1. THE NUCLEIC ACID Dyah Kinasih Wuragil Veterinary Medicine School
University of Brawijaya

2. Friedrich Miescher in 1869
isolated what he called nuclein from the nuclei of pus cells
Nuclein was shown to have acidic properties, hence it became called nucleic acid

3. Contents Composition of nucleic acids Structure and function of DNA
Structures and functions of RNA
Properties of nucleic acid

4. Section 1 Composition of Nucleic Acid

5. Two types of nucleic acid
Deoxyribonucleic acid (DNA)
Ribonucleic acid (RNA)

6. DNA vs RNA DNA 1- Deoxyribose sugar
2- Bases: Adenine, Thymine, Cytosine, Guanine
3- Double-stranded helix arrangement
RNA
1- Ribose sugar
2- Bases: Adenine, Uracyl, Cytosine, Guanine
4- Single stranded

7. The distribution of nucleic acids in the eukaryotic cell
DNA is found in the nucleus
with small amounts in mitochondria and chloroplasts
RNA is found throughout the cell

8. NUCLEOTIDE STRUCTURE NUCLEOTIDE BASE Nucleic acids are polynucleotides
PHOSPATE
SUGAR
Ribose or Deoxyribose
BASE
PURINES
PYRIMIDINES
Adenine (A)
Guanine(G)
Cytocine (C)
Thymine (T)
Uracil (U)
Nucleic acids are polynucleotides
Their building blocks are nucleotides
NUCLEOTIDE

9. Ribose is a pentose C1 C5 C4 C3 C2 O

10. Spot the difference
RIBOSE
DEOXYRIBOSE
CH2OH H OH C O

11. THE SUGAR-PHOSPHATE BACKBONE
The nucleotides are all orientated in the same direction
The phosphate group joins the 3rd Carbon of one sugar to the 5th Carbon of the next in line.

12. The bases are attached to the 1st CarbonP G C A T
ADDING IN THE BASES
The bases are attached to the 1st Carbon
Their order is important It determines the genetic information of the molecule

13. DNA IS MADE OF TWO STRANDS OF POLYNUCLEOTIDEG T A
Hydrogen bonds
DNA IS MADE OF TWO STRANDS OF POLYNUCLEOTIDE

14. DNA IS MADE OF TWO STRANDS OF POLYNUCLEOTIDE
The sister strands of the DNA molecule run in opposite directions (antiparallel)
They are joined by the bases
Each base is paired with a specific partner:
A is always paired with T
G is always paired with C
Purine with Pyrimidine
This the sister strands are complementary but not identical
The bases are joined by hydrogen bonds, individually weak but collectively strong

15. Erwin Chargaff’s Data (1950-51)

16. Purines & Pyrimidines
Adenine
Thymine
Guanine
Cytosine

17. Watson & Crick Base pairing

18. The Double Helix (1953) Public Domain image
© Dr Kalju Kahn USBC Chemistry and Biochemistry

19. DNA as genetic material: The circumstantial evidence
The amount of DNA in somatic cells (body cells) of any given species is constant (like the number of chromosomes)
The DNA content of gametes (sex cells) is half that of somatic cells. In cases of polyploidy (multiple sets of chromosomes) the DNA content increases by a proportional factor
The mutagenic effect of UV light peaks at 253.7nm. The peak for the absorption of UV light by DNA

20. Some important nucleotides
dATP, dGTP, dCTP, dUTP—raw materials for DNA biosynthesis DNA
ATP, GTP, CTP, GTP
raw materials for RNA biosynthesis RNA
energy donor
Important co-enzymes
Cycling nucleotides—cAMP, cGMP –secondary messengers in hormones action.

21. Section 2 Structure and function of DNA

22. Primary structure The base sequence in polydeoxynucleotide chain.
The smallest DNA in nature is virusDNA. The length of φX174 virus DNA is 5,386 bases (a single chain). The DNA length of human genome is 3,000,000,000 pair bases.

23. DNA double helix structure
2. Secondary structure
DNA double helix structure

24. Francis H.C. Crick
James D. Watson

25. Key points on DNA double helic structure
DNA is composed of two strand wound round each other to form a double helix. The two DNA stands are organized in an antiparallel arrangement: the two strands run in opposite directions, one strand is oriented 5’→3’ and the other is oriented 3’ →5’.
The bases on the inside and the sugar-phosphate backbones in the outside.
The diameter of the double helix is 2 nm, the distance between two base is 0.34 nm, each turn of the helix involves 10 bases pairs, 34 nm.

26. (4) The bases of two strands form hydrogen bonds to each other, A pairs with T, G pairs with C. this is called complementary base pairing
(5) stable configuration can be maintained by hydrogen bond and base stacking force.

27. The antiparallel
nature of the DNA
double helix

29. Conformational variation in double-helical structure
B-DNA
A-DNA
Z-DNA

31. 3. Tertiary structure : Supercoils
Supercoils: double-stranded circular DNA form supercoils if the strands are underwound (negatively supercoiled) or overwound (positively supercoiled).

32. The DNA interwinds and wraps about itsself

33. Supercoils in long, linear DNA arranged into loops whose
ends are restrained-model for chromosomal DNA

34. The DNA in a prokaryotic cell is a supercoil.
The DNA in eukaryotic cell is packaged into chromosomes.

35. Functions of DNA The carrier of genetic information.
The template strand involved in replication and transcription.
Gene: the minimum functional unit in DNA
Genome: the total genes in a living cell or living beings.

38. Section 3 Structures and functions of RNA
Types :
mRNA: messenger RNA, the carrier of genetic information from DNA to translate into protein
tRNA: transfer RNA , to transport amino acid to ribosomes to synthesize protein
rRNA: ribosome RNA, the components of ribosomes
hnRNA: Heterogeneous nuclear RNA
snRNA: small nuclear RNA
Ribozyme

39. RNA structure
RNA molecules are largely single-stranded but there are double-stranded regions.

40. Massager RNA( mRNA)
The carrier of genetic information from DNA for the synthesis of protein. Composition: vary considerably in size ( bases in E. coli)

41. Ribosome RNA (rRNA) A component of ribosomes.
Ribosomes are cytoplasmic structures that synthesize protein, composed of both proteins and rRNA.
The ribosomes of prokaryotes and eukaryotes are similar in shape and function. The difference between them is the size and chemical composition.

42. Transfer RNA (tRNA) Function: Transport amino acids to ribosomes for
assembly into proteins.
Primary Structure :
Average length: 75 bases
Modified bases: pseudouridine
methylguanosine
dihydrouridine
The sequence CCA at the 3’ terminus

43. Section 4 Properties of nucleic acid
General physical and chemical properties:
Amphiphilic molecules; normally acidic because of phosphate.
Solid DNA white fiber; RNA white powder. Insoluble in organic solvents, can be precipitate by ethanol.
Can be hydrolyzed by acid/alkaline/enzymes

44. 2. UV Absorption Specific absorption at 260nm.
This can be used to identify nucleic acid

45. 3. Denaturation Concept:
the course of hydrogen bonds broken, 3-D structure was destroyed, the double helix changed into single strand irregular coid
Results:
the value of 260nm absorption is increased
Viscous is decreased
biological functions are lost

46. Heat denaturation and Tm
When DNA were heated to certain temperature, the absorption value at 260nm would increased sharply，which indicates that the double strand helix DNA was separated into single strand. When the absorption value increases to 40%, the value change would low down, which indicates the double strands had been completely separated.

47. Tm: melting temperature of DNA
The temperature of UV absorption increase to an half of maximum value in DNA denaturation.
Factors affect Tm:
G-C content: there are three hydrogen bonds between G-C pair. The more G-C content, the higher Tm value.
(G+C)% = (Tm-69.3) × 2.44

48. 4. Renaturation of DNA
When slowly cooling down the denatured DNA solution, the single strand DNA can reform a double strands helix to recover its biological functions.

49. 5. Molecule hybridization
During the course of lowing down denaturing temperature, between different resource DNAs or single stand DNA and mRNA with complementary bases will repair into a double strands to form a hybrid DNA or DNA-RNA . This course is called molecule hybridization.

51. Thank you...