Biomol3
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Chemical Structures of Nucleic Acids and Lipids
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 Three components of nucleotides -Nitrogenous bases -Pentose (ribose, C5) -Phosphate
Nitrogenous Bases Two types of nitrogenous bases
-Both DNA and RNA contain purine bases and cytosine of pyrimidine bases but thymine is only for DNA and uracil is only for RNA.
Pentoses -Nucleic acids have two kinds of pentoses. -2′-deoxy-D-ribose in deoxyribonucleotides (DNA) -D-ribose in ribonucleotides (RNA) -N-9 of purines and N-1 of pyrimidines are joined with pentoses at 1′carbon of pentose (N-β-glycosyl linkage) -Phosphate is esterified at 5 carbon by o-glycosidic bond.
Nucleotides and Nucleic Acid Nomenclature
Base + Pentose = Nucleoside Base + Pentose + Phosphate = Nucleotide 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. OH
O N
HN O
OH
N H
O
N N H
HO
N H
Resonance forms of pyrimidine (Uracil)
Chemical Properties of Nitrogenous Bases Purines and pyrimidines are hydrophobic and exist in neutral form at physiological pH. Hydrophobic bases are stacked similar to a stack of coins with interaction by van der Waals and dipoledipole force. These forces are the most important to stabilized nucleic acid structure.
Chemical Properties of Nitrogenous Bases
Complementary base pairs -Carbonyl and amino substitute groups on purine and pyrimidine bases are important to interaction between nucleic acid molecules via hydrogen bond.
Complementary base pairs
James Watson
Francis Crick
-Hydrogen bonds can allow association of two, three and four strands of nucleic acids. -In 1953, Watson and Crick defined the two types of base pairs A-T (or U) and G-C, called base pairs. -Specific base pairs permits the fidelity of heritages of the genetic information.
Three Dimensional Structure of Nucleic Acids
-In 1950, Rosalin Frankin and Maurice Wilkins used x-ray diffraction to analyze DNA chains as a helical structure. -Watson and Click proposed the structure that consists of two helical DNA chains wound around the same axis with right-handed double helix.
DNA Double Helix Structure -Right–handed double helix -The hydrophilic backbones expose to polar environment. -The hydrophobic aromatic bases of both strands are stacked inside the double helix perpendicular to the long axis. -The geometry in base pairing creates a major and minor groove.
Major and Minor Groove in DNA Structure More hydrophobic environment Base exposure site Major groove
Minor groove Backbone exposure site
Base exposure site Major groove
Minor groove Backbone exposure site
More hydrophilic environment
The Variation of Three Dimensional Structure of Nucleic Acids -The deviations from Watson-Crick DNA structure can be found in cellular DNA but the key properties is still not affected, base complementarity and antiparallel strand. -The variation of structures are caused by different conformation of three things 1. Different conformation of deoxyribose 2. The free rotation of C′-1-N-glycosyl bond 3. The rotation of phosphodeoxyribose backbone
Different conformation of pentose
The Variation of Three Dimensional Structure of Nucleic Acids The free rotation of C′-1-N-glycosyl bond
-Purines are restricted in two stable forms, syn and anti conformation. -Pyrimidines are restricted in to anti conformation because of steric hindrances between sugar ring and carbonyl oxygen.
The Variation of Three Dimensional Structure of Nucleic Acids B form DNA is referred to Watson-crick model. 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 Quadruplex DNA (G tetraplex) -High rich sequence of G -Highly stable -Possible two directions
Lipids Lipids (Greek: lipos = fat) are biological substances soluble in organic solvent. Lipid classification -Fatty acids -Triacylglycerols -Glycerophospholipids -Sphingolipids -Cholesterol
Storage lipid -Fats and oils are energy storage form in living organism. -Hydrocarbon derivatives are very low oxidation state. -Hydrophobic molecule with low water solvation different from polysaccharides and polypeptides. -Organisms can store energy without carrying a lot of mass weight.
Fatty Acids -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 C12C13, 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
•Most fatty acids have an even number of C because biosynthesis is carried out by adding C2 units of acetyl -CoA. •The first double bond of an unsaturated fatty acid commonly occurs between C9 and C10.
Triacylglycerols -Triacylglycerols are fatty acids ester of glycerol. -They are composed of one glycerol molecule with the same (simple) or different kind (mixed) of fatty acids linked by esterification. -Triacylglycerols are nonpolar molecules, insoluble in water. -Most of eukaryotes store energy as form of triacylglycerol (oil droplets) in separated phase in specialized cells, adipocytes (animals) and plants (germinating seeds). -Adipocyte and germinating seeds have enzyme lipase, enzymes that catalyze hydrolysis of ester bond to release fatty acids from triacylglycerols.
Biological Waxes •Biological waxes are esters of long chain fatty acids (14-36) with long chain of alcohols. •Waxes function as water-repellent substances and coating material in skins. •Pharmacoceutical, cosmetic and chemical industries Lanolin from wood Beeswas Extract from spermaceti (from whales)
Structural Lipids in Membranes
Structural Lipids in Membranes -Membrane are lipid bilayer composed of amphipathic molecules: outer is hydrophilic and inner is hydrophobic. Glycerophospholipids (Phosphoglycerides) -Fatty acid components link to C1 and C2 of glycerol via ester bonds. -The highly charged group of phosphate links to C3 of glycerol.
Glycerophospholipids
•Glycerol 3-phosphate is esterified at C1 and C2. •Amphipathic molecules
Glycerophospholipids
Phospholipids with Ether-Linked Fatty Acids Some animal tissues and unicellular organism can synthesize ether phospholipid with two fatty acid chain linked to glycerol 3-phosphate by ether bonds. Plasmalogen: about 50% of heart vertebrate tissue phospholipids are plamalogen, and it can be found in bacteria and invertebrates Platelet-activating factor: substances are released by leukocytes to stimulate platelets aggregation and the release of serotonin resultng in
Glycolipid -Membrane lipids contain a simple sugar or complex oligosaccharides. -Predominate membrane lipid types are found n plant cells Galactolipid -One or two galactose residues connected to C3 of glycerol -Component in thylakoid membrane (chloroplast)
Glycolipid 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 II Sphingoglycolipids: ceramides head groups (no phosphate) that consist of a single sugar residue or more than one residue. -Component of plasma membrane in neuron tissues, brain and certain carbohydrate moieties representing the human blood group -Cerebroside; head group contains a single sugar residue -Glangliosides; head group contains oligosacharides with charateristic sugar derivatives, sialic acid (N-acetylneuraminidate)
Cerebrosides Cerebrosides lack of phosphate groups, and most of them are nonionic compounds.
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 A
D
B
Cyclopentanoperhydrophenanthrene
Sterols •Plants contain sterol component in their membranes, stigmasterol and β-sitosterols. •Yeast and fungi have ergosterols as a membrane component.
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 Three components of nucleotides -Nitrogenous bases -Pentose (ribose, C5) -Phosphate
Nitrogenous Bases Two types of nitrogenous bases
-Both DNA and RNA contain purine bases and cytosine of pyrimidine bases but thymine is only for DNA and uracil is only for RNA.
Pentoses -Nucleic acids have two kinds of pentoses. -2′-deoxy-D-ribose in deoxyribonucleotides (DNA) -D-ribose in ribonucleotides (RNA) -N-9 of purines and N-1 of pyrimidines are joined with pentoses at 1′carbon of pentose (N-β-glycosyl linkage) -Phosphate is esterified at 5 carbon by o-glycosidic bond.
Nucleotides and Nucleic Acid Nomenclature
Base + Pentose = Nucleoside Base + Pentose + Phosphate = Nucleotide 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. OH
O N
HN O
OH
N H
O
N N H
HO
N H
Resonance forms of pyrimidine (Uracil)
Chemical Properties of Nitrogenous Bases Purines and pyrimidines are hydrophobic and exist in neutral form at physiological pH. Hydrophobic bases are stacked similar to a stack of coins with interaction by van der Waals and dipoledipole force. These forces are the most important to stabilized nucleic acid structure.
Chemical Properties of Nitrogenous Bases
Complementary base pairs -Carbonyl and amino substitute groups on purine and pyrimidine bases are important to interaction between nucleic acid molecules via hydrogen bond.
Complementary base pairs
James Watson
Francis Crick
-Hydrogen bonds can allow association of two, three and four strands of nucleic acids. -In 1953, Watson and Crick defined the two types of base pairs A-T (or U) and G-C, called base pairs. -Specific base pairs permits the fidelity of heritages of the genetic information.
Three Dimensional Structure of Nucleic Acids
-In 1950, Rosalin Frankin and Maurice Wilkins used x-ray diffraction to analyze DNA chains as a helical structure. -Watson and Click proposed the structure that consists of two helical DNA chains wound around the same axis with right-handed double helix.
DNA Double Helix Structure -Right–handed double helix -The hydrophilic backbones expose to polar environment. -The hydrophobic aromatic bases of both strands are stacked inside the double helix perpendicular to the long axis. -The geometry in base pairing creates a major and minor groove.
Major and Minor Groove in DNA Structure More hydrophobic environment Base exposure site Major groove
Minor groove Backbone exposure site
Base exposure site Major groove
Minor groove Backbone exposure site
More hydrophilic environment
The Variation of Three Dimensional Structure of Nucleic Acids -The deviations from Watson-Crick DNA structure can be found in cellular DNA but the key properties is still not affected, base complementarity and antiparallel strand. -The variation of structures are caused by different conformation of three things 1. Different conformation of deoxyribose 2. The free rotation of C′-1-N-glycosyl bond 3. The rotation of phosphodeoxyribose backbone
Different conformation of pentose
The Variation of Three Dimensional Structure of Nucleic Acids The free rotation of C′-1-N-glycosyl bond
-Purines are restricted in two stable forms, syn and anti conformation. -Pyrimidines are restricted in to anti conformation because of steric hindrances between sugar ring and carbonyl oxygen.
The Variation of Three Dimensional Structure of Nucleic Acids B form DNA is referred to Watson-crick model. 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 Quadruplex DNA (G tetraplex) -High rich sequence of G -Highly stable -Possible two directions
Lipids Lipids (Greek: lipos = fat) are biological substances soluble in organic solvent. Lipid classification -Fatty acids -Triacylglycerols -Glycerophospholipids -Sphingolipids -Cholesterol
Storage lipid -Fats and oils are energy storage form in living organism. -Hydrocarbon derivatives are very low oxidation state. -Hydrophobic molecule with low water solvation different from polysaccharides and polypeptides. -Organisms can store energy without carrying a lot of mass weight.
Fatty Acids -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 C12C13, 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
•Most fatty acids have an even number of C because biosynthesis is carried out by adding C2 units of acetyl -CoA. •The first double bond of an unsaturated fatty acid commonly occurs between C9 and C10.
Triacylglycerols -Triacylglycerols are fatty acids ester of glycerol. -They are composed of one glycerol molecule with the same (simple) or different kind (mixed) of fatty acids linked by esterification. -Triacylglycerols are nonpolar molecules, insoluble in water. -Most of eukaryotes store energy as form of triacylglycerol (oil droplets) in separated phase in specialized cells, adipocytes (animals) and plants (germinating seeds). -Adipocyte and germinating seeds have enzyme lipase, enzymes that catalyze hydrolysis of ester bond to release fatty acids from triacylglycerols.
Biological Waxes •Biological waxes are esters of long chain fatty acids (14-36) with long chain of alcohols. •Waxes function as water-repellent substances and coating material in skins. •Pharmacoceutical, cosmetic and chemical industries Lanolin from wood Beeswas Extract from spermaceti (from whales)
Structural Lipids in Membranes
Structural Lipids in Membranes -Membrane are lipid bilayer composed of amphipathic molecules: outer is hydrophilic and inner is hydrophobic. Glycerophospholipids (Phosphoglycerides) -Fatty acid components link to C1 and C2 of glycerol via ester bonds. -The highly charged group of phosphate links to C3 of glycerol.
Glycerophospholipids
•Glycerol 3-phosphate is esterified at C1 and C2. •Amphipathic molecules
Glycerophospholipids
Phospholipids with Ether-Linked Fatty Acids Some animal tissues and unicellular organism can synthesize ether phospholipid with two fatty acid chain linked to glycerol 3-phosphate by ether bonds. Plasmalogen: about 50% of heart vertebrate tissue phospholipids are plamalogen, and it can be found in bacteria and invertebrates Platelet-activating factor: substances are released by leukocytes to stimulate platelets aggregation and the release of serotonin resultng in
Glycolipid -Membrane lipids contain a simple sugar or complex oligosaccharides. -Predominate membrane lipid types are found n plant cells Galactolipid -One or two galactose residues connected to C3 of glycerol -Component in thylakoid membrane (chloroplast)
Glycolipid 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 II Sphingoglycolipids: ceramides head groups (no phosphate) that consist of a single sugar residue or more than one residue. -Component of plasma membrane in neuron tissues, brain and certain carbohydrate moieties representing the human blood group -Cerebroside; head group contains a single sugar residue -Glangliosides; head group contains oligosacharides with charateristic sugar derivatives, sialic acid (N-acetylneuraminidate)
Cerebrosides Cerebrosides lack of phosphate groups, and most of them are nonionic compounds.
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 A
D
B
Cyclopentanoperhydrophenanthrene
Sterols •Plants contain sterol component in their membranes, stigmasterol and β-sitosterols. •Yeast and fungi have ergosterols as a membrane component.
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