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36 Cards in this Set

  • Front
  • Back
the genetic code
triplet code
codons specify aa
its degenerative
its universal
structure of tRNA
nucleotide sequences in a clover shape(acceptor stem,TC loop,anticodon,D loop)
continuous code
the way NA are arranged to present the genetic code
how is an aa matched w/ its proper tRNA
2nd genetic code
aminoacyl-tRNA synthetases interpret the 2nd code and discriminate bw tRNA and aa
the aminoacyl-tRNA synthetase reaction
pyrophosphotases hydrolyze the PP
1.formation of aminoacyl-adenylate
2.transfer activated aa of anhydride to 2'-OH of ribose or the 3'-CCA terminus common to all tRNA's
mirror-symmetric interaction of 2 classes of aminoacyl-tRNA synthetase with tRNA substrates
I:bind to side of tRNA substrates (glutaminyl)
II:bind to side of tRNA closest (aspartyl)
major identity elements in 4 tRNA species
(areas where tRNA synthetase is located)
yeast:1 top,1 left,3 bottom
met:3 bottom
ser:7 top, 2 left
ala:2 top
rules in codon-anticodon pairing
cricks wobble hypothesis
nonsense suppression occurs when suppressor tRNA read nonsense codons
codon-anticodon pairing ie
complementary trinucleotide sequence elements align in antiparallel fashion
structure of ribosomes and how they are assembled
ecoli's is 2 unequal subunits
30S has 21 prot
50S has 31 prot
are roughly 2/3 RNA
20,000 ribos in cell, 20% of cell mass
7 rRNA operons in e.coli
give a precursor RNA cleaved by RNase III to generate 23S,16S,5S.(combos of ala,glu)
ribosomal proteins
1 of each per ribo except L7/L12 w/ 4
L7/L12 identical except for extent of acetylation at N-terminus
4 7/12 plus L10 makes L8
one prot is common to all subunits S20=L26
ribosome assembly and structure
prot + rRNA=ribosomes
tunnel thru large subunit
peptide chain thru tunnel during protein synthesis
eukaryotic ribosomes
mito & chloro similar to prok
cyto are larger/complex
mechanisms of mRNA translation
protein synthesis:
initiation:binds mRNA,initiates aminoacyl-tRNA to small subunit
elongation:moves ribos w/ mRNA and synthesis of pep bond
termination:when stop codon is reached
basic steps in protein synthesis.
ribosome has 3 binding sites for tRNA:
A:acceptor site
P:peptidyl site
E:exit site
location of binding sites on ribosome
A and P: where the anticodon ends of the tRNA are located
P center: on the 40S subunit which lies at the lower tips(acceptor ends).
prokaryotic initiation
tRNA initiator:methionine
formyl transferase adds formyl
N-formyl-met-tRNA is only used for initiation
N-formyl methionine is 1st aa of all ecoli proteins
top of acceptor strand R group:
methionyl-tRNA formyl transferase
catalyzes the transformylation of methionyl-tRNA using N10-formyl-THF as formyl donor. The tRNNA for reading met coddons within a protein is not a substrate for this transformylase.
more initiation
alignment of pyrimidine-rich seq on 3' of 16S RNA w/ purine-rich 5' of mRNA
purine-rich:ribo binding site(shine-dalgarno seq)
initiation factor prot:GTP,N-formyl-met-tRNA,mRNA and 30S
shine-dalgarno sequences recognized by e.coli ribosomes
lie ~10nucleotides upstream from AUG codon and are complementary to the UCCU core seq element of e.coli 16S rRNA.
events of initiation
30S w/ IF-1 and IF-3 binds mRNA,IF-2,GTP and f-met-tRNA
IF-2 delivers the initiator tRNA in a GTP-dependent process
loss of initiation factors leads to binding of 50S
acceptor site now accepts incoming aminoacyl-tRNA
the elongation cycle
factors coincide with prot synthesis
EF-Tu binds aminoacyl-tRNA and GTP
aminoacyl-tRNA binds to A site of ribosome as complex w/ 2EF-Tu and 2GTP
GTP is then hydrolyzed and EF-Tu:GDP dissociates
EF-T's are guanine nucleotide exchange factor(GEF) that recycles EF-Tu by exchanging GTP for GDP
peptidyl transferase
central rxn of protein making
23S rRNA is the peptidyl transferase
rxn center has very conserved bases
translocation of peptidyl-tRNA from the A site to the P site
ribosome life cycle
(CCW with dynamic equilibrium at the top)
pool of 70S ribosomes(top R)
dynamic equilibrium (top)
free subunits (top L)
30S w/ IF-1 & 3 binds mRNAand IF-3 blocks 50S binding (center L)
IF-3 released before 50S can join (bottom L)
termination(cycles to top L)
how proteins are synthesized in eukaryotic cells
5'-methyl-GTP cap and the polyA tail
initition has >12 IF's
intiator tRNA carries only met and isnt formylated
characteristic structure of the eukaryotic mRNA
untranslated regions bw 40-150bp at both 5' & 3' ends of mature mRNA. An initiation codon at 5' (AUG) signals the translation start site.
eukaryotic initiation
begins w/ eIF-2,GTP,met-tRNA
binds to 40S eIF-1A & eIF-3 to from 40S pre-initiation
no mRNA yet
ATP required
prot scan to find AUG
peptide bond formation in protein synthesis
nucleophilic attack by the amino group of the A site aminoacyl-tRNA on the carbonyl-C of the P site is facilitated when 23S rRNA purine A abstracts a proton
peptidyl transferase center of 23S rRNA
highly conserved 2dary structure w/ 16S in it.
central region isnt conserved
purine A:catalysis of rxn
The 3dary structure brings P loop into interaction w/ base U2585 in the central region.
role of GTP hydrolysis
2GTP hydrolyzed/aa in a peptide
hydrolysis drives conformational changes
total of 4high-E P bonds are expended per aa residue
peptide chain termination
release factors(prot):recognize stop codon at A site
release factors w/ nonsense codoon at A transforms peptidyl transferase into hydrolase which cleaves the chain from the tRNA carrier
regulation of initiation
7 prot(4 IF,2elongation,and ribosomal prot S6) are activated by P-ylation
P-ylation of eIF-2a causes it to bind eIF-2b
inhibitors of protein synthesis
those that affect prok but no euk prot making are effective antibiotics.
streptomycin:induces mRNA misreading(bacterial growth)
puromycin:binds at A site terminates protein synthesis from the P site.
diptheria toxin
(an NAD+dependent ADP ribosylase)
target is EF-2(has dipthamide sidechain)
EF-2 doesn't function in making proteins but still binds GTP
ADP(toxin) ribosylates many EF-2's...LETHAL!!