Download nucleic acid

THE
NUCLEIC
ACID
Dyah Ayu Oktavianie
Veterinary Medicine School
University of Brawijaya
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
Contents
1.
2.
3.
4.
Composition of nucleic acids
Structure and function of DNA
Structures and functions of RNA
Properties of nucleic acid
• Section 1 Composition of Nucleic
Acid
Two types of nucleic acid
• Deoxyribonucleic acid (DNA)
• Ribonucleic acid (RNA)
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
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
NUCLEOTIDE STRUCTURE
PHOSPATE
SUGAR
BASE
Ribose or
Deoxyribose
PURINES PYRIMIDINES
Adenine
(A)
Guanine(
G)
NUCLEOTIDE
Cytocine (C)
Thymine (T)
Uracil (U)
Nucleic acids are
polynucleotides
Their building blocks
are nucleotides
Ribose is a pentose
C5
O
C1
C4
C3
C2
Spot the difference
DEOXYRIBOSE
RIBOSE
CH2OH
O
C
H
H
H
C
OH
OH
CH2OH
C
C
H
H
OH
O
C
H
H
C
C
C
OH
OH
H
H
THE SUGAR-PHOSPHATE
BACKBONE
P
P
• 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.
P
P
P
P
P
G
ADDING IN THE BASES
P
C
• The bases are
attached to the 1st
Carbon
• Their order is
important
It determines the
genetic information
of the molecule
P
C
P
A
P
T
P
T
Hydrogen bonds
P
G
C
P
DNA IS MADE OF
TWO STRANDS OF
POLYNUCLEOTIDE
P
C
G
P
P
C
G
P
P
A
T
P
P
T
A
P
P
T
A
P
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
Erwin Chargaff’s Data (1950-51)
Purines & Pyrimidines
Adenine
Guanine
Thymine
Cytosine
Watson & Crick Base pairing
The Double Helix (1953)
© Dr Kalju Kahn USBC Chemistry and Biochemistry
Public Domain image
DNA as genetic material: The
circumstantial evidence
1.
2.
3.
4.
Present in all cells and virtually restricted to the
nucleus
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
Some important nucleotides
•
dATP, dGTP, dCTP, dUTP—raw materials for
DNA biosynthesis DNA
• ATP, GTP, CTP, GTP
(1) raw materials for RNA biosynthesis RNA
(2) energy donor
(3) Important co-enzymes
• Cycling nucleotides—cAMP, cGMP –secondary
messengers in hormones action.
• Section 2 Structure and function of
DNA
1. 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.
• 2. Secondary structure
DNA double helix structure
Francis H.C. Crick
James D. Watson
•
Key points on DNA double helic structure
(1) 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’.
(2) The bases on the inside and the sugar-phosphate
backbones in the outside.
(3) 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, 3,4 nm.
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
•
(4)
•
(5) stable configuration can be maintained by
hydrogen bond and base stacking force.
The antiparallel
nature of the DNA
double helix
• Conformational variation in
double-helical structure
• B-DNA
• A-DNA
• Z-DNA
•
3. Tertiary structure : Supercoils
Supercoils: double-stranded circular DNA
form supercoils if the strands are
underwound (negatively supercoiled) or
overwound (positively supercoiled).
The DNA interwinds and wraps about itsself
Supercoils in long, linear DNA arranged into loops whose
ends are restrained-model for chromosomal DNA
• The DNA in a prokaryotic cell is a supercoil.
• The DNA in eukaryotic cell is packaged into
chromosomes.
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.
Section 3 Structures and functions of RNA
1. 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
RNA structure
• RNA molecules are largely single-stranded
but there are double-stranded regions.
Massager RNA( mRNA)
• The carrier of genetic information from
DNA for the synthesis of protein.
Composition: vary considerably in size
(500-6000bases in E. coli)
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.
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
Section 4 Properties of nucleic acid
1. General physical and chemical properties:
(1) Amphiphilic molecules; normally acidic
because of phosphate.
(2) Solid DNA white fiber; RNA white powder.
Insoluble in organic solvents, can be
precipitate by ethanol.
(3) Can be hydrolyzed by
acid/alkaline/enzymes
2. UV Absorption
• Specific absorption at 260nm.
• This can be used to identify nucleic acid
3. Denaturation
•
•
Concept:
the course of hydrogen bonds broken, 3-D
structure was destroyed, the double helix
changed into single strand irregular coid
• Results:
(1) the value of 260nm absorption is increased
(2) Viscous is decreased
(3) biological functions are lost
• 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.
•
•
•
•
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
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.
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.