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Nucleotides and Nucleic Acids - Coggle Diagram
Nucleotides and Nucleic Acids
Functions
Nucleic acids are polymers of nucleotides used for:
storage of genetic info (DNA)
transmission of genetic info (mRNA)
processing of genetic information (ribozymes)
protein synthesis (tRNA and rRNA)
Nucleotides are also used in the monomer form
energy for metabolism (ATP)
enzyme cofactors (NAD+)
signal transduction (cAMP)
Nucleotides and Nucleosides
Nucleotide
(Nucleoside without phosphate)
nitrogeneous base
pyrimidine or purine
Cytosine, adenine, and guanine are found in both DNA and RNA.
Thymine is found only in DNA.
Unusual occurrence in RNA
Uracil is found only in RNA.
good H-bond donors and acceptors
Neutral molecules at pH 7
heteroaromatic
(雜芳族)
Planar
Absorb UV light around 250—270 nm
測DNA(RNA)濃度
decay rapidly
Protect genetic material
no fluorescence
Tautomerism
(互變異構性)
(H+跑動)
Lactam-lactim tautomerism(heterocycles)
Keto-enol tautomerism(ketones)
pentose
ß-d-ribofuranose in RNA
β-2'-deoxy-d-ribofuranose in DNA
C-3' endo/exo
C-2’ endo/exo
phosphate
Negatively charged
attached to 5’ position
5'-triphosphates
Some attach to 2’ or 3’
五碳糖+’
ß-N-Glycosidic Bond
anomeric carbon of the sugar in β configuration.
嘧啶N1 /嘌呤N9
syn conformation(同向)
anti conformation(反向)
normal B-DNA
Minor nucleosides
DNA
Modification is done after DNA synthesis.
5-MethyIcytosine is common in eukaryotes and is also found in bacteria.
N6-Methyladenosine is common in bacteria but not found in eukaryotes.
Epigenetic marker(表觀基因)
Prokaryotes：degrade foreign DNA
Eukaryotes：which genes should be active
RNA
Inosine(肌苷) is sometimes found in the "wobble position(搖擺位置)" of the anticodon in tRNA.
provides richer genetic code
Pseudouridine(Ψ)(假尿苷) is found widely in tRNA and rRNA.
stabilize the structure of tRNA
help in folding of rRNA
Polynucleotides
phosphodiester linkages
negatively charged backbone
DNA backbone is fairly stable.
DNAse
In cells, mRNA is degraded in a few hours.
Linear polymers
no branching or cross-links
read the sequence from 5' to 3'
Hydrolysis of RNA
unstable under alkaline(鹼)
RNase enzymes are abundant
S-RNase
(植物防雜交)
Dicer is an enzyme that cleaves double-stranded RNA into oligonucleotides.
RNA interference technology
-OH attack phosphate
Mixture of 2'- and 3' -monophosphate derivatives
Hydrogen-Bonding
A-T C-G
Purine pairs with pyrimidine.
Waston-Crick Model of B-DNA
Major/Minor groove
A/B/Z form
Non-Watson- Crick Base-Pair Interactions (stabilization )
DNA strands
Complementarity
Replication of Genetic Code
Parent/Daughter strand
RNA
Messenger RNA:
Code Carrier for the Sequence of Proteins
generally occurs as a single strand
One for more than one protein
Together with transfer RNA (tRNA)
Palindromic Sequences
(Stabilization )
Hairpins and Cruciforms
DNA Denaturation
Covalent bonds remain intact.
Hydrogen bonds are broken.
UV absorbance increases.
induced by high temperature, or change in pH.
Thermal DNA Denaturation (Melting) (PCR)
reversible: annealing
Affecting Factors
High CG increases Tm.
Longer DNA has higher Tm(愈短影響愈大)
High salt increases Tm
AT-rich 先打開
Mutagenesis
Spontaneous
Deamination
very slow reactions
(100 C—>U events/day in a mammalian cell)
Depurination
N-glycosidic bond is hydrolyzed
Significant for purines:(10,000 purines lost/day in a mammalian cell)
Oxidative and Chemical
(可矯正)
Oxidative damage
hydroxylation of guanine
mitochondrial DNA is most susceptible
Chemical alkylation
(抗癌藥)
methylation of guanine
Radiation-Induced
(difficult to fix)
UV light induces dimerization of pyrimidines
(skin cancers)
Ionizing radiation (x rays and y rays) causes ring opening and strand breaking.
Other Functions of Nucleotides:
Energy Source
Coenzymes
Regulatory Molecules