1. STRUCTURE OF DNA 1. primary structure 2. secondary structure 3
STRUCTURE OF DNA 1. primary structure 2. secondary structure 3. tertiary structure

2. PRIMARY STRUCTURE OF DNA

3. James Watson Francis Crick 1962 Nobel Prize

4. Polynucletide chain of DNA (primary/covalent structure)
The polynucleotide chain of DNA consist of nucleotides joined together by 3’,5’ phosphodiester bonds.
Phosphodiester bonds link the 3’- and 5’-sugar carbons of adiacent monomer.
Polynucleotides are directional macromolecules: each end of a polymer is distinct.
3’ –end is one with a free 3’-hydroxyl.
5’ –end is one with a free or phosphorilated 5’-hydroxyl.
Polynucleotides bear a negative charge at physiological pH 1’
3’linkage
5’linkage

5. Simplified representation of DNA chainOH
Sugar: horisontal line
Base: single letter
Phosphodiester bond:
oblique line with P 3’ 5’ G P 3’ 5’ C P P 3’ 5’ T OH

6. Simplified representation of DNA chain
Convention dictates that a single-stranded DNA sequence is written in the
5’ to 3’ direction.
e.g. GCT means 5’GCT 3’

7. Quick Quiz Question :
Identify which is the 3’end of this oligonucleotide?
Write the simplified representation of this oligonucleotide.

8. SECONDARY STRUCTURE OF DNA

9. Double helix of DNA
Watson and Crick discovered the secondary structure of DNA: a double helix – two sugar phosphate chains wrapping round each other, with the phosphate groups sticking out – the nucleotide from strand 1 meets the nucleotide from strand 2 in the middle. These pairs of nucleotides are complementary – where one strand has a C, the other has a G and vice versa; where one strand has an A the other has a T and vice versa.
Human DNA consists of approximately 3 x 109 such “base pairs”.

10. (secondary structure)
The DNA double helix
(secondary structure)
DNA is double stranded: each molecule of DNA is composed of two polynucleotide chain that are joined together by formation of hydrogen bonds between the bases.
DNA strands are twisted to form a double helix.
DNA strands are antiparallel (one strand runs in the 5’ to 3’ direction and the other in the 3’ to 5’ direction, analogous to two street lanes carrying traffic in opposite direction).

11. (secondary structure)
The DNA double helix
(secondary structure)
G-C pairs have 3 hydrogen bonds
A-T pairs have 2 hydrogen bonds
One strand is the complement of the other, as they are formed by complementary bases (G is complementary to C, while A is complementary to T).
The concentration of deoxyadenosine (A) nucleotides equals that of thymidine (T) nucleotides (A=T), while the concentration of deoxyguanosine (G) nucleotides equals that of deoxycytidine (C) nucleotides (G=C)

12. Quick Quiz Question
1. Write the complementary strand of the following DNA strand: ATTTTAAGCTAAGGCCCTTT
2. Calculate the number of the hydrogen bonds existing beteen the complementary strands
3. Specify which base is at the 3’end of this strand and which base is at the 3’ end of its complementary strand.

13. (secondary structure)
The DNA double helix
(secondary structure)
The B form of DNA described by Watson and Crick is right handed.
The distance spanned by one complete turn of the B-DNA double helix is 34 Å.
One turn of B-DNA includes 10 base pairs.
Oter forms of DNA include:
- A-DNA which is more compact than B-DNA
- Z-DNA is left handed and its bases are positioned more toward the periphery of the helix.

14. Quick Quiz Question DNA
Is composed of nucleosides joined by phosphodiester bonds
Contains negatively charged phosphate groups
Contains base pairs A/T and G/C
Consists of two strands which run in the same direction.

15. What are the hydrogen bonds inside the DNA double helix?
Hydrogen bonds represent non-covalent (relatively weak) intermolecular bonds which are caused by the polarity of H-O bond.
3 hydrogen bonds between G & C; 2 between A & T

16. “TERTIARY” STRUCTURE OF DNA: the polynucleosome

17. From DNA to Chromosomes
In eukaryotes, the DNA is stored in the nucleus. Since there is not much space and DNA molecules are extremely large (the length of DNA from one singlehuman cell is 2m!!!), the DNA must be highly organised.
There are five levels of DNA compaction (or packing) that result in a –fold decrease in DNA length.

18. Levels of packing of DNA in the nucleus -the first level-
The DNA double helix is wrapped around protein complexes called histones- each unit of DNA wrapped round a histone complex is called a nucleosome.
Histones are small proteins, rich in basic aminoacids (Arg, Lys). r

19. Levels of packing of DNA in the nucleus - the first level-
Nucleosome contains an octameric core formed by two molecules of each histones H2A, H2B, H3, H4, around which 140 base pairs of DNA are wrapped.
The nucleosomes are separated by a small distance (DNA linker formed by 30 base paires). H1 histones interact with DNA linker.
The polynuceosome structure of DNA are similar to the “beads on a string” (=10nm fibrils of chromatin). r

20. Amethyst Beads on a String

21. r
“Beads on a string” appearance of DNA

22. Levels of packing of DNA in the nucleus -the second level-r
The polynucleosome chain is further compacted to form solenoid structures.
Solenoid structure has 6-7 nucleosomes pe turn.
Solenoid structure form the 30 nm fiber of chromatin.

23. Levels of packing of DNA in the nucleus -the third, fourth and fifth levels-
- The chromatin fibres fold together to form large looped domains.
- These looped domains are then supercoiled and organised into distinct structures called chromosomes.
- The human nuclear DNA ( genome) consists of 23 pairs of chromosomes.

24. The difference between diploid and haploid cells
Many eukaryotic cells contain pairs of chromosomes and are hence called diploid.
Other cells contain single chromosomes and are called haploid.

25. The chromosomes of the human genome

26. 1
DNA
The illustration is a ‘model’ of the double helix forming part of a DNA molecule
(Slide 14)

27. DNA stands for deoxyribose nucleic acid2
DNA stands for deoxyribose nucleic acid
This chemical substance is present in the nucleus
of all cells in all living organisms
DNA controls all the chemical changes which
take place in cells
The kind of cell which is formed, (muscle, blood,
nerve etc) is controlled by DNA
The kind of organism which is produced (buttercup,
giraffe, herring, human etc) is controlled by DNA

28. DNA is a very large molecule made up of a long chain of sub-units
DNA molecule 3
DNA is a very large molecule made up of a long
chain of sub-units
The sub-units are called nucleotides
Each nucleotide is made up of
a sugar called deoxyribose
a phosphate group -PO4 and
an organic base

29. Ribose is a sugar, like glucose, but with only five
Ribose & deoxyribose 4
Ribose is a sugar, like glucose, but with only five
carbon atoms in its molecule
Deoxyribose is almost the same but lacks one
oxygen atom
Both molecules may be represented by the symbol

30. The most common organic bases are
The bases 5
The most common organic bases are
Adenine
(A)
Thymine
(T)
Cytosine
(C)
Guanine
(G)

31. Combine to form a nucleotide
Nucleotides 6
The deoxyribose,
the phosphate
and one of the bases
Combine to form a nucleotide
adenine
deoxyribose
PO4
It is the phosphate group which gives DNA its acidic properties

32. Joined nucleotides 7
PO4
sugar-phosphate
backbone
+ bases
A molecule of DNA is formed by millions of nucleotides joined together in a long chain

33. In fact, the DNA usually consists of a double strand of nucleotides8
In fact, the DNA usually consists of a double
strand of nucleotides
The sugar-phosphate chains are on the outside
and the strands are held together by chemical
bonds between the bases

34. 2-stranded DNA 9
PO4
PO4
PO4
PO4
PO4
PO4
PO4
PO4
PO4

35. The bases always pair up in the same way
Bonding 1 10
The bases always pair up in the same way
Adenine forms a bond with Thymine
Adenine
Thymine
and Cytosine bonds with Guanine
Cytosine
Guanine

36. Bonding 2 11
PO4
adenine
cytosine
PO4
thymine
PO4
guanine
PO4
PO4

37. Pairing up 12
PO4
PO4
PO4
PO4
PO4
PO4
PO4
PO4
PO4

38. The paired strands are coiled into a spiral called13
The paired strands are coiled into a spiral called
A DOUBLE HELIX

39. 14
THE DOUBLE HELIX
bases
sugar-phosphate
chain

40. A DIY model of part of a DNA molecule15
A DIY model of part of a DNA molecule
This is a teaching model. The colours of the bases do not conform to the accepted
scheme today

41. During a cell divides, the DNA strands unwind and separate
replication 16
During a cell divides, the DNA strands unwind
and separate
Each strand makes a new partner by adding
the appropriate nucleotides
The result is that there are now two double-stranded DNA molecules in the nucleus
So that when the cell divides, each nucleus
contains identical DNA
This process is called replication

42. 17
The strands separate
PO4
PO4

43. 18
Each strand builds up its partner by adding the appropriate nucleotides
PO4
PO4
PO4
PO4
PO4
PO4
PO4
PO4
PO4
PO4
PO4
PO4
The nucleotides are present in the nucleoplasm. The nuclear equivalent of cytoplasm
PO4
PO4
PO4
PO4
PO4

44. The sequence of bases in DNA forms the
Genetic code 1 19
The sequence of bases in DNA forms the
Genetic Code
A group of three bases (a triplet) controls
the production of a particular amino acid in
the cytoplasm of the cell
The different amino acids and the order in which they are joined up determines the sort of protein being produced

45. This is a small, imaginary protein molecule showing
Genetic code 2 20
This is a small, imaginary protein molecule showing
how a sequence of 5 different amino acids could determine the shape and identity of the molecule
Ser-Cyst-Val-Gly-Ser-Cyst Ala
Val
Val-Cyst-Ser-Ala-Ser-Cyst-Gly
Val- Cyst-Ala-Ala-Ser-Gly
Each amino acid (Serine, Cysteine, Valine, Glycine and
Alanine) is coded for by a particular triplet of bases

46. Valine Alanine For example Codes for Codes for Coding 21 Cytosine
Adenine
Valine
Codes for
Thymine
Cytosine (C)
Alanine
Codes for
Guanine (G)
Adenine (A)

47. This is known as the triplet code22
This is known as the triplet code
Each triplet codes for a specific amino acid
CGA - CAA - CCA - CCA - GCT - GGG - GAG - CCA -
Ala
Val
Gly
Gly
Arg
Pro
Leu
Gly
The amino acids are joined together in the correct
sequence to make part of a protein
Although the DNA in the nucleus specifies the amino acids and their sequence, it is in the cytoplasm that the protein build-up takes place. The DNA of the nucleus makes a single strand of messenger RNA (ribo-nucleic acid) which leaves the nucleus and builds up the protein in the cytoplasm. The RNA code is complementary, but not identical, to the nuclear DNA. Text books usually give the coding for the RNA but in this presentation it is for the DNA itself
Ala
Val
Gly
Gly
Arg
Pro
Leu
Gly

48. The proteins build the cell structures
DNA and enzymes 23
The proteins build the cell structures
They also make enzymes
The DNA controls which enzymes are made and
the enzymes determine what reactions take place
The structures and reactions in the cell determine
what sort of a cell it is and what its function is
So DNA exerts its control through the enzymes

49. A sequence of triplets in the DNA molecule may
Genes 24
A sequence of triplets in the DNA molecule may
code for a complete protein
Such a sequence forms a gene
There may be a thousand or more bases in
one gene

50. Question 1 Which of the following are components of nucleotides?
(a) deoxyribose
(b) amino acids
(c) phosphate
(d) enzymes
(e) organic bases

51. Question 2 Which of the following represent a correct
pairing of bases?
(a) adenine with thymine
(b) adenine with guanine
(c) thymine with adenine
(d) guanine with cytosine
(e) thymine with thymine

52. Question 3 DNA molecules are formed from (a) organic bases
(b) amino acids
(c) deoxyribose
(d) nucleotides

53. Question 4 Which of the following are organic bases? (a) Valine
(b) Guanine
(c) Thymine
(d) Serine

54. Question 5 Replication of DNA occurs (a) During cell division
(b) before cell division
(c) at any time

55. Question 6 A nucleotide triplet codes for (a) a protein
(b) an amino acid
(c) an enzyme
(d) an organic base

56. Answer
CORRECT

57. Answer
INCORRECT

58. Perbedaan
DNA
RNA
Letak
Sebagian besar di nukleus, sedikit di mitochondria dan kloroplast
Dalam sitoplasma, nucleolus dan kromosom
Pyrimidine bases
Cytosine
Thymine
Urasil
Purine bases
Adenine
Guanine
Pentose
deoxyribose
ribose
Hydrolizing enzyme
Deoxyribonuclease (DNase)
Ribonuclease (RNase)
Peranan
Genetic information
Synthesis of proteins