13 What is chemical biology (Inglés) (Presentación) autor University of Zurich

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What is chemical biology? 
The term “chemical biology” was published in 1930 by J. B. Leathes, (1930) “The birth of chemical biology”, in 
Lancet, 889–895. However, the usage of the term has changed dramatically with time, and the current definition 
cannot be traced back to a single source.
Here we will adopt the broad definition that chemical biology is the application of chemical tools and ideas to 
biological problems. It is interesting also to look at the leading journals in this field, all of which have appeared 
over the past few years. These include:
Nature Chemical Biology (est. 2005) http://www.nature.com/nchembio/index.html
"Nature Chemical Biology welcomes submissions from chemists who are applying the principles, language and tools 
of chemistry to biological systems and from biologists who are interested in understanding biological processes 
at the molecular level. The scope of the journal will emphasize four major themes of contemporary research in 
chemical biology: Chemical synthesis, Chemical Mechanisms in Biology, Expanding Biology through 
Chemistry, Expanding Chemistry through Biology.” (edited for length)
ACS Chemical Biology (est. 2006) http://pubs.acs.org/journals/acbcct/index.html
"ACS Chemical Biology is establishing a community approach to foster interactions between scientists exploring 
cellular function from both a biological and chemical perspective. Results will be published in which 
molecular reasoning has been used to probe questions through in vitro investigations, cell biological methods, or 
organismal studies. We welcome mechanistic studies on proteins, nucleic acids, sugars, lipids, and non-
biological polymers. The journal serves a large scientific community, exploring cellular function from both 
chemical and biological perspectives.” ACS Chemical Biology is “a forum for the publication of 
interdisciplinary research.”
What is chemical biology? 
Chemistry and Biology (est. 1995) http://www.chembiol.com/
"Chemistry & Biology publishes reports of novel investigations in all areas at the interface of chemistry and 
biology. Chemistry & Biology strongly encourages submission of articles in which chemical tools are used to 
provide unique insight into biological function and mechanism. 
ChemBioChem (est. 2006) http://www3.interscience.wiley.com/cgi-bin/jhome/72510898
"Contributions in ChemBioChem cover chemical biology and biological chemistry, bioinorganic and bioorganic 
chemistry, biochemistry, molecular and structural biology. That is, research at the interface of chemistry and 
biology that deals with the application of chemical methods to biological problems or uses life science tools to 
address questions in chemistry."
OK, so how is Chemical Biology different from Biochemistry? Here is one possible model:
Chemistry Chemical Biology Biochemistry Biological Chemistry Biology
Chemical Biology
More than 50% of Nobel Prizes awarded in chemistry are for topics at the chemistry / biology interface:
2008: R. TSIEN, O. SHIMOMURA, and M. CHALFIE for the discovery and modification of fluorescent proteins.
2006: R. D. KORNBERG for his studies of the molecular basis of eukaryotic transcription. 
2004: A. CIECHANOVER, A. HERSHKO , and I. ROSE for the discovery of ubiquitin-mediated protein degradation
2003: P. AGRE, for the discovery of water channels and R. MACKINNON for ion channels. 
“nuclein” protein
Discovery of DNA
“....nuclein bodies will prove tantamount in importance to proteins”
Med.-Chem. Unters. 1871, 4, 441-460.
OO
O
P
O
HO
N
OO
O
P
O
HO
NH
N
N
O
NH2N
NH
O
O
phosphodiester
pKa = 
H3PO4: 2.15, 7.20, 12.35
Discovery of DNA 
Friedrich Miescher (MD, born 1844 Basel) 
Studied under organic chemist Adolf Strecker.
While at the Hoppe-Seyler Laboratory he subjected purified leucocyte nuclei 
from white blood cells to an alkaline extraction followed by acidification.
Miescher showed that the “nuclein” precipitate was a large molecule, acidic, 
resistant to pepsin, and rich in phosphorus. 
O
R
NH3 HCN
NH2
R CN
H3O
+
∆
NH3
R CO2H
+
Albrecht Kossel: From 1879 to 1901 he and his students used hydrolysis and 
chromatography to isolate and characterize the five most abundant nucleobases
from nuclein: 
N
N
NH2
N
N
H
N
NH
NH2
O
N
N
H
N
H
NH
O
O
Adenine Guanine Uracil
N
H
NH
O
O
Thymine
N
H
N
NH2
O
Cytosine
pyrimidinespurines
N
NH
NH
N
N
H
N
N
NH2
OH
N
N
H
N
H
N
OH
O
Imino-A Enol-G Enol-U
N
H
N
OH
O
Enol-T
N
H
NH
NH
O
Imino-C
Composition of DNA 
OO
O
P
O
HO
N
OO
O
P
O
HO
NH
N
N
O
NH2N
NH
O
O
pH < 0
∆
Phoebus Levene: Discovered ribose in 1909 and 
deoxyribose in 1929 and showed that the 
components were linked together in the order 
phosphate-sugar-base to form “nucleotide” units. 
These discoveries lead to the terms ribonucleic 
acid (RNA) and deoxyribonucleic acid (DNA).
Composition of DNA 
J Biol Chem, 1919, 40, 415–24.
OO
O
P
O
HO
N
OO
O
P
O
HO
NH
N
N
O
NH2N
OH
OH
NH
O
O
RNA
J Biol Chem, 1929, 83, 793–802.
DNA
OO
O
P
O
HO
N
OO
O
P
O
HO
NH
N
N
O
NH2N
NH
O
O
NH
N
N
O
NH2NO
O
O
P
OH
O
O
N
N
N N
O
O
P OH
O
O
H2N
N
O
O P
HO
O
N
O
O
O
PHO O
NNH
O
O
NH2
O
Adenosine Guanosine
Thymidine Cytidine
In Levene 1911 published the 
"tetranucleotide hypothesis“
which proposed that nucleic 
acids were made of equal 
amounts of adenine, guanine, 
cytidine, and thymidine.
0.351.001.0837.112.437.113.4Sarcinalutea
2.701.091.0112.836.314.036.9Clostridiumperfringens
1.791.090.9517.132.918.731.3Yeast
1.380.951.0221.529.220.528.8Chicken
1.521.001.0519.829.419.930.9Human
G/CA/TCTGA
Ratio 
(A+T)/(G+C)
Base RatiosBase Composition (mole %)
Organism
Erwin Chargaff: In 1950 reported that the amount of G = C, 
and that the amount of A = T.
Composition of DNA 
NN
H2N
N
N
N
NH
NH2
O
N
N
Adenosine
Guanosine
N
NH
O
O
Thymidine
NN
H2N
O
Cytidine
R
R
R
R
(G) (T)
(C)
(A)
N
NH
NH2
O
N
N
Guanosine (keto)
N
NH
O
O
Thymidine (keto)
N
N
NH2
OH
N
N
Guanosine (enol)
N
N
OH
O
Thymidine (enol)
R RRR
Jerry Donohue: In 1953 he informed Watson that, contrary to published work, the keto structures of 
guanine and thymidine were more important than the enol forms. Note that in the gas phase both 
forms are observed, but in solution the keto form of guanosine dominates by a factor of 104 – 105. 
Base-Pairing Interactions 
Linus Pauling: Published a triple helix DNA model using Astbury’s X-ray 
diffraction data.
Proc Natl Acad Sci U S A. 1953, 39, 84-97.
0.34 x 109 m
William Astbury: Using X-ray diffraction data, Astbury reported that DNA's 
structure repeated every ~30 Å and that the bases lay flat, stacked. 3.4 Å apart. 
DNA Structure 
X-rays
Diffraction 
pattern
Aligned DNA
“Photo 51”
Nature, 1953, 4356, 740-741.
B-form
Rudolf Signer:
Professor of organic chemistry at Bern University, provided Maurice Wilkins with high quality DNA.
Maurice Wilkins:
Started DNA diffraction studies with Ray Gosling in 1950 under Sir John Randal. Focused his work on B-form DNA.
Rosalind Franklin:
Obtained Signer’s DNA from Wilkins in 1951. Focused her work on A-form (low humidity) DNA.
DNA Structure 
Nature, 1953, 4356, 737-738.
“We were not aware of the details of the results presented 
there (from King’s College) when we devised our structure....
We have also been stimulated by a knowledge of the general 
nature of the unpublished experimental results and ideas of 
Dr. Wilkins and Dr. Franklin and their co-workers.”
EMBO reports, 2003, 4, 11, 1025–1026.
vertical axis, bases inside
“Photo 51”B-formMaurice Wilkins showed “Photo 51” to James Watson, 
without Franklin’s knowledge, in early 1953 or late 1952.
In February 1953 a written scientific report, including 
Franklin’s interpretation of “Photo 51” was given to 
Francis Crick by his thesis supervisor Max Perutz.
Rudolf Signer:
Professor of organic chemistry atBern University, provided Maurice Wilkins with high quality DNA.
Maurice Wilkins:
Started DNA diffraction studies with Ray Gosling in 1950 under Sir John Randal. Focused his work on B-form DNA.
Rosalind Franklin:
Obtained Signer’s DNA from Wilkins in 1951. Focused her work on A-form (low humidity) DNA.
DNA Structure 
James Watson & Francis Crick in 1953 published their 
model for the B-form double helix. 
Received Nobel Prize for Medicine or Physiology, along 
with Maurice Wilkins, in 1962. 
Nature, 1953, 4356, 737-738.
“It has not escaped our notice that the specific pairing we 
have postulated immediately suggests a possible copying 
mechanism for the genetic material.”
DNA Structure 
Alfred Hershey and Martha Chase: reported their “blender experiment” in 1953, and DNA was 
finally accepted as the molecule of inheritance.
DNA Function
The Central Dogma of Molecular Biology
F. Crick’s Model (1958):
Models for the flow of genetic information illustrating all possible 
transfers of (A) and those that are permitted (B). Crick concluded 
that once information was transferred from nucleic acid (DNA or 
RNA) to protein it could not flow back to nucleic acids.
J. Watson’s Model (1965):
Many exceptions to Watson’s (simplified) model are known: non-coding RNA (tRNA, rRNA, etc.), reverse 
transcription (RNA viruses), “junk” DNA, epigenetics, prions, trans-splicing, transposons, gene rearrangements 
(information transfer that is independent of duplication), and the one-gene-one-protein hypothesis. 
(A) (B)
http://en.wikipedia.org/wiki/Central_dogma_of_molecular_biology
One Current Model (2008):
Human Genome
Human Genome Project
Projected cost ≈ 4 x 109 CHF 
Craig Venter & Celera Genomics:
Final cost ≈ 4 x 108 CHF 
85% complete in 2001.
92% complete in 2005.
Sequences can not be patent protected.
Near-term cost projections ≈ 1’000 CHF 
per human
genome
Genome vs. Proteome
According to Molecular 
Biology of the Gene, 5th ed., 
Peason Benjamin Cummings 
(Cold Spring Harbor 
Laboratory Press, 2005).
Species
Mycoplasma genitalium (bacterium)
Streptococcus pneumoniae (bacterium)
Escherichia coli (bacterium)
Saccharomyces cerevisiae (yeast)
Arabidopsis thaliana (plant)
Caenorhabditis elegans (worm)
Drosophila melanogaster (fruit fly)
Mus musculus (mouse)
Homo sapiens (human)
Oryza sativa (rice plant)
Genome size (Mb)
0.58
2.2
4.6
12
125
97
180
2500
2900
466
Estimated Number of genes
500
2300
4400
5800
25,500
19,000
13,700
29,000
27,000
45-55,000 
What is the “gene density” (in base pairs per gene) of H. sapiens compared to C. elegans? 
Why does the number of genes estimated from genomic DNA sequences underestimate the number proteins?
Genome vs. Proteome
This is called alternative splicing, and can produce different 
forms of a protein from the same gene. The different forms 
of the mRNA are called “transcript variants,” “splice 
variants,” or “isoforms.” The current record-holder for 
alternative splicing is a Drosophila gene called Dscam
which has ~38’000 splice variants. This gene has 95 
alternate exons and encodes an axon guidance receptor. 
Alternative Splicing of RNA Splicing of Protein
An intein is the protein equivalent of intron. A self-
splicing intein catalyzes its own removal from the host 
protein through a posttranslational process of protein
splicing. A mobile intein displays a site-specific 
endonuclease activity that confers genetic mobility to 
the intein through intein homing. Inteins can evolve 
into new structures and new functions, such as split 
inteins that do trans-splicing.
Annu. Rev. Genet. 2000. 34:61–76
* = to be covered in this course
*
Acetylation: the addition of an acetyl group, usually at the N-terminus of the protein 
Methylation: the addition of a methyl group, usually at lysine or arginine residues.
Biotinylation: acylation of conserved lysine residues with a biotin appendage 
Glutamylation: covalent linkage of glutamic acid residues to tubulin and some other proteins
Glycylation: covalent linkage of one to more than 40 glycine residues to the tubulin C-terminal tail 
Glycosylation: the addition of a glycosyl group to either asparagine, hydroxylysine, serine, or threonine, resulting in a glycoprotein 
Isoprenylation: the addition of an isoprenoid group (e.g. farnesol and geranylgeraniol) 
Lipoylation: attachment of a lipoate functionality 
Phosphopantetheinylation: the addition of a 4'-phosphopantetheinyl (ppan) moiety from coenzyme A, as in fatty acid, polyketide, 
non-ribosomal peptide and leucine biosynthesis 
Phosphorylation: the addition of a phosphate group, usually to serine, tyrosine, threonine or histidine
Sulfation: the addition of a sulfate group to a tyrosine
Selenation: the exchange of a sulfur group with selenium
Citrullination: or deimination, the conversion of arginine to citrulline
Deamidation: the conversion of glutamine to glutamic acid or asparagine to aspartic acid 
Disulfide bridges: the covalent linkage of two cysteine amino acids 
C-terminal amidation
Genome vs. Proteome
Known post-translational protein modifications involving the addition or modification of functional groups:
*
*
*
*
*
*
* = to be covered in this course
*
Important Challenges to Proteomics
1. Which proteins are encoded by the genome and under what conditions?
2. What are the sequences and post-translational modifications of each protein?
3. What does each protein do?
(a) Is it an enzyme, a structural scaffold, a mediator of signal transduction, an antibiotic, a hormone?
(b) To which molecules does each protein bind?
(c) How does over-expression or under-expression of each protein affect the cell and the expression of other 
genes? 
(d) Where in the cell is the protein localized? 
(e) How is its activity regulated?
The study of natural proteins and the creation of non-natural ones require the ability to produce and manipulate 
proteins. The production of proteins using biochemical methods (recombinant DNA technology) can, in favorable 
cases, provide access to large amounts of protein and allow for site-specific mutations. However, the natural genetic 
code is typically limited (not always) to the 21 natural proteinogenic amino acids. To probe the questions above, other 
types of modifications are often required like the site-specific incorporation non-proteinogenic amino acids, 
phosphorylated residues, novel glycosylation patterns, fluorescent labels, photochemical triggers, lipid anchors, etc. 
Over the past 10 years a number of powerful methodologies have been developed for producing proteins with such 
modified groups. The first part of Chemistry 434 will focus on these methodologies. 
Some Relationships Between Analytical and Preparative Chemical Tools
Chemical tools 
Analytical
Protein sequencing.
Identification of post-translational
modifications.
Protein conformation and 
structure.
Protein localization, and catalysis.
Identification of protein-protein,
protein-DNA, protein-RNA,
protein-small molecule binding 
interactions.
Preparative 
Protein synthesis.
Site-specific introduction of 
post-translational modifications.
Chemical cross-linking and 
rational design/modification.
Site-specific protein labeling with 
spectroscopic probes.
Protein-capture through binding 
interactions, and the preparation 
of mutants to probe the contributions
of individual residues for binding. 
* = to be covered in this course
*
*
*
*
*
*
*
Examples of Problems in Preparative Chemistry
For example: how would you make the 
36-residue peptide T20 (1) (also called 
Fuzeon, a new anti-HIV drug from 
Roche); or the glycopeptide 2, which is a 
model of the repeating C-terminal domain 
of RNA polymerase II, in order to study 
the structure and function of this enzyme; 
or the antimicrobial glycoprotein 
diptericin (3) isolated from insects, to 
study the mechanism of its antimicrobial 
action; or an analogue of ribonuclease A 
containing a 5,5-dimethylproline(4) 
residue in place of proline, to examine the 
effects on folding; or a modified form of a 
kinase containing a caged 
photoactivatable phospho-group (5), in 
order to use time-resolved techniques to 
study the function of the phosphoprotein
in cell migration; or a lipidated version of 
green fluorescent protein (6) to study its 
mobility in membranes; or replace site 
specifically an amino acid in a protein for 
a p-benzoyl-L-phenylalanine residue (7) 
to allow photo-crosslinking ???
Ac-Ser-Tyr-Ser-Pro-Thr-Ser-Pro-Ser-Tyr-Ser-NH2
O
H
HO
H
HO
H
NHAc
H
O
OH
1
NH3 CONH2
O
HO
H
H
HO
H
O
AcHN
H
H
OH
Thr11
O
HO
H
H
HO
H
O
AcHN
H
H
OH
Thr54
diptericin (1-82)
2
Ac-YTSLIHSLIEESQNQQEKNEQELLELDKWASLWNWF-NH2
3
O
N O
HN
5,5-dimethylproline (4)
P
O O
O
O2N
Kinase
(5)
GFP
O
P
O
O O
O
O
O
O
C15H31
C15H31
(6)
O
Protein
(7)
Proteinogenic amino acids 
There are over 500 naturally occurring α-amino acids (ignoring 
β-, γ- and δ-amino acids), but the genetic code in nearly all 
organisms encode for only 21 different α-amino acids. All of 
these except glycine have a chiral center at the α-position, 
which has the S absolute configuration. The exception is 
cysteine, which according to the CIP-nomenclature system is 
R. Two others (2S,3R-threonine and 2S,3S-isoleucine) have 
chiral centers at the ß-position. All the proteinogenic amino 
acids are classified as L-amino acids. Bacteria also produce D-
amino acids, which are needed amongst other things, for the 
biosynthesis of the cell wall peptidoglycan. 
NH3 OH
NH
NH2
NH2
OH
NH NH
SH
HOOC COOH
12.5 10.5 10.1
6.0 8.2 14.0 3.7 4.3
The side chains (R) of many amino acids contain charged groups:
These pKa values apply only in free aqueous solution. In 
Other environments, the pKa values may change dramatically.
Back to the Basics: Amino Acids, Peptide Bonds, and Proteins
Amino acids are zwitterionic in neutral aqueous solution:
H3N
OH
O
R
H3N
O
O
R
H2N
O
O
R
+ +
_ _
H2N
OH
O
H2N
OH
O
H2N
OH
O
H2N
OH
O
H2N
OH
O
G - glycine (Gly) A - alanine (Ala)
L - leucine (Leu) V - valine (Val)
I - isoleucine (Ile)
H2N
OH
O
N - asparagine (Asn)
H2N
OH
O
D - aspartic acid (Asp)
H2N
OH
O
Q - glutamine (Gln)
NH2O
H2N
OH
O
OHO
E - glutamic acid (Glu)
OH
O
NH2
O
H2N
OH
O
K - lysine (Lys)
H2N
OH
O
R - arginine (Arg)
HN
NH2 NH
NH2
H2N
OH
O
H - histidine (His)
NH
N
H2N
OH
O
OH
H2N
OH
O
NH
Y - tyrosine (Tyr) W - tryptophane (Trp)
OH
O
P - proline (Pro)
N
H
H2N
OH
O
OH
H2N
OH
O
OH
S - serine (Ser)T - threonine (Thr)
H2N
OH
O
P - phenylalanine (Phe)
Aliphatic Amide and Acidic
Aromatic
Basic
Hydroxyl, Seleneum, or Sulfur
H2N
OH
O
M - methionine (Met)
S
H2N
OH
O
SH
C - cysteine (Cys)
H2N
OH
O
SeH
U - selenocysteine (Sec)
Amide Bonds
Formal Dehydration Reaction:
Amides are synthesized from carboxylic acids and amines. This reaction formally involves the loss of a water molecule. 
R OH
O
Carboxylic Acid
H2N
R
Amine
R
H
N
O
R + H2O+
Amide Water
R O
O
Salt
H3N
R+
-
∆
Synthesis:
It is possible to use dehydration for amide bond synthesis, but it requires very high temperatures (200 oC) and does 
not work for complex “R” groups (like most amino acids). 
R OH
O
Carboxylic Acid
H2N
R
Amine
R
H
N
O
R + H2O +
Amide Water
Reverse Reaction:
The reverse reaction is extremely slow in neutral water at RT, with an estimated half life of 7 years. 
R OH
O
Carboxylic Acid
H2N
R
Amine
R
H
N
O
R + H2O+
Amide Water
For phosphodiester bonds, estimated half life = 1’000 years (RNA), 200 x 106 years (DNA): O
P
Phosphodiester
OO
O
-
Peptide Bonds
LG
O
H2N
R2
O
N
H
R R
R1
O
H
N
R2
O
N
H
R
R
R1
O
H2
N
R2
O
N
H
R
R
R1
LG
-H+
-LG-
LG = tRNA or ppan
R1 = polypeptide
 chain or H
Biosynthesis:
Chemical
Synthesis:
R1 = protecting group
LG = chloride, succinate, 
HOBt, urea, etc.
R2 = tRNA or ppan
R2 = polypeptide 
chain and linker 
to a solid-support
+
-
Tetrahedral Intermediate New Peptide BondActivated Carboxylic Acid and Aliphatic Amine
+
Both chemical and biosyntheic peptide bonds are synthesized from “activated” carboxylic acids and an amine 
nucleophile: 
Growing chain formed in N C terminal direction
Growing chain formed in C N terminal direction
..
Addition
At pH = 7.0 what is the fraction of the ammonium (–NH3+)
versus amine (–NH2) form?
Elimination
Henderson-Hasselbach equation: pH = pKa + log ([A] / [HA])
How is this pKa value different than free amino acids?
pKa ~8
H3N
O
R
H2N
O
R
+
peptidepeptide
Biosynthesis of Polypeptides
Biosynthesis:
Amino acids are converted into esters by the ATP-dependent catalysis of Aminoacyl-tRNA Synthetase in a 
two-step process. Each amino acid requires a different Aminoacyl-tRNA Synthetase. Peptide bonds are 
formed in a portion of the ribosome that contains only RNA. 
1 Reversible.
This is one of
two key steps 
needed for 
accurate 
translation of 
mRNA.
2
Driven by 
subsequent PPi
hydrolysis. 
H2O
2 PiPyrophosphatase
99.98% accurate! How can small differences is codon-anticodon base pairing lead to such high fidelity?
The Ribosome and Translation
At least two proofreading mechanisms exist to prevent errors: 
1. Proofreading of aminoacyl-AMP and tRNA pair. 
2. Kinetic proofreading before peptide bond formation. 
See movies: 
http://pubs.acs.org/isubscribe/journals/cen/85/i08/html/8508cover.html
A delay is introduced between the binding of an 
aminoacyl-tRNA to the codon and the formation of the 
peptide bond to allow errors to be corrected: 
EF-Tu-GTP binds an aminoacyl-tRNA and bring it into 
the A-site. EF-Tu allows the anticodon to interact with 
the codon but prevents peptide bond formation. An 
incorrect tRNA will bind weakly to the codon and will 
dissociate from the codon before an incorrect amino acid 
is incorporated into the polypeptide. Correct codon-
anticodon matching triggers hydrolysis of GTP by the EF-
Tu, after which EF-Tu-GDP dissociates. 
Peptide bond formation proceeds. 
The Ribosome and Translation
“If genomic DNA is the cell's planning authority, 
then the ribosome is its factory, churning out the 
proteins of life”.
The ribosome found in the bacterium Escherichia 
coli is made up of three RNA components and 
more than 50 proteins. It weighs about 2.5 million 
daltons. Eukaryotic versions have four RNAs and 
about 80 proteins and weigh about 4 MDa. 
The rate of translation in E. coli is about 15 amino acids per second. 
What is the rate of translation?
Since the average weight of an amino acid is ~100 
daltons, this is equivalent to a 80 kg person 
working with an object weighing 3 grams.
What is the accuracy (fidelity) of translation?
For E. coli : 99.2 – 99.98% accurate! 
Chemical synthesis is ~ 1 amino acid per hour.
The yield for a typical chemical synthesis is ~96 % per amino acid.
from: Science, 2000 Vol. 289. no. 5481, pp. 947 – 950.
Proposed Mechanisms for Peptide Bond Formation
“During the early stages of model building on the 50S ribosome crystal structure, Moore, Steitz, and co-workers 
came to the anticipated, but hitherto unproven, conclusion that the peptidyl transferase center of the ribosome is 
composed exclusively of RNA.” (see: Science, August 2000, Vol. 289. no. 5481, pp. 905 - 920). 
N
N N
N
NH2
aa-tRNA NH2
..
HN
N N
N
NH2
aa-tRNA NH
+
-
(pKa = 4 - 7)
(pKa = 40)
Problem:
Revised mechanism from author’s current website.
RNA, 2001, 7, 1365–1369.
-Peter Sandler and Erik C. Bottger, et. al.
“…..We concluded that the proposed unusual pKa
of A2451, if existing, may not be crucial for the 
ribosome activity and that the previously reported 
pH-dependent alterations in the DMS modification 
of A2451 do not necessarily reveal an unusual pKa
of this nucleotide.”
Codon Table
http://teachline.ls.huji.ac.il/72693/codon.jpg
Importance of third base?
Notice: three different stop codons.
Or, UGA can 
encode for a 
21stamino acid
like Sec, or an 
unnatural one.
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 /ConvertImagesToIndexed true
 /PassThroughJPEGImages true
 /CreateJDFFile false
 /CreateJobTicket false
 /DefaultRenderingIntent /Default
 /DetectBlends true
 /ColorConversionStrategy /LeaveColorUnchanged
 /DoThumbnails false
 /EmbedAllFonts true
 /EmbedJobOptions true
 /DSCReportingLevel 0
 /EmitDSCWarnings false
 /EndPage -1
 /ImageMemory 1048576
 /LockDistillerParams false
 /MaxSubsetPct 100
 /Optimize true
 /OPM 1
 /ParseDSCComments true
 /ParseDSCCommentsForDocInfo true
 /PreserveCopyPage true
 /PreserveEPSInfo true
 /PreserveHalftoneInfo false
 /PreserveOPIComments false
 /PreserveOverprintSettings true
 /StartPage 1
 /SubsetFonts true
 /TransferFunctionInfo /Apply
 /UCRandBGInfo /Preserve
 /UsePrologue false
 /ColorSettingsFile ()
 /AlwaysEmbed [ true
 ]
 /NeverEmbed [ true
 ]
 /AntiAliasColorImages false
 /DownsampleColorImages true
 /ColorImageDownsampleType /Bicubic
 /ColorImageResolution 300
 /ColorImageDepth -1
 /ColorImageDownsampleThreshold 1.50000
 /EncodeColorImages true
 /ColorImageFilter /DCTEncode
 /AutoFilterColorImages true
 /ColorImageAutoFilterStrategy /JPEG
 /ColorACSImageDict <<
 /QFactor 0.15
 /HSamples [1 1 1 1] /VSamples [1 1 1 1]
 >>
 /ColorImageDict <<
 /QFactor 0.15
 /HSamples [1 1 1 1] /VSamples [1 1 1 1]
 >>
 /JPEG2000ColorACSImageDict <<
 /TileWidth 256
 /TileHeight 256
 /Quality 30
 >>
 /JPEG2000ColorImageDict <<
 /TileWidth 256
 /TileHeight 256
 /Quality 30
 >>
 /AntiAliasGrayImages false
 /DownsampleGrayImages true
 /GrayImageDownsampleType /Bicubic
 /GrayImageResolution 300
 /GrayImageDepth -1
 /GrayImageDownsampleThreshold 1.50000
 /EncodeGrayImages true
 /GrayImageFilter /DCTEncode
 /AutoFilterGrayImages true
 /GrayImageAutoFilterStrategy /JPEG
 /GrayACSImageDict <<
 /QFactor 0.15
 /HSamples [1 1 1 1] /VSamples [1 1 1 1]
 >>
 /GrayImageDict <<
 /QFactor 0.15
 /HSamples [1 1 1 1] /VSamples [1 1 1 1]
 >>
 /JPEG2000GrayACSImageDict <<
 /TileWidth 256
 /TileHeight 256
 /Quality 30
 >>
 /JPEG2000GrayImageDict <<
 /TileWidth 256
 /TileHeight 256
 /Quality 30
 >>
 /AntiAliasMonoImages false
 /DownsampleMonoImages true
 /MonoImageDownsampleType /Bicubic
 /MonoImageResolution 1200
 /MonoImageDepth -1
 /MonoImageDownsampleThreshold 1.50000
 /EncodeMonoImages true
 /MonoImageFilter /CCITTFaxEncode
 /MonoImageDict <<
 /K -1
 >>
 /AllowPSXObjects false
 /PDFX1aCheck false
 /PDFX3Check false
 /PDFXCompliantPDFOnly false
 /PDFXNoTrimBoxError true
 /PDFXTrimBoxToMediaBoxOffset [
 0.00000
 0.00000
 0.00000
 0.00000
 ]
 /PDFXSetBleedBoxToMediaBox true
 /PDFXBleedBoxToTrimBoxOffset [
 0.00000
 0.00000
 0.00000
 0.00000
 ]
 /PDFXOutputIntentProfile ()
 /PDFXOutputCondition ()
 /PDFXRegistryName (http://www.color.org)
 /PDFXTrapped /Unknown
 /Description <<
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 /ENU (Use these settings to create PDF documents with higher image resolution for improved printing quality. The PDF documents can be opened with Acrobat and Reader 5.0 and later.)
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 /NLD <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>/ESP <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>
 /SUO <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>
 /ITA <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>
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 /SVE <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>
 >>
>> setdistillerparams
<<
 /HWResolution [2400 2400]
 /PageSize [612.000 792.000]
>> setpagedevice