Biochem Chapter 30

Front 1

the genetic code

Back 1

triplet code
codons specify aa
its degenerative
its universal

Front 2

structure of tRNA

Back 2

nucleotide sequences in a clover shape(acceptor stem,TC loop,anticodon,D loop)

Front 3

continuous code

Back 3

the way NA are arranged to present the genetic code

Front 4

how is an aa matched w/ its proper tRNA

Back 4

2nd genetic code
aminoacyl-tRNA synthetases interpret the 2nd code and discriminate bw tRNA and aa

Front 5

the aminoacyl-tRNA synthetase reaction

Back 5

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

Front 6

mirror-symmetric interaction of 2 classes of aminoacyl-tRNA synthetase with tRNA substrates

Back 6

I:bind to side of tRNA substrates (glutaminyl)
II:bind to side of tRNA closest (aspartyl)

Front 7

major identity elements in 4 tRNA species
(areas where tRNA synthetase is located)

Back 7

yeast:1 top,1 left,3 bottom
met:3 bottom
ser:7 top, 2 left
ala:2 top

Front 8

rules in codon-anticodon pairing

Back 8

cricks wobble hypothesis
nonsense suppression occurs when suppressor tRNA read nonsense codons

Front 9

codon-anticodon pairing ie

Back 9

complementary trinucleotide sequence elements align in antiparallel fashion
3'-F-G-G-5'(anti)
5'-G-C-C-3'(codon)

Front 10

structure of ribosomes and how they are assembled

Back 10

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

Front 11

7 rRNA operons in e.coli

Back 11

give a precursor RNA cleaved by RNase III to generate 23S,16S,5S.(combos of ala,glu)

Front 12

ribosomal proteins

Back 12

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

Front 13

ribosome assembly and structure

Back 13

prot + rRNA=ribosomes
tunnel thru large subunit
peptide chain thru tunnel during protein synthesis

Front 14

eukaryotic ribosomes

Back 14

mito & chloro similar to prok
cyto are larger/complex

Front 15

mechanisms of mRNA translation

Back 15

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

Front 16

basic steps in protein synthesis.

Back 16

ribosome has 3 binding sites for tRNA:
A:acceptor site
P:peptidyl site
E:exit site

Front 17

location of binding sites on ribosome

Back 17

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).

Front 18

prokaryotic initiation

Back 18

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

Front 19

N-formyl-methionyl-tRNA

Back 19

top of acceptor strand R group:
O=CH-NH-Met

Front 20

methionyl-tRNA formyl transferase

Back 20

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.

Front 21

more initiation

Back 21

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

Front 22

shine-dalgarno sequences recognized by e.coli ribosomes

Back 22

lie ~10nucleotides upstream from AUG codon and are complementary to the UCCU core seq element of e.coli 16S rRNA.

Front 23

events of initiation

Back 23

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

Front 24

the elongation cycle

Back 24

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

Front 25

peptidyl transferase

Back 25

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

Front 26

ribosome life cycle
(CCW with dynamic equilibrium at the top)

Back 26

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)
elongation
termination(cycles to top L)

Front 27

how proteins are synthesized in eukaryotic cells

Back 27

5'-methyl-GTP cap and the polyA tail
initition has >12 IF's
intiator tRNA carries only met and isnt formylated

Front 28

characteristic structure of the eukaryotic mRNA

Back 28

untranslated regions bw 40-150bp at both 5' & 3' ends of mature mRNA. An initiation codon at 5' (AUG) signals the translation start site.

Front 29

eukaryotic initiation

Back 29

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

Front 30

peptide bond formation in protein synthesis

Back 30

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

Front 31

peptidyl transferase center of 23S rRNA

Back 31

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.

Front 32

role of GTP hydrolysis

Back 32

2GTP hydrolyzed/aa in a peptide
hydrolysis drives conformational changes
total of 4high-E P bonds are expended per aa residue

Front 33

peptide chain termination

Back 33

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

Front 34

regulation of initiation

Back 34

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

Front 35

inhibitors of protein synthesis

Back 35

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.

Front 36

diptheria toxin
(an NAD+dependent ADP ribosylase)

Back 36

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!!