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Nucleic acids: DNA and RNA
Done By
Majed Felemban
2
DNA
• Double helix– 2 chains
• Building blocks– Nucleotides
• DNA directs– Is own replication– Directs RNA synthesis → protein synthesis
Campbell and Reece, P86
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In Eukaryotes (animals, plants, fungi)
Complete human genome
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In Prokaryotes (bacteria, archaea)
• Main chromosome is one large, continuous loop– Hundreds to thousands
of genes
• May have smaller loops, with a few genes each– May be swapped
between bacteria– Antibiotic resistance, etc.
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Replication
Transcription
Translation
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Roles of Nucleic Acids• DNA
– Responsible for inheritance– Codes for proteins and functional RNAs
• Genes
– Regulatory sequences• Control which genes are transcribed, and when
– Other unknown functions• 80-90% of the human genome has no known function
Campbell and Reece, P86, 87
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Roles of Nucleic Acids• RNA
– Information transmission (mRNA)– Processing and transport (tRNA, rRNA, snRNA)– Catalytic (ribozymes)– Regulation and feedback (siRNA)– Unit of inheritance (retroviruses)– Other…?
Campbell and Reece, P86, 87
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• Nucleic Acid chemistry is the same for all life on earth.• DNA & RNA are polymers of monomers - nucleotides.• Each nucleotide has three components
(Deoxy)ribonucleic Acid
NUCLEIC ACID STRUCTURES
Campbell and Reece, 86
OH
O-
O
PO-
O
O-
O
PO- OH
O
OHOH
O
O-
O
PO- N
O
OHOH
N
NN
NH2
2. (DEOXY)RIBOSE SUGAR = STRUCTURAL
3. NITROGENOUS BASES = INFORMATIONAL
O
O
O
PO- N
O
OHO
N
NN
NH2
O NO
OH
O
O
PO-
X
X
1. PHOSPHORIC ACID = STRUCTURAL
9Campbell and Reece, P87
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Phosphoric Acid & Related Compounds
• Phosphoric acid isTriprotic.
• Reacts with CHO’s or alcohols to form esters.
D
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Phosphoric Acid & Related Compounds
• Phosphoric acid isTriprotic.
• Reacts with alcohols to form esters.
As found in DNA& RNA at pH7
-
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The sugar may be Ribose (in RNA) or Deoxyribose (in DNA)
H
Ribose Deoxyribose
Phosphate can covalently bond to C3 and C5
Bases (A,C,G,T or U) can covalently bond to C1
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Bases in DNA and RNA
(RNA) (DNA)
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A Base Joined To A Ribose SugarIs Called A Nucleoside
Pyrimidines bond at N-1 to C-1’
Purines bond N-9 to 1’ Carbon of sugar
The carbons in the ribose are now designated as C prime (or C’) to distinguish them from those in the base.
or H
or H
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When Phosphate is Bound to a Nucleoside it is Called a Nucleotide
• ATP, GTP, CTP, UTP (NTPs) are substrates for RNA synthesis• dATP, dGTP, dCTP, dTTP (dNTPs) are substrates for DNA synthesis
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Mononucleotides as they Occur in DNA & RNA
DNA
RNA
A,C,G or T (DNA)orA,C,G or U (RNA)
All nucleotides are asymmetrical
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5’C =
Four Nucleotides With 5’ to 3’ Phosphodiester Linkages
3’C =
DNA & RNA are Polymers of Nucleotides
All DNA and RNA polymers are asymmetrical with 5’ to 3’ direction.
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Properties of DNA and RNA
• They may be informational eg genomic DNA, mRNA.
• They may be structural eg rRNA & tRNA.
• Retain 5’& 3’ molecular orientation due to nucleotide asymmetry.
• They are often single stranded (typically RNA).
• They may be extremely long. Movie*
• Two polymers (or strands) may become double stranded when
certain conditions are met ie they are antiparallel &
complementary in nucleotide sequence (typically nuclear DNA).
* Terao et al., 2008: Lab on a chip DOI: 10.1039/b803753a
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Duplex DNA is Antiparallel
Duplex DNA is NEVER Parallel!
5’Phosphate
3’OH
3’OH
5’Phosphate
or
5’3’
3’
5’
or
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Duplex DNA has Complementarity because of Hydrogen Bonds
• H bonds are weak (~1/20th of a covalent bond):– Often allows transient contact between molecules (biological
signalling systems).– May allow stable contact that can be disrupted and reformed (eg
DNA).
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Hydrogen Bonds
• Form between O &/or N with H between them
eg O-H…O, N…H-N or O-H…N.
• Are due to electrostatic forces.
H is slightly +ve.
O &/or N are slightly -ve.
• Are very weak compared to covalent bonds
• May be broken & reform under various chemical or physical conditions.
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Two representations of duplex DNA showing:
• H bonds between bases and,
• Covalently bonded Sugar Phosphate backbones.
• ~10 basepairs per turn of the helix.
• Duplex DNA width = 2nm.
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Double Stranded (or Duplex) DNA
• Is characteristic of genomic DNA.
• Consists of two separate nucleic acid polymers (“strands”).
• The two strands are Antiparallel wrt 5’& 3’ ends.
• They are held together by Hydrogen Bonds between the bases.
• H-Bond energies are weak BUT there are many of them which makes the duplex DNA very stable.
• Bases are Complementary such that:
– A always pairs with T (2 H Bonds).
– C always pairs with G (3 H Bonds).
• Two strands of complementary antiparallel DNA form a Double Helix eg as found in a chromosome.
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History of The Double Helix of DNA
• The structure of the double helix was found by Rosalind Franklin using X-ray crystallography and correctly interpreted by Watson & Crick in 1953 who also used Chargaff’s rule.
• The bases are Hydrophobic and are in the Centre of the helix where complementary bases pair via H-bonding.
• The Ribose Sugar and Phosphate groups are on the Outside of the helix where they can H bond to polar solvents like water.
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Xray diffraction pattern of DNA similar to Franklin’s data (above, 1953).
Watson & Crick’s structure for DNA
Key data that Watson & Crick worked with
Chargaff’s Rule: there is a 1:1 ratio of purines to pyrimidines (because A=T, GC always).
1GATC