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2. Brief history
 1869: isolated DNA from salmon sperm (Friedrich
Miescher)
 1944: proved DNA is genetic materials (Avery et al.)
 1953: discovered DNA double helix (Watson and Crick)
 1968: decoded the genetic codes (Nirenberg)
 1981: invented DNA sequencing method (Gilbert and
Sanger)
 1987: launched the human genome project
 2001: accomplished the draft map of human genome

3. Nucleic acid
Deoxyribonucleic acid, DNA
Ribonucleic acid, RNA

4. •DNA and RNA are polymers of nucleotide
units.
• DNA (RNA) consists of 4 kinds of
ribonucleotide units linked together through
covalent bonds.
• Each nucleotide unit is composed of
a nitrogenous base
a pentose sugar
a phosphate group
The components of DNA and RNA

5. Bases
• Purines :
– Adenine (A)
– Guanine (G)
• Pyrimidines :
– Cytosine (C)
– Uracil (U)
– Thymine (T)
Thymine (T) is a 5-methyluracil (U)
DNA: A,G,C,T
RNA: A,G,C,U

6. Ribose (in RNA) and deoxyribose (in DNA)
•
• Ribose and deoxyribose predominantly
exist in the cyclic form.

7. •The bases are covalently attached to the 1’ position
of a pentose sugar ring, to form a nucleoside
Glycosidic bond
R Ribose or2’-deoxyribose
Nucleosides =ribose/deoxyribose + bases
1

8. Adenosine, guanosine, cytidine, thymidine, uridine

9. •A nucleotide is a nucleoside with one or more phosphate
groups bound covalently to the 3’-, 5’, or ( in
ribonucleotides only) the 2’-position. In the case of 5’-
position, up to three phosphates may be attached.
Deoxynucleotides
(containing deoxyribose)
Ribonucleotides
(containing ribose)
Phosphate ester bonds
Nucleotides = nucleoside + phosphate

11. BASES NUCLEOSIDES NUCLEOTIDES
Adenine (A) Adenosine Adenosine 5’-triphosphate (ATP)
Deoxyadenosine Deoxyadenosine 5’-triphosphate
(dATP)
Guanine (G) Guanosine Guanosine 5’-triphosphate (GTP)
Deoxyguanosine Deoxy-guanosine 5’-triphosphate
(dGTP)
Cytosine
(C)
Cytidine Cytidine 5’-triphosphate (CTP)
Deoxycytidine Deoxy-cytidine 5’-triphosphate
(dCTP)
Uracil (U) Uridine Uridine 5’-triphosphate (UTP)
Thymine
(T)
Thymidine/
Deoxythymidie
Thymidine/deoxythymidie
5’-triphosphate (dTTP)

12. P
O
O
OH
OH
O
CH2
OHOH
N
N
NH2
O
nucleic acid nucleotides
phosphate
nucleosides
pentose
bases

13. Nucleic
acid
base ribose
DNA A 、 G 、 C 、 T deoxyribose
RNA A 、 G 、 C 、 U ribose
Composition of DNA and RNA

14. Some important nucleotides
• dATP, dGTP, dCTP, dUTP
– Raw materials for DNA biosynthesis.
• ATP, GTP, CTP, UTP
– Raw materials for RNA biosynthesis
– Energy donor
– Important co-enzymes
• Cycling nucleotides—cAMP, cGMP
– Secondary messengers in hormones action.

15. Nucleic acid derivatives
Multiple phosphate nucleotides
adenosine monophosphate (AMP)
adenosine diphosphate (ADP)
adenosine triphosphate (ATP)
N
O
CH2O
OHOH
N
N
N
NH2
P
O
OH
OH
AMPAMP
N
O
CH2O
OHOH
N
N
N
NH2
P
O
OH
OP
O
OH
OH
ADPADP
N
O
CH2O
OHOH
N
N
N
NH2
P
O
OH
OP
O
OH
OP
O
OH
OH
ATPATP

16. Primary structure
 Definition: the base sequence (or the
nucleotide sequence) in
polydeoxynucleotide chain.
 The smallest DNA in nature is virus DNA.
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.
Structure and function of DNA

17. • 3’,5’ phosphodiester bond link nucleotides
together to form polynucleotide chains
5’end
3’ end: free hydroxyl
(-OH) group
Phosphodiester
bond

18. The structure of a DNA chain can be
concisely represented
• An even more abbreviated notation for
this chain is
– pApCpGpTpA
– pACGTA
• The base chain is written in the 5’ 3’→
direction

19. Secondary structure
The secondary structure is defined as the
relative spatial position of all the atoms of
nucleotide residues.

20. •Watson and Crick , 1953
•The genetic material of
all organisms except for
some viruses.
•The foundation of the
molecular biology.
James D. Watson
Francis H.C. Crick
Secondary structure
— DNA double helix structure

21. The discovery of DNA double helix
 Chargaff's Rule
(A=T, G=C in DNA)
 Franklin, Wilkins:
X-ray Diffraction
Refined Structure

22. •Two separate strands
•Antiparellel (5’→3’
direction)
•Base pairing:
hydrogen bonding
that holds two
strands together
•Complementary
(sequence)
Essential for replicating DNA
and transcribing RNA
5’
3’
3’
5’
• Sugar-phosphate
backbones (negatively
charged): outside
• Base pairs (stack one
above the other): inside
DNA double helix

23. Base pairing
A:T G:C
1
23
4
8
9
7 65
43 2
1

24. B form of DNA double
helix
• Right-handed helix;
•The diameter of the
double helix ： 2 nm
• The distance
between two base
pairs: 0.34 nm;
• Each turn of the
helix involves 10 bases
pairs, 3.4 nm.
 Stable configuration
can be maintained by
hydrogen bond and base
stacking force
(hydrophobic

25. Groove binding
• Small molecules like drugs bind in the minor
groove, whereas particular protein motifs can
interact with the major grooves.

26. • Watson, Crick, and Wilkins
shared the Nobel Prize in
medicine or physiology in 1962
for this brilliant
accomplishment.
• The discovery of the DNA
double helix revolutionized
biology: it led the way to an
understanding of gene function
in molecular terms (their work is
recognized to mark the
beginning of molecular biology).

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

28. • B-form: the duplex structure proposed by Watson and Crick is
referred as the B-form DNA.
•It is the standard structure for DNA molecules.
•A-form: at low humidity the DNA molecule will take the A-
form:
•The A-form helix is wider and shorter, with a shorter more compact
helical structure, than the B-form helix.
• Z-form: the Z-form DNA is adopted by short oligonucleotides.
•It is a left-handed double helix in which backbone phosphates zigzag.

29. 2.3 Tertiary structure :
• Supercoils: double-stranded circular DNA
form supercoils if the strands are
underwound (negatively supercoiled) or
overwound (positively supercoiled).
Relaxed supercoiled
Increasing degree of supercoiling

30. • If the strands
are overwound,
form positively
supercoiled;
• If the strands
are underwound,
form negatively
supercoiled.

31.  The DNA in a prokaryotic cell is a
supercoil.
• Supercoiling makes the DNA molecule more
compact thus important for its packaging
in cells.

32. Eukaryotic DNA
• DNA in eukaryotic cells is highly
packed.
• DNA appears in a highly ordered form
called chromosomes during metaphase,
whereas shows a relatively loose form
of chromatin in other phases.
• The basic unit of chromatin is
nucleosome.
• Nucleosomes are composed of DNA
and histone proteins.

33. Nucleosome
• The chromosomal DNA
is complexed with five
types of histone.
•H1, H2A, H2B, H3 and
H4.
•Histons are very basic
proteins, rich in Arginine
and Lysine.
•Nucleosomes: regular association of DNA with
histones to form a structure effectively compacting
DNA. ”beads”

34. Beads on a string
• 146 bp of
negatively
supercoiled DNA
winds 1 ¾ turns
around a histone
octomer.
• H1 histone binds
to the DNA
spacer.

36. The importance of packing of DNA
into chromosomes
 Chromosome is a compact form of the DNA
that readily fits inside the cell
 To protect DNA from damage
 DNA in a chromosome can be transmitted
efficiently to both daughter cells during
cell division
 Chromosome confers an overall organization
to each molecule of DNA, which facilitates
gene expression as well as recombination.

37. 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.

39. Structures and functions of RNA
Conformational variability of RNA is important
for the much more diverse roles of RNA in
the cell, when compared to DNA.
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: ribosomal RNA, the components of
ribosomes
• hnRNA: Heterogeneous nuclear RNA
• snRNA: small nuclear RNA

40. Classes of eukaryotic RNAs

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

42. Messenger RNA( mRNA)
• Function: the carrier of genetic
information from DNA for the
synthesis of protein.
• Comprises only about 5% of the
RNA in the cell.
• Composition: vary considerably in
size (500-6000 bases in E. coli)

43. Eukaryotic mRNA Structure
(1) Capping: linkage of 7-
methylguanosine to the 5’ terminal
residue.
(2) Tailing: attachment of an
adennylate polymer (poly A, 20~250
nucleotides) at the 3’ terminal.

44. 3.2 Transfer RNA (tRNA)
• Primary Structure :
– 74~95 bases, the smallest of the three major
RNA.
– Modified bases: pseudouridine (ψ)
methylguanosine
dihydrouridine (D)
– The sequence CCA at the 3’ terminus
• They make up 15% of the RNA in the cell.
• Function: Transport amino acids to ribosomes for
assembly into proteins.
• There are at least 20 types of tRNA in one cell.

45. Secondary structure: cloverleaf
• Four loops and
four arms
– Amino acid arm
(7bp): to bide
amino acid
– D loop(8-14bp) and
D arm(3-4bp):
– Anticoden loop(5bp)
and arm(7bp): to
recognize amino
acid coden on the
mRNA.
– TψC loop （ 7bp ）
and arm(5bp)
– Variable loop(4-5bp

46. •Tertiary structure of tRNA

47. * The species of rRNA
•Eukaryotes
•5S rRNA
•28S rRNA
•18S rRNA
•5.8S rRNA
•Prokaryotes
•5S rRNA
•23S rRNA
•16S rRNA
• S represents Svedberg units, they represent
measures of sedimentation rate.
Ribosomal RNA (rRNA)
• Components of ribosomes.
• They make up 80% of the RNA in the cell.

48. The proposed
secondary structure
for E.coli 16S rRNA

49. Ribosomes
• Ribosomes are cytoplasmic structures that
synthesize protein, composed of RNA (2/3)
and protein (1/3).
• The ribosomes of prokaryotes and
eukaryotes are similar in shape and
function. The difference between them is
the size and chemical composition.

50. ThreeThree rRNA
5252 proteins
FourFour rRNA
8383 proteins
• Ribosomes are ribonucleoprotein particles for
synthesizing proteins.

51. Other RNAs
 Small nuclear RNA (snRNA)
Involved in mRNA processing
 Small nucleolar RNA (snoRNA)
Play a key role in the processing of rRNA molecules
 Small cytoplasmic RNA (scRNA)
Involved in the selection of proteins for export
 Catalytic RNA or Ribozyme
 Small interfering RNA (siRNA)
Interfere with the expression of a specific gene
 RNomics

53. General properties
 Acidity
Amphiphilic molecules; normally acidic because of
phosphate.
 Viscosity
Solid DNA: white fiber; RNA: white powder.
Insoluble in organic solvents, can be precipitate by
ethanol.
 Optical absorption
UV absorption due to aromatic groups.
 Thermal stability
Disassociation of dsDNA (double-stranded DNA)
into two ssDNAs (single-stranded DNA).

54. UV Absorption
• Specific absorption at 260nm.
• This can be used to identify nucleic
acid.
The UV absorption spectra of the common ribonucleotides

55. Denaturation
• Concept:
• The course of hydrogen bonds
broken, 3-D structure was destroyed, the
double helix changed into single strand
irregular coil.
• Results:
(1) the value of 260nm absorption is
increased;
(2) biological functions are lost.

56. • 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.
•Tm (melting temperature of DNA):
• The temperature of UV absorption increase to an
half of maximum value in DNA denaturation.

57. • Factors affect Tm:
G-C content:
Higher G+C
Less G+C
Temperature
Tm of
two DNA
molecules with
different G+C
content
•There are three hydrogen bonds between G-C
pair. The more G-C content, the higher Tm
value.

58. Renaturation of DNA
• When slowly cooling down (Annealing)
the denatured DNA solution, the single
strand DNA can reform a double strands
helix to recover its biological functions.

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

60. Points
 The components of DNA and RNA
Nucleotide: base (A,G,C,T,U), pentose sugar (Ribose
and deoxyribose), phosphate group
 Structure and function of DNA
Primary structure: 3’,5’ phosphodiester bond
Secondary structure: DNA double helix
Tertiary structure: supercoil
Eukaryotic chromosomes: nucleosome
 Structures and functions of RNA
mRNA, tRNA, rRNA
 Properties of nucleic acid
UV absorption, denaturation and renaturation, molecule
hybridization