The carbohydrate structures.
The structure of nucleic acids.
Department of Medical Chemistry and Clinical Biochemistry
Charles University in Prague – 2nd Faculty of Medicine and
University Hospital in Motol
Matej Kohutiar, Bruno Sopko
Content
I. Structure of saccharides 1. Monosaccharides
Saccharides reactions
2. Oligosaccharides
3. Polysaccharides
4. Complex saccharides
II. Structure of nucleic acids 1.Basic components of nucleic acids
2.Nucleosides and nucleotides
3.DNA chain structures
4.RNA
I. Structure of saccharides
Saccharides
• Polyhydroxaldehydes and polyhydroxyketons with, at
minimum 3 carbon chain
• Division according to the number os saccharide units:
Monosaccharides
Oligosascharides (2-10)
Polysaccharides
Complex saccharides
Monosaccharide structure CH=O
OHH
CH2OH
C O
CH2OH
OHH
CH2OH
Monosaccharide structure CH=O
OHH
CH2OH
C O
CH2OH
OHH
CH2OH
Monosaccharide structure CH=O
OHH
CH2OH
C O
CH2OH
OHH
CH2OH
Monosaccharide structure CH=O
OHH
CH2OH
C O
CH2OH
OHH
CH2OH
CH=O
OHH
CH2OH
C O
CH2OH
HOH
CH2OH
CH=O
OHH
CH2OH
Monosaccharide structure CH=O
OHH
CH2OH
C O
CH2OH
OHH
CH2OH
C O
CH2OH
HOH
CH2OH
Chiral carbons
H
F
Cl Br
Chiral carbons
H
F
Cl Br
H
F
Cl Br
Chiral carbons
CH2OH
H OHOH HH OHH
H OHCH=O
OH
CH2OH
H OHOH HH OHH
H OHCH=O
OH
Chiral carbons
2
CH2OH
H OHOH HH OHH
H OHCH=O
OH
Chiral carbons
2
CH2OH
H OHOH HH OHH
H OHCH=O
OH
Chiral carbons
2
CH2OH
H OHOH HH OHH
H OHCH=O
OH
Chiral carbons
2
CH2OH
H OHOH HH OHH
H OHCH=O
OH
Chiral carbons
4
CH2OH
H OHOH HH OHH
H OHCH=O
OH
2
CH2OH
H OHOH HH OHH
H OHCH=O
OH
Chiral carbons
4
CH2OH
H OHOH HH OHH
H OHCH=O
OH
Chiral carbons
4
CH2OH
H OHOH HH OHH
H OHCH=O
OH
Chiral carbons
4
CH2OH
H OHOH HH OHH
H OHCH=O
OH
Chiral carbons
4
CH2OH
H OHOH HH OHH
H OHCH=O
OH
Chiral carbons
4
CH2OH
H OHOH HH OHH
H OHCH=O
OH
Chiral carbons
Monosaccharide structure
CH=O
CH2OH
H OH
D-glyceraldehyde
Monosaccharide structure
CH=O
CH2OH
H OH
CH=O
CH2OH
OH
H OH
H
D-glyceraldehyde
D-erythrose
Monosaccharide structure
CH=O
CH2OH
H OH
CH=O
CH2OH
OH
H OH
H
CH=O
CH2OH
H
H OH
OH
D-glyceraldehyde
D-erythrose D-threose
Monosaccharide structure CH=O
CH2OH
OH
H OH
H
D-erythrose
Monosaccharide structure CH=O
CH2OH
OH
H OH
H
CH=O
CH2OH
H OH
H OH
H OH
D-erythrose
D-ribose
Monosaccharide structure CH=O
CH2OH
OH
H OH
H
CH=O
CH2OH
H OH
H OH
H OH
CH=O
CH2OH
OH H
H OH
H OH
D-ribose D-arabinose
D-erythrose
Monosaccharide structure CH=O
CH2OH
H
H OH
OH
D-threose
Monosaccharide structure CH=O
CH2OH
H
H OH
OH
CH=O
CH2OH
H OH
OH H
H OH
D-threose
D-xylose
Monosaccharide structure CH=O
CH2OH
H
H OH
OH
CH=O
CH2OH
H OH
OH H
H OH
CH=O
CH2OH
OH H
OH H
H OH
D-threose
D-xylose D-lyxose
Monosaccharide structure
CH=O
CH2OH
H OH
H OH
H OH
CH=O
CH2OH
OH H
OH H
H OH
CH=O
CH2OH
OH H
H OH
H OH
CH=O
CH2OH
H OH
OH H
H OH
D-xylose
D-lyxose D-ribose
D-arabinose
Monosaccharide structure
CH=O
CH2OH
H OH
H OH
H OH
H OH
CH=O
CH2OH
OH H
OH H
OH H
H OH
CH=O
CH2OH
H OH
H OH
OH H
H OH
CH=O
CH2OH
OH H
OH H
H OH
H OH
CH=O
CH2OH
H OH
OH H
H OH
H OH
D-allose D-talose D-glucose D-idose
D-gulose D-mannose D-altrose D-galactose
CH=O
CH2OH
OH H
H OH
OH H
H OH
CH=O
CH2OH
OH H
H OH
H OH
H OH
CH=O
CH2OH
H OH
OH H
OH H
H OH
Monosaccharide structure
CH=O
CH2OH
H OH
H OH
H OH
H OH
Monosaccharide structure
H OH
H OH
H OH
CH=O
CH2OH
H OH
H OH
H OH
H OH
Monosaccharide structure
H OH
H OH
H OH
CH=O
CH2OH
H OH
H OH
H OH
H OH
Monosaccharide structure
Monosaccharide structure
Monosaccharide structure
D-glucose
D-mannose
D-galactose
Monosaccharide structure
ketoses
CH2OH
CH2OH
O
OH
H OH
H OH
O
OH
OH
OH H
H OH
O
OH
OH
OH H
H OH
H OH
O
OH
dihydroxyacetone
D-ribulose D-xylulose D-fructose
Monosaccharide structure
CH=O
CH2OH
H OH
H OH
H OH
H
OH
CH2OH
H OH
H OH
H OH
H
H OH
O
D-allose D-allose
O
OHH
HH
OHH
OH OH
H
OH
Monosaccharide structure
CH=O
CH2OH
H OH
H OH
H OH
H
OH
CH2OH
H OH
H OH
H OH
H
H OH
O
D-allose D-allose α-D-allopyranose
Monosaccharide structure
CH=O
CH2OH
H OH
H OH
H OH
H
OH
CH2OH
H OH
H OH
H OH
H
H OH
O
O
OHH
HH
OHH
OH OH
H
OH
D-allose D-allose α-D-allopyranose
Monosaccharide structure
• In crystals only cyclic forms (α-, β-anomers)
acyclic form
pyranose -pyranose
-furanose -furanose
Saccharides reactions
• Redox reactions
• Esterification
• Glycosides formation
Redox reactions of saccharides
OH
O
H OH
OH H
H OH
H OH
OH
OH H
H OH
H OH
O
OH
OH
OH
H OH
OH H
H OH
H OH
D-glucose D-fructose D-glucitol
Redox reactions of saccharides
CH=O
CH2OH
H OHOH HH OHH OH
D-glucose
Redox reactions of saccharides
CH=O
CH2OH
H OHOH HH OHH OH
COOH
CH2OH
H OHOH HH OHH OH
D-glucose
D-gluconic acid
CH=O
CH2OH
H OHOH HH OHH OH
Redox reactions of saccharides
COOH
CH2OH
H OHOH HH OHH OH
CH=O
COOH
H OHOH HH OHH OH
D-glucose
D-gluconic acid D-glucuronic acid
CH=O
CH2OH
H OHOH HH OHH OH
Redox reactions of saccharides
COOH
CH2OH
H OHOH HH OHH OH
CH=O
COOH
H OHOH HH OHH OH
COOH
COOH
H OHOH HH OHH OH
D-glucose
D-gluconic acid D-glucuronic acid D-glucaric acid
Redox reactions of saccharides
O
OHOHOH
OH
H
OH
D-glucose
Redox reactions of saccharides
O
OHOHOH
OH
H
OH
O
OHOHOH
OH
H
COOH
D-glucose
D-glucuronic acid
Redox reactions of saccharides
O
OHOHOH
OH
H
OH
O
OHOHOH
OH
H
COOH
O
OHOH
OH
OH
O
D-glucose
D-glucuronic acid δ-gluconolactone
Esterification
O
OHOHOH
OH
H
OH
D-glucose
Esterification
O
OHOHOH
OH
H
OH
O
OHOHOH
OH
H
O
PO
O-
O-
D-glucose D-glucose-6-phosphate
Glycosides formation
O
OHOHOH
OH
H
OH
D-glucose
Glycosides formation
O
OHOHOH
OH
H
OH
O
OOHOH
OH
H
OH
CH3
D-glucose α-methyl-D-glucopyranoside
Monosaccharides derivates deoxysaccharides and aminosaccharides
O
OHOHOH
NH
H
OH
O
CH3
O H
OH
HOH
OH
N-acetylglucosamine 2-deoxy-D-ribose
Oligosaccharides
• Contain 2-10 monosaccharide units bound by glycosidic bond
• Homo/heteroglycosides
• Reducing/nonreducing
O
1
OH
OH
OH
O
OH
O4
OH
OH
OH
OH
Oligosaccharides
maltose Sucrose (saccharose)
lactose
O14
OHOH
OH
OH
O
O
14
OHOH
OH
OH
O14
OHOH
OH
OH
O
O2
OH
OH
OH
OH
OH
Polysaccharides
• Contain more than 10 monosaccharide units
• Homo/heteropolysaccharides
• Linear and cyclic polysaccharides
• Branched and non-branched polysaccharides
• Pentosans, hexosans…
Plant polysaccharides starch
• Amylose structure
Non-reducing end Reducing end
O14
OHOH
OH
OH
O14
OH
OH
OH
O
O
O14
OH
OH
OH
O
O4
OHOH
OH
OH
http://bioanalyse.wikispaces.com/Homopolysaccharider
OH
O1
OH
OH
OH
O
O
14
OH
OH
OH
O1
OH
OH
OH
OH
O
O14
OH
OH
6 O
O
O4
OHOH
OH
OH
Plant polysaccharides starch
• Amylopektin
Main chain
branch
http://bioanalyse.wikispaces.com/Homopolysaccharider
Animal polysaccharides
• glycogen
http://www.namrata.co/glycogen-metabolism-subjective-questions-solved-set-1/
http://dstgroupproject.weebly.com/periodic-acid-schiffdiastase.html
http://www.namrata.co/glycogen-metabolism-subjective-questions-solved-set-1/http://www.namrata.co/glycogen-metabolism-subjective-questions-solved-set-1/http://www.namrata.co/glycogen-metabolism-subjective-questions-solved-set-1/http://www.namrata.co/glycogen-metabolism-subjective-questions-solved-set-1/http://www.namrata.co/glycogen-metabolism-subjective-questions-solved-set-1/http://www.namrata.co/glycogen-metabolism-subjective-questions-solved-set-1/http://www.namrata.co/glycogen-metabolism-subjective-questions-solved-set-1/http://www.namrata.co/glycogen-metabolism-subjective-questions-solved-set-1/http://www.namrata.co/glycogen-metabolism-subjective-questions-solved-set-1/http://www.namrata.co/glycogen-metabolism-subjective-questions-solved-set-1/http://www.namrata.co/glycogen-metabolism-subjective-questions-solved-set-1/http://www.namrata.co/glycogen-metabolism-subjective-questions-solved-set-1/http://www.namrata.co/glycogen-metabolism-subjective-questions-solved-set-1/http://www.namrata.co/glycogen-metabolism-subjective-questions-solved-set-1/http://www.namrata.co/glycogen-metabolism-subjective-questions-solved-set-1/http://www.namrata.co/glycogen-metabolism-subjective-questions-solved-set-1/http://dstgroupproject.weebly.com/periodic-acid-schiffdiastase.htmlhttp://dstgroupproject.weebly.com/periodic-acid-schiffdiastase.htmlhttp://dstgroupproject.weebly.com/periodic-acid-schiffdiastase.htmlhttp://dstgroupproject.weebly.com/periodic-acid-schiffdiastase.htmlhttp://dstgroupproject.weebly.com/periodic-acid-schiffdiastase.html
Complex polysaccharides
O
COO-
OH
OH
OH
NH
O
CH3
OH
Hyaluronic acid Chondroitin-4-sulphate
Sialic acid https://wikispaces.psu.edu/display/230/The+Organization+of+Cells+in+Tissue
-+The+Extracellular+Matrix,+Cell+Junctions+and+Cell+Adhesion
II. Structure of nucleic acids
Saccharides present in nucleic acids
O
H
OH
H
OH
H
OH
H
OH
O
H
OH
HH
OH
H
OH
β-D-ribofuranose 2-deoxy-β-D-ribofuranose
Heterocyclic compounds present in
nucleic acids
8
4
9
N3
N1
2 NH5
6
N7
N3
2
4
N1
5
6
pyrimidine purine
Heterocyclic compounds present in
nucleic acids
8
4
9
N3
N1
2 NH5
6
N7
N3
2
4
N1
5
6
N
NH
NH2
O NH
NH
O
O
NH
NH
O
O
CH3
pyrimidine purine
cytosine uracil
thymine
Heterocyclic compounds present in
nucleic acids
8
4
9
N3
N1
2 NH5
6
N7
N3
2
4
N1
5
6
N
N
NH
N
NH2
N
NH
NH
N
NH2
O
N
NH
NH2
O NH
NH
O
O
NH
NH
O
O
CH3
purine pyrimidine
cytosine uracil
thymine
adenine guanine
Keto-enol, and amin-imin
tautomerism
CH3
CH3
NH2
CH3
CH3
NH
CH3
CH3
OH
CH3
CH3
O
Nucleosides
O
OHOH
OH
N
N
N9
N
NH2
O
OHOH
OH
N1
NH
O
O
CH3
adenosine thymidine
Conformation of β-N-glycosidic bond
O
OHOH
OH
N
N
N9
N
NH2
O
OHOH
OH
N
N
N9
N
NH2
adenosine guanosine
Nucleotides
PO-
O
O- O
OHOH
O
N
N
N9
N
NH2
Adenosine monophosphate
Nukleotides
Phosphoanhydride bond
PO-
O
O-
PO
O
O-
PO
O
O- O
OHOH
O
N
N
N9
N
NH2
adenosintriphosphate
Physiologically important nucleotides (NAD+/NADH, FAD/FADH2)
O
OHOH
O N
N
N
N
NH2
P
O
P
O
OHOH
N+
NH2
O
O
OH
OH
OH
O
OHOH
O N
N
N
N
NH2
POPO
N
NNH
NCH3
CH3
O
O
Physiologically important nucleotides
PO-
O
O
OHO
O
N
N
N9
N
NH2
PO-
O
O
OHO
O
N
NH
N9
N
O
NH2
O
OHOH
N
N
N9
N
NH2
O
NH3+
S+
CH3
O-
cAMP cGMP
SAM
Synthetic nucletide analogues
O
HOH
OH
5
N1
NH
O
O
I
O
OHOH
OH
N6N
1
NH
O
O
6
N
N
NH
N
SH
N
N
NH
N
OH
5-iodo-2-deoxyuridine 6-azauridine
6-merkaptopurine allopurinol
DNA chain structure
NO
3´
5´OP N
NHN
NH2
O
OH
NO
3´
5´OP N
NHN
NH2
O
O
NO
3´
5´OP
N
NH2
O
OH
DNA chain structure
NO
3´
5´OP N
NHN
NH2
O
O
NO
3´
5´OP
N
NH2
O
O
NO
3´
5´OP
NH
O
O
CH3
OH
DNA chain structure
NO
3´
5´OP N
NHN
NH2
O
O
NO
3´
5´OP
N
NH2
O
O
NO
3´
5´OP
NH
O
O
CH3
O
NO
3´
5´OP N
NN
NH2
O
P
DNA chain structure
Stabilisation of base pairs
NH NH
O
O
CH3
N
N
NH
N
NH2
Stabilisation of base pairs
NH NH
O
O
CH3
N
N
NH
N
NH2
NNH
NH2
O
N
NH
NH
N
NH2
O
Chargaff’s rule
DNA conformations
http://www.biologyexams4u.com/2012/11/different-forms-of-dna.html#.VDZBrsVdVRo
B-form of DNA
Small cleft
Large cleft
Forces stabilizing the nucleic acids
structures
• Denaturation and renaturation
• Hydrophobic interaction
• Electrostatic interaction
http://dspace.jorum.ac.uk/xmlui/bitstream/handle/10949/956/Items/S377_1_section5.html
http://www.atdbio.com/content/53/DNA-duplex-stability
http://dspace.jorum.ac.uk/xmlui/bitstream/handle/10949/956/Items/S377_1_section5.html
Forces stabilizing the nucleic acids
structures
• Denaturation and renaturation
• Hydrophobic interaction
• Electrostatic interaction
http://dspace.jorum.ac.uk/xmlui/bitstream/handle/10949/956/Items/S377_1_section5.html
http://www.atdbio.com/content/53/DNA-duplex-stability
http://dspace.jorum.ac.uk/xmlui/bitstream/handle/10949/956/Items/S377_1_section5.html
RNA
O
H
OH
H
OH
H
OH
H
OH
NH
NH
O
O
•mRNA
•tRNA
•rRNA
•snRNA
•miRNA
•…
http://www.broadinstitute.org/blog/five-questions-david-root-rna-interference-explained
uracil ribose
RNA stability
O
H
OH
H
OH
H
OH
H
O
P O-
O
O
O OH
OH
OH
OH-
RNA stability
O
H
OH
H
OH
H
OH
H
O
P O-
O
O
O OH
OH
OH
OH-
O
H
OH
H
OH
H
OH
H
OH
O
O OHOH
O
P
O-
O
mRNA
• Highly variable in size
• Transcription starts from 5´-end
• 3´-end: polyA (20-250)
N
NH
N
N
NH2
OCH3
O
H
H
OH
H
OH
H
O NO
3´
5´OP N
NHN
NH2
O
O
NO
3´
5´OP
NH
O
O
O
P
OPOP
O-
OO
OH O-
O
OH
OH
cap
tRNA
• Small molecule (73-95)
• 3´-end: CCA
• Playing also other roles
• At least 1 tRNA for each
aminoacid
http://www.wiley.com/college/boyer/0470003790/structure/tRNA/trna_intro.htm
rRNA
• Majority of cell RNA
• Catalytic activity
http://cronodon.com/BioTech/Ribosomes.html
Other RNAs
• Small interfering RNAs (siRNAs) • mediate the downregulation of gene expression -
binding to specific mRNAs labelled them for destruction by enzymes called endonucleases
• MicroRNAs (miRNAs) • downregulate gene expression - binding to messenger
RNAs (mRNAs) causes preventing mRNAs from being translated into proteins
• Small nucleolar RNAs (snoRNAs) • modify ribosomal RNAs (rRNAs) by organizing the
cleavage of the long pre-rRNA into its functional subunits (18S, 5.8S and 28S molecules)
• Small nuclear RNAs (snRNAs) • are constituents of the cellular machinery
(spliceosome) that helps to produce mRNA
Differences between DNA and RNA
DNA RNA
carbohydrate deoxyribose ribose
pyrimidine base thymine uracil
structure double-helix single helix
stability at high pH resistent cleaved