1. Molecular mechanisms of DNA replication. Transcription.
The painting “Dawn of the Double Helix” composes the DNA duplex as human figures. The theme in this painting is “Life forms: The basic structures that make our existence possible”. 1

2. Two types of nucleic acids – DNA and RNA
Genome - the genetic information of an organism. The genomes of all cells are composed of DNA.
Nucleic acids are biopolymers consisting of nucleotides
Nucleotides have three components: (1) A weakly basic nitrogen base (2) A five-carbon sugar (3) Phosphate 2

3. Ribose and Deoxyribose
Рибоза
Дезоксірибоза
Ribose is the constituent of RNA
Deoxyribose is the constituent of DNA 3

4. Nitrogen Bases of Nucleic Acids
Adenine
Guanine
Cytosine
Thymine
Uracil
The nitrogen bases are derivatives of either pyrimidine or purine. 4

5. Nucleosides
Nucleosides are composed of ribose or deoxyribose and a heterocyclic base. 5

6. Structure of mononucleotide
Adenosine mononucleotide 6

7. Formation of DNA chain (5’-3’ direction)7

8. Nucleotides joined by 3’-5’ phosphodi-ester linkages
One end of the polynucleotide chain is said to be 5’ (no residues are attached to 5’-carbon) and other is said to be 3’. Direction from the top to bottom is called 5’→3’, from bottom to top – 3’→5. 8

9. Primary structure of nucleic acids9

10. Two Antiparallel Strands Form a Double Helix
DNA is Double-Stranded
Two Antiparallel Strands Form a Double Helix
Two strands run in opposite directions
Bases in opposite strands pair by complementary hydrogen bonding
Adenine (A) Thymine (T)
Guanine (G) Cytosine (C)
Crick Francis
Watson James
The double helix of DNA was discovered in by Crick F. and Watson J. Nobel prize in 1962. 10

11. Chemical structure of double-stranded DNA
Chemical structure of double-stranded DNA. The two strands run in opposite directions. Adenine in one strand pairs with thymine in the opposite strand, and guanine pairs with cytosine 11

12. Comple-mentary base pairing and stacking in DNA12

13. Two-stranded struc-ture of DNA13

14. DNA in cells is a constituent of chromatin
Chromatin – DNA plus different proteins
Histones – main proteins of chromatin 14

15. Chromatin structure
DNA is packaged by coiling of the into a solenoid (helix) structure 15

16. Types of RNA (1) Transfer RNA (tRNA)
Carries amino acids to translation machinery
Very stable molecules
(2) Ribosomal RNA (rRNA)
Makes up much of the ribosome
Very stable, majority of cellular RNA
(3) Messenger RNA (mRNA)
Encodes message from DNA to ribosomes
Rapidly degraded by nucleases 16

17. DNA Replication 17

18. The flow of genetic information in a typical cell
The main postulate of molecular biology
DNA 
RNA
protein 18

19. Replication – synthesis of DNA on the DNA template
Semiconservative mechanism of DNA replication
The two strands separate, and each strand is copied to generate a comple-mentary strand Each parental strand remains associated with its newly synthesized complement, so each DNA duplex contains one parental strand and one new strand. 19

20. A model for DNA replication20

21. Components which are necessary for replication
Enzymes (most important – DNA-dependent DNA polymerase)
Protein factors
Parental DNA
ATP, GTP, ТТP, CТP
Ions Mg і Zn 21

22. DNA replication
In eukaryotes the replication begins in many points simultaneously
V-shape – replication forks - the point of the beginning of replication
Helicase – enzyme untwisting the double strand 5’ 3’
Helicase
Primase 5’
Okazaki fragments 3’
Primer
Leading strand
Lagging strand 5’ 3’ 22

23. Replisome - protein machinery for replication
Replisome contains: primosome, DNA polymerase III, proteins
Helicase is a constituent of primosome 23

24. Bidirectional DNA replication in E. coli
New strands of DNA are synthesized at the two replication forks where replisomes are located 24

25. DNA polymerase
DNA polymerase III – the main enzyme of replication responsible for the chain elongation
Appropriate nucleotides are inserted in the correct positions according to the complementary principle
DNA polymerases only synthesize new strand in the 5’-3’ direction. 25

26. 26

27. Напрямок синтезу 5’-3’, антипаралельно до матричного ланцюга27

28. DNA polymerase synthesizes two strands simultaneously
Because DNA polymerases only polymerize nucleotides 5 ’3’, both strands must be synthesized in the 5’3’ direction. Thus, the copy of the parental 3’5’ strand is synthesized continuously; this newly made strand is designated the leading strand. As the helix unwinds, the other parental strand (the 5’3’, strand) is copied in a discontinuous fashion through synthesis of a series of fragments - Okazaki fragments; the strand constructed from the Okazaki fragments is called the lagging strands 28

29. Синтез відстаючого ланцюга відбувається дискретно
Lagging strand is copied in a discontinuous fashion (Okazaki fragments)
The formation of a phosphodi-ester linkage between of adjacent Okazaki fragments is catalized by ligase 29

30. Okazaki Model
Reiji Okazaki provided experimental evidence for discontinuous DNA synthesis 30

31. RNA Primer Begins Each Okazaki Fragment
Primosome is a complex containing primase enzyme which synthesizes short pieces of RNA at the replication fork - primer
DNA pol III uses the RNA primer to start the lagging-strand DNA synthesis
Replisome - includes primosome, DNA pol III
Each Okazaki fragment has the primer 31

32. DNA polymerase I activities
Okazaki Fragments Are Joined by Action of DNA Polymerase I and DNA Ligase
DNA polymerase I activities
DNA pol I removes the RNA primer at the beginning of each Okazaki fragment
Synthesizes DNA in place of RNA
DNA ligase
Catalyzes the formation of a phosphodiester linkage between of adjacent Okazaki fragments 32

33. Repair of Damaged DNA
DNA is the only cellular macromolecule that can be repaired
DNA damage includes: -base modifications -nucleotide deletions or insertions -cross-linking of DNA strands -breakage of phosphodiester backbone 33

34. Reparation – enzymatic deletion and synthesis of the damaged DNA fragments
Recombination - exchange or transfer of pieces of DNA from one chromosome to another or within a chromosome
Transposition – dislocation of gene or group of genes from one place to another 34

35. ТРАНСКРИПЦІЯ 35

36. NECESSARY COMPONENTS DNA matrix DNA-dependent RNA-polymerase
АТP, GТP, CТP, UТP
Мg ions 36

37. DIFFERENCE FROM REPLICATION
Only one strand is used as a matrix
Only the part of DNA is transcribed (not the entire chain) 37

38. RNA Polymerase
There are 3 RNA-polymerases in eukaryotes (for mRNA, rRNA, tRNA)
RNA pol is core of a larger transcription complex
Complex assembles at one end of a gene (promoter) when transcription is initiated – transcription initiation
DNA is continuously unwound as RNA pol catalyzes a processive elongation of RNA chain 38

39. The Chain Elongation Reaction
Mechanism almost identical to that for DNA polymerase
Growing RNA chain is base-paired to DNA template strand
Incoming ribonucleotide triphosphates (RTPs) form correct H bonds to template
New phosphodiester bond formed
Direction 5’-3’
Speed nucleotides/sec 39

40. Initiation and
elongation
steps of
transcription 40

41. The transcription bubble41

42. RNA poly-merase reaction42

43. RNA poly-merase reaction43

44. Transcription Termination
Only certain regions of DNA are transcribed
Transcription complexes assemble at promoters and disassemble at the 3’ end of genes at specific termination sequences 44

45. PROCESSING
Transcription occurs in the nucleus, translation in the cytoplasm
Eukaryotic mRNA is processed in the nucleus
In some mRNA, pieces are removed from the middle and the ends joined (splicing) 45

46. Specific enzymes cut out introns and join exons - splicing
Introns - internal sequences that are removed from the primary RNA transcript
Exons - sequences that are present in the primary transcript and the mature mRNA
Specific enzymes cut out introns and join exons - splicing 46

47. 7-methylguanosine (CAP)
mRNA
transcription
splicing
DNA
exons
exones
PROCESSING
7-methylguanosine (CAP)
Poly-A (TAIL) 5’ 3’
introns
Primary transcript 47