1. 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

2. The Biological Code by Martynas Yčas (London, 1969) Биологический код (Mосква, 1971)
191X
1956
18XX
190X
192X
193X

3. To apply mathematics in biology, a mathematician has to understand biology. Israel Gelfand

4. Plan Pre-history Cracking the Code Update Genetics Evolutionary theory
Chemistry
Cracking the Code
Update

5. Genetics: Gregor Mendel (1822-1884)
Attended the Philosophical Institute in Olomouc
Since 1843 – at the Augustinian Abbey of St. Thomas in Brno
– studied in the University of Vienna
– 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

6. The seven traits of pea plants studied by Mendel

7. 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

8. 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

9. (Law of large numbers) F0 F1 F2
The 3:1 ratio is seen only when the number of observations is sufficiently high. F0 F1 F2

10. The third law
Two different traits are inherited independently (in the second generation the ratio is 9:3:3:1) F0 F1 F2

11. F2

12. What if we take a pair with a different assortment of the same traits?

13. Same F1 F0 F0 F1 F1 F2

14. Same F2
… regardless of the initial assortment F0 F0 F1 F1 F2

15. Incomplete dominance

16. Incomplete dominance ?

17. Incomplete dominance ?

18. Incomplete dominance

19. Charles Darwin ( )
in Edinburgh University and in University of Cambridge – natural history, geology, botany
– Voyage of the Beagle
Journal of Researches into the Geology and Natural History of the various countries visited by H.M.S. Beagle (1839)

20. Origin of Species (1859)

21. 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.

22. Thomas Huxley (1825-1895) “Darwin’s Bulldog”

23. Origin of Homo sapiens

24. 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 ( )
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)

25. 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

26. F2
Mutant phenotypes persist in cis (same gene). Mutant phenotypes reappear in trans (different genes)
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

27. DNA Friedrich Miescher (1869) Phoebus Levene (1929)
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

28. Transforming factor (Frederick Griffith,1928)

29. … = DNA (Oswald Avery, Colin McLeod, Maclyn MacCarthy,1944)

30. DNA is the genetic medium of phages (Alfred Hershey and Martha Chase, 1948)
32P – radioactive DNA 35S – radioactive proteins
Only DNA enters the cell

31. … and only DNA is inherited by progeny phages

32. Erwin Schrödinger
“What is life”, 1946: The gene is an aperiodic crystal

33. The structure of DNA …
Maurice Wilkins and Rosalind Franklin: high-resolution crystals ( )

34. … is the double helix
James Watson and Francis Crick (1953)

35. The Nature paper: a few lines more than one page

36. The DNA chain

37. Complementary pairs of nucleotidesС G Т A

38. Figures from the second Watson-Crick paper

39. The main distances are the same

40. One base-pair in the double helix (axial view)

41. The double helix, stick and ball models, axial view

42. The double helix, stick and ball models, side view

43. Three models for the replication of DNA

44. 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?

45. Electron micrograph of replicating DNA

46. The Central Dogma (F.Crick)
DNA  RNA  protein

47. 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

48. Collinearity of the gene and the protein (Charles Yanofsky, 1967)

49. 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

50. 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
insertion
CUACUACUACGUACUACUACUACUACUACUACUACUACU
LeuLeuLeuArgThrThrThrThrThrThrThrThrThr
deletion
CUACUACUACUACUACUACUACUACUACACUACUACUAC
LeuLeuLeuLeuLeuLeuLeuLeuLeuHisTyrTyrTyr G U

51. Double mutants and revertants
Two classes of mutations: (+) and (–)
Double mutants (+)¤(+) and (–)¤(–) still produce loss-of-function phenotypes
Double mutants (+)¤(–) and (–)¤(+) produce leaky phenotypes
CUACUACUACGUACUACUACUACUACUACUACUACUACU
LeuLeuLeuArgThrThrThrThrThrThrThrThrThr
CUACUACUACUACUACUACUACUACUACACUACUACUAC
LeuLeuLeuLeuLeuLeuLeuLeuLeuHisTyrTyrTyr
CUACUACUACGUACUACUACUACUACUACACUACUACUA
LeuLeuLeuArgThrThrThrThrThrThrLeuLeuLeu

55. 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

57. Cracking the Code (F. Crick, M. Nirenberg, J. Matthaei, S. Ochoa, G
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 deamination-caused mutations: CU, AG
Changes in proteins caused random mutations
(tRNA binding in the presense of trinucleotides)

58. 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
Phe
UCU
UAU
UGU
UUC
UCC
UAC
UGC
UUA
UCA
UAA
UGA
UUG
UCG
UAG
UGG
CUU
CCU
CAU
CGU
CUC
CCC
Pro
CAC
CGC
CUA
CCA
CAA
CGA
CUG
CCG
CAG
CGG
AUU
ACU
AAU
AGU
AUC
ACC
AAC
AGC
AUA
ACG
AAA
Lys
AGA
AUG
ACA
AAG
AGG
GUU
GCU
GAU
GGU
GUC
GCC
GAC
GGC
GUA
GCA
GAA
GGA
GUG
GCG
GAG
GGG

59. Triplet binding data (from Crick’s Croonian lecture, 1966)

60. Reading the code: The ribosome

61. Translation

62. Polysomes

63. Adaptors (F.Crick and S.Brenner)

64. tRNA: secondary structure

65. tRNA: three-dimensional structure

66. tRNA and aminoacid-tRNA-synthetase

67. Initiation of translation

68. Translation start sites
dnaN ACATTATCCGTTAGGAGGATAAAAATG
gyrA GTGATACTTCAGGGAGGTTTTTTAATG
serS TCAATAAAAAAAGGAGTGTTTCGCATG
bofA CAAGCGAAGGAGATGAGAAGATTCATG
csfB GCTAACTGTACGGAGGTGGAGAAGATG
xpaC ATAGACACAGGAGTCGATTATCTCATG
metS ACATTCTGATTAGGAGGTTTCAAGATG
gcaD AAAAGGGATATTGGAGGCCAATAAATG
spoVC TATGTGACTAAGGGAGGATTCGCCATG
ftsH GCTTACTGTGGGAGGAGGTAAGGAATG
pabB AAAGAAAATAGAGGAATGATACAAATG
rplJ CAAGAATCTACAGGAGGTGTAACCATG
tufA AAAGCTCTTAAGGAGGATTTTAGAATG
rpsJ TGTAGGCGAAAAGGAGGGAAAATAATG
rpoA CGTTTTGAAGGAGGGTTTTAAGTAATG
rplM AGATCATTTAGGAGGGGAAATTCAATG

69. Translation start sites aligned
dnaN ACATTATCCGTTAGGAGGATAAAAATG
gyrA GTGATACTTCAGGGAGGTTTTTTAATG
serS TCAATAAAAAAAGGAGTGTTTCGCATG
bofA CAAGCGAAGGAGATGAGAAGATTCATG
csfB GCTAACTGTACGGAGGTGGAGAAGATG
xpaC ATAGACACAGGAGTCGATTATCTCATG
metS ACATTCTGATTAGGAGGTTTCAAGATG
gcaD AAAAGGGATATTGGAGGCCAATAAATG
spoVC TATGTGACTAAGGGAGGATTCGCCATG
ftsH GCTTACTGTGGGAGGAGGTAAGGAATG
pabB AAAGAAAATAGAGGAATGATACAAATG
rplJ CAAGAATCTACAGGAGGTGTAACCATG
tufA AAAGCTCTTAAGGAGGATTTTAGAATG
rpsJ TGTAGGCGAAAAGGAGGGAAAATAATG
rpoA CGTTTTGAAGGAGGGTTTTAAGTAATG
rplM AGATCATTTAGGAGGGGAAATTCAATG

70. Elongation

71. Termination of translation

72. 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

73. 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

74. More symmetry AUU Ile AUC Ile AUA IleMet AUG Met AGU Ser AGC Ser
AGA ArgSer
AGG ArgSer
UGU Cys
UGC Cys
UGA stopTrp
UGG Trp

75. Vulnerable codon families
CGU Arg
CGC Arg
CGA Arg  none
CGG Arg  none
AGU Ser
AGC Ser
AGA Arg  Ser Gly stop
AGG Arg  Ser Gly stop none
GGU Gly
GGC Gly
GGA Gly
GGG Gly

76. Stop-containing families
UGU Cys
UGC Cys
UGA stop  Trp Cys Sec
UGG Trp
UAU Tyr
UAC Tyr
UAA stop  Tyr Gln
UAG stop  Gln (Pyl)

77. How many letters are there in the English alphabet?

78. How many letters are there in the English alphabet?
26 (everybody knows) …

79. How many letters are there in the English alphabet?
26 (everybody knows) …
… but we are discussing the book by Yčas …

80. How many letters are there in the English alphabet?
26 (everybody knows) …
… but we are discussing the book by Yčas …
… so everybody are naïve

81. How many amino acids? Chemists: hundreds
many occur in proteins: post-translation modifications
How many amino acids are encoded by DNA?

82. Crick:

83. 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

84. 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)

85. Alignment of SECIS elements

86. The consensus SECIS structure

87. SECIS elements: examples

88. In methanogenic archaea A derivative of lysine
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

89. Thanks Wikipedia Ergito
Authors of papers, photographs and Internet resources
Professor Leong Hon Wai
The organizers
The assistants
The students