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Nucleotides and Nucleic Acids, 330AB918-41F9-47B8-A852-FBEE255FFB2A,…
Nucleotides and Nucleic Acids
UNI
Nucleotides and Nucleosides
Nucleoside
nitrogeneous base
pentose
Carbon AND nitrogen atoms on the nitrogenous base are numbered in cyclic format.
Nucleotide
pentose
phosphate
nitrogeneous base
Carbons of the pentose are designated N’ to alleviate confusion.
Phosphate Group
Nucleic acids are built using the 5’-triphosphates version of the nucleotide.
• ATP, GTP, TTP, CTP
Two of the three phosphates used for building nucleic acids form a leaving group, and completed nucleic acids contain one phosphate moiety per nucleotide.
Typically attached to 5’ position
May be attached to other positions for specialized
function
Negatively charged at neutral pH
Functions
polymers
transmission of genetic info (mRNA)
processing of genetic information (ribozymes)
storage of genetic info (DNA)
protein synthesis (tRNA and rRNA)
monomer
enzyme cofactors (NAD+)
signal transduction (cAMP)
energy for metabolism (ATP)
Other Nucleotides
Monophosphate Group in Different Positions
Pentose Forms Differ in Some Nucleic acids and Nucleotides
β-d-ribofuranose in RNA
β-2’-deoxy-d-ribofuranose in DNA
Different puckered conformations of the sugar ring are possible.
Nitrogenous Bases
Cytosine, adenine, and guanine are found in both DNA and RNA.
Thymine is found only in DNA.
Absorb UV light around 250–270 nm
Uracil is found only in RNA.
Planar or almost planar structures
All are good H-bond donors and acceptors.
Nitrogen-containing heteroaromatic molecules
Neutral molecules at pH 7
Derivatives of pyrimidine or purine
Minor Nucleosides in DNA
N6-Methyladenosine is common in bacteria but not found in
eukaryotes.
Epigenetic marker:
5-Methylcytosine is common in eukaryotes and is also found in bacteria.
way to mark own DNA so that cells can degrade foreign DNA
(prokaryotes)
Modification is done after DNA synthesis.
way to mark which genes should be active (eukaryotes)
Pseudouridine (Ψ) is found widely in tRNA and rRNA.
made from uridine by enzymatic isomerization after RNA synthesis
may stabilize the structure of tRNA
more common in eukaryotes but found also in eubacteria
may help in folding of rRNA
Inosine is sometimes found in the “wobble position” of the anticodon in tRNA.
– made by de-aminating adenosine
– provides richer genetic code
UV Absorption of Nucleobases
Absorption of UV light at 250–270 nm is due to π→π* electronic transitions.
Excited states of common nucleobases decay rapidly
via radiationless transitions.
– effective photoprotection of genetic material
– no fluorescence from nucleic acids
Tautomerism of Nitrogenous Bases
Keto-enol tautomerism is common in ketones.
Lactam-lactim tautomerism occurs in some heterocycles.
Prototropic tautomers are structural isomers that differ in the location of protons.
Both tautomers exist in solution, but the lactam forms are predominant at neutral pH.
β− N-Glycosidic Bond
The bond is formed:
to position N1 in pyrimidines
to position N9 in purines
This bond is quite stable toward hydrolysis, especially in pyrimidines.
The bond is formed to the anomeric carbon of the sugar in β
configuration.
Bond cleavage is catalyzed by acid.
In nucleotides, the pentose ring is attached to the nitrogenous base via a N-glycosidic bond.
Nomenclature
Deoxyribonucleotides
Ribonucleotides
You need to know structures, names, and symbols (both two-letter (dA) and four-letter (dAMP) codes).
Conformation around N-Glycosidic Bond
Angle near 0° corresponds to syn conformation.
Angle near 180° corresponds to anti conformation.
The sequence of atoms chosen to define this angle is O4’-C1’-
N9-C4 for purine, and O4’-C1’-N1-C2 for pyrimidine derivatives.
Anticonformation is found in normal B-DNA.
Relatively free rotation can occur around the N-glycosidic bond
in free nucleotides.
Poly
Hydrolysis of RNA
Hydrolysis is also catalyzed by enzymes (RNase).
RNase enzymes are abundant around us.
RNase P is a ribozyme (enzyme made of RNA) that processes tRNA precursors.
Dicer is an enzyme that cleaves double-stranded RNA into oligonucleotides.
• protection from viral genomes
• RNA interference technology
S-RNase in plants prevents inbreeding.
RNA is unstable under alkaline conditions.
Hydrogen-Bonding Interactions
Two bases can hydrogen bond to form a base pair.
For monomers, a large number of base pairs ispossible.
In polynucleotide, only a few possibilities exist.
Watson-Crick base pairs predominate in double-stranded DNA.
A pairs with T.
C pairs with G.
Purine pairs with pyrimidine.
Mechanism of Base-catalyzed RNA Hydrolysis
Polynucleotides
RNA backbone is unstable.
In water, RNA lasts for a few years.
In cells, mRNA is degraded in a few hours.
Linear polymers
– no branching or cross-links
DNA backbone is fairly stable
Hydrolysis accelerated by enzymes (DNAse)
DNA from mammoths?
Directionality
The 5’ end is different from the 3’ end.
We read the sequence from 5’ to 3’.
Covalent bonds are formed via phosphodiester linkages.
– negatively charged backbone
AT and GC Base Pairs
DNA and Discovery of its Structure
Other Forms of DNA
Watson-Crick Model of B-DNA
Road to the Double Helix
Covalent Structure of DNA (1868–1935)
Hydrolysis of nuclein
phosphate , pentose , and a nitrogenous base
Friedrich Miescher isolates “nuclein” from cell nuclei
Chemical analysis
phosphodiester linkages, pentose is ribofuranoside
DNA&RNA
Palindromic Sequences Can Form
Hairpins and Cruciforms
RNA Molecules Have Quite Complex Structures
Messenger RNA: Code Carrier for
the Sequence of Proteins
Contains uracil instead of thymine
One mRNA may code for more than one protein
Contains ribose instead of deoxyribose
Together with transfer RNA (tRNA), transfers genetic information from DNA to proteins
Is synthesized using DNA template and generally occurs as a single strand
Complex Structures Are Stabilized by Non-Watson-Crick Base-Pair Interactions
Factors Affecting DNA Denaturation
Tm depends on DNA length. – Longer DNA has higher Tm.
– It is important for short DNA.
Tm depends on pH and ionic strength.
– High salt increases Tm.
The midpoint of melting (Tm) depends on basecomposition.
– High CG increases Tm.
Denaturation of Large DNA Molecules Is Not Iniform
Replication of Genetic Code
Each strand serves as a template for the synthesis of a new strand.
Synthesis is catalyzed by enzymes known as DNA polymerases.
Strand separation occurs first.
A newly made DNA molecule has one daughter strand and one parent strand.
DNA Denaturation
Thermal DNA Denaturation (Melting)
Two strands re-anneal when the temperature is lowered.
The reversible thermal denaturation and annealing
form the basis for the polymerase chain reaction.
Two DNA strands dissociate at elevated temperatures.
DNA denaturation is commonly monitored by UV
spectrophotometry at 260 nm.
DNA exists as double helix at normal temperatures.
Factors Affecting DNA Denaturation
Basic
Hydrogen bonds are broken.
– Two strands separate.
Base stacking is lost
– UV absorbance increases.
Covalent bonds remain intact.
– Genetic code remains intact.
Denaturation can be induced by high temperature, or change in pH.
Denaturation may be reversible: annealing.
Denaturation of Large DNA Molecules Is Not Iniform
Complementarity of DNA Strands
Two chains are complementary.
Two chains run antiparallel.
Two chains differ in sequence
(sequence is read from 5’ to 3’).
Molecular Mechanisms
Radiation-Induced Mutagenesis
（輻射光引起的_不可修復）
Oxidative and Chemical Mutagenesis
(化學物質引起的_可修復）
Spontaneous Mutagenesis：Deamination& Depurination（自體發生的）
Other Functions of Nucleotides:
Regulatory Molecules
Energy Source
Coenzymes
