BIOL 300 - Chapter 21

what is a codon?

three-base pair mRNA sequence from the nontemplate that encodes different amino acids

what is an anticodon?

tRNA sequence that’s complementary to its codon

what is the start codon?

AUG - encodes methionine

what are the stop codons?

UAG, UGA, UAA

how many codons encode amino acids?

61. there are 64 possibilities, but three are stop codons

what is the correlation between codons and amino acids in terms of frequency?

one codon encodes one amino acid, but one amino acid encodes multiple proteins

what parts do an amino acid consist of?

N terminus, C terminus, a hydrogen, and a r-group

in which direction is the amino acid arranged from?

N terminus to C terminus

what makes up the translation apparatus?

mRNA, tRNA, ribosome

what is the tRNA structure?

small noncoding RNA, that has one end bound by an amino acid, and the other presents an anticodon

what are the three types of tRNA?

aminoacyl-tRNA, which has a single amino acid, peptidyl-tRNA, which has the growing peptide chain, and deacylated-tRNA, which is ready to exit

what is the ribosome?

large RNP particle that contains rRNA and ribosomal-proteins - has large and small subunits

what is the svedberg unit?

tracks ssedimentation rate, or the reflection of the speed of sedimentation during ultracentrifugation

what are the 3 binding sites for tRNA?

A, which is the entry site for tRNA, P, which enters tRNA with growing peptide, and E, which is where free tRNA exits

where are ribosomes found?

in cytoplasm or the rough ER

what is the first step of translation initiation?

identify the start codon, AUG

how is the first step of translation initiation different for eukaryotes?

one mRNA has one start codon, and has a 5’ cap. the first small subunit binds to the cap, then initiator tRNA joins, and the subunit uses that tRNA to scan mRNA and recognize AUG. the AUG must be read in a special context of the Kozak sequence

how is the first step of translation initiation different for prokaryotes?

mRNA is polycistronic, so there are multiple start codons; also no 5’ cap. 16S rRNA in the small ribosome recognize the shine-dalgarno sequence, so every AUG with that sequence can be the start codon

what is the kozak sequence?

NNNPuNNAUGG - involves a purine 2 bp above the AUG to allow for binding

what is the shine-dalgarno sequence?

consensus sequence that labels start codons

what is the second step of translation initiation?

assembly of the apparatus to mRNA - involves ribosomes, initiator tRNA with methionine, and initiation factors (IF for prok, eIF for euk)

how does the assembly of ribosome occur?

subunit recruitment depends on initiation factors, and small/large subunits are recruited separately (small subunit is first, large subunit is after tRNA). then, initiator factors are released.

how is initiator tRNA-met different from tRNA-met?

different in sequence and shape, as it binds to initiation factor vs elongation factor. initiator enters directly into the p site instead of starting out in the A site like every other tRNA

how does initiator tRNa enter the P site?

with the help of IF-2 or eIF-2

what is the prokaryotic sequence of events for initiator tRNA entering the P site?

IF2-GTP joins, then initiator tRNA

what is the eukaryotic sequence of events for initiator tRNA entering the P site?

the assembly of small unit that’s bound with the initiator, then eIF proteins bind to mRNA to help find the start site and move forward.

what is the activation process for IF2 and eIF2?

as small GTPases (like Ras), they have an active form with GTP, where they bind to ribosome/initiator tRNA, and in their inactive form the large subunit is able to bind

what is the general overview of translation initiation?

start site is identified and assembled, as the small subunit on mRNA binding site is joined by the large subunit and aminoacyl-tRNA

what is the general overview of translation elongation?

peptide bond formation, as ribosome moves long mRNA and extends protein by transferring peptidyl-tRNA to aminoacyl-tRNA

what is the general overview of translation termination?

recognizing the stop codon and disassembling, as the peptide chain is released and the ribosome dissociates from mRNA

what are the four steps of translation elongation?

aminoacyl-tRNA enters empty A site, the peptide in p site is transferred to aminoacyl-tRNA in A site (leaving p uncharged), ribosome translocates by one coodn so the p site has the peptidyl-tRNA and A site is empty, and the cycle then repeats

what is in the A site in the four steps of elongation?

1) aminoacyl tRNA, 2) peptidyl-tRNA, 3) empty, 4) repeat

what is in the A site in the four steps of elongation?

1) peptidyl-tRNA, 2) uncharged tRNA, 3) peptidyl-tRNA again, 4) repeat

what is involved in the first step of translation elongation?

EFTu (prokaryote) or eEF1a (eukaryote) brings in the aminoacyl-tRNA into the empty A site (both of EFTu and eEF1a have the same GTP/GDP cycle, so its active form brings tRNA in, and GDP releases Tu, which is needed for the peptide bond formation)

what is the quality control mechanism of the first step of translation elongation?

peptide transfer can’t occur unless Tu is released

what is involved in the second step of translation elongation?

the peptide in the P site transfers to the aminoacyl-tRNA in A site, and the release of EFTu lets amino acids to enter the catalytic center formed in the large subunit. peptide/amino acid is connected to tRNA, and peptide transfer then occurs in the new tRNA attacking that connection, so the result is deacylated tRNA at the p site and peptidyl-tRNA at A site

what in the second step of translation elongation is reponsible for the action of catalysis

rRNA - called catalytic RNA

what is the puromycin antibiotic?

mimics aminoacyl-tRNA, but not anchored to A site

what is involved in the third step of translation elongation?

the ribosome moves forward one codon relative to the mRNA, which is driven by conformational change from peptidyl-tRNA falling into a hybrid site, and the small subunit shifts relative to mRNA. this is all driven by EF-G (prok) and eEF2 (euk)