 13

What are the 3 steps in transcription

Answer 13

1. Initiation: RNA polymerase and transcription factors bind to the TATA box in the promoter region
2. Elongation: RNA polymerase moves down the DNA template strand in 3’ to 5’ direction, adding complementary nucleotides
3. Termination: Elongation process needs to end and mRNA to separate from DNA template, sometimes using a termination factor protein

Question 14

Name 3 stop codons

Answer 14

1. UAA
2. UAG
3. UGA

Question 15

What binds aa to tRNAs

Answer 15

• Using enzyme aminoacyl-tRNA synthetases
• 20 different enzymes for each aa

Question 16

What makes translation redundant

Answer 16

• some tRNAs are constructed to require accurate basepairing only at the first two positions of the codon and can tolerate a mismatch (or wobble) at the third position
• Thats why aa’s have more than two codons with only a difference in the third base

Question 17

Do tRNAs have the same lifecycle as mRNAs

Answer 17

• Yes
• pre-tRNAs have to get spliced to remove introns (by endonucleases) then become mature tRNA
• Those that do not pass the test are degraded by nuclear exosome

Question 18

How do aa get attached to tRNAs

Answer 18

• Using aminoacyl-tRNA synthetases
• Process is called favourable binding
• The correct aa has the higest affinity for the synthesis pocket on synthetase
• aa joins 3’ end of tRNA

Question 19

How do incorrect aa get removed from tRNAs

Answer 19

• Process called hydrolytic editing
• Incorrect amino acid-tRNA complex goes to editing pocket on tRNA synthetase
• aa is removed by hydrolysis from tRNA

Question 20

How does translation start 5 steps

Answer 20

1. Starts at AUG
2. Initiator tRNA-methionine complex loaded into small ribosomal subunit + eukaryotic initiation factors (eifs)
3. Small ribosomal subunit then binds 5’ end of mRNA molecule – moves along mRNA to find AUG
4. Initiation factors dissociate – allowing large ribosomal subunit to assemble with complex and complete ribosome
5. Initiator tRNA remains at P site, A site vacant and protein synthesis begins

Question 21

How does translation stop 5 steps

Answer 21

1. Three stop codons (UAA, UAG, UGA)
2. Release factors bind to ribosome with stop codon at A site
3. Forces peptidyl transferase to add water molecule instead of aa
4. Frees carboxyl end of pp chain – chain is released into cytoplasm
5. Ribosome releases bound mRNA molecule and
   separates into subunits. New round of synthesis

Question 22

What are polyribosomes

Answer 22

• Multiple ribosomes on a single long mRNA strand
• Most mRNA molecules esp being translated at high rates found as polyribosomes
• polyribosomes ~80 nucleotides apart

Question 23

Name 2 control mechanisms for incorrect mRNA sequences + when it is detected

Answer 23

1. Broken mRNA – missing either 5’ cap or poly-A tail – translation initiation won’t begin
2. Nonsense mediated mRNA decay – prevents mRNA with nonsense of stop codon in wrong place escaping from nuclear envelope

• Happens as mRNA is transported to cytosol.

Question 24

What do proteosomes do

Answer 24

• Found in cytosol & nucleus
• Destroys incorrect/faulty proteins
• ER detects protein, retrotranslocates to cytosol for destruction

Question 25

What are chaperone proteins

Answer 25

• Chaperones ensure proteins are folded correctly
• They are heat-shock proteins, synthesised in increased amounts when cells exposed to higher temperatures but constitutively
  expressed
• hsp60 and hsp70

Question 26

What are 3 steps to prep proteins for degradation

Answer 26

1. Activation of ubiquitin ligase (ubiquitin marks proteins for degradation)
2. Activation of degradation signal
3. Creation of a ubiquitinylation site in response to intracellular or extracellular signals

Question 27

What are signal recognition particles (srp)

Answer 27

• SRP binds the signal sequence to proteins during translation
• Allowing proteins to be transported to to where they are needed
• Signal sequence gets removed once protein reaches destination

Question 28

What happens after signal sequence on proteins gets removed

Answer 28

• N-LINKED GLYCOSYLATION
• Allows for further modification of newly synthesised proteins
• Linkage important for structure and function of eukaryotic proteins
• Attachment of an oligosaccharide (carbohydrate consisting of several sugar molecules) to N (amide nitrogen of asparagine residue (Asn))

Question 29

Where are the ribosomal subunits assembled?

Answer 29

Nucleolus

Question 30

Where are complete ribosomes (both subunits) assembled?

Answer 30

Cytoplasm (only when they encounter a mRNA)

Question 31

Where are the ribosomal proteins transcribed?

Answer 31

Nucleus

Question 32

Where are ribosomal proteins translated?

Answer 32

Cytoplasm

Question 33

How does the circular structure of mRNA increase the efficiency of translation?

Answer 33

1. The circular structure allows ribosomes to cycle on the mRNA, which is time-efficient.
2. Circularization prevents translation of partially degraded mRNA, which lacks a poly-A tail or m7G cap.