tert

anti
syn

OCH3 OCH3
-O
P -O
P
O O
O O
..
-O
:O -
anti syn

H B H O
HO .. B:
NH2 NH3+

N N
- N N
HO: NH2 R O- -O :O - O
R O- NH3+
H B NH
N N N
N N N N
H B ..
R O B: H O - O .. R O- R O R O
NH2 NH2
N N
N N ..
R O- R O-

AG CU UC
3' C U C G G G C U G U C G 5' 3' C U C G G A
G C A C A G C 3' G CC U G U C G 5'
5' GA G C C
CU AG 5' GA G C C GG AG A C A G C 3'
UC

stem loops "kissing complex"

 G CU
A
U U
U C GG
C C
G G UG
3' A C GC U
C CA U G
CGG CUCC
A CG
5' G C C G A G G G
UA U G C C U A AA
G CA CGA
C G C U GA
U A
C G
A A
G U
U G
UG

four types of base pairs: A•T, C•G, G•C, or T•A

5' NN NNN NNNNN

four types of unpaired bases: A, C, G, or T
3' N N N N N N N N N
N

twelve types of mis-matches:

A•A, A•C, A•G, C•A, C•C, C•T, G•A, G•G, G•T, T•C, T•G, T•T

Total possibilities = 47• 44• 12

= 411• 12
= 50,331,648

RNA RNA RNA

O
.. -
O O -
RNA O O O O O O O
-O
.. O
O H :B N N N
CH3 CH3 .. CH
3

H B

RNA RNA
-
O .. O
O O
O O H
N+ N
CH3 CH3
H
 .OH
O H O. O

.
N N N
H H H
.O O.

O O O
H H H
N H N N
. . .
N N H N H
H H H
O O O
.O OH

O
H
N

N
H
O

R S S
R
NH2 SAM NH2
N N N N
(S)-configuration
+H N N N +H N N N
3 O 3 O

-O -O
2C S HO OH 2C S HO OH
:
:

H3C
:

lariat

B
O
O
- O Ade
..O
n O
-O P
O O
O O P O-
this P–O bond is P O
cleaved by -O O
O
exposure to base
5'-GATCCGCACCGAGTTCAAGAACACCTTTTCAAGAGAGGTGTTCTTGAACTCGGTGTTCTTTTTTTCTAGAG-3'

transcription

U UUsense
5'-GAUCCG CACCGAGUUCAAGAACACCU
A
GUGGCUCAAGUUCUUGUGG A
3'-GAGAUCUUUUUUUCUU AG G
antisense A

N N
H N G2447 H N G2447
N H O N H O
N N N N
1 N 1 N
3 N H O 3 N H O
N H : ..N N
..N H H H O P O
N O P O N
A2451 O A2451 O
A2450 A2450

Cyt Ura
N N
H
O N N O N O
Watson–Crick wobble
H
base pair base pair
H H H H
N N O N N O
H H H H
N N R N N R

N N
Gua ManQ

ATG GGC CGC CGC CCC GCC CGT TGT TAC CGG TAT TGT AAG AAC
AUG GGC CGC CGC CCC GCC CGU UGU UAC CGG UAU UGU AAG AAC
Met Gly Arg Arg Pro Ala Arg Cys Tyr Arg Tyr Cys Lys Asn

A A A G G
5'-G CA GCT G CT G CT CCA G TT-3'
C
Ala Thr Asp Gly Ala Ala
or or or or or or
Glu Ala Ala Ala Pro Val
 peptide peptide
deformylase deformylase
active
actinoin
active S protein/peptide
+ + R
site HO site O
Zn
- O
H
O
~
~
Zn
- O
H
O NH
O N HO: N
N N H N N
H H
O hydroxide anion O

A oxocarbenium ion
HO
HO OH HO OH
HO O
N O: O+
+ N+

:
:

Me3N+

:
N
Me3 N+ O
H2NOC NAD+ O N
N H2NOC H
H2NOC H O N
O N NH H
NH H
EF-2

CATAGCTGTCCTCCT
GUAUCGACAGGAGGA
CATGGTGGT
GUACCACCA

*A
5'
3'
*A O ONa 1 M NaOH O ONa
P P + HO
O O O ONa
H 2O
100 °C

*B O ONa 1 M NaOH
P OH O ONa
O O OH + P OH
H2O NaO O
100 °C

A CCG A B CCG A
GG A GG A
A A A A
G G G G
U G U G
A C A C
G C G C
ribozyme U
C A AG ribozyme UC AAG
5'-GGCGACC ACCGU-3' 5'-GCGCAGC ACGGC-3'
3'-CCGCUGGCUGGCA-5' 3'-CGCGUCGCUGCCG-5'
substrate substrate
Introduction to Bioorganic Chemistry and Chemical Biology | A

ACCESSION X69154; Glycine max ENOD40-1 mRNA.

1 gaauuccgcu aaaccaaucu aucaaguccu gauuaaucug gugagcAUGG AGCUUUGUUG
61 GCUCACAACC AUCCAUGGUU CUUGAagaag cuuggagaga aaggggugug agaggagagg
121 gugcucacuc cucacacucc cucacuuaaa acaguuuguu uuggcuuagc uuuggcuucu
181 cugaucaaca agggaugugu ucuaacauuc uuucuugagu ggcggaagca gauacacauu
241 cuccgacgga ggagaggcuu ggcuacagcc uggcaaaccg gcaagucaca aaaaaggcaa
301 uggacuccau uggggucucu auggcuaugu agugcucaug uaguucuucu ugcuguagaa
361 uguaauaaua aacaaaguug gucuuccuuu ugagaaguua ccagcuuuug cuguccaaaa
421 uuacucaauu ugcagcugac uagaauuccu uucucucuuc aguuucugca gaugaguagg
481 uaggcaauuu gugaucacuc ccuucccuuu ucaugucuuc uguguucccu uuuccaugcu
541 uguuuguguu guuaguuaug accuuaugag gaaauaaaag aauaguacaa uucuaguccc
601 ucaguuuagg auuguauucu auugaacuuu auuagaaaag uuuccagagu ccuuucuaaa
661 aaaaaaaaaa aaaaaaaaa

Peptide A (highlighted)
AUGGAGCUUUGUUGGCUCACAACCAUCCAUGGUUCUUGA
MetGluLeuCysTrpLeuThrThrIleHisGlySerSTOP

Peptide B (underlined)
AUGGUUCUUGAagaagcuuggagagaaaggggugugagaggagagggugcucacuccucacacucccucacuuaa
MetValLeuGluGluAlaTrpArgGluArgGlyValArgGlyGluGlyAlaHisSerSerHisSerLeuThrSTOP

HO HO
O O pH 8 O
HO .. + HO
NH2 EtO O OEt N OEt
Tris H
OH OH