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The Genetic Code
Math-CS Camp, 19.07.06, Singapore
Mikhail S. Gelfand
Research and Training Center of Bioinformatics,
Institute for Information Transmission Problems, Moscow, Russia
and
Department of Bioengineering and Bioinformatics,
Moscow State University
The Biological Code by Martynas Yčas
(London, 1969)
Биологический код (Mосква, 1971)
140
120
refs.
100
80
60
40
20
0
1956
1951-55
1946-50
1941-45
193X
192X
191X
190X
18XX
47
49
51
53
55
57
59
year(s)
61
63
65
67
69
71
To apply
mathematics
in biology, a
mathematician
has to
understand
biology.
Israel Gelfand
Plan
• Pre-history
– Genetics
– Evolutionary theory
– Chemistry
• Cracking the Code
• Update
Genetics:
Gregor Mendel (1822-1884)
• Attended the Philosophical Institute
in Olomouc
• Since 1843 – at the Augustinian
Abbey of St. Thomas in Brno
• 1851-1853 – studied in the University
of Vienna
• 1856-1863 – cultivated 28 thousand
pea plants
• The Three Laws of Genetics
(“Experiments on Plant
Hybridization”)
– Read to the Natural History Society of
Brunn in Bohemia (1865)
– Published in Proceedings of the
Natural History Society (1866)
• Since 1866 – abbot, stopped working
in science
The seven traits of pea plants studied by Mendel
The first law
Crossing two pure lines different in some trait (e.g. yellow / green
seeds), one gets only one variant (allele) in the first generation
(the dominant allele)
F0
F1
The second law
Crossing two pure lines different in some trait (e.g. yellow / green
seeds), one gets only one variant (allele) in the first generation
(the dominant allele), and the distribution 3:1 of the dominant
and recessive alleles in the second generation.
F0
F1
F2
(Law of large numbers)
The 3:1 ratio is seen only when the number of observations is sufficiently high.
F0
F1
F2
The third law
Two different traits are inherited independently
(in the second generation the ratio is 9:3:3:1)
F0
F1
F2
F2
What if we take a pair with a different
assortment of the same traits?
F0
F0
F1
?
F2
Same F1
F2
F0
F0
F1
F1
Same F2
… regardless of the initial assortment
F2
F0
F0
F1
F1
Incomplete dominance
Incomplete dominance
?
Incomplete dominance
?
Incomplete dominance
Charles Darwin (1809-1882)
• 1825-27 in Edinburgh
University and 182731 in University of
Cambridge – natural
history, geology,
botany
• 1831-1836 – Voyage
of the Beagle
• Journal of Researches
into the Geology and
Natural History of the
various countries
visited by H.M.S.
Beagle (1839)
Origin of Species (1859)
The Law of Natural Selection
• Species make more offspring than can grow to adulthood.
• Populations remain roughly the same size.
• Food resources are limited, but are relatively constant most of
the time.
• In such an environment there will be a struggle for survival
among individuals.
• In sexually reproducing species, generally no two individuals
are identical.
• Much of the variation is heritable.
• Individuals with the "best" characteristics will be more likely to
survive …
• … those desirable traits will be passed to their offspring …
• … and then inherited by following generations, becoming
prevalent and then fixed among the population through time.
Thomas Huxley (1825-1895) “Darwin’s Bulldog”
Origin of Homo sapiens
Re-discovery of the Mendel laws and
emergence of modern genetics
• Hugo de Vries (1900)
• William Bateson
– genetics, gene, allele
• Walter Sutton
– Link between genes and
chromosomes(1902)
• Archibald Garrod
– Genetic cause of some
human disease (1902-08-23)
• Thomas Morgan, work on
Drosophila.
– Mutants: spontaneous
appearance of new alleles (a
fly with white eyes in a
population of flies with red
eyes) (1908)
– Universal acceptance of
chromosomes (1915)
Gene = a set of non-complementing mutations
Edward Lewis: Do two recessive mutations occur in the same gene?
F1: Mutant
phenotype
F1: Wild-type
phenotype
Mutant phenotypes persist in cis (same gene).
Mutant phenotypes reappear in trans (different genes)
F2
F1: Mutant
phenotype
F2: All mutant phenotypes
F1: Wild-type
phenotype
F2
WT
WT
Mut
WT
WT
Mut
Mut
Mut
Mut
1
2
1
2
4
2
1
2
1
9:7
DNA
• Friedrich Miescher (1869)
– Nucleolin
– Richard Altmann: nucleic acid (1889). Only in chromosomes
• Phoebus Levene (1929)
– Components (four bases, the sugar-phosphate chain)
– Nucleotide: phosophate+sugar+base unit
• Hammarsten and Casperson (1930s)
– DNA is a long polymer; crystals
• Astbury (1938)
– X-ray photographs
• Chargaff rules (1947)
– In many organisms, #A=#T, #C=#G
Transforming factor (Frederick Griffith,1928)
… = DNA (Oswald Avery, Colin McLeod, Maclyn MacCarthy,1944)
DNA is the genetic medium of phages
(Alfred Hershey and Martha Chase, 1948)
– radioactive DNA
35S – radioactive proteins
32P
Only DNA enters the cell
… and only DNA is inherited by progeny phages
Erwin Schrödinger
“What is life”, 1946: The gene is an aperiodic crystal
The structure of DNA …
• Maurice Wilkins and Rosalind Franklin:
high-resolution crystals (1950-1953)
… is the double helix
James Watson and Francis Crick (1953)
The Nature paper: a few lines more than one page
The DNA chain
Complementary pairs of nucleotides
С
Т
G
A
Figures from
the second
Watson-Crick
paper
The main distances are the same
One base-pair in the double helix (axial view)
The double helix, stick and ball models, axial view
The double helix, stick and ball models, side view
Three models for the replication of DNA
The semi-conservative one is correct
(Matthew Meselson and Franklin Stahl, 1958)
Cells are grown on
the 15N (heavy)
medium for
several
generations, then
transferred to 14N
(light) medium
Q: What would
be the outcome
if one of the two
other models
were correct?
Electron micrograph of replicating DNA
The Central Dogma (F.Crick)
DNA  RNA  protein
Crossingover and recombination
• Genes from one chromosome are not inherited independently
• Recombination allows for relative mapping of gene positions
on the chromosome:
if two genes are close, the frequency of recombination will be
lower
Collinearity of the gene and the protein
(Charles Yanofsky, 1967)
The Genetic Code
• The genetic code:
correspondence between DNA and protein
(George Gamow, 1954) (Георгий Гамов)
• Crick and co-authors (1961):
– Non-overlapping (one mutation affects one amino
acid)
– Degenerate (many codons for one amino acid)
– Comma-less (no specific markers between codons)
– Periodic
The codon is a triplet
• Mutations caused by acridine
– Non-leaky (instead of weakened function, simply no function)
– Mechanism: insertions and deletions of nucleotides
(the downstream part of the gene completely scrambled
the code is comma-less)
CUACUACUACUACUACUACUACUACUACUACUACUACUA
LeuLeuLeuLeuLeuLeuLeuLeuLeuLeuLeuLeuLeu
G
insertion
CUACUACUACGUACUACUACUACUACUACUACUACUACU
LeuLeuLeuArgThrThrThrThrThrThrThrThrThr
U
deletion
CUACUACUACUACUACUACUACUACUACACUACUACUAC
LeuLeuLeuLeuLeuLeuLeuLeuLeuHisTyrTyrTyr
Double mutants and revertants
• Two classes of mutations: (+) and (–)
• Double mutants (+)¤(+) and (–)¤(–) still produce loss-offunction phenotypes
• Double mutants (+)¤(–) and (–)¤(+) produce leaky
phenotypes
CUACUACUACGUACUACUACUACUACUACUACUACUACU
LeuLeuLeuArgThrThrThrThrThrThrThrThrThr
¤
CUACUACUACUACUACUACUACUACUACACUACUACUAC
LeuLeuLeuLeuLeuLeuLeuLeuLeuHisTyrTyrTyr
CUACUACUACGUACUACUACUACUACUACACUACUACUA
LeuLeuLeuArgThrThrThrThrThrThrLeuLeuLeu
Triple mutants are revertants!
• Triple mutants of the same class, (+)¤(+)¤(+) and (–)¤(–)¤(–),
produce leaky phenotypes
CUACUACUACGUACUACUACUACUACUACUACUACUACUACU
LeuLeuLeuArgThrThrThrThrThrThrThrThrThrThr
¤
CUACUACUACUACUACUACGUACUACUACUACUACUACUACU
LeuLeuLeuLeuLeuLeuArgThrThrThrThrThrThrThr
double mutant – loss of function phenotype
CUACAUCUACGUACUACUACGUACUACUACUACUACUACUAC
LeuLeuLeuArgThrThrThrTyrTyrTyrTyrTyrTyrTyr
¤
CUACUACUACUACUACUACUACUACUACGUACUACUACUACU
LeuLeuLeuLeuLeuLeuLeuLeuLeuArgThrThrThrThr
triple mutant – leaky phenotype
CUACUACUACGUACUACUACGUACUACUACGUACUACUACUA
LeuLeuLeuArgThrThrThrTyrTyrTyrValLeuLeuLeu
Cracking the Code
(F.Crick, M.Nirenberg, J.Matthaei, S.Ochoa,
G.Khorana, … and you)
• Regular oligonucleotides
– … UUUUUUUUUU …
– … UCUCUCUCUC …
– … UCAUCAUCAU …
• Random oligonucleotides with known composition
• Changes in proteins caused by deaminationcaused mutations: CU, AG
• Changes in proteins caused random mutations
• (tRNA binding in the presense of trinucleotides)
20 amino acids and 64 codons
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
Alanine
Cysteine
Aspartate
Glutamate
Phenylalanine
Glycine
Histidine
Isoleucine
Lysine
Leucine
Methionine
Asparagine
Proline
Glutamine
Arginine
Serine
Threonine
Valine
Tryptophan
Tyrosine
UUU
UUC
UUA
UUG
CUU
CUC
CUA
CUG
AUU
AUC
AUA
AUG
GUU
GUC
GUA
GUG
Phe
UCU
UCC
UCA
UCG
CCU
CCC
CCA
CCG
ACU
ACC
ACG
ACA
GCU
GCC
GCA
GCG
Pro
UAU
UAC
UAA
UAG
CAU
CAC
CAA
CAG
AAU
AAC
AAA
AAG
GAU
GAC
GAA
GAG
Lys
UGU
UGC
UGA
UGG
CGU
CGC
CGA
CGG
AGU
AGC
AGA
AGG
GGU
GGC
GGA
GGG
Triplet binding data
(from Crick’s Croonian lecture, 1966)
Reading the code: The ribosome
Translation
Polysomes
Adaptors (F.Crick and S.Brenner)
tRNA: secondary structure
tRNA: three-dimensional structure
tRNA and aminoacid-tRNA-synthetase
Initiation of translation
Translation start sites
dnaN
gyrA
serS
bofA
csfB
xpaC
metS
gcaD
spoVC
ftsH
pabB
rplJ
tufA
rpsJ
rpoA
rplM
ACATTATCCGTTAGGAGGATAAAAATG
GTGATACTTCAGGGAGGTTTTTTAATG
TCAATAAAAAAAGGAGTGTTTCGCATG
CAAGCGAAGGAGATGAGAAGATTCATG
GCTAACTGTACGGAGGTGGAGAAGATG
ATAGACACAGGAGTCGATTATCTCATG
ACATTCTGATTAGGAGGTTTCAAGATG
AAAAGGGATATTGGAGGCCAATAAATG
TATGTGACTAAGGGAGGATTCGCCATG
GCTTACTGTGGGAGGAGGTAAGGAATG
AAAGAAAATAGAGGAATGATACAAATG
CAAGAATCTACAGGAGGTGTAACCATG
AAAGCTCTTAAGGAGGATTTTAGAATG
TGTAGGCGAAAAGGAGGGAAAATAATG
CGTTTTGAAGGAGGGTTTTAAGTAATG
AGATCATTTAGGAGGGGAAATTCAATG
Translation start sites aligned
dnaN
gyrA
serS
bofA
csfB
xpaC
metS
gcaD
spoVC
ftsH
pabB
rplJ
tufA
rpsJ
rpoA
rplM
ACATTATCCGTTAGGAGGATAAAAATG
GTGATACTTCAGGGAGGTTTTTTAATG
TCAATAAAAAAAGGAGTGTTTCGCATG
CAAGCGAAGGAGATGAGAAGATTCATG
GCTAACTGTACGGAGGTGGAGAAGATG
ATAGACACAGGAGTCGATTATCTCATG
ACATTCTGATTAGGAGGTTTCAAGATG
AAAAGGGATATTGGAGGCCAATAAATG
TATGTGACTAAGGGAGGATTCGCCATG
GCTTACTGTGGGAGGAGGTAAGGAATG
AAAGAAAATAGAGGAATGATACAAATG
CAAGAATCTACAGGAGGTGTAACCATG
AAAGCTCTTAAGGAGGATTTTAGAATG
TGTAGGCGAAAAGGAGGGAAAATAATG
CGTTTTGAAGGAGGGTTTTAAGTAATG
AGATCATTTAGGAGGGGAAATTCAATG
Elongation
Termination of translation
Dialects
•
•
•
•
•
The genetic code is not universal
… but the differences are relatively minor
… occur mainly in small genomes of organelles
… and involve specific codon families.
In many cases symmetry is increased, or entire families
reassigned.
• Many changes involve stop codons
Reassignment
CUN (=CUU, CUC, CUA, CUG): LeuThr
Possible initiation codons in addition to AUG (Met):
NUG (=GUG,UUG,CUG), AUN (=AUU,AUC,AUA)
UAA, UAG: stop  Gln
More symmetry
AUU
AUC
AUA
AUG
Ile
Ile
IleMet
Met
AGU
AGC
AGA
AGG
Ser
Ser
ArgSer
ArgSer
UGU
UGC
UGA
UGG
Cys
Cys
stopTrp
Trp
Vulnerable codon families
CGU
CGC
CGA
CGG
Arg
Arg
Arg  none
Arg  none
AGU
AGC
AGA
AGG
Ser
Ser
Arg
Arg
GGU
GGC
GGA
GGG
Gly
Gly
Gly
Gly
 Ser
 Ser
Gly
Gly
stop
stop
none
Stop-containing families
UGU
UGC
UGA
UGG
Cys
Cys
stop  Trp
Trp
UAU
UAC
UAA
UAG
Tyr
Tyr
stop  Tyr
stop 
Cys
Sec
Gln
Gln
(Pyl)
How many letters are there in the
English alphabet?
How many letters are there in the
English alphabet?
• 26 (everybody knows) …
How many letters are there in the
English alphabet?
• 26 (everybody knows) …
• … but we are discussing the book by Yčas …
How many letters are there in the
English alphabet?
• 26 (everybody knows) …
• … but we are discussing the book by Yčas …
• … so everybody are naïve
How many amino acids?
• Chemists: hundreds
– many occur in proteins:
post-translation modifications
• How many amino acids are encoded
by DNA?
Crick:
Is formyl-methionine a “standard”
amino acid?
• Occurs in bacteria at N-termini of all
recently synthesized proteins (may be
enzymatically removed later on)
• Has three codons: AUG, GUG, UUG
– unlike “inernal” methionine encoded only
by AUG
– by the way, internal GUG encodes Valine
and internal UUG encodes Leucine
Selenocysteine
• In all three domains of life (bacteria, eukaryotes, archaea)
• Encoded by UGA followed by a special hairpin structure
(SECIS)
– without this hairpin UGA is a stop-codon
– several genes for selenoproteins per genome (or none)
– corresponds to cysteine in homologs (more efficient in enzymes)
• Complicated mechanism of incorporation (specific tRNA,
seryl-tRNA-synthetase, conversion to SeCys on tRNA,
specific elongation factor)
Alignment of SECIS elements
The
consensus
SECIS
structure
SECIS
elements:
examples
Pyrrolysine
• In methanogenic archaea
• A derivative of lysine
• Directly encoded (unlike selenocysteine).
Standard mechanism:
– UAG codon
– specific tRNA
– aminoacyl-tRNA
• UAG rarely used as a stop codon
– never as the only stop of a gene
Thanks
• Wikipedia
• Ergito
• Authors of papers,
photographs and Internet
resources
•
•
•
•
Professor Leong Hon Wai
The organizers
The assistants
The students