darrell r. davis department of medicinal chemistry translation and trnas
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D16,17Anticodon ( )Anticodon Region Green ( )Variable Loop Blue- ( )T Loop Region Gold ( )Acceptor Stem Red- ( )D Loop Region Violet
Darrell R. DavisDepartment of Medicinal Chemistry
http://www.pharmacy.utah.edu/medchem/faculty/davis/biol3510.html
Translation and tRNAs
D16,17Anticodon ( )Anticodon Region Green ( )Variable Loop Blue- ( )T Loop Region Gold ( )Acceptor Stem Red- ( )D Loop Region Violet
pGGGUACCACGCUUAA
CCUGΨTm1Am7GCUAG__GCGGAUU
G A C A Cm5C U G U Gm2G2m2GG A G C C U CAAAGDD - T Loop - D Loop Variable Loop Anticodon Loop1510OH15202535m5CΨYCmGmAAAUGGU
CCAGA
3040455560647075 Acceptor Stem
tRNA Phe
e11
-1767574737271706968676665646362616059585756555453
Gmncm5Ucmnm5Ummchm5Umcm5Us2Umcm5s2Ui6Am2At6Am6t6Am1Gm1Io2yWyWms2t6Aio6A
3437
5251504948474645444342414039383635333231302928272625 e23e2
Eukarya24232221
13e12e14
121110987654321
1415161819201717a20b20a
m2Gm1G, m1A, m2Gm2Gψm2 ,Gψ,m22Gψm3 , , , C Cm Umψ, ψmm5 , Cψ , ,Gm Umψ,ψm
,Um m5 ,Um m5 ,Uψψm1A
ψ , , , Gm Am Cm Umm5 ,C ac4C ,Cm ac4 ,Cψm1AD
GmD,Dψ,acp3U,D acp3 ,U mnm5U ψ,m22GmanQgalQm5CCmIUmQf5Cmψm5 ,Cψψm5Cm7 ,G m1G, D acp3Um6 ,A m5Cm5Cm5 ,Cψm5CCmGmψm2Gψ
m5 ,Cψ
e11
-1767574737271706968676665646362616059585756555453
cmnm5UGmcmnm5s2Ucmnm5Ummo5UCmms2i6Ai6Am2At6Am6Am6t6Am1Gms2t6A
3437
5251504948474645444342414039383635333231302928272625 e23e2
Bacteria24232221
13e12e14
121110987654321
1415161819201717a20b20a
s4UψG+m1Aψs2 , ,U Umψ, Cmψ
,T m5s2Um1Am2GD
DGm
Iac4CQmnm5s2Ucmo5Umnm5Uk2C
m7G, D acp3Uψψ
Circles represent nucleosides that areAlways present. Gold are invariant or semivariant
The RNA Modification Databasehttp://medlib.med.utah.edu/RNAmods/
tRNA Modifications in Eukarya and Bacteria
Grosjean, H., Chantrenne, H. (1980) Mol. Biol. Biochem. Biophys.32, 347-367.
RNA(0.1 mM, 1 M NaCl)
G°37
kcal/mol
H°
kcal/mol
Tm
°C
GGGCCC
CCCGGG-7.9 -63.0 60.2
AAAUUU
UUUAAA1.4 -32.1 -12.5
AAA
UUU3.2 -13.2
-87
Intrinsic properties of 3 base-pair RNA hairpin interactions
UUUUCCCAAAAGGA9U9FGAGCUGCGCCCGGGCGCACGUAAGGCGUGA1ACT3FC5GUCCUAAC5DG7GGCUCG2AAGGGCDDF110203040556070Dihdrouridine LoopT-ψ- C Loop Acceptor Stem
tRNALys UAUUUCCAAUUGAA7U8ψGAGCCGGAGGUCCCCGCACAAUCAGCGUAAGCTψGCGUCAC7V7GGCUCGAAGGGDDG110203040556070Dihydrouridine LoopT-ψ-C Loop
Acceptor StemE.coli tRNALys
DU4AUAnticodon Loop
Human tRNALys,3 and E.coli tRNALys
Saenger (1988) “Principles of Nucleic Acid Structure” pp. 347
HO O
HO OH
N
N
N
N
SCH3
NN
COOH
OHH3CO
H
H
HO O
HO OH
N
N
N
N
H2N
HO O
HO OH
N
N
S
OH
NH3C
H
HO O
HO OH
N
N
O
OH
HO O
HO OH
NN
O
OHH
HO O
HO OH
N
N
S
OHCH3O
O
ms2t6A (A9)
Adenosine
UridinePseudouridine (ψ)(F)
mcm5s2U (U9) mnm5s2U (U8)
Codon-Anticodon Interactions
Summary
•The ribosome is a large “molecular machine” for making proteins•tRNAs bind 3 sites on the ribosome, Amino-acyl, Peptidyl, Exit•RNAs (rRNA, tRNA, and mRNA) are seldom “linear”, but fold into complex structures.•tRNAs can all be folded into a “cloverleaf” secondary structure•tRNAs all form an “L-shaped” 3D structure•tRNAs contain many non-canonical pairs and triples•Modifications are clustered in the functionally important areas•Modifications are conserved in the 3 kingdoms of life.•Modification in the tRNA anticodon help normalize the binding affinityfor the mRNA.
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