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Chemistry 20
Chapter 17
Nucleotides and Nucleic acids
Introduction
– Each cell of our bodies contains thousands of different proteins.
– How do cells know which proteins to synthesize out of the extremely
large number of possible amino acid sequences?
– the transmission of hereditary information took place in the nucleus,
more specifically in structures called chromosomes.
– The hereditary information was thought to reside in genes within the
chromosomes.
– Chemical analysis of nuclei showed chromosomes are made up
largely of proteins called histones and nucleic acids.
Nucleic acids
Backbones of chromosomes
Ribonucleic acids (RNA)
Nucleic acids
Deoxyribonucleic acids (DNA)
RNA and DNA are polymers (monomers: nucleotides).
Nucleotide
A nucleotide is composed of:
• Nitrogen-containing bases (amines)
• Sugars (monosaccharides)
• Phosphate
Phosphate
Bases
N H2
O
4
N
3
2
N
5
6
N
O
1
2
5
N
8
N
3
N9
4
H
Puri ne
N
H
Thymine (T)
(DNA onl y)
N
Uraci l (U)
(in RNA only)
O
N
N
N
O
N H2
N
HN
H
Cytosine (C)
(DNA and
some RNA)
7
6
1
O
H
Pyri mi dine
CH3
HN
N
O
N
H
Adenine (A)
(DNA and RNA)
N
HN
H 2N
N
N
H
Guani ne (G)
(DNA and RNA)
Sugars (monosaccharide)
RNA contains:
• Ribose sugar
DNA contains:
• 2-Deoxy-D-ribose sugar (without O on carbon 2)
Nucleoside
When a primidine or purine forms a glycosidic bond to C1’ of a sugar (ether
ribose or deoxyribose).
Base + Sugar
O
Nucleoside
O
CH3
HN
N
O
H
hymine (T)
NA onl y)
uracil
N
-D -ribos ide
H
5'
Uraci l (U)
(in RNA only)
H
N
3'
H
2'
HO
OH
Urid ine
O
HN
1
O
H
4'
HN
O
HOCH 2
N
O
1'
H
a -N -glycosid ic
bond
bonß-N-glycosidic
d
anomeric
carb on
Nucleotide
A nucleotide forms with the −OH on C5’ of a sugar bonds to
phosphoric acid.
NH2
NH2
Phosphate ester bond
N
N
O
O- P OH
O-
5’
+
O
HO CH2
N
1’
deoxycytidine and phosphate
5’
O
O- P O CH2
O
OH
O
-
N
O
O
OH
deoxycytidine
monophosphate (dCMP)
A nucleotide
Primary structure of DNA and RNA
Carry all information
for protein synthesis.
Sequence of nucleotides.
Each phosphate is linked to C3’ and C5’ of two sugars.
Primary structure of DNA and RNA
A nucleoside = Base + Sugar
A nucleotide = Base + Sugar + Phosphate
A nucleic acid = A chain of nucleotides
Like amino acids
(C-terminal and N-terminal):
Base sequence is read from the C5’ (free phosphate) end to the C3’ (free hydroxyl) end.
-ACGU-
Secondary structure of DNA
5’
3’
• Two strands of polynucleotide form a
double helix structure like a spiral.
3D structure
Sugar phosphate
backbone
• Hydrogen bonds link paired bases:
Adenine-Thymine (A–T)
Guanine-Cytosine (G-C)
• Sugar-Phosphate backbone is
hydrophilic and stays on the outside
(bases are hydrophobic).
3’
5’
Secondary structure of DNA
Complementary base pairs
Higher structure of DNA
• DNA is coiled around proteins called histones.
• Histones are rich in the basic amino acids
• Acidic DNA basic histones attract each other and form units
called nucleosomes.
Core of eight histones
Higher structure of DNA
Chromatin:
Condensed nucleosomes
Higher structure of DNA
Chromatin fibers are organized into loops, and the loops into the bands
that provide the superstructure of chromosomes.
Difference between DNA & RNA
1. DNA has four bases: A, G, C, and T.
RNA has four bases: A, G, C, and U.
2. In DNA: Sugar is 2-deoxy-D-ribose.
In RNA: Sugar is D-ribose.
3. DNA is almost always double-stranded (helical structure).
RNA is single strand.
4. RNA is much smaller than DNA.
RNA molecules
Transmits the genetic information needed to operate the cell.
1. Ribosomal RNA (rRNA)
Most abundant RNA – Contains ribosomes: sites for protein synthesis.
2. Messenger RNA (mRNA)
Carries genetic information from DNA (in nucleus) to ribosomes (in cytoplasm)
for protein synthesis. They are produced in “Transcription”.
3. Transfer RNA (tRNA)
Smallest RNA. Translates the genetic information in mRNA and brings specific
Amino acids to the ribosome for protein synthesis.
Genes
A section of a DNA molecule that contains a specific sequence
of the four bases (A, G, T, and C)
1000 to 2000 nucleotides
Base sequence of the gene carries the information
to produce one protein molecule.
Change of sequence
New protein
Functions of DNA
1. It reproduces itself (Replication)
2. It supplied the information to make up RNA, proteins, and enzymes.
(chapter 18)
Replication
Separation of the two original strands and synthesis
of two new daughter strands using the original strands as templates.
By breaking H-bonds
Replication
Replication is bidirectional: takes place at the same speed in both directions.
Replication is semiconservative: each daughter molecule has one parental strand
and one newly synthesized one.
Origin of replication: specific point of DNA where replication begins.
Replication fork: specific point of DNA where replication is proceeding.
Replication
Leading strand: is synthesized continuously in the 3’  5’ direction
toward the replication fork.
Lagging strand: is synthesized discontinuously in the 5’  3’ direction
away from the replication fork.
Replication
Replisomes: assemblies of “enzyme factories”.
Component
Function
Helicas e
Primas e
Clamp protein
DNA polymerase
Ligase
Unwinds the DNA double helix
Synthesizes primers
Threads leading s trand
Joins as sembled nucleotides
Joins Okazaki fragments in
lagging strand
Helicases
Unwinds the DNA double helix.
•Replication of DNA starts with unwinding of the double helix.
•Unwinding can occur at either end or in the middle.
•Attach themselves to one DNA strand and cause separation of the
double helix.
Primases
Catalyze the synthesis of primers.
Primers: are short nucleotides (4 to 15).
•They are required to start the synthesis of both daughter strands.
•Primases are placed at about every 50 nucleotides in the lagging
strand synthesis.
DNA Polymerase
Catalyze the formation of nucleotides.
Joins the nucleotides to produce a new strands