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Nucleotides and Nucleic Acids, DNA, RNA - Coggle Diagram
Nucleotides and Nucleic Acids
Functions
Nucleic Acids (polymers)
ribozymes:processing of genetic information
tRNA and rRNA:protein synthesis
mRNA:transmission of genetic info
DNA:storage of genetic info
Nucleotides (monomer)
NAD+:enzyme cofactors
cAMP:signal transduction
ATP:energy for metabolism
Nucleotides and Nucleosides
Nucleoside
pentose五碳醣
forms differ in some nucleic acids and nucleotides
β-d-ribofuranose in
RNA
β-2’-deoxy-d-ribofuranose in
DNA
(2'指去氧位置)
different puckered conformations of the sugar ring are possible
nitrogegenous bases含氮鹼基
about
All are good H-bond donors and acceptors --> 可跟彼此形成H-bond ==>DNA雙股螺旋
Neutral molecules at pH 7
Uracil
is found only in
RNA
Thymine
is found only in
DNA
Cytosine, Adenine, and Guanine are found in both DNA and RNA
absorb
UV light
around 250–270 nm --> 可測DNA&RNA 濃度
planar or almost planar structures
nitrogen-containing heteroaromatic molecules
derivatives of pyrimidine
or purine
Nomenclature
deoxyribonucleotides
ribonucleotides
summary
β−N-Glycosidic Bond 醣苷鍵
about
In
nucleotides
, the pentose ring is attached to the nitrogenous base via a
N-glycosidic bond
The bond is formed to the anomeric carbon of the sugar in β configuration
--is formed to position
N1
in
pyrimidines
--is formed to position
N9
in
purines
quite stable toward hydrolysis, especially in pyrimidines平常非常穩定
bond cleavage is catalyzed by acid 以酸催化來斷鍵
conformation around
relatively free rotation can occur around the N-glycosidic bond in free nucleotides
angle near 0° corresponds to
syn conformation
同向(朝裡面)
angle near 180° corresponds to
anti conformation
反向(朝外面)
anticonformation
is found in
normal B-DNA
tautomerism of nitrogenous bases 結構上的H+會跑動
UV absorption of nucleobases
excited states of common nucleobases
decay rapidly
via radiationless transitions
--
effective photoprotection of genetic material 保護遺傳物質
--no fluorescence from nucleic acids
absorption of
UV light
(吸收多少光反推濃度)at 250–270 nm is due to
π --> π(能量激發)
electronic transitions
phosphate磷酸根
Typically attached to 5’ position
Nucleic acids are built using the 5’-triphosphates version of the nucleotide.(ATP, GTP, TTP, CTP)
補充:TP-3*phosphate(α, β, γ)
β, γ常形成leaving group
May be attached to other positions for specialized function
Negatively charged
at neutral pH
Other Nucleotides:Monophosphate Group in Different Positions
minor nucleosides(不常出現的)
DNA
N6-Methyladenosine
is common in bacteria but
not found in eukaryotes
.
Epigenetic marker表觀基因學
:不會改變基因的構造與組成,做表面的改變(epi上) --> 影響許多但不做遺傳
。
prokaryotes
: to
mark own DNA
so that cells can degrade foreign DNA 保護
。
eukaryotes
: to
mark
which genes should be active 標示
5-Methylcytosine
is common in
eukaryotes
and is also found in
bacteria
Modification
is done
after DNA synthesis
(DNA出現後才修飾)
RNA
pseudouridine (Ψ
) is found widely in
tRNA
and
rRNA
-->
stabilize
the structure of
tRNA
-->
help in folding
of
rRNA
Inosine
is sometimes found in the “
wobble position
” of the anticodon in tRNA
原本沒有那麼豐富的結構,為了有更多的遺傳密碼子 --> inosine
Nucleotide
polynucleotides
RNA
backbone is
unstable
(e.g.抽RNA不能講話,因為口水裡有酵素)
Linear polymers 本身是一條很直的結構
DNA
backbone is
fairly stable
read the sequence from
5’ to 3’
Covalent bonds
are formed via
phosphodiester
linkages
negatively charged
backbone
因為phosphate groups都帶負電(跑DNA電泳都是由負-->正)
DNA
DNA denaturation
covalent bonds remains intact --> genetic code remains intact
hydrogen bonds are broken --> two strands separate
may be reversible(可逆的):annealing黏合(逆向)
base stacking is lost -->UV absorbance increases
原因may be high temperature, or change in pH
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
forms
other forms
Watson-Crick model of B-DNA(最normal)
complementary(反向互補)
replication of genetic code
RNA
messenger RNA
contains uracil
instead of thymine
不同片段/部分可轉成不同protein
contains ribose
instead of deoxyribose
與mRNA, tRNA拖不了關係
synthesized using
DNA template
and generally occurs as a single strand
DNA template:轉錄來的,也攜帶遺傳密碼子
hydrolysis
RNase enzymes
S-RNase
in
plants
prevents inbreeding防止雜交
RNase P
is a ribozyme (enzyme made of RNA)
cleaves
double-stranded RNA
into
oligonucleotides
protection from viral genomes
catalyzed by enzymes (RNase)
RNA interference technology
s unstable under alkaline conditions
mechanism of base-catalyzed RNA hydrolysis
have quite complex structures
stabilized by non-Watson-Crick base-pair interactions
存在目的:為了穩定整個構造
除了ATCG配,需要額外的氫鍵去穩定e.g.轉彎處