Transcript Chapter 2. Nucleic Acids

BIOCHEMISTRY
Textbook: “A Text Book of Biochemistry”, by
Zhao Baochang, etc, 2004.
Books for reference:
1. “Biochemistry”, by L. Stryer, 6th edition,
W.H. Freeman and Company, 2006.
2. “Instant Notes in Biochemistry”, by B.D.
Hames & N.M. Hooper, 2nd edition, BIOS
Scientific Publishers Limited, 2000.
Important Concepts
1.
Biochemistry is the study of the molecular
composition of living cells, the chemical reactions
of biological compounds, and the regulation of
these reactions.
2. Major components in body include water (55%),
protein (19%), fat (19%), inorganic matter (7%),
carbohydrate (<1%), and nucleic acid (<1%).
3. Metabolism refers to all the chemical reactions of
a living organism.
Why to study?
1. Biochemistry is one of the basic courses
that can help you to understand the
physiological and pathological processes
in the body at molecular levels, and more
importantly, to use the knowledge to .
2. Biochemistry is also a powerful tool in
life-scientific studies—prepares you to be
a good scientist.
How to study?
1. Classroom study: it is impossible for a lecturer to
give all details of the knowledge in a limited
lecturing-time, but it is important for the students to
catch the main points during the class.
2. Your study should not be limited to classroom and
textbook, but be anyway that helps you understand
well the concepts and the principles of biochemistry,
such as discussions between teacher-students and
among students, lab study, scientific journals...
Chapter 1. Structures and
Functions of Nucleic Acids
Nucleic Acids include deoxyribonucleic acid
(DNA) and ribonucleic acid (RNA). The
genes of all cells and many viruses are
made up of DNA, while RNA serves as the
machinery of protein synthesis.
The flow of genetic information:
DNA
transcription
translation
RNA
Protein
1. Composition of nucleic acids
1) Phosphate
DNA: Adenine(A), Guanine(G),
Thymine(T), Cytosine(C)
2) Bases
RNA: Adenine(A), Guanine(G),
Uracil(U), Cytosine(C)
DNA: deoxyribose
3) Pentoses
RNA: ribose
Structures of bases
Purine
Guanine(G)
Pyrimidine
Cytosine(C) uracil(U)
Adenine(A)
Thymine(T)
Structures of pentoses
Deoxyribose
ribose
2. Nucleosides and nucleotides
1) Nucleoside: base-pentose
Deoxyadenosine
Adenosine
2) Nucleotide: base-pentose-phosphate
O
Deoxyadenosine
monophosphate (dAMP)
Adenosine
monophosphate (AMP)
3) Common nucleotides:
A) Deoxyribonucleotides
dAMP
dADP
dATP
B) Ribonucleotides
HO
AMP
ADP
ATP
Names of nucleoside and nucleotides
Base
In RNA:
adenine
guanine
cytosine
uracil
In DNA:
adenine
guanine
cytosine
thymine
Ribonucleoside
Ribonucleotide
Adenosine
Guanosine
Cytidine
Uridine
Adenosine-5’-monophosphate
Guanosine -5’-monophosphate
Cytidine -5’-monophosphate
Uridine -5’-monophosphate
deoxyadenosine
deoxyguanosine
deoxycytidine
deoxythymidine
deoxyadenosine-5’-monophosphate
deoxyguanosine-5’-monophosphate
deoxycytidine-5’-monophosphate
deoxythymidine-5’-monophosphate
Abbreviated names of nucleoside
mono-, di-, tri- phosphates
Base
NMP
Ribonucleotides:
NDP
NTP
A
G
C
U
ADP
GDP
CDP
UDP
ATP
GTP
CTP
UTP
dADP
dGDP
dCDP
dTDP
dATP
dGTP
dCTP
dTTP
AMP
GMP
CMP
UMP
Deoxyribonucleotides:
A
G
C
T
dAMP
dGMP
dCMP
dTMP
Ultraviolet absorption spectra of
ribonucleotides
Ultraviolet absorption of nucleotides is due to
the optical property of the bases. The
wavelength at 260nm is often used to
quantitatively analyze bases, nucleosides,
nucleotides, or nucleic acids.
3. Primary structure of nucleic acids
1) Nucleotides are linked by 3’,5’phosphodiester bonds to form oligo- or
poly- nucleotides.
RNA: polynucleotide chains
DNA: polydeoxynucleotide chains
3’,5’- phosphodiesters
-
O
5’- end
-
O P O
O
CH2
Base
O
H
H
O
H
H
3’,5’- phosphodiesters
-
O P O
O
CH2
Base
O
H
H
O
H
H
-
O P O
O
CH2
3’- end
H
Base
O
H
H
OH H
Direction: 5’  3’
2) Primary structure of nucleic acids refers to
the nucleotide sequence of the
polynucleotide chain. The primary structure
of a DNA chain may be expressed as:
A
5’ P
C
P
T
P
G
P
C
P
Or:
5’ pApCpTpGpCpT 3’
Or:
5’ ACTGCT 3’
T
P
OH 3’
4. Stereo structures of DNA
1) The secondary structure of DNA
Watson-Crick model: DNA double helix.
•
The two polynucleotide chains are coiled around a
common axis in opposite directions.
•
The bases are on the inside of the helix, forming
hydrogen bonds between the two chains by A-T
and G-C complementary pairing.
The phosphate and deoxyribose are on the
outside as the backbones. The base sequence
carries the genetic information.
•
Minor groove
Major groove
The DNA double helix
Double helical structure of DNA
Minor groove
Major groove
34Å
The DNA base pairs
2) The higher-level structures of DNA
• Prokaryotic DNA: is circular double
stranded and may be further folded
into loops or supercoils with or
without DNA binding proteins.
• Eukaryotic DNA: is complexed with
a histone octamer to form a
nucleosome.
Histones
Five main types of histones: H1, H2a, H2b,
H3 and H4. They are basic DNA-binding
proteins.
The histone octamer consists of 8 histones:
two molecules of each H2a, H2b, H3 and
H4, serving as a core of nucleosome.
Prokaryotic DNA loops
Structure of nucleosome
Formation of chromosome
About DNA
 DNA is of paramount importance for storing,
expressing and transmitting genetic information.
 Growth, reproduction and hereditary
characteristics depend on DNA.
 DNA contains the information that directs the
development of an organism.
 DNA is able to replicate each time a cell divides
and also have the information that is to be
selectively expressed.
5. RNA Structure
• Most RNA molecules are single-stranded
polymer chains consisting of ribonucleotides
linked by 3’5’ phosphodiester bonds.
However, some regions of RNA can form
double-stranded structures by A-U and G-C
base pairing within the single chain itself.
RNA and DNA structures
RNAs in the mammalian cell
RNA
rRNA
mRNA
tRNA
HnRNA
Function
component of ribosome
template for Pr. Synthesis
transporter of amino acids
precursor of mRNA
ribosomal RNA
messenger RNA
transfer RNA
heterogeneous
nuclear RNA
SnRNA small nuclear RNA
splicing of HnRNA
SnoRNA small nucleolar RNA processing of rRNA
ScRNA small cytoplasmic RNA signal-peptide recognition
1) Structure of mRNA
The structural characteristics of mRNA:
a) A cap structure at the 5’ end: protects the 5’
end from degradation by nuclease and
helps in the initiation of protein synthesis.
b) A polyA tail at the 3’ end: is not encoded
by DNA but added after transcription. The
polyA tail protects the 3’end from nuclease
digestion and stabilizes the mRNA.
c) A coding sequence at the center: encodes
the amino acid sequence of a polypeptide.
One mRNA only encodes one polypeptide
chain in mammalian cell, but may encode
several polypeptides in bacteria.
Cap Non-coding Coding sequence Non-coding polyA tail
5’
3’
The cap structure of mRNA
2) Structure of tRNA
a) Secondary structure of tRNA: a cloverleaf
structure containing an anticodon arm, a
DHU arm, a TC arm, and an amino acid
acceptor stem.
b) Tertiary structure of tRNA: at the level of
secondary structure the molecule further
folds to form a “L” shape 3-d structure.
Secondary structure of tRNA
Tertiary structure of tRNA
3) Structure of rRNA
A ribosome consists of a small and a large subunit,
each of which contains proteins and rRNAs
forming a site for protein synthesis.
• Types of rRNA:
prokaryotes
eukaryotes
Small subunit
30S
40S
rRNA
16S
18S
Large subunit
50S
60S
rRNA
23S, 5S
28S, 5.8S, 5S
Types of rRNA
b) Secondary structure of rRNA: complex,
different in size, composition, and 3-d
structure.
About RNA
• mRNA participates in the process of
selective expression of genetic information
stored in DNA.
• tRNA serves as carrier of genetic
information to the site of protein synthesis.
• rRNA is an essential component of
ribosomes.
6. Properties of nucleic acids
1) Denaturation and renaturation
 Denaturation: due to the action of some physical
(heat etc.) or chemical (organic solvents etc.)
factors the native structure of a nucleic acid
molecule can be changed, resulting in loss of its
biological functions and showing several
physical changes (increase in viscosity and in
absorbance of UV light).
Renaturation: when the denaturing factors
are removed, the denatured nucleic acid
molecules may restore their native
structures with recovery of their biological
functions and physical properties.
Melting temperature (Tm) of DNA: the
temperature at which 50% of the maximum
optical density is reached.
Relative optical density (260nm)
Melting curve
1.4
1.3
1.2
1.1
Tm
1.0
30
50
70
Temperature (oC)
90
2) Hybridization: a process of association
through base-pairing between two
polynucleotide chains that are
complementary in base sequence to each
other.
Hybridization can occur between DNADNA, RNA-RNA, or DNA-RNA
polynucleotide chains of different origins.
 Hybridization is a powerful technique that
can be used for probing specific genes.
Principles of nucleic acid hybridization