L5. Gene expression & protein synthesis II

Question 1

explain the structure of the eukaryotic ribosome

Answer 1

• it is a complex of 4 rRNAs and >80 proteins
• RNAs account for most of the mass
• it has large and small subunits
• these subunits will come together after the small subunit binds to mRNA

Question 2

eukaryotic ribosome - explain the sites

Answer 2

• A site: Aminoacyl site
• P site: Peptidyl site
• E site: Exit site

Question 3

explain the structure of tRNAs

Answer 3

• it is an RNA with a 3D cloverleaf structure
• it does this through conventional and non-conventional bonds

Question 4

tRNA - what are anticodons

Answer 4

• a set of three nucleotides that bind to the nonelementary codon in an mRNA molecule
• this is how the ribosome understands what the next amino acid is

Question 5

what are aminoacyl-tRNA synthases

Answer 5

• recognition and attachment of amino acids depend on these molecules
• they use ATP to link the correct amino acid to the tRNA based on the anticodon

Question 6

explain the initiation of translation

Answer 6

• translation initiation factors bind 5’ cap and 3’ poly-A tail to insure that the mRNA is intact
• the initiator tRNA with the factors and a methionine (start codon) bound onto it will bind onto the small ribosomal subunit
• next, mRNA will bind to the small subunit
• finally, the factor will dissociate and the large subunit binds with the initiator tRNA in the P site

Question 7

translation initiation - what happens after initiator tRNA binds to ribosome

Answer 7

• a charged tRNA binds to the A site
• a peptide bond forms between the methionine in the P site and the tRNA in the A site
• the bond on the methionine and the initiator tRNA dissociates

Question 8

translation - what happens as the polypeptide chain grows

Answer 8

• the carboxyl end of the polypeptide chain in the P site is uncoupled from the tRNA
• the polypeptide chain is then bound to the amino acid in the A site
• this is catalyzed by the large ribosome subunit

Question 9

translation - what happens to the tRNA in the P site when when the polypeptide chain is removed

Answer 9

• the large subunit shifts and moves the unneeded tRNA in the P site to the E site to be ejected
• the tRNA that is in the A site is moved to the P site
• the small subunit moves 3 nucleotides along the mRNA to allow another tRNA to enter the A site

Question 10

translation - why are the aminoacyl-tRNA’s in the A and P sites close together

Answer 10

• so they can follow the open reading frame without skipping a nucleotide
• makes sure there is no shift in open reading frame

Question 11

what direction is the mRNA and protein translated in

Answer 11

• mRNA: 5’ to 3’
• protein: N-terminal to C-terminal

Question 12

explain the termination of translation

Answer 12

• when a stop codon is encountered, a release factor docks at site A and the mRNA and the ribosome is released
• the release factor has an anticodon with no attached amino acid

Question 13

what is a polyribosome

Answer 13

• the shape the mRNA makes because multiple ribosomes are on a singular mRNA making multiple proteins
• when translation is terminated, it is only terminated in that particular ribosome

Question 14

explain how the ribosome is a ribozyme

Answer 14

• 2/3 of it consist of rRNA while 1/3 is protein
• the A, P, and E sites are rRNAs
• the catalytic site is formed by the 23S rRNA of the large subunit
• the catalytic site in the rRNA is peptidyl transferase

Question 15

the ribosome is a ribozyme - what are the purpose of the proteins and RNA

Answer 15

• proteins form the core, appear on the surface to fill in gaps, and help fold and stabilize the ribosome
• RNA catalyzes protein synthesis

Question 16

where does protein synthesis occur in the eukaryotic cell

Answer 16

• in the rough endoplasmic reticulum and in the cytosol
• proteins created for the rough ER are made in the rough ER
• proteins made for other purposes are made from ribosomes in the cytosol

Question 17

explain how proteins may go post-translational modifications

Answer 17

• some proteins need to change function after being translated
• can do this be adding a phosphate that can interact with other things
• chaperon proteins help the protein fold into certain shapes

Question 18

explain bacterial translation

Answer 18

happens at the same time as transcription bc they do not have a nucleus

Question 19

what are proteasomes

Answer 19

• it is a large protease complex made of many protein subunits
• uses ATP hydrolysis to unfold proteins

Question 20

proteasomes - how is the protein broken down

Answer 20

• the protein is marked with ubiquitin and fed into the proteasome chamber
• the protein is broken down into short peptides then into amino acids

Question 21

proteasome - how is protein breakdown mediated

Answer 21

it is mediated by proteases which hydrolyze peptide bonds

Question 22

explain the RNA world theory

Answer 22

evolution on life stats with RNA

Question 23

RNA world theory - what evidence is there to support it

Answer 23

• many processes are driven by ribozymes
• RNAs serve as a template to produce the complementary strand and the complementary sequence can be used as a template to produce the original sequence
• RNAs catalyze enzymes

Question 24

RNA world theory - how did we go from RNAs to DNA

Answer 24

• RNA can propagate itself
• RNA then evolved to direct protein synthesis
• then RNA evolved to use DNA and make RNA an intermediate since DNA is more stable than RNA