Biochemistry of Medicinals I DNA structrure
Transcription Translation
Part 2 – Nucleic Acids
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Transcription Translation
Tentative Lecture schedule
Biochemistry of Medicinals I
Phar 6151
Part 2 – Nucleic Acids
Instructor: Dr. Natalia Tretyakova, Ph.D. «hyperlink "mailto:Trety001@umn.edu"» - 6-3432
PDB reference correction and design Dr.chem., Ph.D. Aris Kaksis, Associate Prof. e-mail: ariska@latnet.lv
11-05 Introduction. DNA structure. Double helix, A, B, Z – form of DNA. Biophysical properties of DNA.
11-07 DNA topology. Supercoiling. Enzymes that change DNA: endonucleases, exonucleases
11-09 DNA replication. Polymerization reaction. E. Coli Pol I
11-12 DNA replication (continued). Initiation, elongation, and termination.
11-14 DNA repair. Mutations and cancer.
11-16 Transcription.
11-19 RNA structure. RNA synthesis in prokaryotes. RNA Pol. I.
11-21 RNA synthesis in eukaryotes. Transcription factors.
11-23 No class
11-26 Post-transcriptional modifications in eukaryotes. Review of DNA
11-28 Exam I. Nucleic acids. DNA structure and synthesis. Transcription. mRNA .
11-30 RNA splicing.
12-03 Translation. Genetic code. tRNA.
12-05 tRNA activation
12-07 Codon-anticodon interactions
12-10 Protein synthesis – translation
12-12 Protein synthesis – translocation. Drugs inhibiting protein synthesis
12-14 Review of tRNA, Protein synthesis. Course evaluation
12-17 Exam II. tRNA . Protein synthesis.
Course files: «hyperlink "http://www.pharmacy.umn.edu/resgrad/medchem/index.htm"»
Required reading: Stryer 4th ed Chapters 4 and 31
DNA Structure: Take Home Message
• DNA is a double stranded biopolymer containing repeating units of nitrogen base, deoxyribose sugar, and
phosphate.
• DNA can be arranged in 3 types of anti-parallel complementary strands which contain major and
minor grooves.
• DNA can adopt several topological forms.
There are enzymes that will cut DNA, ligate DNA and change the topology of DNA.
Biochemistry of Medicinals I DNA structrure
Part 2 – Nucleic Acids
Transcription Translation
Page 2
The Basics
Nucleic Acids
DNA
RNA
Central Dogma of Biology

DNA  RNA  Proteins  Cellular Action
Replication
transcription

translation
Signal transduction
Why ?
Questions?
•
•
•
•
How is DNA replicated?
How is DNA synthesis initiated
How is DNA fidelity maintained
What kinds of DNA defects can occur?
Relevance:
• Cancer: ex., Xeroderma pigmentosum
• Genetic diseases: ex., cystic fibrosis
• Genetic typing: ex., drug metabolism
• Rational drug design: ex., antitumor drugs, pharmacogenetics
• Biotechnology: ex., growth hormones
DNA nucleobases
H
7
The Building Blocks
H
H
O
H H
O P O 5'
O
O
3'
N 4 N
Purine or
Pyrimidine
Base
H
Purine
2'
5
9
3
4
H or O H
6
Phosphate Pentose sugar
D-ribose or
D-2-de-oxy-ribose
1
N
8
Nucleotide
O
6
N 5
3
N
2
N1
H
Pyrimidine
2
N
O
H
N
N
N
H
N
N
N
N
N
N
H
H
H
H
Adenine (A)
Guanine (G)
H H
O
O
N
H H
H
H
H
N
N
N
O
N
H
Cytosine (C)
O
N
H
Thymine (T)
O
N
H
Uracyl (U)
Biochemistry of Medicinals I DNA structrure
Transcription Translation
Part 2 – Nucleic Acids
DNA is Composed of Purine Nucleotides
Purine Nucleotides
Phosphate
Nitrogen base (adenine, A)
H
N 5
O PO
O
5'
4'
H O
O
H
1
6 N
7
4
2
8N
N 3 Composed
9
H
O
N
Guanine (G)
H
O
H H
H
O
1'
O
Deo xy ribos e
Sugar
H
O
4' H H
9
N
3
N
H
1'
2'
H O 3'
H
Deoxyadenosine 5’-phosphate (dAMP)
N
5'
O PO
2'
3'
8
H
N 5
6 N 1
7
4 2
H
H
Deoxyguanosine 5’-phosphate (dGMP)
DNA is Composed of Pyrimidine Nucleotides
Phosphate
Pyrimidine Nucleotides
Thymine ( T )
Nitrogen base (cytosine, C)
O
HH
3 H
4 N
H
H H
N
3
5 4 N
2
O
O PO
O
6
H
5'
4'
N O Composed
1
H
O
H H
H O 3'
O PO
1'
2'
H
O
O
Deoxyribos e
Su gar
Deoxycytidine 5’-phosphate (dCMP)
H
5
6
2
N
O
1
5'
H
O
4' H H
H O 3'
1'
2'
H
Deoxy thymidine 5’-phosphate (d T MP)
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Biochemistry of Medicinals I DNA structrure
Transcription Translation
Part 2 – Nucleic Acids
Preferred conformations of nucleobases and sugars in DNA
H
N
H
H
H
O 5' H
N
O
H H
H O
3'
4'
O
H H H
O 5'
2'
O
N
O
H
2'
H
Anti conformation
H
5' O 3'
O
H
O
H
N
N
H
N
H
2'
3'
H O
H
Syn conformation
2'
5'
Base
O
4'
1'
H O H
3’ endo RNA
O
H
Base
1'
3'
H
O H
O
H
2’ endo (3’ exo) B-DNA
Nomenclature of nucleobases, nucleosides, and mononucleotides
Nucleobase
(Deoxy) nucleoside
Mononucleotide
Adenine (A)
Deoxyadenosine (dA)
Guanine (G)
Deoxyguanosine (dG)
Thymine ( T )
Deoxy thymidine (d T )
Cytosine (C)
Deoxycytidine (dC)
Deoxyadenosine 5’-monophosphate
(5’-AMP)
Deoxyguanosine 5’-monophosphate
(5’-GMP)
Deoxy thymidine 5’-monophosphate
(5’- T MP)
Deoxycytidine 5’-monophosphate
(5’-CMP)
Uracil ( U )
Uridine
Uridine
5’-monophosphate (5’- U MP)
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Biochemistry of Medicinals I DNA structrure
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Part 2 – Nucleic Acids
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Structural differences between DNA and RNA
H H
H
DNA
O
H
N
O
N
H
Thymine T
H
Base
H O 5' H
O
H H
H O 3'
2'
H
2'-de-oxy-ribose
RNA
O
H
N
O
N
H
Uracil U
H
Base
H O 5' H
O
H H
H O 3'
2'
O H
D-ribose
Nucleosides Must Be Converted to Triphosphates to be Part of DNA and RNA
Nucleosides are converted intracellularly to mono-, di- and tri-phosphates by nucleoside kinases:
H
O
O
H
O
H
H
Base
O P O P O 5' H
H O 5' H
O P O 5' H
Base
Base
ADP3ADP3O
O
O
O
O


O
H H
H H
H H
Kinase 
Kinase 
2'
2'
2'


H O 3' H
H O 3' H
H O 3' H
ATP4-
ATP4-
Nucleoside
Mono phosphate
Di-phosphate ATP 4
Kinase 
O
O
O
H

H
O PO PO PO

Base
5'
O

O
O
O

H
H

2'

H O 3' H
Tri-phosphate NTP 43
ADP 
Biochemistry of Medicinals I DNA structrure
Transcription Translation
Part 2 – Nucleic Acids
Page 6
DNA is Arranged 5’ to 3’ Connected by a Phosphate
H
N H
CN
H
O H
H
O
O N
5' P O 5'
H
H
O
O 3'
O
H
O
N
H
O
N
A
H
O P O 5'
O
H
N
2' H
H
N
N
O
H
3'
2'
H
N
H
G
H
O P O 5'
O
N
O
H
O 3'
2' H H
H
H
O P O 5' H
O
O
H
H
O 3'
3'
H
N
H
O H
O N
5'
H
H
H
O3' 2' 5'
H
O PO H
N
H
2'
H
H
T
N
N
H
O
P
C A G T
5'
C-A-G- T
H
AN
H
5'
N
H
N H
O
H
H
N
N
H
N H
C
N
The 3' hydroxyl of the sugar of one
de-oxy-ribo-nucleotide is joined to the
O
H
H
5' hydroxyl of the other.
DNA / RNA chains have polarity:
H H H
H
2'
N
one end has 5' hydroxyl group
O 3'
H
H 5'
not connected to any base (5' end), and
O PO H
O
O
N
the other end has free or
O
O
H
H
phosphorylated 3'-OH group.
H
N
By convention, DNA sequence is
2'
N
O 3' H
written in 5'  3' direction.
H
H
H
N In DNA, nucleo-base carry
O P O 5'
N H
O N
genetic information, whereas
O
H
H
phosphates and de-oxy-ribose
units play structural role.
2'
O 3' H
DNA chains can be very long (1 cm),
containing ten millions 23 529 410
O PO H
3'
base pairs of nucleotide units
O
O
N
O
O
T
G
3'
Biochemistry of Medicinals I DNA structrure
Part 2 – Nucleic Acids
Transcription Translation
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DNA secondary structure – double helix
J.Watson and F.Crick, 1950s- proposed DNA structure based on the following:
"
"
"
DNA is the molecule of heredity (O.Avery, 1944)
X-ray diffraction (R.Franklin and M. Wilkins)
E. Chargaff (1940s) G  C and A =
T
in DNA
DNA Composed of Complementary Strands
DNA
N
O
H N H
NH
N
N
N
¥
N H O
N
H
G C
H
H
NH O
O
A= T
N
N
¥
5
N
'
3
'
¥
N H O
A
T
G
C
T
A
G C
H
H
N
N
¥
N
N
H N H
O
H
N HN
N
Anti-parallel Strands of DNA
NH
N
N
N
¥
¥
RNA
¥
H
NH O
N HN
N
N
O
¥
3
A= U
'
Base Pairing is Determined by Hydrogen Bonding
A=
T
GC
5
'
Biochemistry of Medicinals I DNA structrure
Transcription Translation
Double Helical DNA has Two Types of Grooves
Major groove
Minor groove
/
\
Part 2 – Nucleic Acids
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Biochemistry of Medicinals I DNA structrure
Transcription Translation
Part 2 – Nucleic Acids
B-DNA 17 bp CPK colors 1D66.PDB
CG; GC; GC; A= T ;GC;CG; T =A;GC; T =A… 17 base pairs 1D66.PDB
B-DNA
B-DNA = prevalent form in chromosomes
•
•
•
•
•
•
right handed helix
planes of bases are perpendicular | to the helix axis. 3.4 Å rise  between base pairs
Sugars are in 2' endo conformation. Bases are anti conformation.
Bases have a helical twist of 36° 10.4 bases per helix turn (360º)
Wide and deep major groove
Narrow and deep minor groove
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Biochemistry of Medicinals I DNA structrure
Transcription Translation
Part 2 – Nucleic Acids
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A-DNA 11 bp 2D47.PDB
A-DNA 11 bp complete turn
A-DNA = prevalent form for dehydrated DNA; RNA-DNA hybrids - Right handed helix.
Glycosidic bonds 3' are anti Bases are tilted 23º with respect to helical axis.
2.56 Å helix rise  between adjacent base pairs.
Differs from B-DNA due to changes in ribose puckering (3'-endo favored over 2’-endo)
11 bases per helix turn

Narrow and deep major groove
Very broad and shallow minor groove
Biochemistry of Medicinals I DNA structrure
Transcription Translation
Part 2 – Nucleic Acids
Page 11
Sugar puckering in different forms of double helix
2'
5'
O
Base
5' O
O
H
4'
H
3'
H
1'
3'
Base
O
H
O
O H
H
2’ endo (3’ exo) B-DNA
4'
1'
O
2'
H O H
3’ endo A-DNA
The size of major and minor groove is associated with the positions of
the bases relative to the helical axis
Major groove
N
ribos e N
oxydeTo
¥
O
H N H
NH
¥
N
N
To
N H O
deH
oxyMinor groove
ribos e ¥
N
B-DNA
Major groove
Helix
N
Axis
ribos e N
oxydeTo
¥
¥
O
H N H
NH
N
N
To
N H O
H
deoxyMinor groove
ribos e ¥
A-DNA
N
Biochemistry of Medicinals I DNA structrure
Transcription Translation
Part 2 – Nucleic Acids
Z-DNA 180D.PDB 6 baise pairs
Z-DNA
Z-DNADNA = prevalent form for short oligonucleotides for sequences of alternating
pyrimidine ( T , C) and purines (G, A)
Left-handed helix
Glycosidic bond alternates between syn (purines) and anti (pyrimidines)
Backbone zig-zags, sugar pucker alternates between
2’ endo and 3’ endo
12 bases per helix turn
Left handed
Flat major groove
Narrow and deep minor groove
Possible conformations of DNA bases in NA
H
N
H
H
H
O 5' H
N
O
H H
H O
3'
2'
H
Anti conformation
H
N
N
H
N
O
H H H
O 5'
O N
O
H H
3'
2'
H O
H
Syn conformation
DNA properties facilitate its recognition by proteins
The edges of base pairs displayed :
to DNA major and minor groove contain potential
-bond donors and acceptors:
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Biochemistry of Medicinals I DNA structrure
Transcription Translation Part 2 – Nucleic Acids
Major groove
N
H
O
N
H N
HN
N
ribose N
oxydeTo
¥
O
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H N H
NH
¥
N
N
To
N H O
deH
oxyMinor groove
ribose ¥
N
N
O
N = Nitrogen hydrogen bond acceptor
O = Oxygen hydrogen bond acceptor
= Amino hydrogen bond donor
Hydrogen Bond donors and acceptors on Each Edge of a Base Pair
A= T
Major groove
N
H
O
GC
Major groove
O
H
N
N
ribose N
oxydeTo
¥
O
NH
¥
N
N
N H O To
deH
oxyMinor groove
ribose ¥
N
N
H N H
ribose N
oxydeTo
¥
H
H
NH O H
H
N HN
N
Minor groove
N
O To
deoxyribose ¥
DNA Characteristics
1. Major Groove : ¥ 12  wide, 8.5  deep (B-DNA) 2. Minor Groove : ¥ 6 wide, 7.5 deep (B-DNA)
¥ A= T -nho N H O
¥ A= T -no N absent O
¥ T =A-ohn O H N
¥ T =A-on O N absent
¥ G C-noh O H N
¥ G C-nho N H O
¥ C G-hon N H O
¥ C G-ohn O H N
Biochemistry of Medicinals I DNA structrure
Transcription Translation
Physical properties of DNA
• UV absorbance (max = 260 nm)
• Denaturation and reassociation (recombination).
A260
T
70
M
80
90
100 T, ΅C
3. Negative charge >PO4(-) – can be separated by gel electrophoresis
Part 2 – Nucleic Acids
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