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Department of Biochemistry
Jeerus Sucharitakul
Nucleotides
Important chemicals in cellar metabolism
2) Energy currency in living organisms: ATP and GTP
3) Intracellular response of hormone and stimuli from
extracellular signaling: cAMP
3) Genetic information in living organisms
Nucleoside
Pentose and Bases Components in DNA and RNA
DNA RNA
Polynucleotides (DNA and RNA)
-Nucleotide units are joined
forming DNA and RNA by
5′-phostphate covalently
linked to 3′-hydroxy group
of the next nucleotide.
-Backbones are an alternating
of phosphates and pentoses.
-The phosphate groups are
ionized with negatively charge.
-the end of 5 carbon and 3
carbon lacking nucleotide are
called 5′ end and 3′ end.
-The direction of nucleic acids
always represented as from
5′ end to 3′ end.
Chemical Properties of Phosphodierter Bonds
-Backbone is very slowly hydrolyzed in nonenzymatic reaction,
and can be accelerated by enzyme nuclease.
-RNA is rapidly hydrolyzed under alkaline condition whereas
DNA is degraded in acidic condition.
Chemical Properties of Nitrogenous Bases
-Purines and pyrimidines are weakly basic compounds.
-Both type are aromatic and highly conjugated resulting in
resonance stabilization.
-The resonance properties result in partial double-bond
character: pyrimidine rings are planar and purine rings are
nearly planar.
O OH OH
HN N N
O O HO
N N N
H H H
A form DNA:
-Right-handed double helix
-Dehydrated form: the most compact form
-Structure of DNA tending to crystallize
Z form DNA:
-Left-handed double helix
-Zigzag appearance in sugar-phosphate backbone
-Purine bases is are syn conformation, alternating with
pyrimidine in anti conformation: the extended form
-Evidenced some structures in living organism, both
prokaryotes and eukaryotes
The Variation of Three Dimensional Structure of
Nucleic Acids
Unusual DNA Structures
Duplex structures
Hairpin or cruciform structure
-Palindrome sequence;
identical reading either
forward or backward (inverted
repeats)
-Self-complementary within
each strand
Unusual DNA Structures
Three- or four-DNA strand structures
-They are important structure to DNA metabolism, repilcation,
recombination and transcription.
Triplex DNA (C≡G•C+ or T=A•T)
Protonated cytidine
Hoogsteen pairing
Unusual DNA Structures
-Fatty acids are carboxylic acids with long carbon chain ranging
from 4-36 carbon atoms.
-The hydrocarbon chains can be fully saturated or unsaturated
with double bonds.
-Notation of fatty acids
C1 is referred to carboxyl carbon
C18 with saturated hydrocarbon chain, 18:0
C20 with two double bonds between C9-C10 and between C12-
C13, 20:2(∆9,12)
-The double bonds of polyunsaturated fatty acid are not
conjugated, (no −CH=CH−CH=CH− but −CH=CH−CH2−CH=CH−).
-All natural fatty acids are synthesized as cis conformation.
-Trans conformation can be occurred in dairy animals because of
the fermentation in rumen of them.
Physical Properties of Natural Fatty Acids
-By length of chains
-By degree of unsaturation
Physical Properties of Natural Fatty Acids
Sulfolipids
-One sulfonated glucose residue connected to C3 of glycerol
-Component of plant cell membranes.
Sphingolipids
•Sphingolipds are composed of one molecule of long chain
of amino alcohol.
• Ceramide is a parent compounds of sphingolipids
I Sphingophospholipid: ceramides containing either
phosphocholine or phosphoethanolamine
-Sphingomyelins is similar to phosphatidylcholine component
in plasma membrane of animal cells surrounding the axon
(myelin sheath) of neuron for insulation some positions for
action potential.
Sphingosine
Sphingolipids
or β-D-glucose, glucocerebroside
Glangliosides
Sphingolipids
Steroids
•Eukaryotic origins
•Derivatives of cyclopentanoperhydrophenanthrene
•Most abundant in animals, cholesterol
•Cholesterol is a major component of plasma membranes but
lesser amounts in the membranes of subcellular organells.
C D
A B
Cyclopentanoperhydrophenanthrene
Sterols
•Plants contain sterol component in their membranes,
stigmasterol and β-sitosterols.
•Yeast and fungi have ergosterols as a membrane component.